@article {pmid39261613,
year = {2024},
author = {Vosseberg, J and van Hooff, JJE and Köstlbacher, S and Panagiotou, K and Tamarit, D and Ettema, TJG},
title = {The emerging view on the origin and early evolution of eukaryotic cells.},
journal = {Nature},
volume = {633},
number = {8029},
pages = {295-305},
pmid = {39261613},
issn = {1476-4687},
mesh = {*Eukaryotic Cells/cytology/metabolism ; *Symbiosis ; *Biological Evolution ; Archaea/genetics/classification/cytology ; Mitochondria/genetics/metabolism ; Bacteria/genetics/cytology/classification/metabolism ; Prokaryotic Cells/cytology/metabolism/classification ; Phylogeny ; Animals ; Eukaryota/genetics/classification/cytology ; },
abstract = {The origin of the eukaryotic cell, with its compartmentalized nature and generally large size compared with bacterial and archaeal cells, represents a cornerstone event in the evolution of complex life on Earth. In a process referred to as eukaryogenesis, the eukaryotic cell is believed to have evolved between approximately 1.8 and 2.7 billion years ago from its archaeal ancestors, with a symbiosis with a bacterial (proto-mitochondrial) partner being a key event. In the tree of life, the branch separating the first from the last common ancestor of all eukaryotes is long and lacks evolutionary intermediates. As a result, the timing and driving forces of the emergence of complex eukaryotic features remain poorly understood. During the past decade, environmental and comparative genomic studies have revealed vital details about the identity and nature of the host cell and the proto-mitochondrial endosymbiont, enabling a critical reappraisal of hypotheses underlying the symbiotic origin of the eukaryotic cell. Here we outline our current understanding of the key players and events underlying the emergence of cellular complexity during the prokaryote-to-eukaryote transition and discuss potential avenues of future research that might provide new insights into the enigmatic origin of the eukaryotic cell.},
}

*Eukaryotic Cells/cytology/metabolism
*Symbiosis
*Biological Evolution
Archaea/genetics/classification/cytology
Mitochondria/genetics/metabolism
Bacteria/genetics/cytology/classification/metabolism
Prokaryotic Cells/cytology/metabolism/classification
Phylogeny
Animals
Eukaryota/genetics/classification/cytology

@article {pmid39252884,
year = {2024},
author = {Thoral, E and Dawson, NJ and Bettinazzi, S and Rodríguez, E},
title = {An evolving roadmap: using mitochondrial physiology to help guide conservation efforts.},
journal = {Conservation physiology},
volume = {12},
number = {1},
pages = {coae063},
doi = {10.1093/conphys/coae063},
pmid = {39252884},
issn = {2051-1434},
abstract = {The crucial role of aerobic energy production in sustaining eukaryotic life positions mitochondrial processes as key determinants of an animal's ability to withstand unpredictable environments. The advent of new techniques facilitating the measurement of mitochondrial function offers an increasingly promising tool for conservation approaches. Herein, we synthesize the current knowledge on the links between mitochondrial bioenergetics, ecophysiology and local adaptation, expanding them to the wider conservation physiology field. We discuss recent findings linking cellular bioenergetics to whole-animal fitness, in the current context of climate change. We summarize topics, questions, methods, pitfalls and caveats to help provide a comprehensive roadmap for studying mitochondria from a conservation perspective. Our overall aim is to help guide conservation in natural populations, outlining the methods and techniques that could be most useful to assess mitochondrial function in the field.},
}

@article {pmid39162337,
year = {2024},
author = {Klirs, Y and Novosolov, M and Gissi, C and Garić, R and Pupko, T and Stach, T and Huchon, D},
title = {Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss.},
journal = {Genome biology and evolution},
volume = {16},
number = {9},
pages = {},
doi = {10.1093/gbe/evae181},
pmid = {39162337},
issn = {1759-6653},
support = {I-1454-203.13/2018//German-Israeli Foundation for Scientific Research and Development/ ; },
mesh = {Animals ; *Genome, Mitochondrial ; *RNA Editing ; *RNA, Transfer/genetics ; *Urochordata/genetics ; *Evolution, Molecular ; *Phylogeny ; Cell Nucleus/genetics ; },
abstract = {Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome of O. dioica by means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned open reading frame that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined.},
}

Animals
*Genome, Mitochondrial
*RNA Editing
*RNA, Transfer/genetics
*Urochordata/genetics
*Evolution, Molecular
*Phylogeny
Cell Nucleus/genetics

@article {pmid39243912,
year = {2024},
author = {Liu, GH and Zuo, YW and Shan, Y and Yu, J and Li, JX and Chen, Y and Gong, XY and Liao, XM},
title = {Structural analysis of the mitochondrial genome of Santalum album reveals a complex branched configuration.},
journal = {Genomics},
volume = {},
number = {},
pages = {110935},
doi = {10.1016/j.ygeno.2024.110935},
pmid = {39243912},
issn = {1089-8646},
abstract = {BACKGROUND: Santalum album L. is an evergreen tree which is mainly distributes throughout tropical and temperate regions. And it has a great medicinal and economic value.

RESULTS: In this study, the complete mitochondrial genome of S. album were assembled and annotated, which could be described by a complex branched structure consisting of three contigs. The lengths of these three contigs are 165,122 bp, 93,430 bp and 92,491 bp. We annotated 34 genes coding for proteins (PCGs), 26 tRNA genes, and 4 rRNA genes. The analysis of repeated elements shows that there are 89 SSRs and 242 pairs of dispersed repeats in S. album mitochondrial genome. Also we found 20 MTPTs among the chloroplast and mitochondria. The 20 MTPTs sequences span a combined length of 22,353 bp, making up 15.52 % of the plastome, 6.37 % of the mitochondrial genome. Additionally, by using the Deepred-mt tool, we found 628 RNA editing sites in 34 PCGs. Moreover, significant genomic rearrangement is observed between S. album and its associated mitochondrial genomes. Finally, based on mitochondrial genome PCGs, we deduced the phylogenetic ties between S. album and other angiosperms.

CONCLUSIONS: We reported the mitochondrial genome from Santalales for the first time, which provides a crucial genetic resource for our study of the evolution of mitochondrial genome.},
}

@article {pmid39232676,
year = {2024},
author = {Ou, T and Wu, Z and Tian, C and Yang, Y and Li, Z},
title = {Complete mitochondrial genome of Agropyron cristatum reveals gene transfer and RNA editing events.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {830},
pmid = {39232676},
issn = {1471-2229},
abstract = {BACKGROUND: As an important forage in arid and semi-arid regions, Agropyron cristatum provides livestock with exceptionally high nutritional value. Additionally, A. cristatum exhibits outstanding genetic characteristics to endure drought and disease. Therefore, rich genetic diversity serves as a cornerstone for the improvement of major food crops. The purposes of this study were to systematically describe mitogenome of A.cristatum and preliminarily analyze its internal variations.

RESULT: The A. cristatum mitogenome was a single-ring molecular structure of 381,065 bp that comprised 52 genes, including 35 protein-coding, 3 rRNA and 14 tRNA genes. Among these, two pseudoprotein-coding genes and multiple copies of tRNA genes were observed. A total of 320 repetitive sequences was found to cover more than 10% of the mitogenome (105 simple sequences, 185 dispersed and 30 tandem repeats), which led to a large number of fragment rearrangements in the mitogenome of A. cristatum. Leucine was the most frequent amino acid (n = 1087,10.8%) in the protein-coding genes of A. cristatum mitogenome, and the highest usage codon was ATG (initiation codon). The number of A/T changes at the third base of the codon was much higher than that of G/C. Among 23 PCGs, the range of Pi values is from 0.0021 to 0.0539, with an average of 0.013. Additionally, 81 RNA editing sites were predicted, which were considerably fewer than those reported in other plant mitogenomes. Most of the RNA editing site base positions were concentrated at the first and second codon bases, which were C to T transitions. Moreover, we identified 95 sequence fragments (total length of 34, 343 bp) that were transferred from the chloroplast to mitochondria genes, introns, and intergenic regions. The stability of the tRNA genes was maintained during this process. Selection pressure analysis of 23 protein-coding genes shared by 15 Poaceae plants, showed that most genes were subjected to purifying selection during evolution, whereas rps4, cob, mttB, and ccmB underwent positive selection in different plants. Finally, a phylogenetic tree was constructed based on 22 plant mitogenomes, which showed that Agropyron plants have a high degree of independent heritability in Triticeae.

CONCLUSION: The findings of this study provide new data for a better understanding of A. cristatum genes, and demonstrate that mitogenomes are suitable for the study of plant classifications, such as those of Agropyron. Moreover, it provides a reference for further exploration of the phylogenetic relationships within Agropyron species, and establishes a theoretical basis for the subsequent development and utilization of A. cristatum plant germplasm resources.},
}

@article {pmid39152292,
year = {2024},
author = {Zhang, Y and Liu, S and Mostert, D and Yu, H and Zhuo, M and Li, G and Zuo, C and Haridas, S and Webster, K and Li, M and Grigoriev, IV and Yi, G and Viljoen, A and Li, C and Ma, LJ},
title = {Virulence of banana wilt-causing fungal pathogen Fusarium oxysporum tropical race 4 is mediated by nitric oxide biosynthesis and accessory genes.},
journal = {Nature microbiology},
volume = {9},
number = {9},
pages = {2232-2243},
pmid = {39152292},
issn = {2058-5276},
support = {IOS-165241//National Science Foundation (NSF)/ ; MASR-2009-04374//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; MAS00532//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; MAS00496//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; R01EY030150//U.S. Department of Health & Human Services | NIH | National Eye Institute (NEI)/ ; },
mesh = {*Fusarium/genetics/pathogenicity/metabolism ; *Musa/microbiology ; *Plant Diseases/microbiology ; *Nitric Oxide/metabolism ; Virulence/genetics ; Virulence Factors/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Gene Expression Regulation, Fungal ; Genes, Fungal ; Phylogeny ; },
abstract = {Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most damaging plant diseases known. Foc race 1 (R1) decimated the Gros Michel-based banana (Musa acuminata) trade, and now Foc tropical race 4 (TR4) threatens global production of its replacement, the Cavendish banana. Here population genomics revealed that all Cavendish banana-infecting Foc race 4 strains share an evolutionary origin distinct from that of R1 strains. Although TR4 lacks accessory chromosomes, it contains accessory genes at the ends of some core chromosomes that are enriched for virulence and mitochondria-related functions. Meta-transcriptomics revealed the unique induction of the entire mitochondrion-localized nitric oxide (NO) biosynthesis pathway upon TR4 infection. Empirically, we confirmed the unique induction of a NO burst in TR4, suggesting that nitrosative pressure may contribute to virulence. Targeted mutagenesis demonstrated the functional importance of fungal NO production and the accessory gene SIX4 as virulence factors.},
}

*Fusarium/genetics/pathogenicity/metabolism
*Musa/microbiology
*Plant Diseases/microbiology
*Nitric Oxide/metabolism
Virulence/genetics
Virulence Factors/genetics/metabolism
Fungal Proteins/genetics/metabolism
Gene Expression Regulation, Fungal
Genes, Fungal
Phylogeny

@article {pmid38924467,
year = {2024},
author = {Menegollo, M and Bentham, RB and Henriques, T and Ng, SQ and Ren, Z and Esculier, C and Agarwal, S and Tong, ETY and Lo, C and Ilangovan, S and Szabadkai, Z and Suman, M and Patani, N and Ghanate, A and Bryson, K and Stein, RC and Yuneva, M and Szabadkai, G},
title = {Multistate Gene Cluster Switches Determine the Adaptive Mitochondrial and Metabolic Landscape of Breast Cancer.},
journal = {Cancer research},
volume = {84},
number = {17},
pages = {2911-2925},
pmid = {38924467},
issn = {1538-7445},
support = {IG13447//Fondazione AIRC per la Ricerca sul Cancro ETS (AIRC)/ ; BB/P018726/1//Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 29264//Cancer Research UK (CRUK)/ ; FC001223/WT_/Wellcome Trust/United Kingdom ; FC0010060//Francis Crick Institute (FCI)/ ; C57633/A25043//Cancer Research UK (CRUK)/ ; FS/20/4/34958//British Heart Foundation (BHF)/ ; //UCLH Biomedical Research Centre (UCL)/ ; IG22221//Fondazione AIRC per la ricerca sul cancro ETS (AIRC)/ ; 204458/Z/16/Z//Wellcome Trust (WT)/ ; BB/L020874/1//Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Humans ; *Breast Neoplasms/genetics/metabolism/pathology ; Female ; *Mitochondria/metabolism/genetics ; *Multigene Family ; Transcriptome ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic ; Prognosis ; Energy Metabolism/genetics ; },
abstract = {Adaptive metabolic switches are proposed to underlie conversions between cellular states during normal development as well as in cancer evolution. Metabolic adaptations represent important therapeutic targets in tumors, highlighting the need to characterize the full spectrum, characteristics, and regulation of the metabolic switches. To investigate the hypothesis that metabolic switches associated with specific metabolic states can be recognized by locating large alternating gene expression patterns, we developed a method to identify interspersed gene sets by massive correlated biclustering and to predict their metabolic wiring. Testing the method on breast cancer transcriptome datasets revealed a series of gene sets with switch-like behavior that could be used to predict mitochondrial content, metabolic activity, and central carbon flux in tumors. The predictions were experimentally validated by bioenergetic profiling and metabolic flux analysis of 13C-labeled substrates. The metabolic switch positions also distinguished between cellular states, correlating with tumor pathology, prognosis, and chemosensitivity. The method is applicable to any large and heterogeneous transcriptome dataset to discover metabolic and associated pathophysiological states. Significance: A method for identifying the transcriptomic signatures of metabolic switches underlying divergent routes of cellular transformation stratifies breast cancer into metabolic subtypes, predicting their biology, architecture, and clinical outcome.},
}

Humans
*Breast Neoplasms/genetics/metabolism/pathology
Female
*Mitochondria/metabolism/genetics
*Multigene Family
Transcriptome
Gene Expression Profiling/methods
Gene Expression Regulation, Neoplastic
Prognosis
Energy Metabolism/genetics

@article {pmid39226386,
year = {2024},
author = {Amaya Romero, JE and Chenal, C and Ben Chehida, Y and Miles, A and Clarkson, CS and Pedergnana, V and Wertheim, B and Fontaine, MC},
title = {Mitochondrial Variation in Anopheles gambiae and Anopheles coluzzii: Phylogeographic Legacy and Mitonuclear Associations With Metabolic Resistance to Pathogens and Insecticides.},
journal = {Genome biology and evolution},
volume = {16},
number = {9},
pages = {},
doi = {10.1093/gbe/evae172},
pmid = {39226386},
issn = {1759-6653},
mesh = {Animals ; *Anopheles/genetics ; *Phylogeography ; *Phylogeny ; *DNA, Mitochondrial/genetics ; *Insecticide Resistance/genetics ; Genome, Mitochondrial ; Evolution, Molecular ; Genetic Variation ; Insecticides/pharmacology ; Mitochondria/genetics ; Africa ; },
abstract = {Mitochondrial DNA has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mitochondrial DNA variation in Anopheles gambiae and Anopheles coluzzii, in relation to other species in the Anopheles gambiae complex, by assembling the mitogenomes of 1,219 mosquitoes across Africa. The mitochondrial DNA phylogeny of the Anopheles gambiae complex was consistent with previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, and Anopheles arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three saltwater-tolerant species (Anopheles merus, Anopheles melas, and Anopheles bwambae) in the Anopheles gambiae complex also suggested that introgression and possibly selection shaped mitochondrial DNA evolution. Mitochondrial DNA variation in An. gambiae and An. coluzzii across Africa revealed significant partitioning among populations and species. A peculiar mitochondrial DNA lineage found predominantly in An. coluzzii and in the hybrid taxon of the African "far-west" exhibited divergence comparable to the interspecies divergence in the Anopheles gambiae complex, with a geographic distribution matching closely An. coluzzii's geographic range. This phylogeographic relict of the An. coluzzii and An. gambiae split was associated with population and species structure, but not with the rare Wolbachia occurrence. The lineage was significantly associated with single nucleotide polymorphisms in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline potential mitonuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticides in Anopheles.},
}

Animals
*Anopheles/genetics
*Phylogeography
*Phylogeny
*DNA, Mitochondrial/genetics
*Insecticide Resistance/genetics
Genome, Mitochondrial
Evolution, Molecular
Genetic Variation
Insecticides/pharmacology
Mitochondria/genetics
Africa

@article {pmid39222118,
year = {2024},
author = {Santos, YS and Vidal, AH and Abreu, EFM and Nogueira, I and Faleiro, FG and Lacorte, CC and Melo, FL and de Araújo Campos, M and de Rezende, RR and Morgan, T and Varsani, A and Alfenas-Zerbini, P and Ribeiro, SG},
title = {Detection and molecular characterization of a novel mitovirus associated with Passiflora edulis Sims.},
journal = {Archives of virology},
volume = {169},
number = {9},
pages = {190},
pmid = {39222118},
issn = {1432-8798},
support = {APQ-00661-18//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; },
mesh = {*Passiflora/virology ; *Phylogeny ; *Open Reading Frames ; *Genome, Viral/genetics ; *Plant Diseases/virology ; Brazil ; *RNA-Dependent RNA Polymerase/genetics ; RNA Viruses/genetics/isolation & purification/classification ; Viral Proteins/genetics ; RNA, Viral/genetics ; Amino Acid Sequence ; },
abstract = {Mitoviruses are cryptic capsidless viruses belonging to the family Mitoviridae that replicate and are maintained in the mitochondria of fungi. Complete mitovirus-like sequences were recently assembled from plant transcriptome data and plant leaf tissue samples. Passion fruit (Passiflora spp.) is an economically important crop for numerous tropical and subtropical countries worldwide, and many virus-induced diseases impact its production. From a large-scale genomic study targeting viruses infecting Passiflora spp. in Brazil, we detected a de novo-assembled contig with similarity to other plant-associated mitoviruses. The contig is ∼2.6 kb long, with a single open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRP). This contig has been named "passion fruit mitovirus-like 1" (PfMv1). An alignment of the predicted amino acid sequence of the RdRP of PfMv1 and those of other plant-associated mitoviruses revealed the presence of the six conserved motifs of mitovirus RdRPs. PfMv1 has 79% coverage and 50.14% identity to Humulus lupulus mitovirus 1. Phylogenetic analysis showed that PfMV1 clustered with other plant-associated mitoviruses in the genus Duamitovirus. Using RT-PCR, we detected a PfMv1-derived fragment, but no corresponding DNA was identified, thus excluding the possibility that this is an endogenized viral-like sequence. This is the first evidence of a replicating mitovirus associated with Passiflora edulis, and it should be classified as a member of a new species, for which we propose the name "Duamitovirus passiflorae".},
}

*Passiflora/virology
*Phylogeny
*Open Reading Frames
*Genome, Viral/genetics
*Plant Diseases/virology
Brazil
*RNA-Dependent RNA Polymerase/genetics
RNA Viruses/genetics/isolation & purification/classification
Viral Proteins/genetics
RNA, Viral/genetics
Amino Acid Sequence

@article {pmid39213749,
year = {2024},
author = {Chen, X and Sun, W and Song, Y and Wu, S and Xie, S and Xiong, W and Peng, C and Peng, Y and Wang, Z and Lek, S and Hogstrand, C and Sørensen, M and Pan, L and Liu, D},
title = {Acute waterborne cadmium exposure induces liver ferroptosis in Channa argus.},
journal = {Ecotoxicology and environmental safety},
volume = {283},
number = {},
pages = {116947},
doi = {10.1016/j.ecoenv.2024.116947},
pmid = {39213749},
issn = {1090-2414},
abstract = {The impact of cadmium (Cd) toxicity on fish liver injury has received much attention in recent years. Currently, autophagy, apoptosis and endoplasmic reticulum stress were reported in Cd exposed fish liver, and if there are other mechanisms (such as ferroptosis) and relevant signaling pathways involved in fish remains unknown. An experiment was conducted to investigate Cd toxicity in Channa argus (Cantor, 1842) exposed to 0, 1.0, and 2.0 mg Cd/L of water for 96 h. Cd disrupted the structure of mitochondria in the liver. Besides, Cd induced ferroptosis by significantly increasing the level of Fe[2+], ROS, MDA and significantly decreasing the level of Ferritin, GSH, GSH-Px, GPX4, GST and SOD (p < 0.05 in all cases). In addition, the mRNA expression of ferroptosis related genes, gpx4 and slc7a11, were significantly downregulated by Cd. Moreover, Cd exposure significantly inhibited the Nrf2/Keap1 signaling pathway, one of the pathways involved in ferroptosis, by upregulating the mRNA levels of keap1a and keap1b, and downregulating the mRNA levels of nrf2 and its target genes (ho-1, nqo1 and cat). Cd exposure also caused extensive accumulation of vacuoles and lipid droplets in liver, as well as an increase in triglyceride content. Cd significantly affected lipid metabolism related enzyme activity and gene expression, which were also regulated by Nrf2/Keap1 signaling pathway. In summary, these results indicate that ferroptosis is a mechanism in waterborne Cd exposed fish liver injury via the Nrf2/Keap1 signaling pathway and the Cd induced hepatic steatosis is also modulated by Nrf2/Keap1 pathway at the whole-body level in fish. These findings provide new insights into the fish liver injury and molecular basis of Cd toxicity.},
}

@article {pmid39202396,
year = {2024},
author = {Wu, H and Qi, S and Fan, S and Li, H and Zhang, Y and Zhang, Y and Xu, Q and Chen, G},
title = {Analysis of the Mitochondrial COI Gene and Genetic Diversity of Endangered Goose Breeds.},
journal = {Genes},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/genes15081037},
pmid = {39202396},
issn = {2073-4425},
support = {[2021YFD1200302]//the National Key Research and Development Program of China/ ; [JBGS [2021]023]//the Jiangsu Provincial Seed Industry Revitalization Announcement Leading Project/ ; },
mesh = {Animals ; *Geese/genetics ; *Endangered Species ; *Phylogeny ; *Haplotypes ; *Electron Transport Complex IV/genetics ; Genetic Variation ; DNA, Mitochondrial/genetics ; Breeding ; China ; Mitochondria/genetics ; },
abstract = {The mitochondrial cytochrome c oxidase subunit I (COI) genes of six endangered goose breeds (Xupu, Yangjiang, Yan, Wuzong, Baizi, and Lingxian) were sequenced and compared to assess the genetic diversity of endangered goose breeds. By constructing phylogenetic trees and evolutionary maps of genetic relationships, the affinities and degrees of genetic variations among the six different breeds were revealed. A total of 92 polymorphic sites were detected in the 741 bp sequence of the mtDNA COI gene after shear correction, and the GC content of the processed sequence (51.11%) was higher than that of the AT content (48.89%). The polymorphic loci within the populations of five of the six breeds (Xupu, Yangjiang, Yan, Baizi, and Lingxian) were more than 10, the haplotype diversity > 0.5, and the nucleotide diversity (Pi) > 0.005, with the Baizi geese being the exception. A total of 35 haplotypes were detected based on nucleotide variation among sequences, and the goose breed haplotypes showed a central star-shaped dispersion; the FST values were -0.03781 to 0.02645, The greatest genetic differentiation (FST = 0.02645) was observed in Yan and Wuzong breeds. The most frequent genetic exchange (Nm > 15.00) was between the Wuzong and Yangjiang geese. An analysis of molecular variance showed that the population genetic variation mainly came from within the population; the base mismatch differential distribution analysis of the goose breeds and the Tajima's D and Fu's Fs neutral detection of the historical occurrence dynamics of their populations were negative (p > 0.10). The distribution curve of the base mismatches showed a multimodal peak, which indicated that the population tended to be stabilised. These results provide important genetic information for the conservation and management of endangered goose breeds and a scientific basis for the development of effective conservation strategies.},
}

Animals
*Geese/genetics
*Endangered Species
*Phylogeny
*Haplotypes
*Electron Transport Complex IV/genetics
Genetic Variation
DNA, Mitochondrial/genetics
Breeding
China
Mitochondria/genetics

@article {pmid39201699,
year = {2024},
author = {Li, H and Liang, T and Liu, Y and Wang, P and Wang, S and Zhao, M and Zhang, Y},
title = {Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
doi = {10.3390/ijms25169013},
pmid = {39201699},
issn = {1422-0067},
support = {31870009//National Natural Science Foundation of China/ ; YNWR-QNBJ-2018-355//Top Young Talents Program of the Ten Thousand Talents Plan in Yunnan Province/ ; 2021KF009//YNCUB/ ; },
mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; Phylogeny ; Introns/genetics ; Mitochondria/genetics ; Basidiomycota/genetics ; DNA, Mitochondrial/genetics ; Genomics/methods ; Gene Transfer, Horizontal ; },
abstract = {Limited exploration in fungal mitochondrial genetics has uncovered diverse inheritance modes. The mitochondrial genomes are inherited uniparentally in the majority of sexual eukaryotes, our discovery of persistent mitochondrial heterogeneity within the natural population of the basidiomycete fungus Thelephora ganbajun represents a significant advance in understanding mitochondrial inheritance and evolution in eukaryotes. Here, we present a comprehensive analysis by sequencing and assembling the complete mitogenomes of 40 samples exhibiting diverse cox1 heterogeneity patterns from various geographical origins. Additionally, we identified heterogeneous variants in the nad5 gene, which, similar to cox1, displayed variability across multiple copies. Notably, our study reveals a distinct prevalence of introns and homing endonucleases in these heterogeneous genes. Furthermore, we detected potential instances of horizontal gene transfer involving homing endonucleases. Population genomic analyses underscore regional variations in mitochondrial genome composition among natural samples exhibiting heterogeneity. Thus, polymorphisms in heterogeneous genes, introns, and homing endonucleases significantly influence mitochondrial structure, structural variation, and evolutionary dynamics in this species. This study contributes valuable insights into mitochondrial genome architecture, population dynamics, and the evolutionary implications of mitochondrial heterogeneity in sexual eukaryotes.},
}

*Genome, Mitochondrial
*Evolution, Molecular
Phylogeny
Introns/genetics
Mitochondria/genetics
Basidiomycota/genetics
DNA, Mitochondrial/genetics
Genomics/methods
Gene Transfer, Horizontal

@article {pmid39199300,
year = {2024},
author = {Wang, X and Wang, D and Zhang, R and Qin, X and Shen, X and You, C},
title = {Morphological Structure Identification, Comparative Mitochondrial Genomics and Population Genetic Analysis toward Exploring Interspecific Variations and Phylogenetic Implications of Malus baccata 'ZA' and Other Species.},
journal = {Biomolecules},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biom14080912},
pmid = {39199300},
issn = {2218-273X},
support = {32072520, 32172538//National Natural Science Foundation of China/ ; ZR2020MC132//Shandong Provincial Natural Science Foundation/ ; 2022YFD1201700//National Key Research and Development Program of China/ ; SDAIT-06-07//Fruit Industry System of Shandong Province/ ; },
mesh = {*Phylogeny ; *Genome, Mitochondrial/genetics ; *Malus/genetics/classification ; Genetics, Population ; Genomics ; Mitochondria/genetics ; },
abstract = {Malus baccata, a valuable germplasm resource in the genus Malus, is indigenous to China and widely distributed. However, little is known about the lineage composition and genetic basis of 'ZA', a mutant type of M. baccata. In this study, we compared the differences between 'ZA' and wild type from the perspective of morphology and ultrastructure and analyzed their chloroplast pigment content based on biochemical methods. Further, the complete mitogenome of M. baccata 'ZA' was assembled and obtained by next-generation sequencing. Subsequently, its molecular characteristics were analyzed using Geneious, MISA-web, and CodonW toolkits. Furthermore, by examining 106 Malus germplasms and 42 Rosaceae species, we deduced and elucidated the evolutionary position of M. baccata 'ZA', as well as interspecific variations among different individuals. In comparison, the total length of the 'ZA' mitogenome (GC content: 45.4%) is 374,023 bp, which is approximately 2.33 times larger than the size (160,202 bp) of the plastome (GC: 36.5%). The collinear analysis results revealed abundant repeats and genome rearrangements occurring between different Malus species. Additionally, we identified 14 plastid-driven fragment transfer events. A total of 54 genes have been annotated in the 'ZA' mitogenome, including 35 protein-coding genes, 16 tRNAs, and three rRNAs. By calculating nucleotide polymorphisms and selection pressure for 24 shared core mitochondrial CDSs from 42 Rosaceae species (including 'ZA'), we observed that the nad3 gene exhibited minimal variation, while nad4L appeared to be evolving rapidly. Population genetics analysis detected a total of 1578 high-quality variants (1424 SNPs, 60 insertions, and 94 deletions; variation rate: 1/237) among samples from 106 Malus individuals. Furthermore, by constructing phylogenetic trees based on both Malus and Rosaceae taxa datasets, it was preliminarily demonstrated that 'ZA' is closely related to M. baccata, M. sieversii, and other proximate species in terms of evolution. The sequencing data obtained in this study, along with our findings, contribute to expanding the mitogenomic resources available for Rosaceae research. They also hold reference significance for molecular identification studies as well as conservation and breeding efforts focused on excellent germplasms.},
}

*Phylogeny
*Genome, Mitochondrial/genetics
*Malus/genetics/classification
Genetics, Population
Genomics
Mitochondria/genetics

@article {pmid39199261,
year = {2024},
author = {Tian, L and Luo, Y and Ren, J and Zhao, C},
title = {The Role of Oxidative Stress in Hypomagnetic Field Effects.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/antiox13081017},
pmid = {39199261},
issn = {2076-3921},
support = {YSBR-097//CAS Project for Young Scientists in Basic Research/ ; 42388101 and 42274099//National Natural Science Foundation of China/ ; },
abstract = {The geomagnetic field (GMF) is crucial for the survival and evolution of life on Earth. The weakening of the GMF, known as the hypomagnetic field (HMF), significantly affects various aspects of life on Earth. HMF has become a potential health risk for future deep space exploration. Oxidative stress is directly involved in the biological effects of HMF on animals or cells. Oxidative stress occurs when there is an imbalance favoring oxidants over antioxidants, resulting in cellular damage. Oxidative stress is a double-edged sword, depending on the degree of deviation from homeostasis. In this review, we summarize the important experimental findings from animal and cell studies on HMF exposure affecting intracellular reactive oxygen species (ROS), as well as the accompanying many physiological abnormalities, such as cognitive dysfunction, the imbalance of gut microbiota homeostasis, mood disorders, and osteoporosis. We discuss new insights into the molecular mechanisms underlying these HMF effects in the context of the signaling pathways related to ROS. Among them, mitochondria are considered to be the main organelles that respond to HMF-induced stress by regulating metabolism and ROS production in cells. In order to unravel the molecular mechanisms of HMF action, future studies need to consider the upstream and downstream pathways associated with ROS.},
}

@article {pmid39192127,
year = {2025},
author = {Bhattacharya, M and Bhowmik, D and Yin, Q},
title = {In Vitro Cleavage Assay to Characterize DENV NS2B3 Antagonism of cGAS.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2854},
number = {},
pages = {153-170},
pmid = {39192127},
issn = {1940-6029},
abstract = {cGAS is a key cytosolic dsDNA receptor that senses viral infection and elicits interferon production through the cGAS-cGAMP-STING axis. cGAS is activated by dsDNA from viral and bacterial origins as well as dsDNA leaked from damaged mitochondria and nucleus. Eventually, cGAS activation launches the cell into an antiviral state to restrict the replication of both DNA and RNA viruses. Throughout the long co-evolution, viruses devise many strategies to evade cGAS detection or suppress cGAS activation. We recently reported that the Dengue virus protease NS2B3 proteolytically cleaves human cGAS in its N-terminal region, effectively reducing cGAS binding to DNA and consequent production of the second messenger cGAMP. Several other RNA viruses likely adopt the cleavage strategy. Here, we describe a protocol for the purification of recombinant human cGAS and Dengue NS2B3 protease, as well as the in vitro cleavage assay.},
}

@article {pmid39146359,
year = {2024},
author = {von Känel, C and Stettler, P and Esposito, C and Berger, S and Amodeo, S and Oeljeklaus, S and Calderaro, S and Durante, IM and Rašková, V and Warscheid, B and Schneider, A},
title = {Pam16 and Pam18 were repurposed during Trypanosoma brucei evolution to regulate the replication of mitochondrial DNA.},
journal = {PLoS biology},
volume = {22},
number = {8},
pages = {e3002449},
doi = {10.1371/journal.pbio.3002449},
pmid = {39146359},
issn = {1545-7885},
mesh = {*Trypanosoma brucei brucei/metabolism/genetics ; *Protozoan Proteins/metabolism/genetics ; *DNA Replication ; *DNA, Mitochondrial/genetics/metabolism ; Mitochondrial Proteins/metabolism/genetics ; Mitochondria/metabolism/genetics ; Evolution, Molecular ; },
abstract = {Protein import and genome replication are essential processes for mitochondrial biogenesis and propagation. The J-domain proteins Pam16 and Pam18 regulate the presequence translocase of the mitochondrial inner membrane. In the protozoan Trypanosoma brucei, their counterparts are TbPam16 and TbPam18, which are essential for the procyclic form (PCF) of the parasite, though not involved in mitochondrial protein import. Here, we show that during evolution, the 2 proteins have been repurposed to regulate the replication of maxicircles within the intricate kDNA network, the most complex mitochondrial genome known. TbPam18 and TbPam16 have inactive J-domains suggesting a function independent of heat shock proteins. However, their single transmembrane domain is essential for function. Pulldown of TbPam16 identifies a putative client protein, termed MaRF11, the depletion of which causes the selective loss of maxicircles, akin to the effects observed for TbPam18 and TbPam16. Moreover, depletion of the mitochondrial proteasome results in increased levels of MaRF11. Thus, we have discovered a protein complex comprising TbPam18, TbPam16, and MaRF11, that controls maxicircle replication. We propose a working model in which the matrix protein MaRF11 functions downstream of the 2 integral inner membrane proteins TbPam18 and TbPam16. Moreover, we suggest that the levels of MaRF11 are controlled by the mitochondrial proteasome.},
}

*Trypanosoma brucei brucei/metabolism/genetics
*Protozoan Proteins/metabolism/genetics
*DNA Replication
*DNA, Mitochondrial/genetics/metabolism
Mitochondrial Proteins/metabolism/genetics
Mitochondria/metabolism/genetics
Evolution, Molecular

@article {pmid38944824,
year = {2024},
author = {Sepúlveda-Espinoza, F and Cofré-Serrano, A and Veloso-Valeria, T and Quesada-Calderon, S and Guillemin, ML},
title = {Characterization of the organellar genomes of Mazzaella laminarioides and Mazzaella membranacea (Gigartinaceae, Rhodophyta).},
journal = {Journal of phycology},
volume = {60},
number = {4},
pages = {797-805},
doi = {10.1111/jpy.13478},
pmid = {38944824},
issn = {1529-8817},
support = {15150003//Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias/ ; NCN2021-033//Agencia Nacional de Investigación y Desarrollo/ ; 1221477//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 3210788//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; },
mesh = {*Rhodophyta/genetics/classification ; *Genome, Mitochondrial ; *Genome, Chloroplast ; Phylogeny ; Chile ; },
abstract = {Mazzaella, a genus with no genomic resources available, has extensive distribution in the cold waters of the Pacific, where they represent ecologically and economically important species. In this study, we aimed to sequence, assemble, and annotate the complete mitochondrial and chloroplast genomes from two Mazzaella spp. and characterize the intraspecific variation among them. We report for the first time seven whole organellar genomes (mitochondria: OR915856, OR947465, OR947466, OR947467, OR947468, OR947469, OR947470; chloroplast: OR881974, OR909680, OR909681, OR909682, OR909683, OR909684, OR909685) obtained through high-throughput sequencing for six M. laminarioides sampled from three Chilean regions and one M. membranacea. Sequenced Mazzaella mitogenomes have identical gene number, gene order, and genome structure. The same results were observed for assembled plastomes. A total of 52 genes were identified in mitogenomes, and a total of 235 genes were identified in plastomes. Although the M. membranacea plastome included a full-length pbsA gene, in all M. laminarioides samples, the pbsA gene was split in three open reading frames (ORFs). Within M. laminarioides, we observed important plastome lineage-specific variations, such as the pseudogenization of the two hypothetical protein-coding genes, ycf23 and ycf45. Nonsense mutations in the ycf23 and ycf45 genes were only detected in the northern lineage. These results are consistent with phylogenetic reconstructions and divergence time estimation using concatenated coding sequences that not only support the monophyly of M. laminarioides but also underscore that the three M. laminarioides lineages are in an advanced stage of divergence. These new results open the question of the existence of still undisclosed species in M. laminarioides.},
}

*Rhodophyta/genetics/classification
*Genome, Mitochondrial
*Genome, Chloroplast
Phylogeny
Chile

@article {pmid38833723,
year = {2024},
author = {Mukhopadhyay, J and Hausner, G},
title = {Interconnected roles of fungal nuclear- and intron-encoded maturases: at the crossroads of mitochondrial intron splicing.},
journal = {Biochemistry and cell biology = Biochimie et biologie cellulaire},
volume = {},
number = {},
pages = {},
doi = {10.1139/bcb-2024-0046},
pmid = {38833723},
issn = {1208-6002},
abstract = {Group I and II introns are large catalytic RNAs (ribozymes) that are frequently encountered in fungal mitochondrial genomes. The discovery of respiratory mutants linked to intron splicing defects demonstrated that for the efficient removal of organellar introns there appears to be a requirement of protein splicing factors. These splicing factors can be intron-encoded proteins with maturase activities that usually promote the splicing of the introns that encode them (cis-acting) and/or nuclear-encoded factors that can promote the splicing of a range of different introns (trans-acting). Compared to plants organellar introns, fungal mitochondrial intron splicing is still poorly explored, especially in terms of the synergy of nuclear factors with intron-encoded maturases that has direct impact on splicing through their association with intron RNA. In addition, nuclear-encoded accessory factors might drive the splicing impetus through translational activation, mitoribosome assembly, and phosphorylation-mediated RNA turnover. This review explores protein-assisted splicing of introns by nuclear and mitochondrial-encoded maturases as a means of mitonuclear interplay that could respond to environmental and developmental factors promoting phenotypic adaptation and potentially speciation. It also highlights key evolutionary events that have led to changes in structure and ATP-dependence to accommodate the dual functionality of nuclear and organellar splicing factors.},
}

@article {pmid39179249,
year = {2024},
author = {Guo, Y and Wen, H and Chen, Z and Jiao, M and Zhang, Y and Ge, D and Liu, R and Gu, J},
title = {Conjoint analysis of succinylome and phosphorylome reveals imbalanced HDAC phosphorylation-driven succinylayion dynamic contibutes to lung cancer.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
doi = {10.1093/bib/bbae415},
pmid = {39179249},
issn = {1477-4054},
support = {20ZR1410800//Science and Technology Commission of Shanghai Municipality/ ; 82373371//National Science Foundation of China/ ; 2020YFC2008402//National Science and Technology Major Project of China/ ; //Program for Professor of Special Appointment/ ; //Shanghai Institutions of Higher Learning/ ; },
mesh = {Humans ; *Lung Neoplasms/metabolism/genetics/pathology ; Phosphorylation ; *Protein Processing, Post-Translational ; *Histone Deacetylases/metabolism ; Succinic Acid/metabolism ; Mitochondria/metabolism ; },
abstract = {Cancerous genetic mutations result in a complex and comprehensive post-translational modification (PTM) dynamics, in which protein succinylation is well known for its ability to reprogram cell metabolism and is involved in the malignant evolution. Little is known about the regulatory interactions between succinylation and other PTMs in the PTM network. Here, we developed a conjoint analysis and systematic clustering method to explore the intermodification communications between succinylome and phosphorylome from eight lung cancer patients. We found that the intermodification coorperation in both parallel and series. Besides directly participating in metabolism pathways, some phosphosites out of mitochondria were identified as an upstream regulatory modification directing succinylome dynamics in cancer metabolism reprogramming. Phosphorylated activation of histone deacetylase (HDAC) in lung cancer resulted in the removal of acetylation and favored the occurrence of succinylation modification of mitochondrial proteins. These results suggest a tandem regulation between succinylation and phosphorylation in the PTM network and provide HDAC-related targets for intervening mitochondrial succinylation and cancer metabolism reprogramming.},
}

Humans
*Lung Neoplasms/metabolism/genetics/pathology
Phosphorylation
*Protein Processing, Post-Translational
*Histone Deacetylases/metabolism
Succinic Acid/metabolism
Mitochondria/metabolism

@article {pmid39163758,
year = {2024},
author = {Sizek, H and Deritei, D and Fleig, K and Harris, M and Regan, PL and Glass, K and Regan, ER},
title = {Unlocking mitochondrial dysfunction-associated senescence (MiDAS) with NAD[+] - A Boolean model of mitochondrial dynamics and cell cycle control.},
journal = {Translational oncology},
volume = {49},
number = {},
pages = {102084},
doi = {10.1016/j.tranon.2024.102084},
pmid = {39163758},
issn = {1936-5233},
abstract = {The steady accumulation of senescent cells with aging creates tissue environments that aid cancer evolution. Aging cell states are highly heterogeneous. 'Deep senescent' cells rely on healthy mitochondria to fuel a strong proinflammatory secretome, including cytokines, growth and transforming signals. Yet, the physiological triggers of senescence such as reactive oxygen species (ROS) can also trigger mitochondrial dysfunction, and sufficient energy deficit to alter their secretome and cause chronic oxidative stress - a state termed Mitochondrial Dysfunction-Associated Senescence (MiDAS). Here, we offer a mechanistic hypothesis for the molecular processes leading to MiDAS, along with testable predictions. To do this we have built a Boolean regulatory network model that qualitatively captures key aspects of mitochondrial dynamics during cell cycle progression (hyper-fusion at the G1/S boundary, fission in mitosis), apoptosis (fission and dysfunction) and glucose starvation (reversible hyper-fusion), as well as MiDAS in response to SIRT3 knockdown or oxidative stress. Our model reaffirms the protective role of NAD[+] and external pyruvate. We offer testable predictions about the growth factor- and glucose-dependence of MiDAS and its reversibility at different stages of reactive oxygen species (ROS)-induced senescence. Our model provides mechanistic insights into the distinct stages of DNA-damage induced senescence, the relationship between senescence and epithelial-to-mesenchymal transition in cancer and offers a foundation for building multiscale models of tissue aging.},
}

@article {pmid39164316,
year = {2024},
author = {García-Merchán, VH and Palero, F and Rufino, M and Macpherson, E and Abelló, P and Pascual, M},
title = {Mitochondrial, nuclear and morphological differentiation in the swimming crab Liocarcinus depurator along the Atlantic-Mediterranean transition.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19342},
pmid = {39164316},
issn = {2045-2322},
support = {PID2020-118550RB//Ministerio de Ciencia, Innovación y Universidades/ ; },
mesh = {Animals ; *Brachyura/genetics ; Mediterranean Sea ; *Microsatellite Repeats/genetics ; *DNA, Mitochondrial/genetics ; Atlantic Ocean ; Mitochondria/genetics ; Genetic Variation ; Genetics, Population ; Cell Nucleus/genetics ; Selection, Genetic ; },
abstract = {Environmental gradients in the sea may coincide with phenotypic or genetic gradients resulting from an evolutionary balance between selection and dispersal. The population differentiation of the swimming crab, Liocarcinus depurator, an important by-catch species in the Mediterranean Sea and North-East Atlantic, was assessed using both genetic and morphometric approaches. A total of 472 specimens were collected along its distribution area, and 17 morphometric landmarks, one mitochondrial gene (COI) and 11 polymorphic microsatellite markers were scored in 350, 287 and 280 individuals, respectively. Morphometric data lacked significant differences, but genetic analyses showed significant genetic differentiation between Atlantic and Mediterranean populations, with a steeper gradient in COI compared to microsatellite markers. Interestingly, nuclear differentiation was due to an outlier locus with a gradient in the Atlantic-Mediterranean transition area overlapping with the mtDNA gradient. Such overlapping clines are likely to be maintained by natural selection. Our results suggest a scenario of past isolation with local adaptation and secondary contact between the two basins. Local adaptation during the process of vicariance may reinforce genetic differentiation at loci maintained by environmental selection even after secondary contact.},
}

Animals
*Brachyura/genetics
Mediterranean Sea
*Microsatellite Repeats/genetics
*DNA, Mitochondrial/genetics
Atlantic Ocean
Mitochondria/genetics
Genetic Variation
Genetics, Population
Cell Nucleus/genetics
Selection, Genetic

@article {pmid38488948,
year = {2024},
author = {Ren, P and Zhang, J and Vijg, J},
title = {Somatic mutations in aging and disease.},
journal = {GeroScience},
volume = {46},
number = {5},
pages = {5171-5189},
pmid = {38488948},
issn = {2509-2723},
support = {AG017242/GF/NIH HHS/United States ; AG047200/GF/NIH HHS/United States ; AG038072/GF/NIH HHS/United States ; ES029519/GF/NIH HHS/United States ; HL145560/GF/NIH HHS/United States ; AG056278/GF/NIH HHS/United States ; 82172461//National Natural Science Foundation of China/ ; BC180689P1//DOD grant/ ; },
mesh = {*Aging/genetics ; Humans ; Animals ; *Mutation ; Mice ; Mutation Rate ; DNA Repair/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Time always leaves its mark, and our genome is no exception. Mutations in the genome of somatic cells were first hypothesized to be the cause of aging in the 1950s, shortly after the molecular structure of DNA had been described. Somatic mutation theories of aging are based on the fact that mutations in DNA as the ultimate template for all cellular functions are irreversible. However, it took until the 1990s to develop the methods to test if DNA mutations accumulate with age in different organs and tissues and estimate the severity of the problem. By now, numerous studies have documented the accumulation of somatic mutations with age in normal cells and tissues of mice, humans, and other animals, showing clock-like mutational signatures that provide information on the underlying causes of the mutations. In this review, we will first briefly discuss the recent advances in next-generation sequencing that now allow quantitative analysis of somatic mutations. Second, we will provide evidence that the mutation rate differs between cell types, with a focus on differences between germline and somatic mutation rate. Third, we will discuss somatic mutational signatures as measures of aging, environmental exposure, and activities of DNA repair processes. Fourth, we will explain the concept of clonally amplified somatic mutations, with a focus on clonal hematopoiesis. Fifth, we will briefly discuss somatic mutations in the transcriptome and in our other genome, i.e., the genome of mitochondria. We will end with a brief discussion of a possible causal contribution of somatic mutations to the aging process.},
}

*Aging/genetics
Humans
Animals
*Mutation
Mice
Mutation Rate
DNA Repair/genetics
High-Throughput Nucleotide Sequencing

@article {pmid39160470,
year = {2024},
author = {Bajić, V and Schulmann, VH and Nowick, K},
title = {mtDNA "nomenclutter" and its consequences on the interpretation of genetic data.},
journal = {BMC ecology and evolution},
volume = {24},
number = {1},
pages = {110},
pmid = {39160470},
issn = {2730-7182},
mesh = {*DNA, Mitochondrial/genetics ; Humans ; *Haplotypes/genetics ; *Phylogeny ; Genetic Variation/genetics ; Terminology as Topic ; },
abstract = {Population-based studies of human mitochondrial genetic diversity often require the classification of mitochondrial DNA (mtDNA) haplotypes into more than 5400 described haplogroups, and further grouping those into hierarchically higher haplogroups. Such secondary haplogroup groupings (e.g., "macro-haplogroups") vary across studies, as they depend on the sample quality, technical factors of haplogroup calling, the aims of the study, and the researchers' understanding of the mtDNA haplogroup nomenclature. Retention of historical nomenclature coupled with a growing number of newly described mtDNA lineages results in increasingly complex and inconsistent nomenclature that does not reflect phylogeny well. This "clutter" leaves room for grouping errors and inconsistencies across scientific publications, especially when the haplogroup names are used as a proxy for secondary groupings, and represents a source for scientific misinterpretation. Here we explore the effects of phylogenetically insensitive secondary mtDNA haplogroup groupings, and the lack of standardized secondary haplogroup groupings on downstream analyses and interpretation of genetic data. We demonstrate that frequency-based analyses produce inconsistent results when different secondary mtDNA groupings are applied, and thus allow for vastly different interpretations of the same genetic data. The lack of guidelines and recommendations on how to choose appropriate secondary haplogroup groupings presents an issue for the interpretation of results, as well as their comparison and reproducibility across studies. To reduce biases originating from arbitrarily defined secondary nomenclature-based groupings, we suggest that future updates of mtDNA phylogenies aimed for the use in mtDNA haplogroup nomenclature should also provide well-defined and standardized sets of phylogenetically meaningful algorithm-based secondary haplogroup groupings such as "macro-haplogroups", "meso-haplogroups", and "micro-haplogroups". Ideally, each of the secondary haplogroup grouping levels should be informative about different human population history events. Those phylogenetically informative levels of haplogroup groupings can be easily defined using TreeCluster, and then implemented into haplogroup callers such as HaploGrep3. This would foster reproducibility across studies, provide a grouping standard for population-based studies, and reduce errors associated with haplogroup nomenclatures in future studies.},
}

*DNA, Mitochondrial/genetics
Humans
*Haplotypes/genetics
*Phylogeny
Genetic Variation/genetics
Terminology as Topic

@article {pmid39158587,
year = {2024},
author = {Ge, J and Li, H and Liang, X and Zhou, B},
title = {SLC30A9: an evolutionarily conserved mitochondrial zinc transporter essential for mammalian early embryonic development.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {81},
number = {1},
pages = {357},
pmid = {39158587},
issn = {1420-9071},
support = {2018YFA0900100//National Key Research and Development Program of China/ ; 31971087//Nationa Natural Science Foundation of China/ ; KQTD20180413181837372//Shenzhen Science and Technology Innovation Program/ ; },
mesh = {Animals ; *Cation Transport Proteins/metabolism/genetics ; Humans ; *Zinc/metabolism ; Mice ; *Mitochondria/metabolism ; *Embryonic Development/genetics ; Drosophila melanogaster/metabolism/genetics/embryology ; Evolution, Molecular ; Mice, Knockout ; Amino Acid Sequence ; Mitochondrial Proteins/metabolism/genetics ; Transcription Factors ; Cell Cycle Proteins ; },
abstract = {SLC30A9 (ZnT9) is a mitochondria-resident zinc transporter. Mutations in SLC30A9 have been reported in human patients with a novel cerebro-renal syndrome. Here, we show that ZnT9 is an evolutionarily highly conserved protein, with many regions extremely preserved among evolutionarily distant organisms. In Drosophila melanogaster (the fly), ZnT9 (ZnT49B) knockdown results in acutely impaired movement and drastic mitochondrial deformation. Severe Drosophila ZnT9 (dZnT9) reduction and ZnT9-null mutant flies are pupal lethal. The phenotype of dZnT9 knockdown can be partially rescued by mouse ZnT9 expression or zinc chelator TPEN, indicating the defect of dZnT9 loss is indeed a result of zinc dyshomeostasis. Interestingly, in the mouse, germline loss of Znt9 produces even more extreme phenotypes: the mutant embryos exhibit midgestational lethality with severe development abnormalities. Targeted mutagenesis of Znt9 in the mouse brain leads to serious dwarfism and physical incapacitation, followed by death shortly. Strikingly, the GH/IGF-1 signals are almost non-existent in these tissue-specific knockout mice, consistent with the medical finding in some human patients with severe mitochondrial deficiecny. ZnT9 mutations cause mitochondrial zinc dyshomeostasis, and we demonstrate mechanistically that mitochondrial zinc elevation quickly and potently inhibits the activities of respiration complexes. These results reveal the critical role of ZnT9 and mitochondrial zinc homeostasis in mammalian development. Based on our functional analyses, we finally discussed the possible nature of the so far identified human SLC30A9 mutations.},
}

Animals
*Cation Transport Proteins/metabolism/genetics
Humans
*Zinc/metabolism
Mice
*Mitochondria/metabolism
*Embryonic Development/genetics
Drosophila melanogaster/metabolism/genetics/embryology
Evolution, Molecular
Mice, Knockout
Amino Acid Sequence
Mitochondrial Proteins/metabolism/genetics
Transcription Factors
Cell Cycle Proteins

@article {pmid38834883,
year = {2024},
author = {Tao, M and Chen, J and Cui, C and Xu, Y and Xu, J and Shi, Z and Yun, J and Zhang, J and Ou, GZ and Liu, C and Chen, Y and Zhu, ZR and Pan, R and Xu, S and Chen, XX and Rokas, A and Zhao, Y and Wang, S and Huang, J and Shen, XX},
title = {Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes.},
journal = {Nature aging},
volume = {4},
number = {8},
pages = {1076-1088},
pmid = {38834883},
issn = {2662-8465},
support = {32071665//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32230015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32325044//National Natural Science Foundation of China (National Science Foundation of China)/ ; DEB-2110404//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Longevity/genetics ; Humans ; *Caenorhabditis elegans/genetics ; *Evolution, Molecular ; Cell Nucleus/genetics/metabolism ; Oxidative Phosphorylation ; Insecta/genetics ; Genome, Insect/genetics ; Mitochondria/genetics/metabolism ; Cellular Senescence/genetics ; },
abstract = {Oxidative phosphorylation, essential for energy metabolism and linked to the regulation of longevity, involves mitochondrial and nuclear genes. The functions of these genes and their evolutionary rate covariation (ERC) have been extensively studied, but little is known about whether other nuclear genes not targeted to mitochondria evolutionarily and functionally interact with mitochondrial genes. Here we systematically examined the ERC of mitochondrial and nuclear benchmarking universal single-copy ortholog (BUSCO) genes from 472 insects, identifying 75 non-mitochondria-targeted nuclear genes. We found that the uncharacterized gene CG11837-a putative ortholog of human DIMT1-regulates insect lifespan, as its knockdown reduces median lifespan in five diverse insect species and Caenorhabditis elegans, whereas its overexpression extends median lifespans in fruit flies and C. elegans and enhances oxidative phosphorylation gene activity. Additionally, DIMT1 overexpression protects human cells from cellular senescence. Together, these data provide insights into the ERC of mito-nuclear genes and suggest that CG11837 may regulate longevity across animals.},
}

Animals
*Longevity/genetics
Humans
*Caenorhabditis elegans/genetics
*Evolution, Molecular
Cell Nucleus/genetics/metabolism
Oxidative Phosphorylation
Insecta/genetics
Genome, Insect/genetics
Mitochondria/genetics/metabolism
Cellular Senescence/genetics

@article {pmid38908469,
year = {2024},
author = {Lu, H and Liu, C and Yang, C and He, Z and Wang, L and Song, L},
title = {Genome-wide identification of the HSP70 genes in Pacific oyster Magallana gigas and their response to heat stress.},
journal = {Cell stress & chaperones},
volume = {29},
number = {4},
pages = {589-602},
pmid = {38908469},
issn = {1466-1268},
mesh = {Animals ; *HSP70 Heat-Shock Proteins/genetics/metabolism ; *Heat-Shock Response/genetics ; Phylogeny ; Ostreidae/genetics/metabolism ; Crassostrea/genetics/metabolism ; Multigene Family ; Genome ; },
abstract = {Heat shock protein 70 (HSP70), the most prominent and well-characterized stress protein in animals, plays an important role in assisting animals in responding to various adverse conditions. In the present study, a total of 113 HSP70 gene family members were identified in the updated genome of Magallana gigas (designated MgHSP70) (previously known as Crassostrea gigas). There were 75, 12, 11, and 8 HSP70s located in the cytoplasm, nucleus, mitochondria, and endoplasmic reticulum, respectively, and 7 HSP70s were located in both the nucleus and cytoplasm. Among 113 MgHSP70 genes, 107 were unevenly distributed in 8 chromosomes of M. gigas with the greatest number in chromosome 07 (61 genes, 57.01%). The MgHSP70 gene family members were mainly assigned into five clusters, among which the HSPa12 subfamily underwent lineage-specific expansion, consisting of 89 members. A total of 68 MgHSP70 genes (60.18%) were tandemly duplicated and formed 30 gene pairs, among which 14 gene pairs were under strong positive selection. In general, the expression of MgHSP70s was tissue-specific, with the highest expression in labial palp and gill and the lowest expression in adductor muscle and hemocytes. There were 35, 31, and 47 significantly upregulated genes at 6, 12, and 24 h after heat shock treatment (28 °C), respectively. The expression patterns of different tandemly duplicated genes exhibited distinct characteristics after shock treatment, indicating that these genes may have different functions. Nevertheless, genes within the same tandemly duplicated group exhibit similar expression patterns. Most of the tandemly duplicated HSP70 gene pairs showed the highest expression levels at 24 h. This study provides a comprehensive description of the MgHSP70 gene family in M. gigas and offers valuable insights into the functions of HSP70 in the mollusc adaptation of oysters to environmental stress.},
}

Animals
*HSP70 Heat-Shock Proteins/genetics/metabolism
*Heat-Shock Response/genetics
Phylogeny
Ostreidae/genetics/metabolism
Crassostrea/genetics/metabolism
Multigene Family
Genome

@article {pmid39145390,
year = {2024},
author = {Kutzer, MAM and Cornish, B and Jamieson, M and Zawistowska, O and Monteith, KM and Vale, PF},
title = {Mitochondrial background can explain variable costs of immune deployment.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voae082},
pmid = {39145390},
issn = {1420-9101},
support = {RPG-2018-369//Leverhulme Trust Research Project/ ; },
abstract = {Organismal health and survival depend on the ability to mount an effective immune response against infection. Yet immune defence may be energy-demanding, resulting in fitness costs if investment in immune function deprives other physiological processes of resources. While evidence of costly immunity resulting in reduced longevity and reproduction is common, the role of energy-producing mitochondria on the magnitude of these costs is unknown. Here, we employed Drosophila melanogaster cybrid lines, where several mitochondrial genotypes (mitotypes) were introgressed onto a single nuclear genetic background, to explicitly test the role of mitochondrial variation on the costs of immune stimulation. We exposed female flies carrying one of nine distinct mitotypes to either a benign, heat-killed bacterial pathogen (stimulating immune deployment while avoiding pathology) or to a sterile control and measured lifespan, fecundity, and locomotor activity. We observed mitotype-specific costs of immune stimulation and identified a positive genetic correlation in immune-stimulated flies between lifespan and the proportion of time cybrids spent moving while alive. Our results suggests that costs of immunity are highly variable depending on the mitochondrial genome, adding to a growing body of work highlighting the important role of mitochondrial variation in host-pathogen interactions.},
}

@article {pmid39132738,
year = {2024},
author = {Leung, A and Patel, R and Chirachon, V and Stata, M and Macfarlane, TD and Ludwig, M and Busch, FA and Sage, TL and Sage, RF},
title = {Tribulus (Zygophyllaceae) as a case study for the evolution of C2 and C4 photosynthesis.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15069},
pmid = {39132738},
issn = {1365-3040},
support = {//Queen Elizabeth II/Charles E. Eckenwalder Graduate Scholarship/ ; NE/W00674X/1//Natural Environment Research Council/ ; DP130102243//Australian Research Council/ ; RGPIN-2020-05925//Natural Sciences and Engineering Research Council/ ; RGPIN-2017-06476//Natural Sciences and Engineering Research Council/ ; },
abstract = {C2 photosynthesis is a photosynthetic pathway in which photorespiratory CO2 release and refixation are enhanced in leaf bundle sheath (BS) tissues. The evolution of C2 photosynthesis has been hypothesized to be a major step in the origin of C4 photosynthesis, highlighting the importance of studying C2 evolution. In this study, physiological, anatomical, ultrastructural, and immunohistochemical properties of leaf photosynthetic tissues were investigated in six non-C4 Tribulus species and four C4 Tribulus species. At 42°C, T. cristatus exhibited a photosynthetic CO2 compensation point in the absence of respiration (C*) of 21 µmol mol[-1], below the C3 mean C* of 73 µmol mol[-1]. Tribulus astrocarpus had a C* value at 42°C of 55 µmol mol[-1], intermediate between the C3 species and the C2 T. cristatus. Glycine decarboxylase (GDC) allocation to BS tissues was associated with lower C*. Tribulus cristatus and T. astrocarpus allocated 86% and 30% of their GDC to the BS tissues, respectively, well above the C3 mean of 11%. Tribulus astrocarpus thus exhibits a weaker C2 (termed sub-C2) phenotype. Increased allocation of mitochondria to the BS and decreased length-to-width ratios of BS cells, were present in non-C4 species, indicating a potential role in C2 and C4 evolution.},
}

@article {pmid39039280,
year = {2024},
author = {An, J and Nam, CH and Kim, R and Lee, Y and Won, H and Park, S and Lee, WH and Park, H and Yoon, CJ and An, Y and Kim, JH and Jun, JK and Bae, JM and Shin, EC and Kim, B and Cha, YJ and Kwon, HW and Oh, JW and Park, JY and Kim, MJ and Ju, YS},
title = {Mitochondrial DNA mosaicism in normal human somatic cells.},
journal = {Nature genetics},
volume = {56},
number = {8},
pages = {1665-1677},
pmid = {39039280},
issn = {1546-1718},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Mosaicism ; *Mutation ; Heteroplasmy/genetics ; Mutation Rate ; Mitochondria/genetics ; Genome, Mitochondrial ; DNA Replication/genetics ; Female ; Male ; },
abstract = {Somatic cells accumulate genomic alterations with age; however, our understanding of mitochondrial DNA (mtDNA) mosaicism remains limited. Here we investigated the genomes of 2,096 clones derived from three cell types across 31 donors, identifying 6,451 mtDNA variants with heteroplasmy levels of ≳0.3%. While the majority of these variants were unique to individual clones, suggesting stochastic acquisition with age, 409 variants (6%) were shared across multiple embryonic lineages, indicating their origin from heteroplasmy in fertilized eggs. The mutational spectrum exhibited replication-strand bias, implicating mtDNA replication as a major mutational process. We evaluated the mtDNA mutation rate (5.0 × 10[-8] per base pair) and a turnover frequency of 10-20 per year, which are fundamental components shaping the landscape of mtDNA mosaicism over a lifetime. The expansion of mtDNA-truncating mutations toward homoplasmy was substantially suppressed. Our findings provide comprehensive insights into the origins, dynamics and functional consequences of mtDNA mosaicism in human somatic cells.},
}

Humans
*DNA, Mitochondrial/genetics
*Mosaicism
*Mutation
Heteroplasmy/genetics
Mutation Rate
Mitochondria/genetics
Genome, Mitochondrial
DNA Replication/genetics
Female
Male

@article {pmid39128009,
year = {2024},
author = {Harry, CJ and Hibshman, JD and Damatac, A and Davidson, PL and Estermann, MA and Flores-Flores, M and Holmes, CM and Lázaro, J and Legere, EA and Leyhr, J and Thendral, SB and Vincent, BA and Goldstein, B},
title = {Protocol for fluorescent live-cell staining of tardigrades.},
journal = {STAR protocols},
volume = {5},
number = {3},
pages = {103232},
doi = {10.1016/j.xpro.2024.103232},
pmid = {39128009},
issn = {2666-1667},
abstract = {Tardigrades are microscopic organisms with exceptional resilience to environmental extremes. Most protocols to visualize the internal anatomy of tardigrades rely on fixation, hampering our understanding of dynamic changes to organelles and other subcellular components. Here, we provide protocols for staining live tardigrade adults and other postembryonic stages, facilitating real-time visualization of structures including lipid droplets, mitochondria, lysosomes, and DNA.},
}

@article {pmid39126033,
year = {2024},
author = {Zhan, L and Chen, Y and He, J and Guo, Z and Wu, L and Storey, KB and Zhang, J and Yu, D},
title = {The Phylogenetic Relationships of Major Lizard Families Using Mitochondrial Genomes and Selection Pressure Analyses in Anguimorpha.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
doi = {10.3390/ijms25158464},
pmid = {39126033},
issn = {1422-0067},
support = {31801963//the National Natural Science Foundation of Chin/ ; LQ16C030001//the Zhejiang Province Natural Science Foundation/ ; },
mesh = {Animals ; *Lizards/genetics/classification ; *Phylogeny ; *Genome, Mitochondrial/genetics ; *Selection, Genetic ; Evolution, Molecular ; },
abstract = {Anguimorpha, within the order Squamata, represents a group with distinct morphological and behavioral characteristics in different ecological niches among lizards. Within Anguimorpha, there is a group characterized by limb loss, occupying lower ecological niches, concentrated within the subfamily Anguinae. Lizards with limbs and those without exhibit distinct locomotor abilities when adapting to their habitats, which in turn necessitate varying degrees of energy expenditure. Mitochondria, known as the metabolic powerhouses of cells, play a crucial role in providing approximately 95% of an organism's energy. Functionally, mitogenomes (mitochondrial genomes) can serve as a valuable tool for investigating potential adaptive evolutionary selection behind limb loss in reptiles. Due to the variation of mitogenome structures among each species, as well as its simple genetic structure, maternal inheritance, and high evolutionary rate, the mitogenome is increasingly utilized to reconstruct phylogenetic relationships of squamate animals. In this study, we sequenced the mitogenomes of two species within Anguimorpha as well as the mitogenomes of two species in Gekkota and four species in Scincoidea. We compared these data with the mitogenome content and evolutionary history of related species. Within Anguimorpha, between the mitogenomes of limbless and limbed lizards, a branch-site model analysis supported the presence of 10 positively selected sites: Cytb protein (at sites 183 and 187), ND2 protein (at sites 90, 155, and 198), ND3 protein (at site 21), ND5 protein (at sites 12 and 267), and ND6 protein (at sites 72 and 119). These findings suggested that positive selection of mitogenome in limbless lizards may be associated with the energy requirements for their locomotion. Additionally, we acquired data from 205 mitogenomes from the NCBI database. Bayesian inference (BI) and Maximum Likelihood (ML) trees were constructed using the 13 mitochondrial protein-coding genes (PCGs) and two rRNAs (12S rRNA and 16S rRNA) from 213 mitogenomes. Our phylogenetic tree and the divergence time estimates for Squamata based on mitogenome data are consistent with results from previous studies. Gekkota was placed at the root of Squamata in both BI and ML trees. However, within the Toxicofera clade, due to long-branch attraction, Anguimorpha and (Pleurodonta + (Serpentes + Acrodonta)) were closely related groupings, which might indicate errors and also demonstrate that mitogenome-based phylogenetic trees may not effectively resolve long-branch attraction issues. Additionally, we reviewed the origin and diversification of Squamata throughout the Mesozoic era, suggesting that Squamata originated in the Late Triassic (206.05 Mya), with the diversification of various superfamilies occurring during the Cretaceous period. Future improvements in constructing squamate phylogenetic relationships using mitogenomes will rely on identifying snake and acrodont species with slower evolutionary rates, ensuring comprehensive taxonomic coverage of squamate diversity, and increasing the number of genes analyzed.},
}

Animals
*Lizards/genetics/classification
*Phylogeny
*Genome, Mitochondrial/genetics
*Selection, Genetic
Evolution, Molecular

@article {pmid39125940,
year = {2024},
author = {Zhang, X and Ding, Z and Lou, H and Han, R and Ma, C and Yang, S},
title = {A Systematic Review and Developmental Perspective on Origin of CMS Genes in Crops.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
doi = {10.3390/ijms25158372},
pmid = {39125940},
issn = {1422-0067},
support = {No. 31200908 and No. 8176140709//the National Natural Science Foundation of China/ ; },
mesh = {*Crops, Agricultural/genetics/growth & development ; *Genome, Mitochondrial ; *DNA, Mitochondrial/genetics ; Plant Infertility/genetics ; Cytoplasm/genetics/metabolism ; Plant Breeding/methods ; Mitochondria/genetics/metabolism ; Genes, Mitochondrial ; },
abstract = {Cytoplasmic male sterility (CMS) arises from the incompatibility between the nucleus and cytoplasm as typical representatives of the chimeric structures in the mitochondrial genome (mitogenome), which has been extensively applied for hybrid seed production in various crops. The frequent occurrence of chimeric mitochondrial genes leading to CMS is consistent with the mitochondrial DNA (mtDNA) evolution. The sequence conservation resulting from faithfully maternal inheritance and the chimeric structure caused by frequent sequence recombination have been defined as two major features of the mitogenome. However, when and how these chimeric mitochondrial genes appear in the context of the highly conserved reproduction of mitochondria is an enigma. This review, therefore, presents the critical view of the research on CMS in plants to elucidate the mechanisms of this phenomenon. Generally, distant hybridization is the main mechanism to generate an original CMS source in natural populations and in breeding. Mitochondria and mitogenomes show pleomorphic and dynamic changes at key stages of the life cycle. The promitochondria in dry seeds develop into fully functioning mitochondria during seed imbibition, followed by massive mitochondria or mitogenome fusion and fission in the germination stage along with changes in the mtDNA structure and quantity. The mitogenome stability is controlled by nuclear loci, such as the nuclear gene Msh1. Its suppression leads to the rearrangement of mtDNA and the production of heritable CMS genes. An abundant recombination of mtDNA is also often found in distant hybrids and somatic/cybrid hybrids. Since mtDNA recombination is ubiquitous in distant hybridization, we put forward a hypothesis that the original CMS genes originated from mtDNA recombination during the germination of the hybrid seeds produced from distant hybridizations to solve the nucleo-cytoplasmic incompatibility resulting from the allogenic nuclear genome during seed germination.},
}

*Crops, Agricultural/genetics/growth & development
*Genome, Mitochondrial
*DNA, Mitochondrial/genetics
Plant Infertility/genetics
Cytoplasm/genetics/metabolism
Plant Breeding/methods
Mitochondria/genetics/metabolism
Genes, Mitochondrial

@article {pmid39122691,
year = {2024},
author = {Williams, SK and Jerlström Hultqvist, J and Eglit, Y and Salas-Leiva, DE and Curtis, B and Orr, RJS and Stairs, CW and Atalay, TN and MacMillan, N and Simpson, AGB and Roger, AJ},
title = {Extreme mitochondrial reduction in a novel group of free-living metamonads.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6805},
pmid = {39122691},
issn = {2041-1723},
support = {FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; },
mesh = {*Mitochondria/metabolism/genetics ; *Phylogeny ; *Proteome/metabolism/genetics ; Transcriptome ; Eukaryota/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Iron-Sulfur Proteins/metabolism/genetics ; },
abstract = {Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.},
}

*Mitochondria/metabolism/genetics
*Phylogeny
*Proteome/metabolism/genetics
Transcriptome
Eukaryota/genetics/metabolism/classification
Gene Transfer, Horizontal
Iron-Sulfur Proteins/metabolism/genetics

@article {pmid39120309,
year = {2024},
author = {Proust, B and Herak Bosnar, M and Ćetković, H and Tokarska-Schlattner, M and Schlattner, U},
title = {Mitochondrial NME6: A Paradigm Change within the NME/NDP Kinase Protein Family?.},
journal = {Cells},
volume = {13},
number = {15},
pages = {},
doi = {10.3390/cells13151278},
pmid = {39120309},
issn = {2073-4409},
support = {ANR-15-IDEX-02 SYMER//Agence Nationale de la Recherche/ ; IP-2022-10-7420//Croatian Science Foundation/ ; },
mesh = {Humans ; Animals ; *Mitochondria/metabolism ; Mitochondrial Proteins/metabolism/genetics ; NM23 Nucleoside Diphosphate Kinases/metabolism/genetics ; Nucleoside Diphosphate Kinase D/metabolism/genetics ; },
abstract = {Eukaryotic NMEs/NDP kinases are a family of 10 multifunctional proteins that occur in different cellular compartments and interact with various cellular components (proteins, membranes, and DNA). In contrast to the well-studied Group I NMEs (NME1-4), little is known about the more divergent Group II NMEs (NME5-9). Three recent publications now shed new light on NME6. First, NME6 is a third mitochondrial NME, largely localized in the matrix space, associated with the mitochondrial inner membrane. Second, while its monomeric form is inactive, NME6 gains NDP kinase activity through interaction with mitochondrial RCC1L. This challenges the current notion that mammalian NMEs require the formation of hexamers to become active. The formation of complexes between NME6 and RCC1L, likely heterodimers, seemingly obviates the necessity for hexamer formation, stabilizing a NDP kinase-competent conformation. Third, NME6 is involved in mitochondrial gene maintenance and expression by providing (d)NTPs for replication and transcription (in particular the pyrimidine nucleotides) and by a less characterized mechanism that supports mitoribosome function. This review offers an overview of NME evolution and structure and highlights the new insight into NME6. The new findings position NME6 as the most comprehensively studied protein in NME Group II and may even suggest it as a new paradigm for related family members.},
}

Humans
Animals
*Mitochondria/metabolism
Mitochondrial Proteins/metabolism/genetics
NM23 Nucleoside Diphosphate Kinases/metabolism/genetics
Nucleoside Diphosphate Kinase D/metabolism/genetics

@article {pmid39119601,
year = {2024},
author = {Zachos, KA and Gamboa, JA and Dewji, AS and Lee, J and Brijbassi, S and Andreazza, AC},
title = {The interplay between mitochondria, the gut microbiome and metabolites and their therapeutic potential in primary mitochondrial disease.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1428242},
doi = {10.3389/fphar.2024.1428242},
pmid = {39119601},
issn = {1663-9812},
abstract = {The various roles of the mitochondria and the microbiome in health and disease have been thoroughly investigated, though they are often examined independently and in the context of chronic disease. However, the mitochondria and microbiome are closely connected, namely, through their evolution, maternal inheritance patterns, overlapping role in many diseases and their importance in the maintenance of human health. The concept known as the "mitochondria-microbiome crosstalk" is the ongoing bidirectional crosstalk between these two entities and warrants further exploration and consideration, especially in the context of primary mitochondrial disease, where mitochondrial dysfunction can be detrimental for clinical manifestation of disease, and the role and composition of the microbiome is rarely investigated. A potential mechanism underlying this crosstalk is the role of metabolites from both the mitochondria and the microbiome. During digestion, gut microbes modulate compounds found in food, which can produce metabolites with various bioactive effects. Similarly, mitochondrial metabolites are produced from substrates that undergo biochemical processes during cellular respiration. This review aims to provide an overview of current literature examining the mitochondria-microbiome crosstalk, the role of commonly studied metabolites serve in signaling and mediating these biochemical pathways, and the impact diet has on both the mitochondria and the microbiome. As a final point, this review highlights the up-to-date implications of the mitochondria-microbiome crosstalk in mitochondrial disease and its potential as a therapeutic tool or target.},
}

@article {pmid39111696,
year = {2024},
author = {Wu, Y and Liu, Y and Feng, Y and Li, X and Lu, Z and Gu, H and Li, W and Hill, LJ and Ou, S},
title = {Evolution of therapeutic strategy based on oxidant-antioxidant balance for Fuchs endothelial corneal dystrophy.},
journal = {The ocular surface},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtos.2024.08.003},
pmid = {39111696},
issn = {1937-5913},
abstract = {Fuchs endothelial corneal dystrophy (FECD) stands as the most prevalent primary corneal endothelial dystrophy worldwide, posing a significant risk to corneal homeostasis and clarity. Corneal endothelial cells exhibit susceptibility to oxidative stress, suggesting a nuanced relationship between oxidant-antioxidant imbalance and FECD pathogenesis, irrespective of FECD genotype. Given the constrained availability of corneal transplants, exploration into non-surgical interventions becomes crucial. This encompasses traditional antioxidants, small molecule compounds, biologics, and diverse non-drug therapies, such as gene-related therapy, hydrogen therapy and near infrared light therapy. This review concentrates on elucidating the mechanisms behind oxidant-antioxidant imbalance and the evolution of strategies to restore oxidant-antioxidant balance in FECD. It provides a comprehensive overview of both conventional and emerging therapeutic approaches, offering valuable insights for the advancement of non-surgical treatment modalities. The findings herein might establish a robust foundation for future research and the therapeutic strategy of FECD.},
}

@article {pmid39107687,
year = {2024},
author = {Raynes, Y and Santiago, JC and Lemieux, FA and Darwin, L and Rand, DM},
title = {Sex, tissue, and mitochondrial interactions modify the transcriptional response to rapamycin in Drosophila.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {766},
pmid = {39107687},
issn = {1471-2164},
mesh = {Animals ; *Sirolimus/pharmacology ; Female ; Male ; *Mitochondria/metabolism/drug effects/genetics ; Drosophila melanogaster/genetics/drug effects ; Sex Factors ; TOR Serine-Threonine Kinases/metabolism ; Organ Specificity/genetics ; Drosophila/genetics/drug effects ; Transcription, Genetic/drug effects ; Gene Expression Profiling ; },
abstract = {BACKGROUND: Many common diseases exhibit uncontrolled mTOR signaling, prompting considerable interest in the therapeutic potential of mTOR inhibitors, such as rapamycin, to treat a range of conditions, including cancer, aging-related pathologies, and neurological disorders. Despite encouraging preclinical results, the success of mTOR interventions in the clinic has been limited by off-target side effects and dose-limiting toxicities. Improving clinical efficacy and mitigating side effects require a better understanding of the influence of key clinical factors, such as sex, tissue, and genomic background, on the outcomes of mTOR-targeting therapies.

RESULTS: We assayed gene expression with and without rapamycin exposure across three distinct body parts (head, thorax, abdomen) of D. melanogaster flies, bearing either their native melanogaster mitochondrial genome or the mitochondrial genome from a related species, D. simulans. The fully factorial RNA-seq study design revealed a large number of genes that responded to the rapamycin treatment in a sex-dependent and tissue-dependent manner, and relatively few genes with the transcriptional response to rapamycin affected by the mitochondrial background. Reanalysis of an earlier study confirmed that mitochondria can have a temporal influence on rapamycin response.

CONCLUSIONS: We found significant and wide-ranging effects of sex and body part, alongside a subtle, potentially time-dependent, influence of mitochondria on the transcriptional response to rapamycin. Our findings suggest a number of pathways that could be crucial for predicting potential side effects of mTOR inhibition in a particular sex or tissue. Further studies of the temporal response to rapamycin are necessary to elucidate the effects of the mitochondrial background on mTOR and its inhibition.},
}

Animals
*Sirolimus/pharmacology
Female
Male
*Mitochondria/metabolism/drug effects/genetics
Drosophila melanogaster/genetics/drug effects
Sex Factors
TOR Serine-Threonine Kinases/metabolism
Organ Specificity/genetics
Drosophila/genetics/drug effects
Transcription, Genetic/drug effects
Gene Expression Profiling

@article {pmid39031116,
year = {2024},
author = {Korábek, O and Hausdorf, B},
title = {Accelerated mitochondrial evolution and asymmetric fitness of hybrids contribute to the persistence of Helix thessalica in the Helix pomatia range.},
journal = {Molecular ecology},
volume = {33},
number = {16},
pages = {e17474},
doi = {10.1111/mec.17474},
pmid = {39031116},
issn = {1365-294X},
support = {UNCE/24/SCI/006//Univerzita Karlova v Praze/ ; },
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Hybridization, Genetic ; *Gene Flow ; *Helix, Snails/genetics ; Genome, Mitochondrial ; Genetic Fitness ; Evolution, Molecular ; Genetics, Population ; Mitochondria/genetics ; Selection, Genetic ; },
abstract = {Interbreeding and introgression between recently diverged species is common. However, the processes that prevent these species from merging where they co-occur are not well understood. We studied the mechanisms that allowed an isolated group of populations of the snail Helix thessalica to persist within the range of the related Helix pomatia despite high gene flow. Using genomic cline analysis, we found that the nuclear gene flow between the two taxa across the mosaic hybrid zone was not different from that expected under neutral admixture, but that the exchange of mtDNA was asymmetric. Tests showed that there is relaxed selection in the mitochondrial genome of H. thessalica and that the substitution rate is elevated compared to that of H. pomatia. A lack of hybrids that combine the mtDNA of H. thessalica with a mainly (>46%) H. pomatia genomic background indicates that the nuclear-encoded mitochondrial proteins of H. pomatia are not well adapted to the more rapidly evolving proteins and RNAs encoded by the mitochondrion of H. thessalica. The presumed reduction of fitness of hybrids with the fast-evolving mtDNA of H. thessalica and a high H. pomatia ancestry, similar to 'Darwin's Corollary to Haldane's rule', resulted in a relative loss of H. pomatia nuclear ancestry compared to H. thessalica ancestry in the hybrid zone. This probably prevents the H. thessalica populations from merging quickly with the surrounding H. pomatia populations and supports the hypothesis that incompatibilities between rapidly evolving mitochondrial genes and nuclear genes contribute to speciation.},
}

Animals
*DNA, Mitochondrial/genetics
*Hybridization, Genetic
*Gene Flow
*Helix, Snails/genetics
Genome, Mitochondrial
Genetic Fitness
Evolution, Molecular
Genetics, Population
Mitochondria/genetics
Selection, Genetic

@article {pmid39101615,
year = {2024},
author = {Veeraragavan, S and Johansen, M and Johnston, IG},
title = {Evolution and maintenance of mtDNA gene content across eukaryotes.},
journal = {The Biochemical journal},
volume = {481},
number = {15},
pages = {1015-1042},
doi = {10.1042/BCJ20230415},
pmid = {39101615},
issn = {1470-8728},
mesh = {Animals ; *DNA, Mitochondrial/genetics/metabolism ; *Evolution, Molecular ; Eukaryota/genetics ; Humans ; Recombination, Genetic ; Mitochondria/genetics/metabolism ; Genes, Mitochondrial ; },
abstract = {Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review, we will discuss some possible answers to these questions, attempting a broad perspective across eukaryotes. We hope to cover some interesting features which may be less familiar from the perspective of particular species, including the ubiquity of recombination outside bilaterian animals, encrypted chainmail-like mtDNA, single genes split over multiple mtDNA chromosomes, triparental inheritance, gene transfer by grafting, gain of mtDNA recombination factors, social networks of mitochondria, and the role of mtDNA dysfunction in feeding the world. We will discuss a unifying picture where organismal ecology and gene-specific features together influence whether organism X retains mtDNA gene Y, and where ecology and development together determine which strategies, importantly including recombination, are used to maintain the mtDNA genes that are retained.},
}

Animals
*DNA, Mitochondrial/genetics/metabolism
*Evolution, Molecular
Eukaryota/genetics
Humans
Recombination, Genetic
Mitochondria/genetics/metabolism
Genes, Mitochondrial

@article {pmid39096545,
year = {2024},
author = {Zhang, Y and Liu, J and Zheng, R and Hou, K and Zhang, Y and Jia, T and Lu, X and Samarawickrama, PN and Jia, S and He, Y and Liu, J},
title = {Curcumin analogue EF24 prevents alveolar epithelial cell senescence to ameliorate idiopathic pulmonary fibrosis via activation of PTEN.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {133},
number = {},
pages = {155882},
doi = {10.1016/j.phymed.2024.155882},
pmid = {39096545},
issn = {1618-095X},
abstract = {BACKGROUND: Treating Idiopathic pulmonary fibrosis (IPF) remains challenging owing to its relentless progression, grim prognosis, and the scarcity of effective treatment options. Emerging evidence strongly supports the critical role of accelerated senescence in alveolar epithelial cells (AECs) in driving the progression of IPF. Consequently, targeting senescent AECs emerges as a promising therapeutic strategy for IPF.

PURPOSE: Curcumin analogue EF24 is a derivative of curcumin and shows heightened bioactivity encompassing anti-inflammatory, anti-tumor and anti-aging properties. The objective of this study was to elucidate the therapeutic potential and underlying molecular mechanisms of EF24 in the treatment of IPF.

METHODS: A549 and ATII cells were induced to become senescent using bleomycin. Senescence markers were examined using different methods including senescence-associated β-galactosidase (SA-β-gal) staining, western blotting, and q-PCR. Mice were intratracheally administrated with bleomycin to induce pulmonary fibrosis. This was validated by micro-computed tomography (CT), masson trichrome staining, and transmission electron microscope (TEM). The role and underlying mechanisms of EF24 in IPF were determined in vitro and in vivo by evaluating the expressions of PTEN, AKT/mTOR/NF-κB signaling pathway, and mitophagy using western blotting or flow cytometry.

RESULTS: We identified that the curcumin analogue EF24 was the most promising candidate among 12 compounds against IPF. EF24 treatment significantly reduced senescence biomarkers in bleomycin-induced senescent AECs, including SA-β-Gal, PAI-1, P21, and the senescence-associated secretory phenotype (SASP). EF24 also effectively inhibited fibroblast activation which was induced by senescent AECs or TGF-β. We revealed that PTEN activation was integral for EF24 to inhibit AECs senescence by suppressing the AKT/mTOR/NF-κB signaling pathway. Additionally, EF24 improved mitochondrial dysfunction through induction of mitophagy. Furthermore, EF24 administration significantly reduced the senescent phenotype induced by bleomycin in the lung tissues of mice. Notably, EF24 mitigates fibrosis and promotes overall health benefits in both the acute and chronic phases of IPF, suggesting its therapeutic potential in IPF treatment.

CONCLUSION: These findings collectively highlight EF24 as a new and effective therapeutic agent against IPF by inhibiting senescence in AECs.},
}

@article {pmid39092472,
year = {2024},
author = {Özdemir, M and Dennerlein, S},
title = {The TOM complex from an evolutionary perspective and the functions of TOMM70.},
journal = {Biological chemistry},
volume = {},
number = {},
pages = {},
pmid = {39092472},
issn = {1437-4315},
abstract = {In humans, up to 1,500 mitochondrial precursor proteins are synthesized at cytosolic ribosomes and must be imported into the organelle. This is not only essential for mitochondrial but also for many cytosolic functions. The majority of mitochondrial precursor proteins are imported over the translocase of the outer membrane (TOM). In recent years, high-resolution structure analyses from different organisms shed light on the composition and arrangement of the TOM complex. Although significant similarities have been found, differences were also observed, which have been favored during evolution and could reflect the manifold functions of TOM with cellular signaling and its response to altered metabolic situations. A key component within these regulatory mechanisms is TOMM70, which is involved in protein import, forms contacts to the ER and the nucleus, but is also involved in cellular defense mechanisms during infections.},
}

@article {pmid39071318,
year = {2024},
author = {Sloan, DB and Broz, AK and Kuster, SA and Muthye, V and Peñafiel-Ayala, A and Marron, JR and Lavrov, DV and Brieba, LG},
title = {Expansion of the MutS Gene Family in Plants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39071318},
issn = {2692-8205},
support = {R35 GM148134/GM/NIGMS NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; },
abstract = {The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1" is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6/MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics.},
}

@article {pmid38950860,
year = {2024},
author = {Box, JM and Higgins, ME and Stuart, RA},
title = {Importance of conserved hydrophobic pocket region in yeast mitoribosomal mL44 protein for mitotranslation and transcript preference.},
journal = {The Journal of biological chemistry},
volume = {300},
number = {8},
pages = {107519},
doi = {10.1016/j.jbc.2024.107519},
pmid = {38950860},
issn = {1083-351X},
abstract = {The mitochondrial ribosome (mitoribosome) is responsible for the synthesis of key oxidative phosphorylation subunits encoded by the mitochondrial genome. Defects in mitoribosomal function therefore can have serious consequences for the bioenergetic capacity of the cell. Mutation of the conserved mitoribosomal mL44 protein has been directly linked to childhood cardiomyopathy and progressive neurophysiology issues. To further explore the functional significance of the mL44 protein in supporting mitochondrial protein synthesis, we have performed a mutagenesis study of the yeast mL44 homolog, the MrpL3/mL44 protein. We specifically investigated the conserved hydrophobic pocket region of the MrpL3/mL44 protein, where the known disease-related residue in the human mL44 protein (L156R) is located. While our findings identify a number of residues in this region critical for MrpL3/mL44's ability to support the assembly of translationally active mitoribosomes, the introduction of the disease-related mutation into the equivalent position in the yeast protein (residue A186) was found to not have a major impact on function. The human and yeast mL44 proteins share many similarities in sequence and structure; however results presented here indicate that these two proteins have diverged somewhat in evolution. Finally, we observed that mutation of the MrpL3/mL44 does not impact the translation of all mitochondrial encoded proteins equally, suggesting the mitochondrial translation system may exhibit a transcript hierarchy and prioritization.},
}

@article {pmid39084221,
year = {2024},
author = {Moreira, D and Blaz, J and Kim, E and Eme, L},
title = {A gene-rich mitochondrion with a unique ancestral protein transport system.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.07.017},
pmid = {39084221},
issn = {1879-0445},
abstract = {Mitochondria originated from an ancient endosymbiosis involving an alphaproteobacterium.[1][,][2][,][3] Over time, these organelles reduced their gene content massively, with most genes being transferred to the host nucleus before the last eukaryotic common ancestor (LECA).[4] This process has yielded varying gene compositions in modern mitogenomes, including the complete loss of this organellar genome in some extreme cases.[5][,][6][,][7][,][8][,][9][,][10][,][11][,][12][,][13][,][14] At the other end of the spectrum, jakobids harbor the most gene-rich mitogenomes, encoding 60-66 proteins.[8] Here, we introduce the mitogenome of Mantamonas sphyraenae, a protist from the deep-branching CRuMs supergroup.[15][,][16] Remarkably, it boasts the most gene-rich mitogenome outside of jakobids, by housing 91 genes, including 62 protein-coding ones. These include rare homologs of the four subunits of the bacterial-type cytochrome c maturation system I (CcmA, CcmB, CcmC, and CcmF) alongside a unique ribosomal protein S6. During the early evolution of mitochondria, gene transfer from the proto-mitochondrial endosymbiont to the nucleus became possible thanks to systems facilitating the transport of proteins synthesized in the host cytoplasm back to the mitochondrion. In addition to the universally found eukaryotic protein import systems, jakobid mitogenomes were reported to uniquely encode the SecY transmembrane protein of the Sec general secretory pathway, whose evolutionary origin was however unclear. The Mantamonas mitogenome not only encodes SecY but also SecA, SecE, and SecG, making it the sole eukaryote known to house a complete mitochondrial Sec translocation system. Furthermore, our phylogenetic and comparative genomic analyses provide compelling evidence for the alphaproteobacterial origin of this system, establishing its presence in LECA.},
}

@article {pmid39080531,
year = {2024},
author = {Liu, YJ and Zhang, TY and Wang, QQ and Draisma, SGA and Hu, ZM},
title = {Comparative structure and evolution of the organellar genomes of Padina usoehtunii (Dictyotales) with the brown algal crown radiation clade.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {747},
pmid = {39080531},
issn = {1471-2164},
abstract = {BACKGROUND: Organellar genomes have become increasingly essential for studying genetic diversity, phylogenetics, and evolutionary histories of seaweeds. The order Dictyotales (Dictyotophycidae), a highly diverse lineage within the Phaeophyceae, is long-term characterized by a scarcity of organellar genome datasets compared to orders of the brown algal crown radiation (Fucophycidae).

RESULTS: We sequenced the organellar genomes of Padina usoehtunii, a representative of the order Dictyotales, to investigate the structural and evolutionary differences by comparing to five other major brown algal orders. Our results confirmed previously reported findings that the rate of structural rearrangements in chloroplast genomes is higher than that in mitochondria, whereas mitochondrial sequences exhibited a higher substitution rate compared to chloroplasts. Such evolutionary patterns contrast with land plants and green algae. The expansion and contraction of the inverted repeat (IR) region in the chloroplast correlated with the changes in the number of boundary genes. Specifically, the size of the IR region influenced the position of the boundary gene rpl21, with complete rpl21 genes found within the IR region in Dictyotales, Sphacelariales and Ectocarpales, while the rpl21 genes in Desmarestiales, Fucales, and Laminariales span both the IR and short single copy (SSC) regions. The absence of the rbcR gene in the Dictyotales may indicate an endosymbiotic transfer from the chloroplast to the nuclear genome. Inversion of the SSC region occurred at least twice in brown algae. Once in a lineage only represented by the Ectocarpales in the present study and once in a lineage only represented by the Fucales. Photosystem genes in the chloroplasts experienced the strongest signature of purifying selection, while ribosomal protein genes in both chloroplasts and mitochondria underwent a potential weak purifying selection.

CONCLUSIONS: Variations in chloroplast genome structure among different brown algal orders are evolutionarily linked to their phylogenetic positions in the Phaeophyceae tree. Chloroplast genomes harbor more structural rearrangements than the mitochondria, despite mitochondrial genes exhibiting faster mutation rates. The position and the change in the number of boundary genes likely shaped the IR regions in the chloroplast, and the produced structural variability is important mechanistically to create gene diversity in brown algal chloroplast.},
}

@article {pmid39080514,
year = {2024},
author = {Lu, G and Wang, W and Zhang, S and Yang, G and Zhang, K and Que, Y and Deng, L},
title = {The first complete mitochondrial genome of Grossulariaceae: Molecular features, structure recombination, and genetic evolution.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {744},
pmid = {39080514},
issn = {1471-2164},
abstract = {BACKGROUND: Mitochondria play crucial roles in the growth, development, and adaptation of plants. Blackcurrant (Ribes nigrum L.) stands out as a significant berry species due to its rich nutritional profile, medicinal properties, and health benefits. Despite its importance, the mitochondrial genome of blackcurrant remains unassembled.

RESULTS: This study presents the first assembly of the mitochondrial genome of R. nigrum in the Grossulariaceae family. The genome spans 450,227 base pairs (bp) and encompasses 39 protein-coding genes (PCGs), 19 transfer RNAs (tRNAs), and three ribosomal RNAs (rRNAs). Protein-coding regions constitute 8.88% of the entire genome. Additionally, we identified 180 simple sequence repeats, 12 tandem repeats, and 432 pairs of dispersed repeats. Notably, the dispersed sequence R1 (cotig3, 1,129 bp) mediated genome recombination, resulting in the formation of two major conformations, namely master and double circles. Furthermore, we identified 731 C-to-U RNA editing sites within the PCGs. Among these, cox1-2, nad1-2, and nad4L-2 were associated with the creation of start codons, whereas atp6-718 and rps10-391 were linked to termination codons. We also detected fourteen plastome fragments within the mitogenome, constituting 1.11% of the total length. Phylogenetic analysis suggests that R. nigrum might have undergone multiple genomic reorganization and/or gene transfer events, resulting in the loss of two PCGs (rps2 and rps11) during its evolutionary history.

CONCLUSIONS: This investigation unveils the molecular characteristics of the R. nigrum mitogenome, shedding light on its evolutionary trajectory and phylogenetic implications. Furthermore, it serves as a valuable reference for evolutionary research and germplasm identification within the genus.},
}

@article {pmid39067796,
year = {2024},
author = {Qu, K and Liu, D and Sun, L and Li, M and Xia, T and Sun, W and Xia, Y},
title = {De novo assembly and comprehensive analysis of the mitochondrial genome of Taxus wallichiana reveals different repeats mediate recombination to generate multiple conformations.},
journal = {Genomics},
volume = {116},
number = {5},
pages = {110900},
doi = {10.1016/j.ygeno.2024.110900},
pmid = {39067796},
issn = {1089-8646},
abstract = {Taxus plants are the exclusive source of paclitaxel, an anticancer drug with significant medicinal and economic value. Interspecies hybridization and gene introgression during evolution have obscured distinctions among Taxus species, complicating their phylogenetic classification. While the chloroplast genome of Taxus wallichiana, a widely distributed species in China, has been sequenced, its mitochondrial genome (mitogenome) remains uncharacterized.We sequenced and assembled the T. wallichiana mitogenome using BGI short reads and Nanopore long reads, facilitating comparisons with other gymnosperm mitogenomes. The T. wallichiana mitogenome spanning 469,949 bp, predominantly forms a circular configuration with a GC content of 50.51%, supplemented by 3 minor configurations mediated by one pair of LRs and two pairs of IntRs. It includes 32 protein-coding genes, 7 tRNA genes, and 3 rRNA genes, several of which exist in multiple copies.We detailed the mitogenome's structure, codon usage, RNA editing, and sequence migration between organelles, constructing a phylogenetic tree to elucidate evolutionary relationships. Unlike typical gymnosperm mitochondria, T. wallichiana shows no evidence of mitochondrial-plastid DNA transfer (MTPT), highlighting its unique genomic architecture. Synteny analysis indicated extensive genomic rearrangements in T. wallichiana, likely driven by recombination among abundant repetitive sequences. This study offers a high-quality T. wallichiana mitogenome, enhancing our understanding of gymnosperm mitochondrial evolution and supporting further cultivation and utilization of Taxus species.},
}

@article {pmid39062690,
year = {2024},
author = {Zhang, Y and Peng, Y and Zhang, H and Gao, Q and Song, F and Cui, X and Mo, F},
title = {Genome-Wide Identification of APX Gene Family in Citrus maxima and Expression Analysis at Different Postharvest Preservation Times.},
journal = {Genes},
volume = {15},
number = {7},
pages = {},
pmid = {39062690},
issn = {2073-4425},
support = {202427060300564//Innovation and Entrepreneurship Training Program for College Students/ ; },
mesh = {*Citrus/genetics ; *Gene Expression Regulation, Plant ; *Ascorbate Peroxidases/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Multigene Family ; *Phylogeny ; Genome, Plant ; Fruit/genetics/metabolism ; Gene Expression Profiling/methods ; },
abstract = {Ascorbate peroxidase (APX) is a crucial enzyme involved in cellular antioxidant defense and plays a pivotal role in modulating reactive oxygen species (ROS) levels under various environmental stresses in plants. This study utilized bioinformatics methods to identify and analyze the APX gene family of pomelo, while quantitative real-time PCR (qRT-PCR) was employed to validate and analyze the expression of CmAPXs at different stages of fruit postharvest. This study identified 96 members of the CmAPX family in the entire pomelo genome, with uneven distribution across nine chromosomes and occurrences of gene fragment replication. The subcellular localization includes peroxisome, cytoplasm, chloroplasts, and mitochondria. The CmAPX family exhibits a similar gene structure, predominantly consisting of two exons. An analysis of the upstream promoter regions revealed a significant presence of cis-acting elements associated with light (Box 4, G-Box), hormones (ABRE, TCA-element), and stress-related (MBS, LTR, ARE) responses. Phylogenetic and collinearity analyses revealed that the CmAPX gene family can be classified into three subclasses, with seven collinear gene pairs. Furthermore, CmAPXs are closely related to citrus, pomelo, and lemon, followed by Arabidopsis, and exhibit low homology with rice. Additionally, the transcriptomic heat map and qPCR results revealed that the expression levels of CmAPX57, CmAPX34, CmAPX50, CmAPX4, CmAPX5, and CmAPX81 were positively correlated with granulation degree, indicating the activation of the endogenous stress resistance system in pomelo cells by these genes, thereby conferring resistance to ROS. This finding is consistent with the results of GO enrichment analysis. Furthermore, 38 miRNAs were identified as potential regulators targeting the CmAPX family for post-transcriptional regulation. Thus, this study has preliminarily characterized members of the APX gene family in pomelo and provided valuable insights for further research on their antioxidant function and molecular mechanism.},
}

*Citrus/genetics
*Gene Expression Regulation, Plant
*Ascorbate Peroxidases/genetics/metabolism
*Plant Proteins/genetics/metabolism
*Multigene Family
*Phylogeny
Genome, Plant
Fruit/genetics/metabolism
Gene Expression Profiling/methods

@article {pmid39062621,
year = {2024},
author = {Aishan, Z and Mu, ZL and Li, ZC and Luo, XY and Huangfu, N},
title = {The First Three Mitochondrial Genomes for the Characterization of the Genus Egeirotrioza (Hemiptera: Triozidae) and Phylogenetic Implications.},
journal = {Genes},
volume = {15},
number = {7},
pages = {},
pmid = {39062621},
issn = {2073-4425},
support = {2022D01C403//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 5244031//Beijing Natural Science Foundation/ ; },
mesh = {Animals ; *Genome, Mitochondrial ; *Phylogeny ; *Hemiptera/genetics/classification ; Evolution, Molecular ; RNA, Transfer/genetics ; },
abstract = {(1) Background: Mitochondrial genomes are important markers for the study of phylogenetics and systematics. Triozidae includes some primary pests of Populus euphratica. The phylogenetic relationships of this group remain controversial due to the lack of molecular data. (2) Methods: Mitochondria of Egeirotrioza Boselli were sequenced and assembled. We analyzed the sequence length, nucleotide composition, and evolutionary rate of Triozidae, combined with the 13 published mitochondrial genomes. (3) Results: The evolutionary rate of protein-coding genes was as follows: ATP8 > ND6 > ND5 > ND2 > ND4 > ND4L > ND1 > ND3 > APT6 > CYTB > COX3 > COX2 > COX1. We reconstructed the phylogenetic relationships of Triozidae based on 16 triozid mitochondrial genomes (thirteen ingroups and three outgroups) using the maximum likelihood (ML) and Bayesian inference (BI) approaches. The phylogenetic analysis of the 16 Triozidae mitochondrial genomes showed that Egeirotrioza was closely related to Leptynoptera. (4) Conclusions: We have identified 13 PCGs, 22 tRNAs, 2 rRNAs, and 1 control region (CR) of all newly sequenced mitochondrial genomes, which were the mitochondrial gene type in animals. The results of this study provide valuable genomic information for the study of psyllid species.},
}

Animals
*Genome, Mitochondrial
*Phylogeny
*Hemiptera/genetics/classification
Evolution, Molecular
RNA, Transfer/genetics

@article {pmid39062606,
year = {2024},
author = {Li, S and Jiao, B and Wang, J and Zhao, P and Dong, F and Yang, F and Ma, C and Guo, P and Zhou, S},
title = {Identification of Wheat Glutamate Synthetase Gene Family and Expression Analysis under Nitrogen Stress.},
journal = {Genes},
volume = {15},
number = {7},
pages = {},
pmid = {39062606},
issn = {2073-4425},
support = {2022KJCXZX-SSS-4//HAAFS Agriculture Science and Technology Innovation Project/ ; },
mesh = {*Triticum/genetics/metabolism ; *Nitrogen/metabolism ; *Gene Expression Regulation, Plant ; *Stress, Physiological/genetics ; *Plant Proteins/genetics/metabolism ; Glutamate Synthase/genetics/metabolism ; Multigene Family ; Promoter Regions, Genetic ; Plant Roots/genetics/metabolism/growth & development ; Seedlings/genetics/growth & development/metabolism ; Plant Leaves/genetics/metabolism ; Phylogeny ; },
abstract = {Nitrogen (N), as the main component of biological macromolecules, maintains the basic process of plant growth and development. GOGAT, as a key enzyme in the N assimilation process, catalyzes α-ketoglutaric acid and glutamine to form glutamate. In this study, six GOGAT genes in wheat (Triticum aestivum L.) were identified and classified into two subfamilies, Fd-GOGAT (TaGOGAT2s) and NADH-GOGAT (TaGOGAT3s), according to the type of electron donor. Subcellular localization prediction showed that TaGOGAT3-D was localized in mitochondria and that the other five TaGOGATs were localized in chloroplasts. Via the analysis of promoter elements, many binding sites related to growth and development, hormone regulation and plant stress resistance regulations were found on the TaGOGAT promoters. The tissue-specificity expression analysis showed that TaGOGAT2s were mainly expressed in wheat leaves and flag leaves, while TaGOGAT3s were highly expressed in roots and leaves. The expression level of TaGOGATs and the enzyme activity of TaGOGAT3s in the leaves and roots of wheat seedlings were influenced by the treatment of N deficiency. This study conducted a systematic analysis of wheat GOGAT genes, providing a theoretical basis not only for the functional analysis of TaGOGATs, but also for the study of wheat nitrogen use efficiency (NUE).},
}

*Triticum/genetics/metabolism
*Nitrogen/metabolism
*Gene Expression Regulation, Plant
*Stress, Physiological/genetics
*Plant Proteins/genetics/metabolism
Glutamate Synthase/genetics/metabolism
Multigene Family
Promoter Regions, Genetic
Plant Roots/genetics/metabolism/growth & development
Seedlings/genetics/growth & development/metabolism
Plant Leaves/genetics/metabolism
Phylogeny

@article {pmid38851187,
year = {2024},
author = {Árnadóttir, ER and Moore, KHS and Guðmundsdóttir, VB and Ebenesersdóttir, SS and Guity, K and Jónsson, H and Stefánsson, K and Helgason, A},
title = {The rate and nature of mitochondrial DNA mutations in human pedigrees.},
journal = {Cell},
volume = {187},
number = {15},
pages = {3904-3918.e8},
doi = {10.1016/j.cell.2024.05.022},
pmid = {38851187},
issn = {1097-4172},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Pedigree ; Female ; Iceland ; Male ; Mutation ; Mutation Rate ; },
abstract = {We examined the rate and nature of mitochondrial DNA (mtDNA) mutations in humans using sequence data from 64,806 contemporary Icelanders from 2,548 matrilines. Based on 116,663 mother-child transmissions, 8,199 mutations were detected, providing robust rate estimates by nucleotide type, functional impact, position, and different alleles at the same position. We thoroughly document the true extent of hypermutability in mtDNA, mainly affecting the control region but also some coding-region variants. The results reveal the impact of negative selection on viable deleterious mutations, including rapidly mutating disease-associated 3243A>G and 1555A>G and pre-natal selection that most likely occurs during the development of oocytes. Finally, we show that the fate of new mutations is determined by a drastic germline bottleneck, amounting to an average of 3 mtDNA units effectively transmitted from mother to child.},
}

Humans
*DNA, Mitochondrial/genetics
*Pedigree
Female
Iceland
Male
Mutation
Mutation Rate

@article {pmid39062730,
year = {2024},
author = {Domínguez-Ruiz, M and Olarte, M and Onecha, E and García-Vaquero, I and Gelvez, N and López, G and Villamar, M and Morín, M and Moreno-Pelayo, MA and Morales-Angulo, C and Polo, R and Tamayo, ML and Del Castillo, I},
title = {Novel Cases of Non-Syndromic Hearing Impairment Caused by Pathogenic Variants in Genes Encoding Mitochondrial Aminoacyl-tRNA Synthetases.},
journal = {Genes},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/genes15070951},
pmid = {39062730},
issn = {2073-4425},
support = {PI20/00619//Instituto de Salud Carlos III/ ; S2017/ BMD3721//Regional Government of Madrid/ ; 00008286//Pontificia Universidad Javeriana/ ; },
abstract = {Dysfunction of some mitochondrial aminoacyl-tRNA synthetases (encoded by the KARS1, HARS2, LARS2 and NARS2 genes) results in a great variety of phenotypes ranging from non-syndromic hearing impairment (NSHI) to very complex syndromes, with a predominance of neurological signs. The diversity of roles that are played by these moonlighting enzymes and the fact that most pathogenic variants are missense and affect different domains of these proteins in diverse compound heterozygous combinations make it difficult to establish genotype-phenotype correlations. We used a targeted gene-sequencing panel to investigate the presence of pathogenic variants in those four genes in cohorts of 175 Spanish and 18 Colombian familial cases with non-DFNB1 autosomal recessive NSHI. Disease-associated variants were found in five cases. Five mutations were novel as follows: c.766C>T in KARS1, c.475C>T, c.728A>C and c.1012G>A in HARS2, and c.795A>G in LARS2. We provide audiograms from patients at different ages to document the evolution of the hearing loss, which is mostly prelingual and progresses from moderate/severe to profound, the middle frequencies being more severely affected. No additional clinical sign was observed in any affected subject. Our results confirm the involvement of KARS1 in DFNB89 NSHI, for which until now there was limited evidence.},
}

@article {pmid39060773,
year = {2024},
author = {Pang, B and Dong, G and Pang, T and Sun, X and Liu, X and Nie, Y and Chang, X},
title = {Emerging insights into the pathogenesis and therapeutic strategies for vascular endothelial injury-associated diseases: focus on mitochondrial dysfunction.},
journal = {Angiogenesis},
volume = {},
number = {},
pages = {},
pmid = {39060773},
issn = {1573-7209},
abstract = {As a vital component of blood vessels, endothelial cells play a key role in maintaining overall physiological function by residing between circulating blood and semi-solid tissue. Various stress stimuli can induce endothelial injury, leading to the onset of corresponding diseases in the body. In recent years, the importance of mitochondria in vascular endothelial injury has become increasingly apparent. Mitochondria, as the primary site of cellular aerobic respiration and the organelle for "energy information transfer," can detect endothelial cell damage by integrating and receiving various external stress signals. The generation of reactive oxygen species (ROS) and mitochondrial dysfunction often determine the evolution of endothelial cell injury towards necrosis or apoptosis. Therefore, mitochondria are closely associated with endothelial cell function, helping to determine the progression of clinical diseases. This article comprehensively reviews the interconnection and pathogenesis of mitochondrial-induced vascular endothelial cell injury in cardiovascular diseases, renal diseases, pulmonary-related diseases, cerebrovascular diseases, and microvascular diseases associated with diabetes. Corresponding therapeutic approaches are also provided. Additionally, strategies for using clinical drugs to treat vascular endothelial injury-based diseases are discussed, aiming to offer new insights and treatment options for the clinical diagnosis of related vascular injuries.},
}

@article {pmid39050895,
year = {2024},
author = {Da Costa, RT and Urquiza, P and Perez, MM and Du, Y and Khong, ML and Zheng, H and Guitart-Mampel, M and Elustondo, PA and Scoma, ER and Hambardikar, V and Ueberheide, B and Tanner, JA and Cohen, A and Pavlov, EV and Haynes, CM and Solesio, ME},
title = {Mitochondrial inorganic polyphosphate is required to maintain proteostasis within the organelle.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1423208},
pmid = {39050895},
issn = {2296-634X},
abstract = {The existing literature points towards the presence of robust mitochondrial mechanisms aimed at mitigating protein dyshomeostasis within the organelle. However, the precise molecular composition of these mechanisms remains unclear. Our data show that inorganic polyphosphate (polyP), a polymer well-conserved throughout evolution, is a component of these mechanisms. In mammals, mitochondria exhibit a significant abundance of polyP, and both our research and that of others have already highlighted its potent regulatory effect on bioenergetics. Given the intimate connection between energy metabolism and protein homeostasis, the involvement of polyP in proteostasis has also been demonstrated in several organisms. For example, polyP is a bacterial primordial chaperone, and its role in amyloidogenesis has already been established. Here, using mammalian models, our study reveals that the depletion of mitochondrial polyP leads to increased protein aggregation within the organelle, following stress exposure. Furthermore, mitochondrial polyP is able to bind to proteins, and these proteins differ under control and stress conditions. The depletion of mitochondrial polyP significantly affects the proteome under both control and stress conditions, while also exerting regulatory control over gene expression. Our findings suggest that mitochondrial polyP is a previously unrecognized, and potent component of mitochondrial proteostasis.},
}

@article {pmid39048023,
year = {2024},
author = {Makiuchi, T and Saito-Nakano, Y and Nozaki, T},
title = {Evidence of γ-secretase complex involved in the regulation of intramembrane proteolysis in Entamoeba histolytica.},
journal = {Parasitology international},
volume = {},
number = {},
pages = {102925},
doi = {10.1016/j.parint.2024.102925},
pmid = {39048023},
issn = {1873-0329},
abstract = {Presenilins (PSNs) are multifunctional membrane proteins involved in signal transduction, lysosomal acidification, and certain physiological processes related to mitochondria. The aspartic protease activity of PSN and the formation of a γ-secretase complex with other subunits such as nicastrin (NCT) are required for the biological functions. Although PSN is widely conserved in eukaryotes, most studies on PSN were conducted in metazoans. Homologous genes for PSN and NCT (EhPSN and EhNCT, respectively) are encoded in the genome of Entamoeba histolytica; however, their functions remain unknown. In this study, we showed that EhPSN and EhNCT form a complex on the cell membrane, demonstrating that the parasite possesses γ-secretase. The predicted structure of EhPSN was similar to the human homolog, demonstrated by the crystal structure, and phylogenetic analysis indicated good conservation between EhPSN and human PSN, supporting the premise that EhPSN functions as a subunit of γ-secretase. By contrast, EhNCT appears to have undergone remarkable structural changes during its evolution. Blue native-polyacrylamide gel electrophoresis combined with western blotting indicated that a 150-kDa single band contains both EhPSN (estimated molecular size: 47-kDa) and EhNCT (64-kDa), suggesting that the complex also contains other unknown components or post-translational modifications. Coimmunoprecipitation from amebic lysates also confirmed that EhPSN and EhNCT formed a complex. Indirect immunofluorescence analysis revealed that the complex localized to the plasma membrane. Moreover, EhPSN exhibited protease activity, which was suppressed by a γ-secretase inhibitor. This is the first report of a γ-secretase complex in protozoan parasites.},
}

@article {pmid38646826,
year = {2024},
author = {Aronowitz, DI and Geoffrion, TR and Piel, S and Benson, EJ and Morton, SR and Starr, J and Melchior, RW and Gaudio, HA and Degani, RE and Widmann, NJ and Weeks, MK and Ko, TS and Licht, DJ and Hefti, M and Gaynor, JW and Kilbaugh, TJ and Mavroudis, CD},
title = {Early Impairment of Cerebral Bioenergetics After Cardiopulmonary Bypass in Neonatal Swine.},
journal = {World journal for pediatric & congenital heart surgery},
volume = {15},
number = {4},
pages = {459-466},
doi = {10.1177/21501351241232077},
pmid = {38646826},
issn = {2150-136X},
mesh = {Animals ; *Cardiopulmonary Bypass/adverse effects ; Swine ; *Energy Metabolism/physiology ; *Animals, Newborn ; *Mitochondria/metabolism ; Disease Models, Animal ; Brain/metabolism ; Lactic Acid/metabolism/blood/analysis ; Pyruvic Acid/metabolism ; Glycerol/metabolism ; },
abstract = {Objectives: We previously demonstrated cerebral mitochondrial dysfunction in neonatal swine immediately following a period of full-flow cardiopulmonary bypass (CPB). The extent to which this dysfunction persists in the postoperative period and its correlation with other markers of cerebral bioenergetic failure and injury is unknown. We utilized a neonatal swine model to investigate the early evolution of mitochondrial function and cerebral bioenergetic failure after CPB. Methods: Twenty piglets (mean weight 4.4 ± 0.5 kg) underwent 3 h of CPB at 34 °C via cervical cannulation and were followed for 8, 12, 18, or 24 h (n = 5 per group). Markers of brain tissue damage (glycerol) and bioenergetic dysfunction (lactate to pyruvate ratio) were continuously measured in cerebral microdialysate samples. Control animals (n = 3, mean weight 4.1 ± 1.2 kg) did not undergo cannulation or CPB. Brain tissue was extracted immediately after euthanasia to obtain ex-vivo cortical mitochondrial respiration and frequency of cortical microglial nodules (indicative of cerebral microinfarctions) via neuropathology. Results: Both the lactate to pyruvate ratio (P < .0001) and glycerol levels (P = .01) increased in cerebral microdialysate within 8 h after CPB. At 24 h post-CPB, cortical mitochondrial respiration was significantly decreased compared with controls (P = .046). The presence of microglial nodules increased throughout the study period (24 h) (P = .01, R[2 ]= 0.9). Conclusion: CPB results in impaired cerebral bioenergetics that persist for at least 24 h. During this period of bioenergetic impairment, there may be increased susceptibility to secondary injury related to alterations in metabolic delivery or demand, such as hypoglycemia, seizures, and decreased cerebral blood flow.},
}

Animals
*Cardiopulmonary Bypass/adverse effects
Swine
*Energy Metabolism/physiology
*Animals, Newborn
*Mitochondria/metabolism
Disease Models, Animal
Brain/metabolism
Lactic Acid/metabolism/blood/analysis
Pyruvic Acid/metabolism
Glycerol/metabolism

@article {pmid35022483,
year = {2022},
author = {Dash, A and Ghag, SB},
title = {Genome-wide in silico characterization and stress induced expression analysis of BcL-2 associated athanogene (BAG) family in Musa spp.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {625},
pmid = {35022483},
issn = {2045-2322},
mesh = {*Musa/genetics/metabolism ; *Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism ; *Stress, Physiological/genetics ; *Phylogeny ; Multigene Family ; Genome, Plant ; Computer Simulation ; Gene Expression Profiling ; },
abstract = {Programmed cell death (PCD) is a genetically controlled process for the selective removal of damaged cells. Though understanding about plant PCD has improved over years, the mechanisms are yet to be fully deciphered. Among the several molecular players of PCD in plants, B cell lymphoma 2 (Bcl-2)-associated athanogene (BAG) family of co-chaperones are evolutionary conserved and regulate cell death, growth and development. In this study, we performed a genome-wide in silico analysis of the MusaBAG gene family in a globally important fruit crop banana. Thirteen MusaBAG genes were identified, out of which MusaBAG1, 7 and 8 genes were found to have multiple copies. MusaBAG genes were distributed on seven out of 11 chromosomes in banana. Except for one paralog of MusaBAG8 all the other 12 proteins have characteristic BAG domain. MusaBAG1, 2 and 4 have an additional ubiquitin-like domain whereas MusaBAG5-8 have a calmodulin binding motif. Most of the MusaBAG proteins were predicted to be localized in the nucleus and mitochondria or chloroplast. The in silico cis-regulatory element analysis suggested regulation associated with photoperiodic control, abiotic and biotic stress. The phylogenetic analysis revealed 2 major clusters. Digital gene expression analysis and quantitative real-time RT-PCR depicted the differential expression pattern of MusaBAG genes under abiotic and biotic stress conditions. Further studies are warranted to uncover the role of each of these proteins in growth, PCD and stress responses so as to explore them as candidate genes for engineering transgenic banana plants with improved agronomic traits.},
}

*Musa/genetics/metabolism
*Gene Expression Regulation, Plant
*Plant Proteins/genetics/metabolism
*Stress, Physiological/genetics
*Phylogeny
Multigene Family
Genome, Plant
Computer Simulation
Gene Expression Profiling

@article {pmid34111145,
year = {2021},
author = {Horoiwa, M and Mandagi, IF and Sutra, N and Montenegro, J and Tantu, FY and Masengi, KWA and Nagano, AJ and Kusumi, J and Yasuda, N and Yamahira, K},
title = {Mitochondrial introgression by ancient admixture between two distant lacustrine fishes in Sulawesi Island.},
journal = {PloS one},
volume = {16},
number = {6},
pages = {e0245316},
pmid = {34111145},
issn = {1932-6203},
mesh = {Animals ; *Haplotypes ; *DNA, Mitochondrial/genetics ; Islands ; Phylogeny ; Polymorphism, Single Nucleotide ; Genetic Introgression ; Mitochondria/genetics ; Genetics, Population ; Fishes/genetics/classification ; Ecosystem ; },
abstract = {Sulawesi, an island located in a biogeographical transition zone between Indomalaya and Australasia, is famous for its high levels of endemism. Ricefishes (family Adrianichthyidae) are an example of taxa that have uniquely diversified on this island. It was demonstrated that habitat fragmentation due to the Pliocene juxtaposition among tectonic subdivisions of this island was the primary factor that promoted their divergence; however, it is also equally probable that habitat fusions and resultant admixtures between phylogenetically distant species may have frequently occurred. Previous studies revealed that some individuals of Oryzias sarasinorum endemic to a tectonic lake in central Sulawesi have mitochondrial haplotypes that are similar to the haplotypes of O. eversi, which is a phylogenetically related but geologically distant (ca. 190 km apart) adrianichthyid endemic to a small fountain. In this study, we tested if this reflects ancient admixture of O. eversi and O. sarasinorum. Population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that O. eversi and O. sarasinorum are substantially reproductively isolated from each other. Comparison of demographic models revealed that the models assuming ancient admixture from O. eversi to O. sarasinorum was more supported than the models assuming no admixture; this supported the idea that the O. eversi-like mitochondrial haplotype in O. sarasinorum was introgressed from O. eversi. This study is the first to demonstrate ancient admixture of lacustrine or pond organisms in Sulawesi beyond 100 km. The complex geological history of this island enabled such island-wide admixture of lacustrine organisms, which usually experience limited migration.},
}

Animals
*Haplotypes
*DNA, Mitochondrial/genetics
Islands
Phylogeny
Polymorphism, Single Nucleotide
Genetic Introgression
Mitochondria/genetics
Genetics, Population
Fishes/genetics/classification
Ecosystem

@article {pmid34061855,
year = {2021},
author = {Cai, C and Gu, K and Zhao, H and Steinhagen, S and He, P and Wichard, T},
title = {Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea.},
journal = {PloS one},
volume = {16},
number = {6},
pages = {e0250968},
pmid = {34061855},
issn = {1932-6203},
mesh = {*Phylogeny ; *Ulva/genetics ; *Genome, Chloroplast/genetics ; Genetic Markers ; *Genome, Mitochondrial ; Evolution, Molecular ; China ; Oceans and Seas ; Chlorophyta/genetics ; },
abstract = {Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.},
}

*Phylogeny
*Ulva/genetics
*Genome, Chloroplast/genetics
Genetic Markers
*Genome, Mitochondrial
Evolution, Molecular
China
Oceans and Seas
Chlorophyta/genetics

@article {pmid39016375,
year = {2024},
author = {Martini, D and De Cesari, C and Digregorio, M and Muscò, A and Giudetti, G and Giannaccini, M and Andreazzoli, M},
title = {Expression analysis of thg1l during Xenopus laevis development.},
journal = {The International journal of developmental biology},
volume = {68},
number = {2},
pages = {85-91},
doi = {10.1387/ijdb.240033ma},
pmid = {39016375},
issn = {1696-3547},
mesh = {Animals ; *Xenopus laevis/metabolism/embryology/genetics ; *Gene Expression Regulation, Developmental ; *Xenopus Proteins/genetics/metabolism ; Nucleotidyltransferases/genetics/metabolism ; Embryo, Nonmammalian/metabolism/embryology ; Embryonic Development/genetics ; RNA, Messenger/genetics/metabolism ; },
abstract = {The tRNA-histidine guanylyltransferase 1-like (THG1L), also known as induced in high glucose-1 (IHG-1), encodes for an essential mitochondria-associated protein highly conserved throughout evolution, that catalyses the 3'-5' addition of a guanine to the 5'-end of tRNA-histidine (tRNA[His]). Previous data indicated that THG1L plays a crucial role in the regulation of mitochondrial biogenesis and dynamics, in ATP production, and is critically involved in the modulation of apoptosis, cell-cycle progression and survival, as well as in cellular stress responses and redox homeostasis. Dysregulations of THG1L expression play a central role in various pathologies, including nephropathies, and neurodevelopmental disorders often characterized by developmental delay and cerebellar ataxia. Despite the essential role of THG1L, little is known about its expression during vertebrate development. Herein, we examined the detailed spatio-temporal expression of this gene in the developing Xenopus laevis. Our results show that thg1l is maternally inherited and its temporal expression suggests a role during the earliest stages of embryogenesis. Spatially, thg1l mRNA localizes in the ectoderm and marginal zone mesoderm during early stages of development. Then, at tadpole stages, thg1l transcripts mostly localise in neural crests and their derivatives, somites, developing kidney and central nervous system, therefore largely coinciding with territories displaying intense energy metabolism during organogenesis in Xenopus.},
}

Animals
*Xenopus laevis/metabolism/embryology/genetics
*Gene Expression Regulation, Developmental
*Xenopus Proteins/genetics/metabolism
Nucleotidyltransferases/genetics/metabolism
Embryo, Nonmammalian/metabolism/embryology
Embryonic Development/genetics
RNA, Messenger/genetics/metabolism

@article {pmid39009246,
year = {2024},
author = {Guttipatti, P and Saadallah, N and Ji, R and Avula, UMR and Goulbourne, CN and Wan, EY},
title = {Quantitative 3D electron microscopy characterization of mitochondrial structure, mitophagy, and organelle interactions in murine atrial fibrillation.},
journal = {Journal of structural biology},
volume = {216},
number = {3},
pages = {108110},
doi = {10.1016/j.jsb.2024.108110},
pmid = {39009246},
issn = {1095-8657},
abstract = {Atrial fibrillation (AF) is the most common clinical arrhythmia, however there is limited understanding of its pathophysiology including the cellular and ultrastructural changes rendered by the irregular rhythm, which limits pharmacological therapy development. Prior work has demonstrated the importance of reactive oxygen species (ROS) and mitochondrial dysfunction in the development of AF. Mitochondrial structure, interactions with other organelles such as sarcoplasmic reticulum (SR) and T-tubules (TT), and degradation of dysfunctional mitochondria via mitophagy are important processes to understand ultrastructural changes due to AF. However, most analysis of mitochondrial structure and interactome in AF has been limited to two-dimensional (2D) modalities such as transmission electron microscopy (EM), which does not fully visualize the morphological evolution of the mitochondria during mitophagy. Herein, we utilize focused ion beam-scanning electron microscopy (FIB-SEM) and perform reconstruction of three-dimensional (3D) EM from murine left atrial samples and measure the interactions of mitochondria with SR and TT. We developed a novel 3D quantitative analysis of FIB-SEM in a murine model of AF to quantify mitophagy stage, mitophagosome size in cardiomyocytes, and mitochondrial structural remodeling when compared with control mice. We show that in our murine model of spontaneous and continuous AF due to persistent late sodium current, left atrial cardiomyocytes have heterogenous mitochondria, with a significant number which are enlarged with increased elongation and structural complexity. Mitophagosomes in AF cardiomyocytes are located at Z-lines where they neighbor large, elongated mitochondria. Mitochondria in AF cardiomyocytes show increased organelle interaction, with 5X greater contact area with SR and are 4X as likely to interact with TT when compared to control. We show that mitophagy in AF cardiomyocytes involves 2.5X larger mitophagosomes that carry increased organelle contents. In conclusion, when oxidative stress overcomes compensatory mechanisms, mitophagy in AF faces a challenge of degrading bulky complex mitochondria, which may result in increased SR and TT contacts, perhaps allowing for mitochondrial Ca[2+] maintenance and antioxidant production.},
}

@article {pmid38995516,
year = {2024},
author = {Lin, YE and Chiu, HL and Wu, CS and Chaw, SM},
title = {Phylogenomics identifies parents of naturally occurring tetraploid bananas.},
journal = {Botanical studies},
volume = {65},
number = {1},
pages = {19},
pmid = {38995516},
issn = {1817-406X},
support = {23-23//Academia Sinica/ ; },
abstract = {BACKGROUND: Triploid bananas are almost sterile. However, we succeeded in harvesting seeds from two edible triploid banana individuals (Genotype: ABB) in our conservation repository where various wild diploid bananas were also grown. The resulting rare offspring survived to seedling stages. DNA content analyses reveal that they are tetraploid. Since bananas contain maternally inherited plastids and paternally inherited mitochondria, we sequenced and assembled plastomes and mitogenomes of these seedlings to trace their hybridization history.

RESULTS: The coding sequences of both organellar genomic scaffolds were extracted, aligned, and concatenated for constructing phylogenetic trees. Our results suggest that these tetraploid seedlings be derived from hybridization between edible triploid bananas and wild diploid Musa balbisiana (BB) individuals. We propose that generating female triploid gametes via apomeiosis may allow the triploid maternal bananas to produce viable seeds.

CONCLUSIONS: Our study suggests a practical avenue towards expanding genetic recombination and increasing genetic diversity of banana breeding programs. Further cellular studies are needed to understand the fusion and developmental processes that lead to formation of hybrid embryos in banana reproduction, polyploidization, and evolution.},
}

@article {pmid38995057,
year = {2024},
author = {Smith, CH and Mejia-Trujillo, R and Havird, JC},
title = {Mitonuclear compatibility is maintained despite relaxed selection on male mitochondrial DNA in bivalves with doubly uniparental inheritance.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpae108},
pmid = {38995057},
issn = {1558-5646},
abstract = {Mitonuclear coevolution is common in eukaryotes, but bivalve lineages that have doubly uniparental inheritance (DUI) of mitochondria may be an interesting example. In this system, females transmit mtDNA (F mtDNA) to all offspring, while males transmit a different mtDNA (M mtDNA) solely to their sons. Molecular evolution and functional data suggest oxidative phosphorylation (OXPHOS) genes encoded in M mtDNA evolve under relaxed selection due to their function being limited to sperm only (vs. all other tissues for F mtDNA). This has led to the hypothesis that mitonuclear coevolution is less important for M mtDNA. Here, we use comparative phylogenetics, transcriptomics, and proteomics to understand mitonuclear interactions in DUI bivalves. We found nuclear OXPHOS proteins coevolve and maintain compatibility similarly with both F and M mtDNA OXPHOS proteins. Mitochondrial recombination did not influence mitonuclear compatibility and nuclear-encoded OXPHOS genes were not upregulated in tissues with M mtDNA to offset dysfunction. Our results support that selection maintains mitonuclear compatibility with F and M mtDNA despite relaxed selection on M mtDNA. Strict sperm transmission, lower effective population size, and higher mutation rates may explain the evolution of M mtDNA. Our study highlights that mitonuclear coevolution and compatibility may be broad features of eukaryotes.},
}

@article {pmid38980999,
year = {2024},
author = {Gammuto, L and Serra, V and Petroni, G and Todaro, MA},
title = {Molecular phylogenetic position and description of a new genus and species of freshwater Chaetonotidae (Gastrotricha: Chaetonotida: Paucitubulatina), and the annotation of its mitochondrial genome.},
journal = {Invertebrate systematics},
volume = {38},
number = {},
pages = {},
doi = {10.1071/IS23059},
pmid = {38980999},
issn = {1447-2600},
mesh = {*Phylogeny ; *Genome, Mitochondrial/genetics ; Animals ; Species Specificity ; Fresh Water ; },
abstract = {Chaetonotidae is the most diversified family of the entire phylum Gastrotricha; it comprises ~430 species distributed across 16 genera. The current classification, established mainly on morphological traits, has been challenged in recent years by phylogenetic studies, indicating that the cuticular ornamentations used to discriminate among species may be misleading when used to identify groupings, which has been the practice until now. Therefore, a consensus is developing toward implementing novel approaches to better define species identity and affiliation at a higher taxonomic ranking. Using an integrative morphological and molecular approach, including annotation of the mitogenome, we report on some freshwater gastrotrichs characterised by a mixture of two types of cuticular scales diagnostic of the genera Aspidiophorus and Heterolepidoderma . Our specimens' overall anatomical characteristics find no correspondence in the taxa of these two genera, calling for their affiliation to a new species. Phylogenetic analyses based on the sequence of the ribosomal RNA genes of 96 taxa consistently found the new species unrelated to Aspidiophorus or Heterolepidoderma but allied with Chaetonotus aff. subtilis, as a subset of a larger clade, including mostly planktonic species. Morphological uniqueness and position along the non-monophyletic Chaetonotidae branch advocate erecting a new genus to accommodate the current specimens; consequently, the name Litigonotus ghinii gen. nov., sp. nov. is proposed. The complete mitochondrial genome of the new taxon resulted in a single circular molecule 14,384 bp long, including 13 protein-coding genes, 17 tRNA genes and 2 rRNAs genes, showing a perfect synteny and collinearity with the only other gastrotrich mitogenome available, a possible hint of a high level of conservation in the mitochondria of Chaetonotidae. ZooBank: urn:lsid:zoobank.org:pub:9803F659-306F-4EC3-A73B-8C704069F24A.},
}

*Phylogeny
*Genome, Mitochondrial/genetics
Animals
Species Specificity
Fresh Water

@article {pmid38970720,
year = {2024},
author = {Shannan, PZT and Suganya, SG and Ramesh, M and Jemima, EA},
title = {Molecular based identification and phylogenetic relationship of the leech Hirudinaria manillensis from India by using mitochondrial cytochrome c oxidase subunit I gene.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {787},
pmid = {38970720},
issn = {1573-4978},
mesh = {Animals ; *Phylogeny ; *Leeches/genetics/enzymology/classification ; *Electron Transport Complex IV/genetics ; India ; DNA, Mitochondrial/genetics ; Sequence Analysis, DNA/methods ; Mitochondria/genetics/enzymology ; Base Sequence ; },
abstract = {BACKGROUND: A molecular approach for the identification of unknown species by the using mitochondrial cox1 gene is an effective and reliable as compared with morphological-based identification. Hirudinaria manillensis referred to as Asian Buffalo Leech, is found in South Asia and traditionally used as medicine owing to its medicinal properties.

METHODS AND RESULTS: The study aimed to isolate and identify the leech species using cox1 gene sequencing and their phylogenetic relationships. The nucleotide sequences of cytochrome c oxidase subunit I (cox1) mitochondrial genes were analyzed for species identification and the phylogenetic relationship of crucial therapeutic leech Hirudinaria manillensis. The isolated DNA from the leech sample was amplified with cox1 gene-specific primers. BLAST results with the H. manillensis sequence showed 89.24% homology with H. manillensis and phylogenetic tree analysis revealed the genetic relationship with other GenBank submitted sequences.

CONCLUSION: The present study concluded that the cox1 gene could be an effective way to identify the leech H. manillensis and provided sufficient phylogenetic information to distinguish H. manillensis indicating a significant mtDNA-based approach to species identification.},
}

Animals
*Phylogeny
*Leeches/genetics/enzymology/classification
*Electron Transport Complex IV/genetics
India
DNA, Mitochondrial/genetics
Sequence Analysis, DNA/methods
Mitochondria/genetics/enzymology
Base Sequence

@article {pmid38946300,
year = {2024},
author = {Elnegris, HM and Abdelrahman, AA and El-Roghy, ES},
title = {The potential therapeutic effects of exosomes derived from bone marrow mesenchymal stem cells on ileum injury of a rat sepsis model (histological and immunohistochemical study).},
journal = {Ultrastructural pathology},
volume = {48},
number = {4},
pages = {274-296},
doi = {10.1080/01913123.2024.2368011},
pmid = {38946300},
issn = {1521-0758},
mesh = {Animals ; *Sepsis/complications ; Rats ; *Ileum/pathology ; *Mesenchymal Stem Cells ; *Disease Models, Animal ; *Exosomes/metabolism ; Male ; Immunohistochemistry ; Rats, Wistar ; Nitric Oxide Synthase Type II/metabolism ; },
abstract = {Sepsis denotes a serious high mortality concern. The study was designed to evaluate the effect of mesenchymal stem cell exosomes (MSC-exosomes) on the evolution of the animal model of sepsis. In this study, 36 rats were distributed into three groups, (I) controls, (II) LPS-treated, and (III) LPS+MSC-EVs. Sepsis was simulated by administering E. coli-LPS to the laboratory animals. Group III was given MSC-exosomes four hours after the LPS injection. Forty-eight hours later rats were sacrificed. Ileum samples were excised, and processed for the histological assessment, immunohistochemical identification of CD44, and inducible nitric oxide synthase (iNOS). Ileum homogenate was used to estimate tumor necrosis factor α (TNF α) besides Cyclooxygenase-2 (COX 2). PCR was used for the detection of interleukin 1α (IL‑1α), and interleukin 17 (IL‑17). Statistical and morphometrical analysis was done. The LPS-treated group showed increased TNF-α, IL‑1α, IL‑17, and decreased COX 2. LPS administration led to cytoplasmic vacuolization of enterocytes, an increase in the vasculature, and cellular infiltrations invaded the lamina propria. There was a significant rise in goblet cells and the proportion of collagen fibers. Ultrastructurally, the enterocytes displayed nuclear irregularity, rough endoplasmic reticulum (rER) dilatation, and increased mitochondria number. Sepsis induces a significant increase in iNOS and a decrease in CD44 immune expressions. LPS+MSC-EVs group restored normal ileum structure and revealed a significant elevation in CD44 and a reduction in iNOS immunoreactions. LPS-sepsis induced an obvious ileum inflammatory deterioration ameliorated by MSC-exosomes, mostly through their antioxidant, anti-inflammatory, and anti-apoptotic properties.},
}

Animals
*Sepsis/complications
Rats
*Ileum/pathology
*Mesenchymal Stem Cells
*Disease Models, Animal
*Exosomes/metabolism
Male
Immunohistochemistry
Rats, Wistar
Nitric Oxide Synthase Type II/metabolism

@article {pmid38940122,
year = {2024},
author = {Sashittal, P and Chen, V and Pasarkar, A and Raphael, BJ},
title = {Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {Supplement_1},
pages = {i218-i227},
pmid = {38940122},
issn = {1367-4811},
support = {U24 CA264027/CA/NCI NIH HHS/United States ; //NIH/ ; U24CA248453/BC/NCI NIH HHS/United States ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; *Cell Lineage/genetics ; *Mitochondria/genetics ; Mutation ; Genome, Mitochondrial ; Algorithms ; Evolution, Molecular ; },
abstract = {MOTIVATION: Eukaryotic cells contain organelles called mitochondria that have their own genome. Most cells contain thousands of mitochondria which replicate, even in nondividing cells, by means of a relatively error-prone process resulting in somatic mutations in their genome. Because of the higher mutation rate compared to the nuclear genome, mitochondrial mutations have been used to track cellular lineage, particularly using single-cell sequencing that measures mitochondrial mutations in individual cells. However, existing methods to infer the cell lineage tree from mitochondrial mutations do not model "heteroplasmy," which is the presence of multiple mitochondrial clones with distinct sets of mutations in an individual cell. Single-cell sequencing data thus provide a mixture of the mitochondrial clones in individual cells, with the ancestral relationships between these clones described by a mitochondrial clone tree. While deconvolution of somatic mutations from a mixture of evolutionarily related genomes has been extensively studied in the context of bulk sequencing of cancer tumor samples, the problem of mitochondrial deconvolution has the additional constraint that the mitochondrial clone tree must be concordant with the cell lineage tree.

RESULTS: We formalize the problem of inferring a concordant pair of a mitochondrial clone tree and a cell lineage tree from single-cell sequencing data as the Nested Perfect Phylogeny Mixture (NPPM) problem. We derive a combinatorial characterization of the solutions to the NPPM problem, and formulate an algorithm, MERLIN, to solve this problem exactly using a mixed integer linear program. We show on simulated data that MERLIN outperforms existing methods that do not model mitochondrial heteroplasmy nor the concordance between the mitochondrial clone tree and the cell lineage tree. We use MERLIN to analyze single-cell whole-genome sequencing data of 5220 cells of a gastric cancer cell line and show that MERLIN infers a more biologically plausible cell lineage tree and mitochondrial clone tree compared to existing methods.

https://github.com/raphael-group/MERLIN.},
}

*Single-Cell Analysis/methods
Humans
*Cell Lineage/genetics
*Mitochondria/genetics
Mutation
Genome, Mitochondrial
Algorithms
Evolution, Molecular

@article {pmid38936100,
year = {2024},
author = {Montoliu Nebot, J and Iradi Casal, A and Cepeda Madrigal, S and Rissi, G and Sanz Saz, S and Molés Gimeno, JD and Miravet Sorribes, LM},
title = {[Physiological assessment and management of post-COVID patients with normal cardiopulmonary imaging and functional tests].},
journal = {Semergen},
volume = {50},
number = {8},
pages = {102282},
doi = {10.1016/j.semerg.2024.102282},
pmid = {38936100},
issn = {1578-8865},
abstract = {OBJECTIVE: Contributing to elucidate the pathophysiology of dyspnoea and exertion intolerance in post-COVID syndrome patients with normal cardiopulmonary imaging and functional tests at rest, while determining their fitness and level of endurance in order to individualize working parameters for physical rehabilitation.

MATERIAL AND METHODS: After an anamnesis and clinical examination at rest, 27 subjects (50±11.9 years) (14 women) with post-COVID syndrome of more than 6 months of evolution performed a continuous maximal-incremental graded cardiopulmonary exercise test (CPET) with breath-by-breath gas-exchange monitoring and continuous ECG registration, on an electromagnetically braked cycle ergometer. The values obtained were compared with those of reference, gender or controls, using the Chi-square, t-Student or ANOVA test.

RESULTS: The clinical examination at rest and the CPET were clinically normal and without adverse events. Reasons for stopping exercise were leg discomfort. It is only worth noting a BMI=29.9±5.8kg/m[2] and a basal lactate concentration of 2.1±0.7mmol/L. The physiological assessment of endurance showed the following results relative to predicted VO2máx: 1)peakVO2=80.5±18.6%; 2)VO2 at ventilatory threshold1 (VO2VT1): 46.0±12.9%; 3)VO2VT2: 57.2±16.4%; 4)working time in acidosis: 5.6±3,0minutes; and 5)maximum lactate concentration: 5.1±2.2mmol/L.

CONCLUSIONS: The CPET identified limited aerobic metabolism and early increase in glycolytic metabolism as causes of dyspnoea and exercise intolerance, determined fitness for physical rehabilitation, and individualized it based on the level of endurance.},
}

@article {pmid38934796,
year = {2024},
author = {Khachaturyan, M and Santer, M and Reusch, TBH and Dagan, T},
title = {Heteroplasmy Is Rare in Plant Mitochondria Compared with Plastids despite Similar Mutation Rates.},
journal = {Molecular biology and evolution},
volume = {41},
number = {7},
pages = {},
pmid = {38934796},
issn = {1537-1719},
support = {HIDSS-0005)//Helmholtz School for Marine Data Science/ ; RGP0011/2022//HFSP/ ; 101043835//ERC/ ; },
mesh = {*Plastids/genetics ; *Mitochondria/genetics/metabolism ; *Mutation Rate ; *Heteroplasmy ; Alleles ; },
abstract = {Plant cells harbor two membrane-bound organelles containing their own genetic material-plastids and mitochondria. Although the two organelles coexist and coevolve within the same plant cells, they differ in genome copy number, intracellular organization, and mode of segregation. How these attributes affect the time to fixation or, conversely, loss of neutral alleles is currently unresolved. Here, we show that mitochondria and plastids share the same mutation rate, yet plastid alleles remain in a heteroplasmic state significantly longer compared with mitochondrial alleles. By analyzing genetic variants across populations of the marine flowering plant Zostera marina and simulating organelle allele dynamics, we examine the determinants of allele segregation and allele fixation. Our results suggest that the bottlenecks on the cell population, e.g. during branching or seeding, and stratification of the meristematic tissue are important determinants of mitochondrial allele dynamics. Furthermore, we suggest that the prolonged plastid allele dynamics are due to a yet unknown active plastid partition mechanism. The dissimilarity between plastid and mitochondrial novel allele fixation at different levels of organization may manifest in differences in adaptation processes. Our study uncovers fundamental principles of organelle population genetics that are essential for further investigations of long-term evolution and molecular dating of divergence events.},
}

*Plastids/genetics
*Mitochondria/genetics/metabolism
*Mutation Rate
*Heteroplasmy
Alleles

@article {pmid38915079,
year = {2024},
author = {Wu, CS and Wang, RJ and Chaw, SM},
title = {Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {140},
pmid = {38915079},
issn = {1741-7007},
support = {No. 2022B1111040003//Guangdong Provincial Key R&D Programme/ ; },
mesh = {*Phylogeny ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Gnetum/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Magnoliopsida/genetics ; },
abstract = {BACKGROUND: Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus.

RESULTS: We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT.

CONCLUSIONS: Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.},
}

*Phylogeny
*Gene Transfer, Horizontal
*Genome, Mitochondrial
*Gnetum/genetics
DNA, Plant/genetics
Evolution, Molecular
Magnoliopsida/genetics

@article {pmid38906137,
year = {2024},
author = {Iwata, R and Vanderhaeghen, P},
title = {Metabolic mechanisms of species-specific developmental tempo.},
journal = {Developmental cell},
volume = {59},
number = {13},
pages = {1628-1639},
doi = {10.1016/j.devcel.2024.05.027},
pmid = {38906137},
issn = {1878-1551},
mesh = {Animals ; *Species Specificity ; Humans ; Mitochondria/metabolism ; Biological Evolution ; Metabolic Networks and Pathways ; Gene Expression Regulation, Developmental ; },
abstract = {Development consists of a highly ordered suite of steps and transitions, like choreography. Although these sequences are often evolutionarily conserved, they can display species variations in duration and speed, thereby modifying final organ size or function. Despite their evolutionary significance, the mechanisms underlying species-specific scaling of developmental tempo have remained unclear. Here, we will review recent findings that implicate global cellular mechanisms, particularly intermediary and protein metabolism, as species-specific modifiers of developmental tempo. In various systems, from somitic cell oscillations to neuronal development, metabolic pathways display species differences. These have been linked to mitochondrial metabolism, which can influence the species-specific speed of developmental transitions. Thus, intermediary metabolic pathways regulate developmental tempo together with other global processes, including proteostasis and chromatin remodeling. By linking metabolism and the evolution of developmental trajectories, these findings provide opportunities to decipher how species-specific cellular timing can influence organism fitness.},
}

Animals
*Species Specificity
Humans
Mitochondria/metabolism
Biological Evolution
Metabolic Networks and Pathways
Gene Expression Regulation, Developmental

@article {pmid38900713,
year = {2024},
author = {Molinet, J and Navarrete, JP and Villarroel, CA and Villarreal, P and Sandoval, FI and Nespolo, RF and Stelkens, R and Cubillos, FA},
title = {Wild Patagonian yeast improve the evolutionary potential of novel interspecific hybrid strains for lager brewing.},
journal = {PLoS genetics},
volume = {20},
number = {6},
pages = {e1011154},
pmid = {38900713},
issn = {1553-7404},
mesh = {*Beer/microbiology ; *Fermentation/genetics ; *Saccharomyces cerevisiae/genetics/metabolism ; *Hybridization, Genetic ; Saccharomyces/genetics/metabolism ; Ethanol/metabolism ; Mitochondria/genetics/metabolism ; Genome, Fungal ; Evolution, Molecular ; Genetic Variation ; Maltose/metabolism ; Mutation ; },
abstract = {Lager yeasts are limited to a few strains worldwide, imposing restrictions on flavour and aroma diversity and hindering our understanding of the complex evolutionary mechanisms during yeast domestication. The recent finding of diverse S. eubayanus lineages from Patagonia offers potential for generating new lager yeasts with different flavour profiles. Here, we leverage the natural genetic diversity of S. eubayanus and expand the lager yeast repertoire by including three distinct Patagonian S. eubayanus lineages. We used experimental evolution and selection on desirable traits to enhance the fermentation profiles of novel S. cerevisiae x S. eubayanus hybrids. Our analyses reveal an intricate interplay of pre-existing diversity, selection on species-specific mitochondria, de-novo mutations, and gene copy variations in sugar metabolism genes, resulting in high ethanol production and unique aroma profiles. Hybrids with S. eubayanus mitochondria exhibited greater evolutionary potential and superior fitness post-evolution, analogous to commercial lager hybrids. Using genome-wide screens of the parental subgenomes, we identified genetic changes in IRA2, IMA1, and MALX genes that influence maltose metabolism, and increase glycolytic flux and sugar consumption in the evolved hybrids. Functional validation and transcriptome analyses confirmed increased maltose-related gene expression, influencing greater maltotriose consumption in evolved hybrids. This study demonstrates the potential for generating industrially viable lager yeast hybrids from wild Patagonian strains. Our hybridization, evolution, and mitochondrial selection approach produced hybrids with high fermentation capacity and expands lager beer brewing options.},
}

*Beer/microbiology
*Fermentation/genetics
*Saccharomyces cerevisiae/genetics/metabolism
*Hybridization, Genetic
Saccharomyces/genetics/metabolism
Ethanol/metabolism
Mitochondria/genetics/metabolism
Genome, Fungal
Evolution, Molecular
Genetic Variation
Maltose/metabolism
Mutation

@article {pmid38892163,
year = {2024},
author = {Hong, YH and Yuan, YN and Li, K and Storey, KB and Zhang, JY and Zhang, SS and Yu, DN},
title = {Differential Mitochondrial Genome Expression of Four Hylid Frog Species under Low-Temperature Stress and Its Relationship with Amphibian Temperature Adaptation.},
journal = {International journal of molecular sciences},
volume = {25},
number = {11},
pages = {},
pmid = {38892163},
issn = {1422-0067},
support = {31801963//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Genome, Mitochondrial ; *Anura/genetics/physiology ; *Phylogeny ; Cold-Shock Response/genetics ; Cold Temperature ; Adaptation, Physiological/genetics ; Gene Expression Regulation ; },
abstract = {Extreme weather poses huge challenges for animals that must adapt to wide variations in environmental temperature and, in many cases, it can lead to the local extirpation of populations or even the extinction of an entire species. Previous studies have found that one element of amphibian adaptation to environmental stress involves changes in mitochondrial gene expression at low temperatures. However, to date, comparative studies of gene expression in organisms living at extreme temperatures have focused mainly on nuclear genes. This study sequenced the complete mitochondrial genomes of five Asian hylid frog species: Dryophytes japonicus, D. immaculata, Hyla annectans, H. chinensis and H. zhaopingensis. It compared the phylogenetic relationships within the Hylidae family and explored the association between mitochondrial gene expression and evolutionary adaptations to cold stress. The present results showed that in D. immaculata, transcript levels of 12 out of 13 mitochondria genes were significantly reduced under cold exposure (p < 0.05); hence, we put forward the conjecture that D. immaculata adapts by entering a hibernation state at low temperature. In H. annectans, the transcripts of 10 genes (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, COX1, COX2 and ATP8) were significantly reduced in response to cold exposure, and five mitochondrial genes in H. chinensis (ND1, ND2, ND3, ND4L and ATP6) also showed significantly reduced expression and transcript levels under cold conditions. By contrast, transcript levels of ND2 and ATP6 in H. zhaopingensis were significantly increased at low temperatures, possibly related to the narrow distribution of this species primarily at low latitudes. Indeed, H. zhaopingensis has little ability to adapt to low temperature (4 °C), or maybe to enter into hibernation, and it shows metabolic disorder in the cold. The present study demonstrates that the regulatory trend of mitochondrial gene expression in amphibians is correlated with their ability to adapt to variable climates in extreme environments. These results can predict which species are more likely to undergo extirpation or extinction with climate change and, thereby, provide new ideas for the study of species extinction in highly variable winter climates.},
}

Animals
*Genome, Mitochondrial
*Anura/genetics/physiology
*Phylogeny
Cold-Shock Response/genetics
Cold Temperature
Adaptation, Physiological/genetics
Gene Expression Regulation

@article {pmid38890582,
year = {2024},
author = {Gendron, EMS and Qing, X and Sevigny, JL and Li, H and Liu, Z and Blaxter, M and Powers, TO and Thomas, WK and Porazinska, DL},
title = {Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {615},
pmid = {38890582},
issn = {1471-2164},
mesh = {Animals ; *Genome, Mitochondrial ; *Nematoda/genetics ; *Selection, Genetic ; *Genomics/methods ; *Phylogeny ; Base Composition ; Evolution, Molecular ; Codon/genetics ; },
abstract = {BACKGROUND: Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures.

RESULTS: Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection.

CONCLUSIONS: Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.},
}

Animals
*Genome, Mitochondrial
*Nematoda/genetics
*Selection, Genetic
*Genomics/methods
*Phylogeny
Base Composition
Evolution, Molecular
Codon/genetics

@article {pmid38882704,
year = {2024},
author = {Tomizawa, Y and Aizawa, M and Jouraku, A and Sonoda, S},
title = {Field survey of reproductive modes and sodium channel mutations associated with pyrethroid resistance in Thrips tabaci.},
journal = {Journal of pesticide science},
volume = {49},
number = {2},
pages = {122-129},
pmid = {38882704},
issn = {1348-589X},
abstract = {Using PCR-Restriction Fragment Length Polymorphism (RFLP) with mitochondrial cytochrome c oxidase subunit I sequences, we examined the reproductive modes of female adults of Thrips tabaci collected at 54 sites across Japan. Results showed the presence of heteroplasmic insects harboring mitochondria associated with arrhenotoky and thelytoky. Using the insects, we also applied PCR-RFLP to examine the genotypes for the amino acid mutation (T929I) site involved in pyrethroid resistance. Findings showed the presence of thelytokous heterozygotes under the circumstance that most arrhenotokous insects are resistant homozygotes, and many thelytokous insects are susceptible homozygotes. These results suggest that, in the field, genetic exchange occurs between insects through of both reproductive modes. A survey of the genotypes for the other amino acid mutations using nucleotide sequencing showed a decline of insects with an M918T and L1014F pair and an increase of insects with M918L. These results suggest the evolutional progression of amino acid mutations associated with pyrethroid resistance in T. tabaci.},
}

@article {pmid38877225,
year = {2024},
author = {Hu, X and Hoffmann, DS and Wang, M and Schuhmacher, L and Stroe, MC and Schreckenberger, B and Elstner, M and Fischer, R},
title = {GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting.},
journal = {Nature microbiology},
volume = {9},
number = {7},
pages = {1752-1763},
pmid = {38877225},
issn = {2058-5276},
support = {FI 459/26-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STR1784/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Caenorhabditis elegans/microbiology/metabolism ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Mitochondria/metabolism ; *Ascomycota/metabolism/genetics ; *Fungal Proteins/metabolism/genetics ; Pheromones/metabolism ; Humans ; Gene Expression Regulation, Fungal ; },
abstract = {Initiation of development requires differential gene expression and metabolic adaptations. Here we show in the nematode-trapping fungus, Arthrobotrys flagrans, that both are achieved through a dual-function G-protein-coupled receptor (GPCR). A. flagrans develops adhesive traps and recognizes its prey, Caenorhabditis elegans, through nematode-specific pheromones (ascarosides). Gene-expression analyses revealed that ascarosides activate the fungal GPCR, GprC, at the plasma membrane and together with the G-protein alpha subunit GasA, reprograms the cell. However, GprC and GasA also reside in mitochondria and boost respiration. This dual localization of GprC in A. flagrans resembles the localization of the cannabinoid receptor CB1 in humans. The C. elegans ascaroside-sensing GPCR, SRBC66 and GPCRs of many fungi are also predicted for dual localization, suggesting broad evolutionary conservation. An SRBC64/66-GprC chimaeric protein was functional in A. flagrans, and C. elegans SRBC64/66 and DAF38 share ascaroside-binding sites with the fungal GprC receptor, suggesting 400-million-year convergent evolution.},
}

Animals
*Caenorhabditis elegans/microbiology/metabolism
*Receptors, G-Protein-Coupled/metabolism/genetics
*Mitochondria/metabolism
*Ascomycota/metabolism/genetics
*Fungal Proteins/metabolism/genetics
Pheromones/metabolism
Humans
Gene Expression Regulation, Fungal

@article {pmid38869631,
year = {2024},
author = {de Jong, TJ and Shmida, A},
title = {Paternal Inheritance of Mitochondrial DNA May Lead to Dioecy in Conifers.},
journal = {Acta biotheoretica},
volume = {72},
number = {2},
pages = {7},
pmid = {38869631},
issn = {1572-8358},
mesh = {*DNA, Mitochondrial/genetics ; *Tracheophyta/genetics ; *Paternal Inheritance ; Reproduction/genetics ; Pollen/genetics ; DNA, Plant/genetics ; },
abstract = {In angiosperms cytoplasmic DNA is typically passed on maternally through ovules. Genes in the mtDNA may cause male sterility. When male-sterile (female) cytotypes produce more seeds than cosexuals, they pass on more copies of their mtDNA and will co-occur with cosexuals with a neutral cytotype. Cytoplasmic gynodioecy is a well-known phenomenon in angiosperms, both in wild and crop plants. In some conifer families (e.g. Pinaceae) mitochondria are also maternally inherited. However in some other families (e.g. Taxaceae and Cupressaceae) mtDNA is paternally inherited through the pollen. With paternal mtDNA inheritance, male cytotypes that produce more pollen than cosexuals are expected to co-occur with cosexuals. This is uncharted territory. An ESS model shows that the presence of male cytotypes selects for more female allocation in the cosexual, i.e. for sexual specialisation. An allele that switches sex from male to female can then invade. This leads to rapid loss of the neutral cytotype of the cosexual, fixation of the male cytotype and dioecy with 50% males and 50% females. The models suggest that paternal inheritance of mtDNA facilitates the evolution dioecy. Consistent with this hypothesis the Pinaceae are 100% monoecious, while dioecy is common in the Taxaceae family and in the genus Juniperus (Cupressaceae). However, no reliable data are yet available on both mode of inheritance of mtDNA and gender variation of the same species. When cosexuals benefit from reproductive assurance (high selfing rate, low inbreeding depression, low fertilisation) they maintain themselves next to males and females. This predicted pattern with three sex types present in the same population is observed in conifers in nature.},
}

*DNA, Mitochondrial/genetics
*Tracheophyta/genetics
*Paternal Inheritance
Reproduction/genetics
Pollen/genetics
DNA, Plant/genetics

@article {pmid38868915,
year = {2024},
author = {Baird, LM and Berndsen, CE and Monroe, JD},
title = {Malate dehydrogenase in plants: evolution, structure, and a myriad of functions.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20230089},
pmid = {38868915},
issn = {1744-1358},
support = {MCB-2322867//National Science Foundation (NSF)/ ; },
abstract = {Malate dehydrogenase (MDH) catalyzes the interconversion of oxaloacetate and malate coupled to the oxidation/reduction of coenzymes NAD(P)H/NAD(P)+. While most animals have two isoforms of MDH located in the cytosol and mitochondria, all major groups of land plants have at least six MDHs localized to the cytosol, mitochondria, plastids, and peroxisomes. This family of enzymes participates in important reactions in plant cells including photosynthesis, photorespiration, lipid metabolism, and NH4+ metabolism. MDH also helps to regulate the energy balance in the cell and may help the plant cope with various environmental stresses. Despite their functional diversity, all of the plant MDH enzymes share a similar structural fold and act as dimers. In this review, we will introduce readers to our current understanding of the plant MDHs, including their evolution, structure, and function. The focus will be on the MDH enzymes of the model plant Arabidopsis thaliana.},
}

@article {pmid38866808,
year = {2024},
author = {Faustino, M and Lourenço, T and Strobbe, S and Cao, D and Fonseca, A and Rocha, I and Van Der Straeten, D and Oliveira, MM},
title = {OsTH1 is a key player in thiamin biosynthesis in rice.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {13591},
pmid = {38866808},
issn = {2045-2322},
mesh = {*Oryza/genetics/metabolism ; *Thiamine/biosynthesis/metabolism ; *Plant Proteins/metabolism/genetics ; Phylogeny ; Gene Expression Regulation, Plant ; },
abstract = {Thiamin is a vital nutrient that acts as a cofactor for several enzymes primarily localized in the mitochondria. These thiamin-dependent enzymes are involved in energy metabolism, nucleic acid biosynthesis, and antioxidant machinery. The enzyme HMP-P kinase/thiamin monophosphate synthase (TH1) holds a key position in thiamin biosynthesis, being responsible for the phosphorylation of HMP-P into HMP-PP and for the condensation of HMP-PP and HET-P to form TMP. Through mathematical kinetic model, we have identified TH1 as a critical player for thiamin biofortification in rice. We further focused on the functional characterization of OsTH1. Sequence and gene expression analysis, along with phylogenetic studies, provided insights into OsTH1 bifunctional features and evolution. The indispensable role of OsTH1 in thiamin biosynthesis was validated by heterologous expression of OsTH1 and successful complementation of yeast knock-out mutants impaired in thiamin production. We also proved that the sole OsTH1 overexpression in rice callus significantly improves B1 concentration, resulting in 50% increase in thiamin accumulation. Our study underscores the critical role of OsTH1 in thiamin biosynthesis, shedding light on its bifunctional nature and evolutionary significance. The significant enhancement of thiamin accumulation in rice callus upon OsTH1 overexpression constitutes evidence of its potential application in biofortification strategies.},
}

*Oryza/genetics/metabolism
*Thiamine/biosynthesis/metabolism
*Plant Proteins/metabolism/genetics
Phylogeny
Gene Expression Regulation, Plant

@article {pmid38864935,
year = {2024},
author = {Mochizuki, H},
title = {Pathological mechanisms and treatment of sporadic Parkinson's disease: past, present, and future.},
journal = {Journal of neural transmission (Vienna, Austria : 1996)},
volume = {131},
number = {6},
pages = {597-607},
pmid = {38864935},
issn = {1435-1463},
support = {JPMJCR18H4//Core Research for Evolutional Science and Technology/ ; JP18dm0207020//Japan Agency for Medical Research and Development/ ; JP22dm0207070//Japan Agency for Medical Research and Development/ ; 22H02951//Japan Society for the Promotion of Science London/ ; 23K18255//Japan Society for the Promotion of Science London/ ; },
mesh = {Humans ; *Parkinson Disease/therapy/pathology/metabolism ; Animals ; Substantia Nigra/pathology/metabolism ; alpha-Synuclein/metabolism ; },
abstract = {For a special issue, we review studies on the pathogenesis of nigral cell death and the treatment of sporadic Parkinson's disease (sPD) over the past few decades, with a focus on the studies performed by Prof. Mizuno and our group. Prof. Mizuno proposed the initial concept that mitochondrial function may be impaired in sPD. When working at Jichi Medical School, he found a decrease in complex I of the mitochondrial electron transfer complex in the substantia nigra of patients with Parkinson's disease (PD) and MPTP models. After moving to Juntendo University as a professor and chairman, he continued to study the mechanisms of cell death in the substantia nigra of patients with sPD. Under his supervision, I studied the relationships between PD and apoptosis, PD and iron involvement, mitochondrial dysfunction and apoptosis, and PD and neuroinflammation. Moving to Kitasato University, we focused on PD and the cytotoxicity of alpha synuclein (αSyn) as well as brain neuropathology. Eventually, I moved to Osaka University, where I continued working on PD and αSyn projects to promote therapeutic research. In this paper, we present the details of these studies in the following order: past, present, and future.},
}

Humans
*Parkinson Disease/therapy/pathology/metabolism
Animals
Substantia Nigra/pathology/metabolism
alpha-Synuclein/metabolism

@article {pmid38853081,
year = {2024},
author = {Rackham, O and Saurer, M and Ban, N and Filipovska, A},
title = {Unique architectural features of mammalian mitochondrial protein synthesis.},
journal = {Trends in cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tcb.2024.05.001},
pmid = {38853081},
issn = {1879-3088},
abstract = {Mitochondria rely on coordinated expression of their own mitochondrial DNA (mtDNA) with that of the nuclear genome for their biogenesis. The bacterial ancestry of mitochondria has given rise to unique and idiosyncratic features of the mtDNA and its expression machinery that can be specific to different organisms. In animals, the mitochondrial protein synthesis machinery has acquired many new components and mechanisms over evolution. These include several new ribosomal proteins, new stop codons and ways to recognise them, and new mechanisms to deliver nascent proteins into the mitochondrial inner membrane. Here we describe the mitochondrial protein synthesis machinery in mammals and its unique mechanisms of action elucidated to date and highlight the technologies poised to reveal the next generation of discoveries in mitochondrial translation.},
}

@article {pmid38851366,
year = {2024},
author = {Tapanainen, R and Aasumets, K and Fekete, Z and Goffart, S and Dufour, E and L O Pohjoismäki, J},
title = {Species-specific variation in mitochondrial genome tandem repeat polymorphisms in hares (Lepus spp., Lagomorpha, Leporidae) provides insight into their evolution.},
journal = {Gene},
volume = {926},
number = {},
pages = {148644},
doi = {10.1016/j.gene.2024.148644},
pmid = {38851366},
issn = {1879-0038},
mesh = {Animals ; *Hares/genetics ; *Genome, Mitochondrial ; *Tandem Repeat Sequences/genetics ; *DNA, Mitochondrial/genetics ; *Polymorphism, Genetic ; *Evolution, Molecular ; *Species Specificity ; Phylogeny ; },
abstract = {The non-coding regions of the mitochondrial DNAs (mtDNAs) of hares, rabbits, and pikas (Lagomorpha) contain short (∼20 bp) and long (130-160 bp) tandem repeats, absent in related mammalian orders. In the presented study, we provide in-depth analysis for mountain hare (Lepus timidus) and brown hare (L. europaeus) mtDNA non-coding regions, together with a species- and population-level analysis of tandem repeat variation. Mountain hare short tandem repeats (SRs) as well as other analyzed hare species consist of two conserved 10 bp motifs, with only brown hares exhibiting a single, more variable motif. Long tandem repeats (LRs) also differ in sequence and copy number between species. Mountain hares have four to seven LRs, median value five, while brown hares exhibit five to nine LRs, median value six. Interestingly, introgressed mountain hare mtDNA in brown hares obtained an intermediate LR length distribution, with median copy number being the same as with conspecific brown hare mtDNA. In contrast, transfer of brown hare mtDNA into cultured mtDNA-less mountain hare cells maintained the original LR number, whereas the reciprocal transfer caused copy number instability, suggesting that cellular environment rather than the nuclear genomic background plays a role in the LR maintenance. Due to their dynamic nature and separation from other known conserved sequence elements on the non-coding region of hare mitochondrial genomes, the tandem repeat elements likely to represent signatures of ancient genetic rearrangements. clarifying the nature and dynamics of these rearrangements may shed light on the possible role of NCR repeated elements in mitochondria and in species evolution.},
}

Animals
*Hares/genetics
*Genome, Mitochondrial
*Tandem Repeat Sequences/genetics
*DNA, Mitochondrial/genetics
*Polymorphism, Genetic
*Evolution, Molecular
*Species Specificity
Phylogeny

@article {pmid38842420,
year = {2024},
author = {Dorrell, RG and Zhang, Y and Liang, Y and Gueguen, N and Nonoyama, T and Croteau, D and Penot, M and Adiba, S and Bailleul, B and Gros, V and Pierella Karlusich, JJ and Zweig, N and Fernie, AR and Jouhet, J and Maréchal, E and Bowler, C},
title = {Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koae168},
pmid = {38842420},
issn = {1532-298X},
abstract = {Organic carbon fixed in chloroplasts through the Calvin-Benson-Bassham Cycle can be diverted towards different metabolic fates, including cyoplasmic and mitochondrial respiration, gluconeogenesis, and synthesis of diverse plastid metabolites via the pyruvate hub. In plants, pyruvate is principally produced via cytoplasmic glycolysis, although a plastid-targeted lower glycolytic pathway is known to exist in non-photosynthetic tissue. Here, we characterized a lower plastid glycolysis-gluconeogenesis pathway enabling the direct interconversion of glyceraldehyde-3-phosphate and phospho-enol-pyruvate in diatoms, ecologically important marine algae distantly related to plants. We show that two reversible enzymes required to complete diatom plastid glycolysis-gluconeogenesis, Enolase and bis-phospho-glycerate mutase (PGAM), originated through duplications of mitochondria-targeted respiratory isoforms. Through CRISPR-Cas9 mutagenesis, integrative 'omic analyses, and measured kinetics of expressed enzymes in the diatom Phaeodactylum tricornutum, we present evidence that this pathway diverts plastid glyceraldehyde-3-phosphate into the pyruvate hub, and may also function in the gluconeogenic direction. Considering experimental data, we show that this pathway has different roles dependent in particular on day length and environmental temperature, and show that the cpEnolase and cpPGAM genes are expressed at elevated levels in high latitude oceans where diatoms are abundant. Our data provide evolutionary, meta-genomic and functional insights into a poorly understood yet evolutionarily recurrent plastid metabolic pathway.},
}

@article {pmid38835243,
year = {2024},
author = {Zwahlen, SM and Hayward, JA and Maguire, CS and Qin, AR and van Dooren, GG},
title = {A myzozoan-specific protein is an essential membrane-anchoring component of the succinate dehydrogenase complex in Toxoplasma parasites.},
journal = {Open biology},
volume = {14},
number = {6},
pages = {230463},
doi = {10.1098/rsob.230463},
pmid = {38835243},
issn = {2046-2441},
support = {//National Health and Medical Research Council/ ; },
mesh = {*Toxoplasma/metabolism/genetics/enzymology ; *Succinate Dehydrogenase/metabolism/genetics ; *Protozoan Proteins/metabolism/genetics/chemistry ; Humans ; Mitochondrial Proteins/metabolism/genetics ; Mitochondria/metabolism ; Phylogeny ; Animals ; },
abstract = {Succinate dehydrogenase (SDH) is a protein complex that functions in the tricarboxylic acid cycle and the electron transport chain of mitochondria. In most eukaryotes, SDH is highly conserved and comprises the following four subunits: SdhA and SdhB form the catalytic core of the complex, while SdhC and SdhD anchor the complex in the membrane. Toxoplasma gondii is an apicomplexan parasite that infects one-third of humans worldwide. The genome of T. gondii encodes homologues of the catalytic subunits SdhA and SdhB, although the physiological role of the SDH complex in the parasite and the identity of the membrane-anchoring subunits are poorly understood. Here, we show that the SDH complex contributes to optimal proliferation and O2 consumption in the disease-causing tachyzoite stage of the T. gondii life cycle. We characterize a small membrane-bound subunit of the SDH complex called mitochondrial protein ookinete developmental defect (MPODD), which is conserved among myzozoans, a phylogenetic grouping that incorporates apicomplexan parasites and their closest free-living relatives. We demonstrate that TgMPODD is essential for SDH activity and plays a key role in attaching the TgSdhA and TgSdhB proteins to the membrane anchor of the complex. Our findings highlight a unique and important feature of mitochondrial energy metabolism in apicomplexan parasites and their relatives.},
}

*Toxoplasma/metabolism/genetics/enzymology
*Succinate Dehydrogenase/metabolism/genetics
*Protozoan Proteins/metabolism/genetics/chemistry
Humans
Mitochondrial Proteins/metabolism/genetics
Mitochondria/metabolism
Phylogeny
Animals

@article {pmid38827288,
year = {2024},
author = {Liu, Y and Fu, X and Wang, Y and Liu, J and Liu, Y and Li, C and Dong, J},
title = {Exploring Barbronia species diversity and phylogenetic relationship within Suborder Erpobdelliformes (Clitellata: Annelida).},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17480},
pmid = {38827288},
issn = {2167-8359},
mesh = {Animals ; *Phylogeny ; Genome, Mitochondrial/genetics ; Leeches/genetics/classification ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 28S/genetics ; },
abstract = {BACKGROUND: Barbronia, a genus of freshwater macrophagous leeches, belongs to Erpobdelliformes (Salifidae: Clitellata: Annelida), and B. weberi, a well-known leech within this genus, has a worldwide distribution. However, the systematics of Barbronia have not yet been adequately investigated, primarily due to a few molecular markers, and only 20 Barbronia sequences available in the GenBank database. This gap significantly limits our understanding of the Barbronia species identification, as well as the phylogenetic placement of the genus Barbronia within Salifidae.

METHODS: Next-generation sequencing (NGS) was used to simultaneously capture the entire mitochondrial genome and the full-length 18S/28S rDNA sequences. The species boundary of Barbronia species was estimated using bGMYC and bPTP methods, based on all available Barbronia COI sequences. Uncorrected COI p-distance was calculated in MEGA. A molecular data matrix consisting of four loci (COI, 12S, 18S, and 28S rDNA) for outgroups (three Haemopis leeches) and 49 erpobdellid leeches, representing eight genera within the Suborder Erpobdelliformes was aligned using MAFFT and LocARNA. This matrix was used to reconstruct the phylogenetic relationship of Barbronia via Bayesian inference (BI) and the maximum likelihood (ML) method.

RESULTS: The full lengths of the mitochondrial genome, 18S and 28S rDNAs of B. cf. gwalagwalensis, are 14847 bp, 1876 bp 1876 bp, and 2863 bp, respectively. Both bGMYC and bPTP results based on COI data are generally congruent, suggesting that the previously proposed taxa (B. arcana, B. weberi formosana, and B. wuttkei or Erpobdella wuttkei) are synonyms of B. weberi. The specimens listed in the B. gwalagwalensis group, however, are split into at least two Primary Species Hypotheses (PSHs). The p-distance of the first PSH is less than 1.3% but increased to 4.5% when including the secondary PSH (i.e., B. cf. gwalagwalensis). In comparison, the interspecific p-distance between the B. weberi group and the B. gwalagwalensis group ranged from 6.4% to 8.7%, and the intraspecific p-distance within the B. weberi group is less than 0.8%. Considering the species delimitation results and the sufficient large p-distance, the specimen sampled in China is treated as B. cf. gwalagwalensis. The monophyly of the four Erpobdelliformes families Salifidae, Orobdellidae, Gastrostomobdellidae sensu stricto and Erpobdellidae is well supported in ML and BI analysis based on a data of four markers. Within the Salifidae, a well-supported Barbronia is closely related to a clade containing Odontobdella and Mimobdella, and these three genera are sister to a clade consisted of Salifa and Linta. According to the results of this study, the strategy of simultaneous obtaining both whole mitochondria and nuclear markers from extensively sampled Salifids species using NGS is expected to fathom both the species diversity of B. gwalagwalensis and the evolutionary relationship of Salifidae.},
}

Animals
*Phylogeny
Genome, Mitochondrial/genetics
Leeches/genetics/classification
High-Throughput Nucleotide Sequencing
RNA, Ribosomal, 28S/genetics

@article {pmid38825738,
year = {2024},
author = {Boscaro, V and James, ER and Fiorito, R and Del Campo, J and Scheffrahn, RH and Keeling, PJ},
title = {Updated classification of the phylum Parabasalia.},
journal = {The Journal of eukaryotic microbiology},
volume = {71},
number = {4},
pages = {e13035},
doi = {10.1111/jeu.13035},
pmid = {38825738},
issn = {1550-7408},
support = {RGPIN-2014-03994//Natural Sciences and Engineering Research Council of Canada/ ; //Gordon and Betty Moore Foundation/ ; },
mesh = {*Phylogeny ; Animals ; Parabasalidea/classification/genetics ; Symbiosis ; },
abstract = {The phylum Parabasalia includes very diverse single-cell organisms that nevertheless share a distinctive set of morphological traits. Most are harmless or beneficial gut symbionts of animals, but some have turned into parasites in other body compartments, the most notorious example being Trichomonas vaginalis in humans. Parabasalians have garnered attention for their nutritional symbioses with termites, their modified anaerobic mitochondria (hydrogenosomes), their character evolution, and the wholly unique features of some species. The molecular revolution confirmed the monophyly of Parabasalia, but considerably changed our view of their internal relationships, prompting a comprehensive reclassification 14 years ago. This classification has remained authoritative for many subgroups despite a greatly expanded pool of available data, but the large number of species and sequences that have since come out allow for taxonomic refinements in certain lineages, which we undertake here. We aimed to introduce as little disruption as possible but at the same time ensure that most taxa are truly monophyletic, and that the larger clades are subdivided into meaningful units. In doing so, we also highlighted correlations between the phylogeny of parabasalians and that of their hosts.},
}

*Phylogeny
Animals
Parabasalidea/classification/genetics
Symbiosis

@article {pmid38818026,
year = {2024},
author = {Tower, J},
title = {Selectively advantageous instability in biotic and pre-biotic systems and implications for evolution and aging.},
journal = {Frontiers in aging},
volume = {5},
number = {},
pages = {1376060},
pmid = {38818026},
issn = {2673-6217},
abstract = {Rules of biology typically involve conservation of resources. For example, common patterns such as hexagons and logarithmic spirals require minimal materials, and scaling laws involve conservation of energy. Here a relationship with the opposite theme is discussed, which is the selectively advantageous instability (SAI) of one or more components of a replicating system, such as the cell. By increasing the complexity of the system, SAI can have benefits in addition to the generation of energy or the mobilization of building blocks. SAI involves a potential cost to the replicating system for the materials and/or energy required to create the unstable component, and in some cases, the energy required for its active degradation. SAI is well-studied in cells. Short-lived transcription and signaling factors enable a rapid response to a changing environment, and turnover is critical for replacement of damaged macromolecules. The minimal gene set for a viable cell includes proteases and a nuclease, suggesting SAI is essential for life. SAI promotes genetic diversity in several ways. Toxin/antitoxin systems promote maintenance of genes, and SAI of mitochondria facilitates uniparental transmission. By creating two distinct states, subject to different selective pressures, SAI can maintain genetic diversity. SAI of components of synthetic replicators favors replicator cycling, promoting emergence of replicators with increased complexity. Both classical and recent computer modeling of replicators reveals SAI. SAI may be involved at additional levels of biological organization. In summary, SAI promotes replicator genetic diversity and reproductive fitness, and may promote aging through loss of resources and maintenance of deleterious alleles.},
}

@article {pmid38816808,
year = {2024},
author = {Xing, J and Zhang, Y and Song, W and Ali, NA and Su, K and Sun, X and Sun, Y and Jiang, Y and Zhao, X},
title = {Comprehensive identification, characterization, and expression analysis of the MORF gene family in Brassica napus.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {475},
pmid = {38816808},
issn = {1471-2229},
support = {32170556//National Natural Science Foundation of China/ ; the Hundred-Talent Program//Zhejiang University/ ; },
mesh = {*Brassica napus/genetics/metabolism ; *Multigene Family ; *Phylogeny ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Genes, Plant ; RNA Editing ; Gene Expression Profiling ; Chloroplasts/genetics/metabolism ; },
abstract = {BACKGROUND: RNA editing in chloroplast and mitochondrion transcripts of plants is an important type of post-transcriptional RNA modification in which members of the multiple organellar RNA editing factor gene family (MORF) play a crucial role. However, a systematic identification and characterization of MORF members in Brassica napus is still lacking.

RESULTS: In this study, a total of 43 MORF genes were identified from the genome of the Brassica napus cultivar "Zhongshuang 11". The Brassica napus MORF (BnMORF) family members were divided into three groups through phylogenetic analysis. BnMORF genes distributed on 14 chromosomes and expanded due to segmental duplication and whole genome duplication repetitions. The majority of BnMORF proteins were predicted to be localized to mitochondria and chloroplasts. The promoter cis-regulatory element analysis, spatial-temporal expression profiling, and co-expression network of BnMORF genes indicated the involvement of BnMORF genes in stress and phytohormone responses, as well as growth and development.

CONCLUSION: This study provides a comprehensive analysis of BnMORF genes and lays a foundation for further exploring their physiological functions in Brassica napus.},
}

*Brassica napus/genetics/metabolism
*Multigene Family
*Phylogeny
*Plant Proteins/genetics/metabolism
Gene Expression Regulation, Plant
Genes, Plant
RNA Editing
Gene Expression Profiling
Chloroplasts/genetics/metabolism

@article {pmid38813885,
year = {2024},
author = {Bennett, GM and Kwak, Y and Maynard, R},
title = {Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again.},
journal = {Genome biology and evolution},
volume = {16},
number = {6},
pages = {},
pmid = {38813885},
issn = {1759-6653},
support = {NSF-1347116//National Science Foundation/ ; GT15982/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Symbiosis ; *Biological Evolution ; Animals ; Bacteria/genetics ; Biodiversity ; Evolution, Molecular ; },
abstract = {Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.},
}

*Symbiosis
*Biological Evolution
Animals
Bacteria/genetics
Biodiversity
Evolution, Molecular

@article {pmid38813783,
year = {2024},
author = {Wolyniak, MJ and Frazier, RH and Gemborys, PK and Loehr, HE},
title = {Malate dehydrogenase: a story of diverse evolutionary radiation.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20230076},
pmid = {38813783},
issn = {1744-1358},
support = {//Hampden-Sydney College Office of Undergraduate Research/ ; },
abstract = {Malate dehydrogenase (MDH) is a ubiquitous enzyme involved in cellular respiration across all domains of life. MDH's ubiquity allows it to act as an excellent model for considering the history of life and how the rise of aerobic respiration and eukaryogenesis influenced this evolutionary process. Here, we present the diversity of the MDH family of enzymes across bacteria, archaea, and eukarya, the relationship between MDH and lactate dehydrogenase (LDH) in the formation of a protein superfamily, and the connections between MDH and endosymbiosis in the formation of mitochondria and chloroplasts. The development of novel and powerful DNA sequencing techniques has challenged some of the conventional wisdom underlying MDH evolution and suggests a history dominated by gene duplication, horizontal gene transfer, and cryptic endosymbiosis events and adaptation to a diverse range of environments across all domains of life over evolutionary time. The data also suggest a superfamily of proteins that do not share high levels of sequential similarity but yet retain strong conservation of core function via key amino acid residues and secondary structural components. As DNA sequencing and 'big data' analysis techniques continue to improve in the life sciences, it is likely that the story of MDH will continue to refine as more examples of superfamily diversity are recovered from nature and analyzed.},
}

@article {pmid38812744,
year = {2024},
author = {Marques, E and Kramer, R and Ryan, DG},
title = {Multifaceted mitochondria in innate immunity.},
journal = {NPJ metabolic health and disease},
volume = {2},
number = {1},
pages = {6},
pmid = {38812744},
issn = {2948-2828},
abstract = {The ability of mitochondria to transform the energy we obtain from food into cell phosphorylation potential has long been appreciated. However, recent decades have seen an evolution in our understanding of mitochondria, highlighting their significance as key signal-transducing organelles with essential roles in immunity that extend beyond their bioenergetic function. Importantly, mitochondria retain bacterial motifs as a remnant of their endosymbiotic origin that are recognised by innate immune cells to trigger inflammation and participate in anti-microbial defence. This review aims to explore how mitochondrial physiology, spanning from oxidative phosphorylation (OxPhos) to signalling of mitochondrial nucleic acids, metabolites, and lipids, influences the effector functions of phagocytes. These myriad effector functions include macrophage polarisation, efferocytosis, anti-bactericidal activity, antigen presentation, immune signalling, and cytokine regulation. Strict regulation of these processes is critical for organismal homeostasis that when disrupted may cause injury or contribute to disease. Thus, the expanding body of literature, which continues to highlight the central role of mitochondria in the innate immune system, may provide insights for the development of the next generation of therapies for inflammatory diseases.},
}

@article {pmid38812151,
year = {2024},
author = {Zhang, XY and Yu, JC and Chen, WT and Zhou, DY and Yuan, Y and Liu, HG and Liang, YL},
title = {[Identification of HSP70 gene family members in Fritillaria cirrhosa and expression analysis in different tissues under high temperature stress].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {9},
pages = {2422-2433},
doi = {10.19540/j.cnki.cjcmm.20240214.101},
pmid = {38812151},
issn = {1001-5302},
mesh = {*HSP70 Heat-Shock Proteins/genetics/metabolism/chemistry ; *Plant Proteins/genetics/metabolism/chemistry ; *Fritillaria/genetics/chemistry ; *Phylogeny ; *Gene Expression Regulation, Plant ; Hot Temperature ; Stress, Physiological/genetics ; Gene Expression Profiling ; Multigene Family ; },
abstract = {The heat shock protein 70 family contains the stress proteins ubiquitous in plants. These proteins are involved in the responses to different abiotic stress conditions and have highly conserved gene sequences. However, little is known about the molecular mechanisms of Fritillaria cirrhosa in response to high-temperature stress. Here, 26 HSP70s, FcHSP70-1 to FcHSP70-26, were identified from the transcriptome data of root, bulb, stem, leaf, and fruit samples of F. cirrhosa. The proteins encoded by FcHSP70s had the lengths ranging from 560 aa to 944 aa, with the molecular weight of 61.64-100.01 kDa and the theoretical isoelectric point between 5.00 and 6.59. The secondary structural elements of HSP70s were mainly random coils and α-helixes. Subcellular localization prediction revealed that FcHSP70s were distributed in mitochondria, chloroplasts, nuclei, endoplasmic reticulum, and cytoplasm. The phylogenetic tree showed that 7 members of the HSP70 family belonged to the Dnak subfamily and 19 members belonged to the HSP110/SSE subfamily. In addition, the qRT-PCR results showed that the expression of FcHSP70-5, FcHSP70-8, FcHSP70-17, FcHSP70-18, and FcHSP70-23 in F. cirrhosa was significantly up-regulated at 35 ℃, which indicated that these genes might play a role in the response to high temperature stress. In addition, compared with other tissues, stems and leaves were sensitive to high temperature stress, with the expression of 18 genes up-regulated by 18.18 and 8.03 folds on average, respectively. These findings provide valuable information about the molecular mechanism of HSP70s of F. cirrhosa in response to high temperature stress.},
}

*HSP70 Heat-Shock Proteins/genetics/metabolism/chemistry
*Plant Proteins/genetics/metabolism/chemistry
*Fritillaria/genetics/chemistry
*Phylogeny
*Gene Expression Regulation, Plant
Hot Temperature
Stress, Physiological/genetics
Gene Expression Profiling
Multigene Family

@article {pmid38809522,
year = {2024},
author = {Li, W and Cai, Z and Schindler, F and Afjehi-Sadat, L and Montsch, B and Heffeter, P and Heiss, EH and Weckwerth, W},
title = {Elevated PINK1/Parkin-Dependent Mitophagy and Boosted Mitochondrial Function Mediate Protection of HepG2 Cells from Excess Palmitic Acid by Hesperetin.},
journal = {Journal of agricultural and food chemistry},
volume = {72},
number = {23},
pages = {13039-13053},
pmid = {38809522},
issn = {1520-5118},
mesh = {Humans ; Hep G2 Cells ; *Palmitic Acid/pharmacology ; *Hesperidin/pharmacology ; *Mitophagy/drug effects ; *Ubiquitin-Protein Ligases/metabolism/genetics ; *Mitochondria/drug effects/metabolism ; *Protein Kinases/metabolism/genetics ; Reactive Oxygen Species/metabolism ; Hepatocytes/drug effects/metabolism ; Membrane Potential, Mitochondrial/drug effects ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics ; Non-alcoholic Fatty Liver Disease/metabolism/drug therapy ; Protective Agents/pharmacology ; },
abstract = {Deregulation of mitochondrial functions in hepatocytes contributes to many liver diseases, such as nonalcoholic fatty liver disease (NAFLD). Lately, it was referred to as MAFLD (metabolism-associated fatty liver disease). Hesperetin (Hst), a bioactive flavonoid constituent of citrus fruit, has been proven to attenuate NAFLD. However, a potential connection between its preventive activities and the modulation of mitochondrial functions remains unclear. Here, our results showed that Hst alleviates palmitic acid (PA)-triggered NLRP3 inflammasome activation and cell death by inhibition of mitochondrial impairment in HepG2 cells. Hst reinstates fatty acid oxidation (FAO) rates measured by seahorse extracellular flux analyzer and intracellular acetyl-CoA levels as well as intracellular tricarboxylic acid cycle metabolites levels including NADH and FADH2 reduced by PA exposure. In addition, Hst protects HepG2 cells against PA-induced abnormal energetic profile, ATP generation reduction, overproduction of mitochondrial reactive oxygen species, and collapsed mitochondrial membrane potential. Furthermore, Hst improves the protein expression involved in PINK1/Parkin-mediated mitophagy. Our results demonstrate that it restores PA-impaired mitochondrial function and sustains cellular homeostasis due to the elevation of PINK1/Parkin-mediated mitophagy and the subsequent disposal of dysfunctional mitochondria. These results provide therapeutic potential for Hst utilization as an effective intervention against fatty liver disease.},
}

Humans
Hep G2 Cells
*Palmitic Acid/pharmacology
*Hesperidin/pharmacology
*Mitophagy/drug effects
*Ubiquitin-Protein Ligases/metabolism/genetics
*Mitochondria/drug effects/metabolism
*Protein Kinases/metabolism/genetics
Reactive Oxygen Species/metabolism
Hepatocytes/drug effects/metabolism
Membrane Potential, Mitochondrial/drug effects
NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics
Non-alcoholic Fatty Liver Disease/metabolism/drug therapy
Protective Agents/pharmacology

@article {pmid38805695,
year = {2024},
author = {McElroy, KE and Masonbrink, R and Chudalayandi, S and Severin, AJ and Serb, JM},
title = {A chromosome-level genome assembly of the disco clam, Ctenoides ales.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae115},
pmid = {38805695},
issn = {2160-1836},
abstract = {The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales, which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and report a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, will be valuable resources for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.},
}

@article {pmid38804831,
year = {2024},
author = {Wang, J and Taki, M and Ohba, Y and Arita, M and Yamaguchi, S},
title = {Fluorescence Lifetime Imaging of Lipid Heterogeneity in the Inner Mitochondrial Membrane with a Super-photostable Environment-Sensitive Probe.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {63},
number = {28},
pages = {e202404328},
doi = {10.1002/anie.202404328},
pmid = {38804831},
issn = {1521-3773},
support = {19H02849//Japan Society for the Promotion of Science/ ; 23K06101//Japan Society for the Promotion of Science/ ; JP22H04926//Japan Society for the Promotion of Science/ ; JPMJCR21O5//Core Research for Evolutional Science and Technology/ ; JPMJER2101//Exploratory Research for Advanced Technology/ ; },
mesh = {*Fluorescent Dyes/chemistry ; *Mitochondrial Membranes/metabolism/chemistry ; *Optical Imaging ; Humans ; Lipids/chemistry ; Microscopy, Fluorescence ; Reactive Oxygen Species/metabolism/analysis ; HeLa Cells ; Mitochondria/metabolism/chemistry ; },
abstract = {The inner mitochondrial membrane (IMM) undergoes dynamic morphological changes, which are crucial for the maintenance of mitochondrial functions as well as cell survival. As the dynamics of the membrane are governed by its lipid components, a fluorescent probe that can sense spatiotemporal alterations in the lipid properties of the IMM over long periods of time is required to understand mitochondrial physiological functions in detail. Herein, we report a red-emissive IMM-labeling reagent with excellent photostability and sensitivity to its environment, which enables the visualization of the IMM ultrastructure using super-resolution microscopy as well as of the lipid heterogeneity based on the fluorescence lifetime at the single mitochondrion level. Combining the probe and fluorescence lifetime imaging microscopy (FLIM) showed that peroxidation of unsaturated lipids in the IMM by reactive oxygen species caused an increase in the membrane order, which took place prior to mitochondrial swelling.},
}

*Fluorescent Dyes/chemistry
*Mitochondrial Membranes/metabolism/chemistry
*Optical Imaging
Humans
Lipids/chemistry
Microscopy, Fluorescence
Reactive Oxygen Species/metabolism/analysis
HeLa Cells
Mitochondria/metabolism/chemistry

@article {pmid38791655,
year = {2024},
author = {Zhou, S and Wang, X and Wang, L and Gao, X and Lyu, T and Xia, T and Shi, L and Dong, Y and Mei, X and Zhang, Z and Zhang, H},
title = {Different Evolutionary Trends of Galloanseres: Mitogenomics Analysis.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {10},
pages = {},
pmid = {38791655},
issn = {2076-2615},
support = {32200407//National Natural Science Foundation of China/ ; 32270444//National Natural Science Foundation of China/ ; ZR2023ZD47//Natural Science Foundation of Shandong Province/ ; GZC20231394//Postdoctoral Fellowship Program of CPSF/ ; GZC20231395//Postdoctoral Fellowship Program of CPSF/ ; GZC20231396//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {The two existing clades of Galloanseres, orders Galliformes (landfowl) and Anseriformes (waterfowl), exhibit dramatically different evolutionary trends. Mitochondria serve as primary sites for energy production in organisms, and numerous studies have revealed their role in biological evolution and ecological adaptation. We assembled the complete mitogenome sequences of two species of the genus Aythya within Anseriformes: Aythya baeri and Aythya marila. A phylogenetic tree was constructed for 142 species within Galloanseres, and their divergence times were inferred. The divergence between Galliformes and Anseriformes occurred ~79.62 million years ago (Mya), followed by rapid evolution and diversification after the Middle Miocene (~13.82 Mya). The analysis of selective pressure indicated that the mitochondrial protein-coding genes (PCGs) of Galloanseres species have predominantly undergone purifying selection. The free-ratio model revealed that the evolutionary rates of COX1 and COX3 were lower than those of the other PCGs, whereas ND2 and ND6 had faster evolutionary rates. The CmC model also indicated that most PCGs in Anseriformes exhibited stronger selective constraints. Our study suggests that the distinct evolutionary trends and energy requirements of Galliformes and Anseriformes drive different evolutionary patterns in the mitogenome.},
}

@article {pmid38791521,
year = {2024},
author = {Singh, MK and Shin, Y and Han, S and Ha, J and Tiwari, PK and Kim, SS and Kang, I},
title = {Molecular Chaperonin HSP60: Current Understanding and Future Prospects.},
journal = {International journal of molecular sciences},
volume = {25},
number = {10},
pages = {},
pmid = {38791521},
issn = {1422-0067},
support = {NRF-2018R1A6A1A03025124//National Research Foundation/ ; },
mesh = {*Chaperonin 60/metabolism/genetics ; Humans ; Animals ; *Oxidative Stress ; *Mitochondria/metabolism ; Neoplasms/metabolism/genetics/pathology ; Apoptosis ; Neurodegenerative Diseases/metabolism ; Protein Folding ; Reactive Oxygen Species/metabolism ; },
abstract = {Molecular chaperones are highly conserved across evolution and play a crucial role in preserving protein homeostasis. The 60 kDa heat shock protein (HSP60), also referred to as chaperonin 60 (Cpn60), resides within mitochondria and is involved in maintaining the organelle's proteome integrity and homeostasis. The HSP60 family, encompassing Cpn60, plays diverse roles in cellular processes, including protein folding, cell signaling, and managing high-temperature stress. In prokaryotes, HSP60 is well understood as a GroEL/GroES complex, which forms a double-ring cavity and aids in protein folding. In eukaryotes, HSP60 is implicated in numerous biological functions, like facilitating the folding of native proteins and influencing disease and development processes. Notably, research highlights its critical involvement in sustaining oxidative stress and preserving mitochondrial integrity. HSP60 perturbation results in the loss of the mitochondria integrity and activates apoptosis. Currently, numerous clinical investigations are in progress to explore targeting HSP60 both in vivo and in vitro across various disease models. These studies aim to enhance our comprehension of disease mechanisms and potentially harness HSP60 as a therapeutic target for various conditions, including cancer, inflammatory disorders, and neurodegenerative diseases. This review delves into the diverse functions of HSP60 in regulating proteo-homeostasis, oxidative stress, ROS, apoptosis, and its implications in diseases like cancer and neurodegeneration.},
}

*Chaperonin 60/metabolism/genetics
Humans
Animals
*Oxidative Stress
*Mitochondria/metabolism
Neoplasms/metabolism/genetics/pathology
Apoptosis
Neurodegenerative Diseases/metabolism
Protein Folding
Reactive Oxygen Species/metabolism

@article {pmid38789593,
year = {2024},
author = {Qu, K and Chen, Y and Liu, D and Guo, H and Xu, T and Jing, Q and Ge, L and Shu, X and Xin, X and Xie, X and Tong, B},
title = {Comprehensive analysis of the complete mitochondrial genome of Lilium tsingtauense reveals a novel multichromosome structure.},
journal = {Plant cell reports},
volume = {43},
number = {6},
pages = {150},
pmid = {38789593},
issn = {1432-203X},
support = {2020070316//National Forestry and Grassland Administration/ ; 2021070307//National Forestry and Grassland Administration/ ; Lu Financial Preliminary Guide [2021] No. 1//Shandong provincial department of finance/ ; 2021LZGC023//Department of Science and Technology of Shandong Province/ ; 2005-DKA21003//Chinese Academy of Forestry/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Lilium/genetics ; *Chromosomes, Plant/genetics ; *Phylogeny ; RNA, Transfer/genetics ; Genome, Plant/genetics ; Base Composition/genetics ; },
abstract = {Lilium tsingtauense mitogenome comprises 27 independent chromosome molecules, it undergoes frequent genomic recombination, and the rate of recombination and mutation between different repetitive sequences affects the formation of multichromosomal structures. Given the extremely large genome of Lily, which likely harbors additional genetic resources, it serves as an ideal material for studying the phylogenetic evolution of organisms. Although the Lilium chloroplast genome has been documented, the sequence of its mitochondrial genome (mitogenome) remains uncharted. Using BGI short reads and Nanopore long reads, we sequenced, assembled, and annotated the mitogenome of Lilium tsingtauense. This effort culminated in the characterization of Lilium's first complete mitogenome. Comparative analysis with other angiosperms revealed the unique multichromosomal structure of the L. tsingtauense mitogenome, spanning 1,125,108 bp and comprising 27 independent circular chromosomes. It contains 36 protein-coding genes, 12 tRNA genes, and 3 rRNA genes, with a GC content of 44.90%. Notably, three chromosomes in the L. tsingtauense mitogenome lack identifiable genes, hinting at the potential existence of novel genes and noncoding elements. The high degree of observed genome fragmentation implies frequent reorganization, with recombination and mutation rates among diverse repetitive sequences likely driving the formation of multichromosomal structures. Our comprehensive analysis, covering genome size, coding genes, structure, RNA editing, repetitive sequences, and sequence migration, sheds light on the evolutionary and molecular biology of multichromosomal mitochondria in Lilium. This high-quality mitogenome of L. tsingtauense not only enriches our understanding of multichromosomal mitogenomes but also establishes a solid foundation for future genome breeding and germplasm innovation in Lilium.},
}

*Genome, Mitochondrial/genetics
*Lilium/genetics
*Chromosomes, Plant/genetics
*Phylogeny
RNA, Transfer/genetics
Genome, Plant/genetics
Base Composition/genetics

@article {pmid38782915,
year = {2024},
author = {Hanson, SE and Dowdy, T and Larion, M and Doyle, MT and Bernstein, HD},
title = {The patatin-like protein PlpD forms structurally dynamic homodimers in the Pseudomonas aeruginosa outer membrane.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4389},
pmid = {38782915},
issn = {2041-1723},
support = {Intramural Program//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; Intramural Program//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; Intramural Program//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
mesh = {*Pseudomonas aeruginosa/metabolism/genetics ; *Bacterial Outer Membrane Proteins/metabolism/chemistry/genetics ; *Protein Multimerization ; Periplasm/metabolism ; Protein Domains ; Bacterial Outer Membrane/metabolism ; Models, Molecular ; Bacterial Proteins/metabolism/chemistry/genetics ; },
abstract = {Members of the Omp85 superfamily of outer membrane proteins (OMPs) found in Gram-negative bacteria, mitochondria and chloroplasts are characterized by a distinctive 16-stranded β-barrel transmembrane domain and at least one periplasmic POTRA domain. All previously studied Omp85 proteins promote critical OMP assembly and/or protein translocation reactions. Pseudomonas aeruginosa PlpD is the prototype of an Omp85 protein family that contains an N-terminal patatin-like (PL) domain that is thought to be translocated across the OM by a C-terminal β-barrel domain. Challenging the current dogma, we find that the PlpD PL-domain resides exclusively in the periplasm and, unlike previously studied Omp85 proteins, PlpD forms a homodimer. Remarkably, the PL-domain contains a segment that exhibits unprecedented dynamicity by undergoing transient strand-swapping with the neighboring β-barrel domain. Our results show that the Omp85 superfamily is more structurally diverse than currently believed and suggest that the Omp85 scaffold was utilized during evolution to generate novel functions.},
}

*Pseudomonas aeruginosa/metabolism/genetics
*Bacterial Outer Membrane Proteins/metabolism/chemistry/genetics
*Protein Multimerization
Periplasm/metabolism
Protein Domains
Bacterial Outer Membrane/metabolism
Models, Molecular
Bacterial Proteins/metabolism/chemistry/genetics

@article {pmid38776415,
year = {2024},
author = {Liao, T and Wang, S and Zhang, H and Stüeken, EE and Luo, H},
title = {Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils.},
journal = {Molecular biology and evolution},
volume = {41},
number = {5},
pages = {},
pmid = {38776415},
issn = {1537-1719},
support = {14107823//Hong Kong Research Grants Council (RGC) General Research Fund/ ; 42293294//Natural Science Foundation of China/ ; AoE/M-403/16//Hong Kong Research Grants Council Area of Excellence Scheme/ ; 2022A1515010844//Guangdong Basic and Applied Basic Research Foundation/ ; 2021M702296//China Postdoctoral Science Foundation/ ; },
mesh = {*Ammonia/metabolism ; *Oxidation-Reduction ; *Fossils ; Gammaproteobacteria/metabolism/genetics ; Bacteria/metabolism/genetics ; Biological Evolution ; Phylogeny ; Symbiosis ; Eukaryota/metabolism/genetics ; Nitrogen Cycle ; },
abstract = {Evolution of a complete nitrogen (N) cycle relies on the onset of ammonia oxidation, which aerobically converts ammonia to nitrogen oxides. However, accurate estimation of the antiquity of ammonia-oxidizing bacteria (AOB) remains challenging because AOB-specific fossils are absent and bacterial fossils amenable to calibrate molecular clocks are rare. Leveraging the ancient endosymbiosis of mitochondria and plastid, as well as using state-of-the-art Bayesian sequential dating approach, we obtained a timeline of AOB evolution calibrated largely by eukaryotic fossils. We show that the first AOB evolved in marine Gammaproteobacteria (Gamma-AOB) and emerged between 2.1 and 1.9 billion years ago (Ga), thus postdating the Great Oxidation Event (GOE; 2.4 to 2.32 Ga). To reconcile the sedimentary N isotopic signatures of ammonia oxidation occurring near the GOE, we propose that ammonia oxidation likely occurred at the common ancestor of Gamma-AOB and Gammaproteobacterial methanotrophs, or the actinobacterial/verrucomicrobial methanotrophs which are known to have ammonia oxidation activities. It is also likely that nitrite was transported from the terrestrial habitats where ammonia oxidation by archaea took place. Further, we show that the Gamma-AOB predated the anaerobic ammonia-oxidizing (anammox) bacteria, implying that the emergence of anammox was constrained by the availability of dedicated ammonia oxidizers which produce nitrite to fuel anammox. Our work supports a new hypothesis that N redox cycle involving nitrogen oxides evolved rather late in the ocean.},
}

*Ammonia/metabolism
*Oxidation-Reduction
*Fossils
Gammaproteobacteria/metabolism/genetics
Bacteria/metabolism/genetics
Biological Evolution
Phylogeny
Symbiosis
Eukaryota/metabolism/genetics
Nitrogen Cycle