@article {pmid39264945,
year = {2024},
author = {Zang, C and Wang, X and Liu, Y and Wang, H and Sun, Q and Cheng, P and Zhang, Y and Gong, M and Liu, H},
title = {Wolbachia and mosquitoes: Exploring transmission modes and coevolutionary dynamics in Shandong Province, China.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {9},
pages = {e0011944},
doi = {10.1371/journal.pntd.0011944},
pmid = {39264945},
issn = {1935-2735},
abstract = {Vector-borne diseases leave a large footprint on global health. Notable culprits include West Nile virus (WNV), St. Louis encephalitis virus (SLEV), and Japanese encephalitis virus (JEV), all transmitted by Culex mosquitoes. Chemical insecticides have been widely used to reduce the spread of mosquito-borne diseases. Still, mosquitoes are becoming more and more resistant to most chemical insecticides which cause particular harm to the ecology. Wolbachia belongs to the family Ehrlichiaceae in the order Rickettsiales and is a matrilineally inherited endosymbiont present in 60% of insects in nature. Wolbachia is capable of inducing a wide range of reproductive abnormalities in its hosts, such as cytoplasmic incompatibility, and can alter mosquito resistance to pathogen infection. Wolbachia has been proposed as a biological alternative to chemical vector control, and specific research progress and effectiveness have been achieved. Despite the importance of Wolbachia, this strategy has not been tested in Culex pipiens pallens, the most prevalent mosquito species in Shandong Province, China. Little is known about how the mass release of Wolbachia-infected mosquitoes may impact the genetic structure of Culex pipiens pallens, and how the symbiotic bacterium Wolbachia interacts with mitochondria during host mosquito transmission. Based on the population genetic structure of Culex pipiens pallens in Shandong Province, this study investigated the infection rate and infection type of Wolbachia in Shandong Province and jointly analysed the evolutionary relationship between the host mosquito and the symbiotic bacterium Wolbachia. Our study showed that Wolbachia naturally infected by Culex pipiens pallens in Shandong Province was less homologous to Wolbachia infected by Aedes albopictus released from mosquito factory in Guangzhou. Our results also show that Culex pipiens pallens is undergoing demographic expansion in Shandong Province. The overall Wolbachia infection rate of Culex pipiens pallens was 92.8%, and a total of 15 WSP haplotypes were detected. We found that the genetic diversity of Wolbachia was low in Culex pipiens pallens from Shandong Province, and the mosquitoes were infected only with type B Wolbachia. Visualizing the relationship between Culex pipiens pallens and Wolbachia using a tanglegram revealed patterns of widespread associations. A specific coevolutionary relationship exists between the host mosquito and Wolbachia. Knowledge of this mosquito-Wolbachia relationship will provide essential scientific information required for Wolbachia-based vector control approaches in Shandong Province and will lead to a better understanding of the diversity and evolution of Wolbachia for its utility as a biocontrol agent.},
}
@article {pmid39127314,
year = {2024},
author = {Zhang, L and Liu, ZS and Dong, YZ and He, CF and Zhang, DD and Jiang, GZ and Liu, WB and Li, XF},
title = {Molecular cloning and functional characterization of mitochondrial RNA splicing 2 in fish Megalobrama amblycephala, and its potential roles in magnesium homeostasis and mitochondrial function.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {297},
number = {},
pages = {111727},
doi = {10.1016/j.cbpa.2024.111727},
pmid = {39127314},
issn = {1531-4332},
mesh = {Animals ; *Magnesium/metabolism ; *Homeostasis ; *Cloning, Molecular ; *Mitochondria/metabolism/genetics ; *Amino Acid Sequence ; Fish Proteins/genetics/metabolism ; Cyprinidae/genetics/metabolism ; Phylogeny ; Base Sequence ; RNA Splicing ; },
abstract = {Mitochondrial function can be regulated by ion channels. Mitochondrial RNA splicing 2 (Mrs2) is a magnesium ion (Mg[2+]) channel located in the inner mitochondrial membrane, thereby mediating the Mg[2+] influx into the mitochondrial matrix. However, its potential role in regulating the Mg homeostasis and mitochondrial function in aquatic species is still unclear. This study molecularly characterizes the gene encoding Mrs2 in fish M. amblycephala with its functions in maintaining the Mg homeostasis and mitochondrial function verified. The mrs2 gene is 2133 bp long incorporating a 1269 bp open reading frame, which encodes 422 amino acids. The Mrs2 protein includes two transmembrane domains and a conserved tripeptide Gly-Met-Asn, and has a high homology (65.92-97.64%) with those of most vertebrates. The transcript of mrs2 was relatively high in the white muscle, liver and kidney. The inhibition of mrs2 reduces the expressions of Mg[2+] influx/efflux-related proteins, mitochondrial Mg content, and the activities of mitochondrial complex I and V in hepatocytes. However, the over-expression of mrs2 increases the expressions of Mg[2+] influx/efflux-related proteins, mitochondrial Mg content, and the complex V activity, but decreases the activities of mitochondrial complex III and IV and citrate synthase in hepatocytes. Collectively, Mrs2 is highly conserved among different species, and is prerequisite for maintaining Mg homeostasis and mitochondrial function in fish.},
}
@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.},
}
@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.},
}
@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.<br><br>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&#x202f;bp, 93,430&#x202f;bp and 92,491&#x202f;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&#x202f;bp, making up 15.52&#x202f;% of the plastome, 6.37&#x202f;% 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.<br><br>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.<br><br>RESULT: The A. cristatum mitogenome was a single-ring molecular structure of 381,065&#xa0;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&#x2009;=&#x2009;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&#xa0;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.<br><br>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 &amp; 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.},
}
@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},
doi = {10.1158/0008-5472.CAN-23-3172},
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.},
}
@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.},
}
@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//Funda&#xe7;&#xe3;o de Amparo &#xe0; 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 &amp; 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".},
}
@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.},
}
@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.},
}
@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.},
}
@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},
mesh = {Humans ; *Viral Nonstructural Proteins/metabolism ; *Nucleotidyltransferases/metabolism/antagonists &amp; inhibitors ; *Dengue Virus ; Proteolysis ; Recombinant Proteins/metabolism/genetics/isolation &amp; purification ; Nucleotides, Cyclic/metabolism ; Dengue/virology/metabolism ; },
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.},
}
@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 Investigaci&#xf3;n en &#xc1;reas Prioritarias/ ; NCN2021-033//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; 1221477//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 3210788//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; },
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.},
}
@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.},
}
@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, Innovaci&#xf3;n 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.},
}
@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 {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.},
}
@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.},
}
@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.},
}
@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.},
}
@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 &amp; 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.},
}
@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 &amp; 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.},
}
@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.},
}
@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 &amp; 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.},
}
@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 Sant&#xe9; 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.},
}
@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.},
}
@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.<br><br>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.<br><br>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.},
}
@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.},
}
@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.},
}
@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.<br><br>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.<br><br>METHODS: A549 and ATII cells were induced to become senescent using bleomycin. Senescence markers were examined using different methods including senescence-associated &#x3b2;-galactosidase (SA-&#x3b2;-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-&#x3ba;B signaling pathway, and mitophagy using western blotting or flow cytometry.<br><br>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-&#x3b2;-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-&#x3b2;. We revealed that PTEN activation was integral for EF24 to inhibit AECs senescence by suppressing the AKT/mTOR/NF-&#x3ba;B 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.<br><br>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).<br><br>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.<br><br>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.<br><br>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&#xa0;bp) mediated genome recombination, resulting in the formation of two major conformations, namely master and double circles. Furthermore, we identified 731&#xa0;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.<br><br>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.},
}
@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.},
}
@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 &amp; development ; Seedlings/genetics/growth &amp; 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).},
}
@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.},
}
@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 &amp; 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.},
}
@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.},
}
@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.},
}
@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.},
}
@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.},
}
@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.<br><br>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.<br><br>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.},
}
@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.<br><br>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.<br><br>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.},
}
@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.},
}
@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.<br><br>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.<br><br>https://github.com/raphael-group/MERLIN.},
}
@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.<br><br>MATERIAL AND METHODS: After an anamnesis and clinical examination at rest, 27 subjects (50&#xb1;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.<br><br>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&#xb1;5.8kg/m[2] and a basal lactate concentration of 2.1&#xb1;0.7mmol/L. The physiological assessment of endurance showed the following results relative to predicted VO2m&#xe1;x: 1)peakVO2=80.5&#xb1;18.6%; 2)VO2 at ventilatory threshold1 (VO2VT1): 46.0&#xb1;12.9%; 3)VO2VT2: 57.2&#xb1;16.4%; 4)working time in acidosis: 5.6&#xb1;3,0minutes; and 5)maximum lactate concentration: 5.1&#xb1;2.2mmol/L.<br><br>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.},
}
@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&amp;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.<br><br>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.<br><br>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.},
}
@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.},
}
@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.},
}
@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.},
}
@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.<br><br>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.<br><br>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.},
}
@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.},
}
@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.},
}
@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.},
}
@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.},
}
@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.},
}
@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.},
}
@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.<br><br>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.<br><br>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.},
}
@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.},
}
@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.<br><br>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.<br><br>CONCLUSION: This study provides a comprehensive analysis of BnMORF genes and lays a foundation for further exploring their physiological functions in Brassica napus.},
}
@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.},
}
@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.},
}
@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.},
}
@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.},
}
@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.},
}
@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.},
}
@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 &amp; Human Services | National Institutes of Health (NIH)/ ; Intramural Program//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; Intramural Program//U.S. Department of Health &amp; 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.},
}
@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.},
}
@article {pmid38773202,
year = {2024},
author = {Pfingstl, T and Hiruta, SF and Shimano, S},
title = {Mitochondrial metagenomics reveal the independent colonization of the world's coasts by intertidal oribatid mites (Acari, Oribatida, Ameronothroidea).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11634},
pmid = {38773202},
issn = {2045-2322},
support = {I 3815//Austrian Science Fund/ ; },
mesh = {Animals ; *Mites/genetics/classification ; *Phylogeny ; *Metagenomics/methods ; Genome, Mitochondrial ; Mitochondria/genetics ; Metagenome ; Evolution, Molecular ; Ecosystem ; },
abstract = {Oribatid mites are an ancient group that already roamed terrestrial ecosystems in the early and middle Devonian. The superfamily of Ameronothroidea, a supposedly monophyletic lineage, represents the only group of oribatid mites that has successfully invaded the marine coastal environment. By using mitogenome data and nucleic ribosomal RNA genes (18S, 5.8S, 28S), we show that Ameronothroidea are a paraphyletic assemblage and that the land-to-sea transition happened three times independently. Common ancestors of the tropical Fortuyniidae and Selenoribatidae were the first to colonize the coasts and molecular calibration of our phylogeny dates this event to a period in the Triassic and Jurassic era (225-146 mya), whereas present-day distribution indicates that this event might have happened early in this period during the Triassic, when the supercontinent Pangaea still existed. The cold temperate northern hemispheric Ameronothridae colonized the marine littoral later in the late Jurassic-Early Cretaceous and had an ancient distribution on Laurasian coasts. The third and final land-to-sea transition happened in the same geological period, but approx. 30 my later when ancestors of Podacaridae invaded coastal marine environments of the Gondwanan landmasses.},
}
@article {pmid38772414,
year = {2024},
author = {Dohnálek, V and Doležal, P},
title = {Installation of LYRM proteins in early eukaryotes to regulate the metabolic capacity of the emerging mitochondrion.},
journal = {Open biology},
volume = {14},
number = {5},
pages = {240021},
doi = {10.1098/rsob.240021},
pmid = {38772414},
issn = {2046-2441},
support = {//Gordon and Betty Moore Foundation and Simons Foundation/ ; //Czech Science Foundation/ ; },
mesh = {*Mitochondria/metabolism ; *Mitochondrial Proteins/metabolism/genetics ; Animals ; Evolution, Molecular ; Eukaryota/metabolism ; Acyl Carrier Protein/metabolism/genetics ; Phylogeny ; Models, Molecular ; Humans ; Amino Acid Sequence ; },
abstract = {Core mitochondrial processes such as the electron transport chain, protein translation and the formation of Fe-S clusters (ISC) are of prokaryotic origin and were present in the bacterial ancestor of mitochondria. In animal and fungal models, a family of small Leu-Tyr-Arg motif-containing proteins (LYRMs) uniformly regulates the function of mitochondrial complexes involved in these processes. The action of LYRMs is contingent upon their binding to the acylated form of acyl carrier protein (ACP). This study demonstrates that LYRMs are structurally and evolutionarily related proteins characterized by a core triplet of α-helices. Their widespread distribution across eukaryotes suggests that 12 specialized LYRMs were likely present in the last eukaryotic common ancestor to regulate the assembly and folding of the subunits that are conserved in bacteria but that lack LYRM homologues. The secondary reduction of mitochondria to anoxic environments has rendered the function of LYRMs and their interaction with acylated ACP dispensable. Consequently, these findings strongly suggest that early eukaryotes installed LYRMs in aerobic mitochondria as orchestrated switches, essential for regulating core metabolism and ATP production.},
}
@article {pmid38758976,
year = {2024},
author = {Giannakis, K and Richards, L and Dauda, KA and Johnston, IG},
title = {Connecting Species-Specific Extents of Genome Reduction in Mitochondria and Plastids.},
journal = {Molecular biology and evolution},
volume = {41},
number = {6},
pages = {},
pmid = {38758976},
issn = {1537-1719},
support = {//BBSRC/ ; //MIBTP Doctoral Training Scheme/ ; /ERC_/European Research Council/International ; 805046//European Union's Horizon 2020/ ; //EvoConBiO/ ; TMS2021TMT09//Trond Mohn Foundation/ ; //Centre for Antimicrobial Resistance in Western Norway/ ; TMS2020TMT11//CAMRIA/ ; },
mesh = {*Genome, Mitochondrial ; *Genome, Plastid ; *Plastids/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Mitochondria/genetics ; Species Specificity ; Biological Evolution ; Eukaryota/genetics ; },
abstract = {Mitochondria and plastids have both dramatically reduced their genomes since the endosymbiotic events that created them. The similarities and differences in the evolution of the two organelle genome types have been the target of discussion and investigation for decades. Ongoing work has suggested that similar mechanisms may modulate the reductive evolution of the two organelles in a given species, but quantitative data and statistical analyses exploring this picture remain limited outside of some specific cases like parasitism. Here, we use cross-eukaryote organelle genome data to explore evidence for coevolution of mitochondrial and plastid genome reduction. Controlling for differences between clades and pseudoreplication due to relatedness, we find that extents of mtDNA and ptDNA gene retention are related to each other across taxa, in a generally positive correlation that appears to differ quantitatively across eukaryotes, for example, between algal and nonalgal species. We find limited evidence for coevolution of specific mtDNA and ptDNA gene pairs, suggesting that the similarities between the two organelle types may be due mainly to independent responses to consistent evolutionary drivers.},
}
@article {pmid38753873,
year = {2024},
author = {Thielen, M and Gärtner, B and Knoop, V and Schallenberg-Rüdinger, M and Lesch, E},
title = {Conquering new grounds: plant organellar C-to-U RNA editing factors can be functional in the plant cytosol.},
journal = {The Plant journal : for cell and molecular biology},
volume = {119},
number = {2},
pages = {895-915},
doi = {10.1111/tpj.16804},
pmid = {38753873},
issn = {1365-313X},
support = {SCHA 1952 2-2//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*RNA Editing ; *Chloroplasts/metabolism/genetics ; *Cytosol/metabolism ; *Bryopsida/genetics/metabolism ; *Mitochondria/metabolism/genetics ; *RNA, Plant/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Cytidine/metabolism/genetics ; RNA-Binding Proteins/metabolism/genetics ; Gene Expression Regulation, Plant ; Uridine/metabolism/genetics ; },
abstract = {Plant mitochondrial and chloroplast transcripts are subject to numerous events of specific cytidine-to-uridine (C-to-U) RNA editing to correct genetic information. Key protein factors for this process are specific RNA-binding pentatricopeptide repeat (PPR) proteins, which are encoded in the nucleus and post-translationally imported into the two endosymbiotic organelles. Despite hundreds of C-to-U editing sites in the plant organelles, no comparable editing has been found for nucleo-cytosolic mRNAs raising the question why plant RNA editing is restricted to chloroplasts and mitochondria. Here, we addressed this issue in the model moss Physcomitrium patens, where all PPR-type RNA editing factors comprise specific RNA-binding and cytidine deamination functionalities in single proteins. To explore whether organelle-type RNA editing can principally also take place in the plant cytosol, we expressed PPR56, PPR65 and PPR78, three editing factors recently shown to also function in a bacterial setup, together with cytosolic co-transcribed native targets in Physcomitrium. While we obtained unsatisfying results upon their constitutive expression, we found strong cytosolic RNA editing under hormone-inducible expression. Moreover, RNA-Seq analyses revealed varying numbers of up to more than 900 off-targets in other cytosolic transcripts. We conclude that PPR-mediated C-to-U RNA editing is not per se incompatible with the plant cytosol but that its limited target specificity has restricted its occurrence to the much less complex transcriptomes of mitochondria and chloroplast in the course of evolution.},
}
@article {pmid38750703,
year = {2024},
author = {Gong, Y and Luo, X and Zhang, T and Zhou, G and Li, J and Zhang, B and Li, P and Huang, H},
title = {Assembly and comparative analysis of the complete mitochondrial genome of white towel gourd (Luffa cylindrica).},
journal = {Genomics},
volume = {116},
number = {3},
pages = {110859},
doi = {10.1016/j.ygeno.2024.110859},
pmid = {38750703},
issn = {1089-8646},
mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Luffa/genetics ; RNA, Transfer/genetics ; Genome, Plant ; Plant Proteins/genetics/metabolism ; },
abstract = {Mitochondria play an important role in the energy production of plant cells through independent genetic systems. This study has aimed to assemble and annotate the functions of the mitochondrial (mt) genome of Luffa cylindrica. The mt genome of L. cylindrica contained two chromosomes with lengths of 380,879 bp and 67,982 bp, respectively. Seventy-seven genes including 39 protein-coding genes, 34 tRNA genes, 3 rRNA genes, and 1 pseudogene, were identified. About 90.63% of the codons ended with A or U bases, and 98.63% of monomers contained A/T, which contributed to the high A/T content (55.91%) of the complete mt genome. Six genes (ATP8, CCMFC, NAD4, RPL10, RPL5 and RPS4) showed positive selection. Phylogenetic analysis indicates that L. cylindrica is closely related to L. acutangula. The present results provide the mt genome of L. cylindrica, which may facilitate possible genetic variation, evolutionary, and molecular breeding studies of L. cylindrica.},
}
@article {pmid38750421,
year = {2024},
author = {Wang, X and Pei, J and Xiong, L and Bao, P and Chu, M and Ma, X and La, Y and Liang, C and Yan, P and Guo, X},
title = {Genetic diversity, phylogeography, and maternal origin of yak (Bos grunniens).},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {481},
pmid = {38750421},
issn = {1471-2164},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; 25-LZIHPS-01//the Innovation Project of Chinese Academy of Agricultural Sciences/ ; },
mesh = {Animals ; Cattle/genetics ; *Phylogeography ; *Genetic Variation ; *Haplotypes ; *Phylogeny ; *Genome, Mitochondrial ; Maternal Inheritance ; Female ; DNA, Mitochondrial/genetics ; },
abstract = {BACKGROUND: There is no consensus as to the origin of the domestic yak (Bos grunniens). Previous studies on yak mitochondria mainly focused on mitochondrial displacement loop (D-loop), a region with low phylogenetic resolution. Here, we analyzed the entire mitochondrial genomes of 509 yaks to obtain greater phylogenetic resolution and a comprehensive picture of geographical diversity.<br><br>RESULTS: A total of 278 haplotypes were defined in 509 yaks from 21 yak breeds. Among them, 28 haplotypes were shared by different varieties, and 250 haplotypes were unique to specific varieties. The overall haplotype diversity and nucleotide diversity of yak were 0.979&#x2009;&#xb1;&#x2009;0.0039 and 0.00237&#x2009;&#xb1;&#x2009;0.00076, respectively. Phylogenetic tree and network analysis showed that yak had three highly differentiated genetic branches with high support rate. The differentiation time of clades I and II were about 0.4328&#xa0;Ma, and the differentiation time of clades (I and II) and III were 0.5654&#xa0;Ma. Yushu yak is shared by all haplogroups. Most (94.70%) of the genetic variation occurred within populations, and only 5.30% of the genetic variation occurred between populations. The classification showed that yaks and wild yaks were first clustered together, and yaks were clustered with American bison as a whole. Altitude had the highest impact on the distribution of yaks.<br><br>CONCLUSIONS: Yaks have high genetic diversity and yak populations have experienced population expansion and lack obvious phylogeographic structure. During the glacial period, yaks had at least three or more glacial refugia.},
}
@article {pmid38741523,
year = {2024},
author = {Hervas, LS and do Amaral-Silva, L and Sartori, MR and Guadalupe-Silva, A and Gargaglioni, LH and Lerchner, J and Oliveira, MT and Bícego, KC},
title = {Mitochondrial function in skeletal muscle contributes to reproductive endothermy in tegu lizards (Salvator merianae).},
journal = {Acta physiologica (Oxford, England)},
volume = {240},
number = {7},
pages = {e14162},
doi = {10.1111/apha.14162},
pmid = {38741523},
issn = {1748-1716},
support = {2021/10910-0//S&#xe3;o Paulo State Research Foundation-FAPESP/ ; 2021/06711-2//S&#xe3;o Paulo State Research Foundation-FAPESP/ ; 2020/10961-1//S&#xe3;o Paulo State Research Foundation-FAPESP/ ; 2020/07520-3//S&#xe3;o Paulo State Research Foundation-FAPESP/ ; 309899/2022-2//CNPq/ ; 148915/2019-1//CNPq/ ; 147536/2018-9//CNPq/ ; 88887.194785/2018-00//CAPES PrInt/ ; },
mesh = {Animals ; *Lizards/physiology/metabolism ; *Muscle, Skeletal/metabolism/physiology ; *Reproduction/physiology ; Thermogenesis/physiology ; Female ; Male ; Seasons ; Mitochondria, Muscle/metabolism ; Energy Metabolism/physiology ; },
abstract = {AIM: In cyclic climate variations, including seasonal changes, many animals regulate their energy demands to overcome critical transitory moments, restricting their high-demand activities to phases of resource abundance, enabling rapid growth and reproduction. Tegu lizards (Salvator merianae) are ectotherms with a robust annual cycle, being active during summer, hibernating during winter, and presenting a remarkable endothermy during reproduction in spring. Here, we evaluated whether changes in mitochondrial respiratory physiology in skeletal muscle could serve as a mechanism for the increased thermogenesis observed during the tegu's reproductive endothermy.<br><br>METHODS: We performed high-resolution respirometry and calorimetry in permeabilized red and white muscle fibers, sampled during summer (activity) and spring (high activity and reproduction), in association with citrate synthase measurements.<br><br>RESULTS: During spring, the muscle fibers exhibited increased oxidative phosphorylation. They also enhanced uncoupled respiration and heat production via adenine nucleotide translocase (ANT), but not via uncoupling proteins (UCP). Citrate synthase activity was higher during the spring, suggesting greater mitochondrial density compared to the summer. These findings were consistent across both sexes and muscle types (red and white).<br><br>CONCLUSION: The current results highlight potential cellular thermogenic mechanisms in an ectothermic reptile that contribute to transient endothermy. Our study indicates that the unique feature of transitioning to endothermy through nonshivering thermogenesis during the reproductive phase may be facilitated by higher mitochondrial density, function, and uncoupling within the skeletal muscle. This knowledge contributes significant elements to the broader picture of models for the evolution of endothermy, particularly in relation to the enhancement of aerobic capacity.},
}
@article {pmid38740928,
year = {2024},
author = {Rakotonirina, A and Dauga, C and Pol, M and Hide, M and Vuth, L and Ballan, V and Kilama, S and Russet, S and Marcombe, S and Boyer, S and Pocquet, N},
title = {Speciation patterns of Aedes mosquitoes in the Scutellaris Group: a mitochondrial perspective.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10930},
pmid = {38740928},
issn = {2045-2322},
mesh = {Animals ; *Aedes/genetics/classification ; *Genetic Speciation ; *Phylogeny ; *Electron Transport Complex IV/genetics ; *Mitochondria/genetics ; Genetic Variation ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Asia ; },
abstract = {The Scutellaris Group of Aedes comprises 47 mosquito species, including Aedes albopictus. While Ae. albopictus is widely distributed, the other species are mostly found in the Asia-Pacific region. Evolutionary history researches of Aedes species within the Scutellaris Group have mainly focused on Ae. albopictus, a species that raises significant public health concerns, neglecting the other species. In this study, we aimed to assess genetic diversity and estimate speciation times of several species within the Scutellaris Group. Mosquitoes were therefore collected from various Asia-Pacific countries. Their mitochondrial cytochrome c oxidase subunit 1 (cox1) and subunit 3 (cox3) sequences were analyzed alongside those of other Scutellaris Group species available in the GenBank database. To estimate the divergence time, we analyzed 1849 cox1 gene sequences from 21 species, using three species (Aedes aegypti, Aedes notoscriptus and Aedes vigilax) as outgroups. We found that most of the speciation dates occurred during the Paleogene and the Neogene periods. A separation between the Scutellaris Subgroup and the Albopictus Subgroup occurred approximately 64-61 million years ago (MYA). We also identified a split between species found in Asia/Micronesia and those collected in Melanesia/Polynesia approximately 36-35 MYA. Our findings suggest that the speciation of Aedes species within the Scutellaris Group may be driven by diversity in mammalian hosts, climate and environmental changes, and geological dynamics rather than human migration.},
}
@article {pmid38740227,
year = {2024},
author = {Zhang, M and Li, W and Zhang, X and Bi, M and Wang, X and Sun, F and Lu, J and Chi, Y and Han, Y and Li, Q and Li, T},
title = {Lamprey VDAC2: Suppressing hydrogen peroxide-induced 293T cell apoptosis by downregulating BAK expression.},
journal = {Fish &amp; shellfish immunology},
volume = {150},
number = {},
pages = {109622},
doi = {10.1016/j.fsi.2024.109622},
pmid = {38740227},
issn = {1095-9947},
mesh = {Animals ; Humans ; Amino Acid Sequence ; *Apoptosis ; bcl-2 Homologous Antagonist-Killer Protein/metabolism ; Down-Regulation/drug effects ; *Fish Proteins/genetics/immunology ; Gene Expression Profiling/veterinary ; Gene Expression Regulation ; HEK293 Cells ; Hydrogen Peroxide ; *Lampreys/genetics/immunology ; Phylogeny ; Sequence Alignment/veterinary ; *Voltage-Dependent Anion Channel 2/metabolism ; },
abstract = {The voltage-dependent anion channel 2 (VDAC2) is the abundant protein in the outer mitochondrial membrane. Opening VDAC2 pores leads to the induction of mitochondrial energy and material transport, facilitating interaction with various mitochondrial proteins implicated in essential processes such as cell apoptosis and proliferation. To investigate the VDAC2 in lower vertebrates, we identified Lr-VDAC2, a homologue of VDAC2 found in lamprey (Lethenteron reissneri), sharing a sequence identity of greater than 50 % with its counterparts. Phylogenetic analysis revealed that the position of Lr-VDAC2 aligns with the lamprey phylogeny, indicating its evolutionary relationship within the species. The Lr-VDAC2 protein was primarily located in the mitochondria of lamprey cells. The expression of the Lr-VDAC2 protein was elevated in high energy-demanding tissues, such as the gills, muscles, and myocardial tissue in normal lampreys. Lr-VDAC2 suppressed H2O2 (hydrogen peroxide)-induced 293 T cell apoptosis by reducing the expression levels of Caspase 3, Caspase 9, and Cyt C (cytochrome c). Further research into the mechanism indicated that the Lr-VDAC2 protein inhibited the pro-apoptotic activity of BAK (Bcl-2 antagonist/killer) protein by downregulating its expression at the protein translational level, thus exerting an anti-apoptotic function similar to the role of VDAC2 in humans.},
}
@article {pmid38735623,
year = {2024},
author = {Strücker, GK and Jaramillo, ML and de Quadros, T and Nazari, EM},
title = {UVB radiation exposure modulates mitophagy in embryonic cells of freshwater prawn Macrobrachium olfersii: Exploring a protective organelle quality control mechanism.},
journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology},
volume = {295},
number = {},
pages = {111664},
doi = {10.1016/j.cbpa.2024.111664},
pmid = {38735623},
issn = {1531-4332},
mesh = {Animals ; *Ultraviolet Rays/adverse effects ; *Mitophagy/radiation effects ; *Palaemonidae/radiation effects/embryology/genetics ; Mitochondria/metabolism/radiation effects ; Embryo, Nonmammalian/radiation effects/metabolism ; Arthropod Proteins/metabolism/genetics ; Phylogeny ; Organelles/metabolism/radiation effects ; },
abstract = {Aquatic environments are subject to ultraviolet B (UVB) radiation incidence, and its effects on organisms are dose-dependent. Besides DNA, mitochondria are an important target of this radiation that causes structural damage and impairs its functional dynamics. Here, we hypothesize that mitophagy acts as an organelle quality control mechanism to mitigate UVB impacts in embryonic cells. Then, freshwater prawn Macrobrachium olfersii embryos was used as a model to investigate the effects of UVB on genes (Tomm20, Opa1, Pink, Prkn, Sqstm1, and Map1lc3) and proteins (TOM20, PINK1, p62 and LC3B) involved in mitophagy modulation. The choice of genes and proteins was based on the identification of mitochondrial membrane (Tomm20, Opa1 and TOM20), mediation of mitophagy (Pink1, Prkn and PINK1), and recognition of mitochondria by the autophagosome membrane (Sqstm1, Map1lc3, p62 and LC3B). First, the phylogeny of all genes presented bootstrap values >80 and conserved domains among crustacean species. Gene expression was inherently modulated during development, with transcripts (Tomm20, Opa1, Pink, Prkn, Sqstm1, and Map1lc3) overexpressed in the initial and final stages of development. Moreover, UVB radiation induced upregulation of Tomm20, Opa1, Pink, Prkn, Sqstm1, and Map1lc3 genes at 6 h after exposure. Interestingly, after 12 h, the protein content of PINK1, p62, and LC3B increased, while TOM20 was not responsive. Despite UVB radiation's harmful effects on embryonic cells, the chronology of gene expression and protein content indicates rapid activation of mitophagy, serving as an organelle quality control mechanism, given the analyzed cells' integrity.},
}
@article {pmid38733988,
year = {2024},
author = {Sangineto, M and Ciarnelli, M and Colangelo, T and Moola, A and Bukke, VN and Duda, L and Villani, R and Romano, A and Giandomenico, S and Kanwal, H and Serviddio, G},
title = {Monocyte bioenergetics: An immunometabolic perspective in metabolic dysfunction-associated steatohepatitis.},
journal = {Cell reports. Medicine},
volume = {5},
number = {5},
pages = {101564},
pmid = {38733988},
issn = {2666-3791},
mesh = {Humans ; *Energy Metabolism ; Animals ; *Monocytes/metabolism/immunology ; Mice ; *Mitochondria/metabolism ; Fatty Liver/metabolism/pathology/immunology ; Male ; Glycolysis ; Reactive Oxygen Species/metabolism ; Mice, Inbred C57BL ; Macrophages/metabolism/immunology ; Female ; Liver/metabolism/pathology ; },
abstract = {Monocytes (Mos) are crucial in the evolution of metabolic dysfunction-associated steatotic liver disease (MASLD) to metabolic dysfunction-associated steatohepatitis (MASH), and immunometabolism studies have recently suggested targeting leukocyte bioenergetics in inflammatory diseases. Here, we reveal a peculiar bioenergetic phenotype in circulating Mos of patients with MASH, characterized by high levels of glycolysis and mitochondrial (mt) respiration. The enhancement of mt respiratory chain activity, especially complex II (succinate dehydrogenase [SDH]), is unbalanced toward the production of reactive oxygen species (ROS) and is sustained at the transcriptional level with the involvement of the AMPK-mTOR-PGC-1α axis. The modulation of mt activity with dimethyl malonate (DMM), an SDH inhibitor, restores the metabolic profile and almost abrogates cytokine production. Analysis of a public single-cell RNA sequencing (scRNA-seq) dataset confirms that in murine models of MASH, liver Mo-derived macrophages exhibit an upregulation of mt and glycolytic energy pathways. Accordingly, the DMM injection in MASH mice contrasts Mo infiltration and macrophagic enrichment, suggesting immunometabolism as a potential target in MASH.},
}
@article {pmid38731291,
year = {2024},
author = {Zhang, J and Xu, C and Wang, S and Wang, S and Li, Y},
title = {Variations in Genetic Diversity of Invasive Species Lithobates catesbeianus in China.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {9},
pages = {},
pmid = {38731291},
issn = {2076-2615},
support = {32030070//National Science Foundation of China/ ; 2019QZKK0501//Second Tibetan Plateau Scientific Expedition and Research (STEP) Program/ ; 050001-521100222045//the High-Level Talents Research Start-Up Project of Hebei University/ ; C2022201042//Hebei Natural Science Foundation/ ; Sino-BON//China's Biodiversity Observation Network/ ; },
abstract = {The introduction and subsequent range expansion of the American bullfrog (Lithobates catesbeianus) is part of a rising trend of troublesome biological invasions happening in China. This detrimental amphibious invasive species has strong adaptability. After its introduction and spread, it established its own ecological niche in many provinces of China, and its range has continued to expand to more areas. Previous studies recorded the introduction time of bullfrogs and calculated the changes in their genetic diversity in China using mitochondria, but the specific introduction route in China is still unknown. Expanding upon previous research, we employed whole-genome scans (utilizing 2b-RAD genomic sequencing) to examine single nucleotide polymorphisms (SNPs) and microsatellites within Lithobates catesbeianus to screen the genomes of these invasive amphibian species from eight Chinese provinces and two U.S. states, including Kansas, where bullfrogs originate. A total of 1,336,475 single nucleotide polymorphic loci and 17 microsatellite loci were used to calculate the genetic diversity of bullfrogs and their migration pathways. Our results suggest that the population in Hunan was the first to be introduced and to spread, and there may have been multiple introductions of subpopulations. Additionally, the genetic diversity of both the SNP and microsatellite loci in the Chinese bullfrog population was lower than that of the US population due to bottleneck effects, but the bullfrogs can adapt and spread rapidly. This study will offer crucial insights for preventing and controlling future introductions into the natural habitats in China. Additionally, it will assist in devising more precise strategies to manage the existing populations and curtail their continued expansion, as well as aim to improve clarity and originality while mitigating plagiarism risk.},
}
@article {pmid38713727,
year = {2024},
author = {K Raval, P and MacLeod, AI and Gould, SB},
title = {A molecular atlas of plastid and mitochondrial proteins reveals organellar remodeling during plant evolutionary transitions from algae to angiosperms.},
journal = {PLoS biology},
volume = {22},
number = {5},
pages = {e3002608},
pmid = {38713727},
issn = {1545-7885},
mesh = {*Plastids/metabolism/genetics ; *Magnoliopsida/genetics/metabolism ; *Mitochondrial Proteins/metabolism/genetics ; *Phylogeny ; Evolution, Molecular ; Biological Evolution ; Mitochondria/metabolism/genetics ; Plant Proteins/metabolism/genetics ; Proteome/metabolism ; Symbiosis/genetics ; Organelles/metabolism/genetics ; },
abstract = {Algae and plants carry 2 organelles of endosymbiotic origin that have been co-evolving in their host cells for more than a billion years. The biology of plastids and mitochondria can differ significantly across major lineages and organelle changes likely accompanied the adaptation to new ecological niches such as the terrestrial habitat. Based on organelle proteome data and the genomes of 168 phototrophic (Archaeplastida) versus a broad range of 518 non-phototrophic eukaryotes, we screened for changes in plastid and mitochondrial biology across 1 billion years of evolution. Taking into account 331,571 protein families (or orthogroups), we identify 31,625 protein families that are unique to primary plastid-bearing eukaryotes. The 1,906 and 825 protein families are predicted to operate in plastids and mitochondria, respectively. Tracing the evolutionary history of these protein families through evolutionary time uncovers the significant remodeling the organelles experienced from algae to land plants. The analyses of gained orthogroups identifies molecular changes of organelle biology that connect to the diversification of major lineages and facilitated major transitions from chlorophytes en route to the global greening and origin of angiosperms.},
}
@article {pmid38692277,
year = {2024},
author = {Kumar, A and Gok, MO and Nguyen, KN and Connor, OM and Reese, ML and Wideman, JG and Muñoz-Gómez, SA and Friedman, JR},
title = {A dynamin superfamily-like pseudoenzyme coordinates with MICOS to promote cristae architecture.},
journal = {Current biology : CB},
volume = {34},
number = {12},
pages = {2606-2622.e9},
pmid = {38692277},
issn = {1879-0445},
support = {S10 OD021685/OD/NIH HHS/United States ; S10 OD028630/OD/NIH HHS/United States ; P30 CA142543/CA/NCI NIH HHS/United States ; R01 AI150715/AI/NIAID NIH HHS/United States ; R21 AI171227/AI/NIAID NIH HHS/United States ; R35 GM137894/GM/NIGMS NIH HHS/United States ; },
mesh = {*Schizosaccharomyces/metabolism/genetics ; *Schizosaccharomyces pombe Proteins/metabolism/genetics ; *Mitochondrial Membranes/metabolism ; *Mitochondrial Proteins/metabolism/genetics ; Dynamins/metabolism/genetics ; Mitochondria/metabolism ; Mitochondria Associated Membranes ; },
abstract = {Mitochondrial cristae architecture is crucial for optimal respiratory function of the organelle. Cristae shape is maintained in part by the mitochondrial contact site and cristae organizing system (MICOS) complex. While MICOS is required for normal cristae morphology, the precise mechanistic role of each of the seven human MICOS subunits, and how the complex coordinates with other cristae-shaping factors, has not been fully determined. Here, we examine the MICOS complex in Schizosaccharomyces pombe, a minimal model whose genome only encodes for four core subunits. Using an unbiased proteomics approach, we identify a poorly characterized inner mitochondrial membrane protein that interacts with MICOS and is required to maintain cristae morphology, which we name Mmc1. We demonstrate that Mmc1 works in concert with MICOS to promote normal mitochondrial morphology and respiratory function. Mmc1 is a distant relative of the dynamin superfamily of proteins (DSPs), GTPases, which are well established to shape and remodel membranes. Similar to DSPs, Mmc1 self-associates and forms high-molecular-weight assemblies. Interestingly, however, Mmc1 is a pseudoenzyme that lacks key residues required for GTP binding and hydrolysis, suggesting that it does not dynamically remodel membranes. These data are consistent with the model that Mmc1 stabilizes cristae architecture by acting as a scaffold to support cristae ultrastructure on the matrix side of the inner membrane. Our study reveals a new class of proteins that evolved early in fungal phylogeny and is required for the maintenance of cristae architecture. This highlights the possibility that functionally analogous proteins work with MICOS to establish cristae morphology in metazoans.},
}
@article {pmid38673928,
year = {2024},
author = {Aleshina, YA and Aleshin, VA},
title = {Evolutionary Changes in Primate Glutamate Dehydrogenases 1 and 2 Influence the Protein Regulation by Ligands, Targeting and Posttranslational Modifications.},
journal = {International journal of molecular sciences},
volume = {25},
number = {8},
pages = {},
pmid = {38673928},
issn = {1422-0067},
support = {23-74-10036//Russian Science Foundation/ ; },
mesh = {Animals ; Humans ; *Evolution, Molecular ; *Glutamate Dehydrogenase/metabolism/genetics/chemistry ; Ligands ; Mutation ; Primates/genetics ; *Protein Processing, Post-Translational ; },
abstract = {There are two paralogs of glutamate dehydrogenase (GDH) in humans encoded by the GLUD1 and GLUD2 genes as a result of a recent retroposition during the evolution of primates. The two human GDHs possess significantly different regulation by allosteric ligands, which is not fully characterized at the structural level. Recent advances in identification of the GDH ligand binding sites provide a deeper perspective on the significance of the accumulated substitutions within the two GDH paralogs. In this review, we describe the evolution of GLUD1 and GLUD2 after the duplication event in primates using the accumulated sequencing and structural data. A new gibbon GLUD2 sequence questions the indispensability of ancestral R496S and G509A mutations for GLUD2 irresponsiveness to GTP, providing an alternative with potentially similar regulatory features. The data of both GLUD1 and GLUD2 evolution not only confirm substitutions enhancing GLUD2 mitochondrial targeting, but also reveal a conserved mutation in ape GLUD1 mitochondrial targeting sequence that likely reduces its transport to mitochondria. Moreover, the information of GDH interactors, posttranslational modification and subcellular localization are provided for better understanding of the GDH mutations. Medically significant point mutations causing deregulation of GDH are considered from the structural and regulatory point of view.},
}
@article {pmid38668970,
year = {2024},
author = {Muthye, V and Lavrov, DV},
title = {Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2757},
number = {},
pages = {239-257},
pmid = {38668970},
issn = {1940-6029},
mesh = {Animals ; *Ctenophora/metabolism/genetics ; *Proteome ; *Mitochondrial Proteins/metabolism/genetics ; Computational Biology/methods ; Mitochondria/metabolism ; Proteomics/methods ; Software ; },
abstract = {Mitochondrial proteomes have been experimentally characterized for only a handful of animal species. However, the increasing availability of genomic and transcriptomic data allows one to infer mitochondrial proteins using computational tools. MitoPredictor is a novel random forest classifier, which utilizes orthology search, mitochondrial targeting signal (MTS) identification, and protein domain content to infer mitochondrial proteins in animals. MitoPredictor's output also includes an easy-to-use R Shiny applet for the visualization and analysis of the results. In this article, we provide a guide for predicting and analyzing the mitochondrial proteome of the ctenophore Mnemiopsis leidyi using MitoPredictor.},
}
@article {pmid38668357,
year = {2024},
author = {Martinez, P and Baghli, I and Gourjon, G and Seyfried, TN},
title = {Mitochondrial-Stem Cell Connection: Providing Additional Explanations for Understanding Cancer.},
journal = {Metabolites},
volume = {14},
number = {4},
pages = {},
pmid = {38668357},
issn = {2218-1989},
abstract = {The cancer paradigm is generally based on the somatic mutation model, asserting that cancer is a disease of genetic origin. The mitochondrial-stem cell connection (MSCC) proposes that tumorigenesis may result from an alteration of the mitochondria, specifically a chronic oxidative phosphorylation (OxPhos) insufficiency in stem cells, which forms cancer stem cells (CSCs) and leads to malignancy. Reviewed evidence suggests that the MSCC could provide a comprehensive understanding of all the different stages of cancer. The metabolism of cancer cells is altered (OxPhos insufficiency) and must be compensated by using the glycolysis and the glutaminolysis pathways, which are essential to their growth. The altered mitochondria regulate the tumor microenvironment, which is also necessary for cancer evolution. Therefore, the MSCC could help improve our understanding of tumorigenesis, metastases, the efficiency of standard treatments, and relapses.},
}
@article {pmid38658571,
year = {2024},
author = {Xing, L and Gkini, V and Nieminen, AI and Zhou, HC and Aquilino, M and Naumann, R and Reppe, K and Tanaka, K and Carmeliet, P and Heikinheimo, O and Pääbo, S and Huttner, WB and Namba, T},
title = {Functional synergy of a human-specific and an ape-specific metabolic regulator in human neocortex development.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3468},
pmid = {38658571},
issn = {2041-1723},
support = {340179, 351966, 336234//Academy of Finland (Suomen Akatemia)/ ; },
mesh = {*Neocortex/metabolism/embryology/growth &amp; development/cytology ; Humans ; Animals ; *Glutamate Dehydrogenase/metabolism/genetics ; *GTPase-Activating Proteins/metabolism/genetics ; Ketoglutaric Acids/metabolism ; Neuroglia/metabolism ; Glutamic Acid/metabolism ; Mitochondria/metabolism/genetics ; Mice ; Citric Acid Cycle/genetics ; Female ; },
abstract = {Metabolism has recently emerged as a major target of genes implicated in the evolutionary expansion of human neocortex. One such gene is the human-specific gene ARHGAP11B. During human neocortex development, ARHGAP11B increases the abundance of basal radial glia, key progenitors for neocortex expansion, by stimulating glutaminolysis (glutamine-to-glutamate-to-alpha-ketoglutarate) in mitochondria. Here we show that the ape-specific protein GLUD2 (glutamate dehydrogenase 2), which also operates in mitochondria and converts glutamate-to-αKG, enhances ARHGAP11B's ability to increase basal radial glia abundance. ARHGAP11B + GLUD2 double-transgenic bRG show increased production of aspartate, a metabolite essential for cell proliferation, from glutamate via alpha-ketoglutarate and the TCA cycle. Hence, during human evolution, a human-specific gene exploited the existence of another gene that emerged during ape evolution, to increase, via concerted changes in metabolism, progenitor abundance and neocortex size.},
}
@article {pmid38658152,
year = {2024},
author = {Fan, C and Yang, J and Chen, R and Liu, W and Xiang, X},
title = {[Identification and expression analysis of the HSP70 gene family under abiotic stresses in Litchi chinensis].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {40},
number = {4},
pages = {1102-1119},
doi = {10.13345/j.cjb.230450},
pmid = {38658152},
issn = {1872-2075},
mesh = {*Litchi/genetics/metabolism ; *HSP70 Heat-Shock Proteins/genetics/metabolism ; *Stress, Physiological/genetics ; *Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism/biosynthesis ; *Phylogeny ; *Droughts ; Multigene Family ; Salt Stress/genetics ; },
abstract = {HSP70 protein, as an important member of the heat shock protein (HSP) family, plays an important role in plant growth, development, and response to biotic and abiotic stresses. In order to explore the role of HSP70 gene family members in Litchi chinensis under low temperature, high temperature, drought, and salt stress, bioinformatics methods were used to identify the HSP70 gene family members within the entire L. chinensis genome. The expression of these genes under various abiotic stresses was then detected using quantitative real-time PCR (qRT-PCR). The results showed that the LcHSP70 gene family consisted of 18 members, which were unevenly distributed across ten L. chinensis chromosomes. The LcHSP70 protein contained 479-851 amino acids, with isoelectric points ranging from 5.07 to 6.95, and molecular weights from 52.44 kDa to 94.07 kDa. The predicted subcellular localization showed that LcHSP70 protein was present in the nucleus, cytoplasm, endoplasmic reticulum, mitochondria, and chloroplast. Phylogenetic analysis divided the LcHSP70 proteins into five subgroups, namely Ⅰ, Ⅱ, Ⅲ, Ⅳ, and Ⅵ. The promoter regions of the LcHSP70 genes contained various cis-acting elements related to plant growth, development, hormone response, and stress response. Moreover, the expression of LcHSP70 genes displayed distint tissue-specific expression level, categorized into universal expression and specific expression. From the selected 6 LcHSP70 genes (i.e., LcHSP70-1, LcHSP70-5, LcHSP70-10, LcHSP70-14, LcHSP70-16, and LcHSP70-18), their relative expression levels were assessed under different abiotic stresses using qRT-PCR. The results indicated that the gene family members exhibited diverse responses to low temperature, high temperature, drought, and salt stress, with significant variations in their expression levels across different time periods. These results provide a foundation for further exploration of the function of the LcHSP70 gene family.},
}
@article {pmid38652016,
year = {2024},
author = {Kwok van der Giezen, FM and Viljoen, A and Campbell-Clause, L and Dao, NT and Colas des Francs-Small, C and Small, I},
title = {Insights into U-to-C RNA editing from the lycophyte Phylloglossum drummondii.},
journal = {The Plant journal : for cell and molecular biology},
volume = {119},
number = {1},
pages = {445-459},
doi = {10.1111/tpj.16775},
pmid = {38652016},
issn = {1365-313X},
support = {DP200102981//Australian Research Council/ ; },
mesh = {*RNA Editing/genetics ; *RNA, Plant/genetics ; Genome, Mitochondrial/genetics ; Transcriptome ; Uridine/metabolism/genetics ; Genome, Chloroplast ; Phylogeny ; Mitochondria/genetics/metabolism ; },
abstract = {The lycophyte Phylloglossum drummondii is the sole inhabitant of its genus in the Huperzioideae group and one of a small minority of plants which perform uridine to cytidine RNA editing. We assembled the P. drummondii chloroplast and mitochondrial genomes and used RNA sequence data to build a comprehensive profile of organellar RNA editing events. In addition to many C-to-U editing events in both organelles, we found just four U-to-C editing events in the mitochondrial transcripts cob, nad1, nad5 and rpl2. These events are conserved in related lycophytes in the genera Huperzia and Phlegmariurus. De novo transcriptomes for three of these lycophytes were assembled to search for putative U-to-C RNA editing enzymes. Four putative U-to-C editing factors could be matched to the four mitochondrial U-to-C editing sites. Due to the unusually few numbers of U-to-C RNA editing sites, P. drummondii and related lycophytes are useful models for studying this poorly understood mechanism.},
}
@article {pmid38630841,
year = {2024},
author = {Gonzalez, RC and Bezerra de Lima, LC and Passos, P and Silva, MJJ},
title = {The good, the bad and the boa: An unexpected new species of a true boa revealed by morphological and molecular evidence.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0298159},
pmid = {38630841},
issn = {1932-6203},
mesh = {Animals ; Male ; Phylogeny ; *Boidae/genetics ; Mitochondria/genetics ; Brazil ; *Lepidoptera ; },
abstract = {Snakes of the genus Boa are outstanding elements of the New World biota with a broad sociological influence on pop culture. Historically, several taxa have been recognized in the past 300 years, being mostly described in the early days of binomial nomenclature. As a rule, these taxa were recognized based on a suite of phenotypic characters mainly those from the external morphology. However, there is a huge disagreement with respect to the current taxonomy and available molecular phylogenies. In order to reconcile both lines of evidence, we investigate the phylogenetic reconstruction (using mitochondrial and nuclear genes) of the genus in parallel to the detailed study of some phenotypic systems from a geographically representative sample of the cis-Andean mainland Boa constrictor. We used cyt-b only (744bp) from 73 samples, and cyt-b, ND4, NTF3, and ODC partial sequences (in a total of 2305 bp) from 35 samples, comprising nine currently recognized taxa (species or subspecies), to infer phylogenetic relationships of boas. Topologies recovered along all the analyses and genetic distances obtained allied to a unique combination of morphological traits (colouration, pholidosis, meristic, morphometric, and male genitalia features) allowed us to recognize B. constrictor lato sensu, B. nebulosa, B. occidentalis, B. orophias and a distinct lineage from the eastern coast of Brazil, which we describe here as a new species, diagnosing it from the previously recognized taxa. Finally, we discuss the minimally necessary changes in the taxonomy of Boa constrictor complex; the value of some usually disregarded phenotypic character system; and we highlight the urgency of continuing environmental policy to preserve one of the most impacted Brazilian hotspots, the Atlantic Forest, which represents an ecoregion full of endemism.},
}
@article {pmid38611479,
year = {2024},
author = {Qian, F and Zuo, D and Zeng, T and Gu, L and Wang, H and Du, X and Zhu, B and Ou, J},
title = {Identification, Evolutionary Dynamics, and Gene Expression Patterns of the ACP Gene Family in Responding to Salt Stress in Brassica Genus.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {38611479},
issn = {2223-7747},
support = {32060463//National Natural Science Foundation of China/ ; 32260460//National Natural Science Foundation of China/ ; Qian Kehe Support [2022] key 026//Guizhou Provincial Science and Technology Plan Project/ ; Qiankehezhicheng&#x3010;2022&#x3011;Key 031//The Scientific and Technological Key Program of Guizhou province/ ; },
abstract = {Acyl carrier proteins (ACPs) have been reported to play a crucial role in responding to biotic and abiotic stresses, regulating growth and development. However, the biological function of the ACP gene family in the Brassica genus has been limited until now. In this study, we conducted a comprehensive analysis and identified a total of 120 ACP genes across six species in the Brassica genus. Among these, there were 27, 26, and 30 ACP genes in the allotetraploid B. napus, B. juncea, and B. carinata, respectively, and 14, 13, and 10 ACP genes in the diploid B. rapa, B. oleracea, and B. nigra, respectively. These ACP genes were further classified into six subclades, each containing conserved motifs and domains. Interestingly, the majority of ACP genes exhibited high conservation among the six species, suggesting that the genome evolution and polyploidization processes had relatively minor effects on the ACP gene family. The duplication modes of the six Brassica species were diverse, and the expansion of most ACPs in Brassica occurred primarily through dispersed duplication (DSD) events. Furthermore, most of the ACP genes were under purifying selection during the process of evolution. Subcellular localization experiments demonstrated that ACP genes in Brassica species are localized in chloroplasts and mitochondria. Cis-acting element analysis revealed that most of the ACP genes were associated with various abiotic stresses. Additionally, RNA-seq data revealed differential expression levels of BnaACP genes across various tissues in B. napus, with particularly high expression in seeds and buds. qRT-PCR analysis further indicated that BnaACP genes play a significant role in salt stress tolerance. These findings provide a comprehensive understanding of ACP genes in Brassica plants and will facilitate further functional analysis of these genes.},
}
@article {pmid38603509,
year = {2024},
author = {Coale, TH and Loconte, V and Turk-Kubo, KA and Vanslembrouck, B and Mak, WKE and Cheung, S and Ekman, A and Chen, JH and Hagino, K and Takano, Y and Nishimura, T and Adachi, M and Le Gros, M and Larabell, C and Zehr, JP},
title = {Nitrogen-fixing organelle in a marine alga.},
journal = {Science (New York, N.Y.)},
volume = {384},
number = {6692},
pages = {217-222},
doi = {10.1126/science.adk1075},
pmid = {38603509},
issn = {1095-9203},
mesh = {*Cyanobacteria/genetics/metabolism ; *Haptophyta/microbiology ; *Nitrogen/metabolism ; *Nitrogen Fixation/genetics ; Seawater/microbiology ; Symbiosis ; *Mitochondria/metabolism ; Chloroplasts/metabolism ; },
abstract = {Symbiotic interactions were key to the evolution of chloroplast and mitochondria organelles, which mediate carbon and energy metabolism in eukaryotes. Biological nitrogen fixation, the reduction of abundant atmospheric nitrogen gas (N2) to biologically available ammonia, is a key metabolic process performed exclusively by prokaryotes. Candidatus Atelocyanobacterium thalassa, or UCYN-A, is a metabolically streamlined N2-fixing cyanobacterium previously reported to be an endosymbiont of a marine unicellular alga. Here we show that UCYN-A has been tightly integrated into algal cell architecture and organellar division and that it imports proteins encoded by the algal genome. These are characteristics of organelles and show that UCYN-A has evolved beyond endosymbiosis and functions as an early evolutionary stage N2-fixing organelle, or "nitroplast."},
}
@article {pmid38601302,
year = {2024},
author = {Fukasawa, Y and Driguez, P and Bougouffa, S and Carty, K and Putra, A and Cheung, MS and Ermini, L},
title = {Plasticity of repetitive sequences demonstrated by the complete mitochondrial genome of Eucalyptus camaldulensis.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1339594},
pmid = {38601302},
issn = {1664-462X},
abstract = {The tree Eucalyptus camaldulensis is a ubiquitous member of the Eucalyptus genus, which includes several hundred species. Despite the extensive sequencing and assembly of nuclear genomes from various eucalypts, the genus has only one fully annotated and complete mitochondrial genome (mitogenome). Plant mitochondria are characterized by dynamic genomic rearrangements, facilitated by repeat content, a feature that has hindered the assembly of plant mitogenomes. This complexity is evident in the paucity of available mitogenomes. This study, to the best of our knowledge, presents the first E. camaldulensis mitogenome. Our findings suggest the presence of multiple isomeric forms of the E. camaldulensis mitogenome and provide novel insights into minor rearrangements triggered by nested repeat sequences. A comparative sequence analysis of the E. camaldulensis and E. grandis mitogenomes unveils evolutionary changes between the two genomes. A significant divergence is the evolution of a large repeat sequence, which may have contributed to the differences observed between the two genomes. The largest repeat sequences in the E. camaldulensis mitogenome align well with significant yet unexplained structural variations in the E. grandis mitogenome, highlighting the adaptability of repeat sequences in plant mitogenomes.},
}
@article {pmid38597829,
year = {2024},
author = {Regina-Ferreira, L and Valdivieso-Rivera, F and Angelim, MKSC and Menezes Dos Reis, L and Furino, VO and Morari, J and Maia de Sousa, L and Consonni, SR and Sponton, CH and Moraes-Vieira, PM and Velloso, LA},
title = {Inhibition of Crif1 protects fatty acid-induced POMC neuron-like cell-line damage by increasing CPT-1 function.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {326},
number = {5},
pages = {E681-E695},
doi = {10.1152/ajpendo.00420.2023},
pmid = {38597829},
issn = {1522-1555},
support = {2013/07607-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; },
mesh = {Animals ; Mice ; *Carnitine O-Palmitoyltransferase/metabolism/genetics ; Cell Line ; *Fatty Acids/metabolism ; Hypothalamus/metabolism/drug effects ; *Mitochondria/metabolism/drug effects ; Neurons/drug effects/metabolism ; Pro-Opiomelanocortin/metabolism/genetics ; Reactive Oxygen Species/metabolism ; *Cell Cycle Proteins/antagonists &amp; inhibitors/metabolism ; },
abstract = {Hypothalamic proopiomelanocortin (POMC) neurons are sensors of signals that reflect the energy stored in the body. Inducing mild stress in proopiomelanocortin neurons protects them from the damage promoted by the consumption of a high-fat diet, mitigating the development of obesity; however, the cellular mechanisms behind these effects are unknown. Here, we induced mild stress in a proopiomelanocortin neuron cell line by inhibiting Crif1. In proopiomelanocortin neurons exposed to high levels of palmitate, the partial inhibition of Crif1 reverted the defects in mitochondrial respiration and ATP production; this was accompanied by improved mitochondrial fusion/fission cycling. Furthermore, the partial inhibition of Crif1 resulted in increased reactive oxygen species production, increased fatty acid oxidation, and reduced dependency on glucose for mitochondrial respiration. These changes were dependent on the activity of CPT-1. Thus, we identified a CPT-1-dependent metabolic shift toward greater utilization of fatty acids as substrates for respiration as the mechanism behind the protective effect of mild stress against palmitate-induced damage of proopiomelanocortin neurons.NEW &amp; NOTEWORTHY Saturated fats can damage hypothalamic neurons resulting in positive energy balance, and this is mitigated by mild cellular stress; however, the mechanisms behind this protective effect are unknown. Using a proopiomelanocortin cell line, we show that under exposure to a high concentration of palmitate, the partial inhibition of the mitochondrial protein Crif1 results in protection due to a metabolic shift warranted by the increased expression and activity of the mitochondrial fatty acid transporter CPT-1.},
}
@article {pmid38594641,
year = {2024},
author = {Shen, B and Shen, A and Liu, L and Tan, Y and Li, S and Tan, Z},
title = {Assembly and comparative analysis of the complete multichromosomal mitochondrial genome of Cymbidium ensifolium, an orchid of high economic and ornamental value.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {255},
pmid = {38594641},
issn = {1471-2229},
support = {Xiangzi Caihuan Zhi (2022) No. 64; Xiangzi Caihuan Zhi (2022) No. 67; Xiangzi Caihuan Zhi (2023) No. 26; Xiangzi Caihuan Zhi (2023) No. 72//the Hunan Provincial Forestry Ecological Protection, Restoration and Development Special Fund Project/ ; 2023JJ50073//the Hunan Provincial Natural Science Foundation/ ; },
mesh = {*Genome, Mitochondrial/genetics ; Phylogeny ; Mitochondria/genetics ; DNA ; *Orchidaceae/genetics ; },
abstract = {BACKGROUND: Orchidaceae is one of the largest groups of angiosperms, and most species have high economic value and scientific research value due to their ornamental and medicinal properties. In China, Chinese Cymbidium is a popular ornamental orchid with high economic value and a long history. However, to date, no detailed information on the mitochondrial genome of any species of Chinese Cymbidium has been published.<br><br>RESULTS: Here, we present the complete assembly and annotation of the mitochondrial genome of Cymbidium ensifolium (L.) Sw. The mitogenome of C. ensifolium was 560,647&#xa0;bp in length and consisted of 19 circular subgenomes ranging in size from 21,995&#xa0;bp to 48,212&#xa0;bp. The genome encoded 35 protein-coding genes, 36 tRNAs, 3 rRNAs, and 3405 ORFs. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 915 dispersed repeats, 162 simple repeats, 45 tandem repeats, and 530 RNA editing sites. Analysis of codon usage showed a preference for codons ending in A/T. Interorganellar DNA transfer was identified in 13 of the 19 chromosomes, with plastid-derived DNA fragments representing 6.81% of the C. ensifolium mitochondrial genome. The homologous fragments of the mitochondrial genome and nuclear genome were also analysed. Comparative analysis showed that the GC content was conserved, but the size, structure, and gene content of the mitogenomes varied greatly among plants with multichromosomal mitogenome structure. Phylogenetic analysis based on the mitogenomes reflected the evolutionary and taxonomic statuses of C. ensifolium. Interestingly, compared with the mitogenomes of Cymbidium lancifolium Hook. and Cymbidium macrorhizon Lindl., the mitogenome of C. ensifolium lost 8 ribosomal protein-coding genes.<br><br>CONCLUSION: In this study, we assembled and annotated the mitogenome of C. ensifolium and compared it with the mitogenomes of other Liliidae and plants with multichromosomal mitogenome structures. Our findings enrich the mitochondrial genome database of orchid plants and reveal the rapid structural evolution of Cymbidium mitochondrial genomes, highlighting the potential for mitochondrial genes to help decipher plant evolutionary history.},
}
@article {pmid38592734,
year = {2024},
author = {Kwasniak-Owczarek, M and Janska, H},
title = {Experimental approaches to studying translation in plant semi-autonomous organelles.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erae151},
pmid = {38592734},
issn = {1460-2431},
abstract = {Plant mitochondria and chloroplasts are semi-autonomous organelles originated from free-living bacteria and retaining respective reduced genomes during evolution. As a consequence, relatively few of the mitochondrial and chloroplast proteins are encoded in the organellar genomes and synthesized by the organellar ribosomes. Since the both organellar genomes encode mainly components of the energy transduction systems, oxidative phosphorylation in mitochondria and photosynthetic apparatus in chloroplasts, understanding the organellar translation is critical to a thorough comprehension of the key aspects of mitochondrial and chloroplast activity affecting plant growth and development. Recent studies have clearly shown that translation is a key regulatory node in the expression of plant organellar genes, underscoring the need for an adequate methodology to study this unique stage of gene expression. The organellar translatome can be analysed by studying newly synthesized proteins or the mRNA pool recruited to the organellar ribosomes. In this review, we present in some detail the experimental approaches used to date for studying translation in the plant bioenergetic organelles. Their benefits and limitations, as well as the critical steps are discussed. Additionally, we briefly mention several recently developed strategies to study organellar translation that have not yet been applied to plants.},
}
@article {pmid38587065,
year = {2024},
author = {Shen, C and Xu, H and Huang, WZ and Zhao, Q and Zhu, RL},
title = {Is RNA editing truly absent in the complex thalloid liverworts (Marchantiopsida)? Evidence of extensive RNA editing from Cyathodium cavernarum.},
journal = {The New phytologist},
volume = {242},
number = {6},
pages = {2817-2831},
doi = {10.1111/nph.19750},
pmid = {38587065},
issn = {1469-8137},
support = {//East China Normal University/ ; 31970215//National Natural Science Foundation of China/ ; 32370218//National Natural Science Foundation of China/ ; },
mesh = {*RNA Editing/genetics ; *Hepatophyta/genetics ; *Phylogeny ; Plant Proteins/genetics/metabolism ; Chloroplasts/genetics/metabolism ; Mitochondria/genetics/metabolism ; Genes, Plant ; Amino Acid Sequence ; },
abstract = {RNA editing is a crucial modification in plants' organellar transcripts that converts cytidine to uridine (C-to-U; and sometimes uridine to cytidine) in RNA molecules. This post-transcriptional process is controlled by the PLS-class protein with a DYW domain, which belongs to the pentatricopeptide repeat (PPR) protein family. RNA editing is widespread in land plants; however, complex thalloid liverworts (Marchantiopsida) are the only group reported to lack both RNA editing and DYW-PPR protein. The liverwort Cyathodium cavernarum (Marchantiopsida, Cyathodiaceae), typically found in cave habitats, was newly found to have 129 C-to-U RNA editing sites in its chloroplast and 172 sites in its mitochondria. The Cyathodium genus, specifically C. cavernarum, has a large number of PPR editing factor genes, including 251 DYW-type PPR proteins. These DYW-type PPR proteins may be responsible for C-to-U RNA editing in C. cavernarum. Cyathodium cavernarum possesses both PPR DYW proteins and RNA editing. Our analysis suggests that the remarkable RNA editing capability of C. cavernarum may have been acquired alongside the emergence of DYW-type PPR editing factors. These findings provide insight into the evolutionary pattern of RNA editing in land plants.},
}
@article {pmid38568891,
year = {2024},
author = {D'Ercole, J and Dapporto, L and Opler, P and Schmidt, CB and Ho, C and Menchetti, M and Zakharov, EV and Burns, JM and Hebert, PDN},
title = {A genetic atlas for the butterflies of continental Canada and United States.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0300811},
pmid = {38568891},
issn = {1932-6203},
mesh = {Animals ; United States ; *Butterflies/genetics ; Phylogeography ; DNA, Mitochondrial/genetics/chemistry ; Mitochondria/genetics ; Haplotypes ; Genetic Variation ; DNA Barcoding, Taxonomic ; Phylogeny ; },
abstract = {Multi-locus genetic data for phylogeographic studies is generally limited in geographic and taxonomic scope as most studies only examine a few related species. The strong adoption of DNA barcoding has generated large datasets of mtDNA COI sequences. This work examines the butterfly fauna of Canada and United States based on 13,236 COI barcode records derived from 619 species. It compiles i) geographic maps depicting the spatial distribution of haplotypes, ii) haplotype networks (minimum spanning trees), and iii) standard indices of genetic diversity such as nucleotide diversity (π), haplotype richness (H), and a measure of spatial genetic structure (GST). High intraspecific genetic diversity and marked spatial structure were observed in the northwestern and southern North America, as well as in proximity to mountain chains. While species generally displayed concordance between genetic diversity and spatial structure, some revealed incongruence between these two metrics. Interestingly, most species falling in this category shared their barcode sequences with one at least other species. Aside from revealing large-scale phylogeographic patterns and shedding light on the processes underlying these patterns, this work also exposed cases of potential synonymy and hybridization.},
}
@article {pmid38561677,
year = {2024},
author = {Chen, L and Dong, X and Huang, H and Xu, H and Rono, PC and Cai, X and Hu, G},
title = {Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {322},
pmid = {38561677},
issn = {1471-2164},
mesh = {*Genome, Mitochondrial ; Phylogeny ; DNA, Mitochondrial/genetics ; *Lamiales/genetics ; Mitochondria/genetics ; *Genome, Chloroplast ; },
abstract = {BACKGROUND: Primulina hunanensis, a troglobitic plant within the Primulina genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work of chloroplast genome (cpDNA) has been recently accomplished, however, the mitochondrial genome (mtDNA) that is crucial for plant evolution has not been reported.<br><br>RESULTS: In this study, we sequenced and assembled the P. hunanensis complete mtDNA, and elucidated its evolutionary and phylogenetic relationships. The assembled mtDNA spans 575,242&#xa0;bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA genes, and 3 rRNA genes. Notably, high number of repetitive sequences in the mtDNA and substantial sequence translocation from chloroplasts to mitochondria were observed. To determine the evolutionary and taxonomic positioning of P. hunanensis, a phylogenetic tree was constructed using mitochondrial PCGs from P. hunanensis and 32 other taxa. Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted.<br><br>CONCLUSIONS: This study reports the initial assembly and annotation of P. hunanensis mtDNA, contributing to the limited mtDNA repository for Gesneriaceae plants and advancing our understanding of their evolution for improved utilization and conservation.},
}
@article {pmid38555796,
year = {2024},
author = {Casimir, P and Iwata, R and Vanderhaeghen, P},
title = {Linking mitochondria metabolism, developmental timing, and human brain evolution.},
journal = {Current opinion in genetics &amp; development},
volume = {86},
number = {},
pages = {102182},
pmid = {38555796},
issn = {1879-0380},
mesh = {Humans ; *Mitochondria/metabolism/genetics ; *Brain/growth &amp; development/metabolism ; Animals ; *Biological Evolution ; *Neurons/metabolism/cytology ; Species Specificity ; Neurogenesis/genetics ; Mice ; },
abstract = {Changes in developmental timing are an important factor of evolution in organ shape and function. This is particularly striking for human brain development, which, compared with other mammals, is considerably prolonged at the level of the cerebral cortex, resulting in brain neoteny. Here, we review recent findings that indicate that mitochondria and metabolism contribute to species differences in the tempo of cortical neuron development. Mitochondria display species-specific developmental timeline and metabolic activity patterns that are highly correlated with the speed of neuron maturation. Enhancing mitochondrial activity in human cortical neurons results in their accelerated maturation, while its reduction leads to decreased maturation rates in mouse neurons. Together with other global and gene-specific mechanisms, mitochondria thus act as a cellular hourglass of neuronal developmental tempo and may thereby contribute to species-specific features of human brain ontogeny.},
}
@article {pmid38554118,
year = {2024},
author = {Laugier, F and Saclier, N and Béthune, K and Braun, A and Konecny, L and Lefébure, T and Luquet, E and Plénet, S and Romiguier, J and David, P},
title = {Both nuclear and cytoplasmic polymorphisms are involved in genetic conflicts over male fertility in the gynodioecious snail, Physa acuta.},
journal = {Evolution; international journal of organic evolution},
volume = {78},
number = {7},
pages = {1227-1236},
doi = {10.1093/evolut/qpae053},
pmid = {38554118},
issn = {1558-5646},
support = {ANR-19-CE02-0017//MINIGAN/ ; //French National Research Agency/ ; },
mesh = {Animals ; *Polymorphism, Genetic ; Male ; *Snails/genetics/physiology ; *Genome, Mitochondrial ; Cell Nucleus/genetics ; Fertility/genetics ; Hermaphroditic Organisms/genetics ; Evolution, Molecular ; Female ; Cytoplasm/genetics ; Infertility, Male/genetics ; },
abstract = {Gynodioecy, the coexistence of hermaphrodites with females, often reflects conflicts between cytoplasmic male sterility (CMS) genes and nuclear genes restoring male fertility. CMS is frequent in plants and has been recently discovered in one animal: the freshwater snail, Physa acuta. In this system, CMS was linked to a single divergent mitochondrial genome (D), devoid of apparent nuclear restoration. Our study uncovers a second, novel CMS-associated mitogenome (K) in Physa acuta, demonstrating an extraordinary acceleration of molecular evolution throughout the entire K mitochondrial genome, akin to the previously observed pattern in D. This suggests a pervasive occurrence of accelerated evolution in both CMS-associated lineages. Through a 17-generation introgression experiment, we further show that nuclear polymorphisms in K-mitogenome individuals contribute to the restoration of male function in natural populations. Our results underscore shared characteristics in gynodioecy between plants and animals, emphasizing the presence of multiple CMS mitotypes and cytonuclear conflicts. This reaffirms the pivotal role of mitochondria in influencing male function and in generating genomic conflicts that impact reproductive processes in animals.},
}
@article {pmid38548188,
year = {2024},
author = {He, X and Qian, Z and Gichira, AW and Chen, J and Li, Z},
title = {Assembly and comparative analysis of the first complete mitochondrial genome of the invasive water hyacinth, Eichhornia crassipes.},
journal = {Gene},
volume = {914},
number = {},
pages = {148416},
doi = {10.1016/j.gene.2024.148416},
pmid = {38548188},
issn = {1879-0038},
mesh = {*Genome, Mitochondrial ; *Eichhornia/genetics ; *Phylogeny ; Introduced Species ; RNA, Transfer/genetics ; Base Composition ; RNA Editing ; Genome, Plant ; },
abstract = {Eichhornia crassipes is an aquatic plant in tropical and subtropical regions, renowned for its notorious invasive tendencies. In this study, we assembled the complete mitogenome of E. crassipes into a single circle molecule of 397,361 bp. The mitogenome has 58 unique genes, including 37 protein-coding genes (PCGs), 18 tRNA genes, three rRNA genes, and 47 % GC content. Sixteen (6.93 %) homologous fragments, ranging from 31 bp to 8548 bp, were identified, indicating the transfer of genetic material from chloroplasts to mitochondria. In addition, we detected positive selection in six PCGs (ccmB, ccmC, ccmFC, nad3, nad4 and sdh4), along with the identification of 782 RNA editing sites across 37 mt-PCGs. These findings suggest a potential contribution to the robust adaptation of this invasive plant to the stressful environment. Lastly, we inferred that phylogenetic conflicts of E. crassipes between the plastome and mitogenome may be attributed to the difference in nucleotide substitution rates between the two organelle genomes. In conclusion, our study provided vital genomic resources for further understanding the invasive mechanism of this species and exploring the dynamic evolution of mitogenomes within the monocot clade.},
}
@article {pmid38547729,
year = {2024},
author = {Queiroz, MIC and Lazaro, CM and Dos Santos, LMB and Rentz, T and Virgilio-da-Silva, JV and Moraes-Vieira, PMM and Cunha, FAS and Santos, JCC and Vercesi, AE and Leite, ACR and Oliveira, HCF},
title = {In vivo chronic exposure to inorganic mercury worsens hypercholesterolemia, oxidative stress and atherosclerosis in the LDL receptor knockout mice.},
journal = {Ecotoxicology and environmental safety},
volume = {275},
number = {},
pages = {116254},
doi = {10.1016/j.ecoenv.2024.116254},
pmid = {38547729},
issn = {1090-2414},
mesh = {Animals ; Mice ; *Atherosclerosis/chemically induced ; Hydrogen Peroxide ; *Hypercholesterolemia ; Kidney Diseases ; *Mercury/toxicity ; Mice, Knockout ; Oxidative Stress/physiology ; Receptors, LDL/genetics ; },
abstract = {Heavy metal exposure leads to multiple system dysfunctions. The mechanisms are likely multifactorial and involve inflammation and oxidative stress. The aim of this study was to evaluate markers and risk factors for atherosclerosis in the LDL receptor knockout mouse model chronically exposed to inorganic mercury (Hg) in the drinking water. Results revealed that Hg exposed mice present increased plasma levels of cholesterol, without alterations in glucose. As a major source and target of oxidants, we evaluated mitochondrial function. We found that liver mitochondria from Hg treated mice show worse respiratory control, lower oxidative phosphorylation efficiency and increased H2O2 release. In addition, Hg induced mitochondrial membrane permeability transition. Erythrocytes from Hg treated mice showed a 50% reduction in their ability to take up oxygen, lower levels of reduced glutathione (GSH) and of antioxidant enzymes (SOD, catalase and GPx). The Hg treatment disturbed immune system cells counting and function. While lymphocytes were reduced, monocytes, eosinophils and neutrophils were increased. Peritoneal macrophages from Hg treated mice showed increased phagocytic activity. Hg exposed mice tissues present metal impregnation and parenchymal architecture alterations. In agreement, increased systemic markers of liver and kidney dysfunction were observed. Plasma, liver and kidney oxidative damage indicators (MDA and carbonyl) were increased while GSH and thiol groups were diminished by Hg exposure. Importantly, atherosclerotic lesion size in the aorta root of Hg exposed mice were larger than in controls. In conclusion, in vivo chronic exposure to Hg worsens the hypercholesterolemia, impairs mitochondrial bioenergetics and redox function, alters immune cells profile and function, causes several tissues oxidative damage and accelerates atherosclerosis development.},
}
@article {pmid38547143,
year = {2024},
author = {Charrasse, S and Racine, V and Saint-Omer, C and Poquillon, T and Lionnard, L and Ledru, M and Gonindard, C and Delaunois, S and Kissa, K and Frye, RE and Pastore, M and Reynes, C and Frechet, M and Chajra, H and Aouacheria, A},
title = {Quantitative imaging and semiotic phenotyping of mitochondrial network morphology in live human cells.},
journal = {PloS one},
volume = {19},
number = {3},
pages = {e0301372},
pmid = {38547143},
issn = {1932-6203},
mesh = {Humans ; *Hydrogen Peroxide/pharmacology/metabolism ; *Mitochondria/metabolism ; Software ; Image Processing, Computer-Assisted/methods ; Algorithms ; },
abstract = {The importance of mitochondria in tissue homeostasis, stress responses and human diseases, combined to their ability to transition between various structural and functional states, makes them excellent organelles for monitoring cell health. There is therefore a need for technologies to accurately analyze and quantify changes in mitochondrial organization in a variety of cells and cellular contexts. Here we present an innovative computerized method that enables accurate, multiscale, fast and cost-effective analysis of mitochondrial shape and network architecture from confocal fluorescence images by providing more than thirty features. In order to facilitate interpretation of the quantitative results, we introduced two innovations: the use of Kiviat-graphs (herein named MitoSpider plots) to present highly multidimensional data and visualization of the various mito-cellular configurations in the form of morphospace diagrams (called MitoSigils). We tested our fully automated image analysis tool on rich datasets gathered from live normal human skin cells cultured under basal conditions or exposed to specific stress including UVB irradiation and pesticide exposure. We demonstrated the ability of our proprietary software (named MitoTouch) to sensitively discriminate between control and stressed dermal fibroblasts, and between normal fibroblasts and other cell types (including cancer tissue-derived fibroblasts and primary keratinocytes), showing that our automated analysis captures subtle differences in morphology. Based on this novel algorithm, we report the identification of a protective natural ingredient that mitigates the deleterious impact of hydrogen peroxide (H2O2) on mitochondrial organization. Hence we conceived a novel wet-plus-dry pipeline combining cell cultures, quantitative imaging and semiotic analysis for exhaustive analysis of mitochondrial morphology in living adherent cells. Our tool has potential for broader applications in other research areas such as cell biology and medicine, high-throughput drug screening as well as predictive and environmental toxicology.},
}
@article {pmid38543688,
year = {2024},
author = {Ramos-González, PL and Alexandre, MAV and Potsclam-Barro, M and Duarte, LML and Michea Gonzalez, GL and Chabi-Jesus, C and Ramos, AF and Harakava, R and Lorenzi, H and Freitas-Astúa, J and Kitajima, EW},
title = {Two Novel Betarhabdovirins Infecting Ornamental Plants and the Peculiar Intracellular Behavior of the Cytorhabdovirus in the Liana Aristolochia gibertii.},
journal = {Viruses},
volume = {16},
number = {3},
pages = {},
pmid = {38543688},
issn = {1999-4915},
support = {PNPD20132154 - 33141010001P4 - PNPD - IBSP, 88882.157041/2017-01//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 17/50334-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/25078-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/02179-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {*Aristolochia/genetics ; *Mirabilis/genetics ; Genome, Viral ; *Rhabdoviridae ; Plants/genetics ; Phylogeny ; Plant Diseases ; },
abstract = {Two novel members of the subfamily Betarhabdovirinae, family Rhabdoviridae, were identified in Brazil. Overall, their genomes have the typical organization 3'-N-P-P3-M-G-L-5' observed in mono-segmented plant-infecting rhabdoviruses. In aristolochia-associated cytorhabdovirus (AaCV), found in the liana aristolochia (Aristolochia gibertii Hook), an additional short orphan ORF encoding a transmembrane helix was detected between P3 and M. The AaCV genome and inferred encoded proteins share the highest identity values, consistently < 60%, with their counterparts of the yerba mate chlorosis-associated virus (Cytorhabdovirus flaviyerbamate). The second virus, false jalap virus (FaJV), was detected in the herbaceous plant false jalap (Mirabilis jalapa L.) and represents together with tomato betanucleorhabdovirus 2, originally found in tomato plants in Slovenia, a tentative new species of the genus Betanucleorhabdovirus. FaJV particles accumulate in the perinuclear space, and electron-lucent viroplasms were observed in the nuclei of the infected cells. Notably, distinct from typical rhabdoviruses, most virions of AaCV were observed to be non-enclosed within membrane-bounded cavities. Instead, they were frequently seen in close association with surfaces of mitochondria or peroxisomes. Unlike FaJV, AaCV was successfully graft-transmitted to healthy plants of three species of the genus Aristolochia, while mechanical and seed transmission proved unsuccessful for both viruses. Data suggest that these viruses belong to two new tentative species within the subfamily Betarhabdovirinae.},
}
@article {pmid38540407,
year = {2024},
author = {Zhang, G and Jiao, Y and Zhao, Z and Chen, Q and Wang, Z and Zhu, J and Lv, N and Sun, G},
title = {Genome-Wide and Expression Pattern Analysis of the HIT4 Gene Family Uncovers the Involvement of GHHIT4_4 in Response to Verticillium Wilt in Gossypium hirsutum.},
journal = {Genes},
volume = {15},
number = {3},
pages = {},
pmid = {38540407},
issn = {2073-4425},
mesh = {*Gossypium/metabolism ; *Verticillium/genetics ; Phylogeny ; Disease Resistance/genetics ; Chromosome Mapping ; },
abstract = {Chromatin remodelers are essential for regulating plant growth, development, and responses to environmental stresses. HIT4 (HEAT-INTOLERANT 4) is a novel stress-induced chromatin remodeling factor that has been less studied in abiotic stress and stress resistance, particularly in cotton. In this study, we conducted a comprehensive analysis of the members of the HIT4 gene family in Gossypium hirsutum using bioinformatics methods, including phylogenetic relationships, gene organization, transcription profiles, phylogenetic connections, selection pressure, and stress response. A total of 18 HIT4 genes were identified in four cotton species, with six HIT4 gene members in upland cotton. Based on the evolutionary relationships shown in the phylogenetic tree, the 18 HIT4 protein sequences were classified into four distinct subgroups. Furthermore, we conducted chromosome mapping to determine the genomic locations of these genes and visually represented the structural characteristics of HIT4 in G. hirsutum. In addition, we predicted the regulatory elements in HIT4 in G. hirsutum and conducted an analysis of repetitive sequences and gene collinearity among HIT4 in four cotton species. Moreover, we calculated the Ka/Ks ratio for homologous genes to assess the selection pressure acting on HIT4. Using RNA-seq, we explored the expression patterns of HIT4 genes in G. hirsutum and Gossypium barbadense. Through weighted gene co-expression network analysis (WGCNA), we found that GHHIT4_4 belonged to the MEblue module, which was mainly enriched in pathways such as DNA replication, phagosome, pentose and glucuronate interconversions, steroid biosynthesis, and starch and sucrose metabolism. This module may regulate the mechanism of upland cotton resistance to Verticillium wilt through DNA replication, phagosome, and various metabolic pathways. In addition, we performed heterologous overexpression of GH_D11G0591 (GHHIT4_4) in tobacco, and the results showed a significant reduction in disease index compared to the wild type, with higher expression levels of disease resistance genes in the transgenic tobacco. After conducting a VIGS (virus-induced gene silencing) experiment in cotton, the results indicated that silencing GHHIT4_4 had a significant impact, the resistance to Verticillium wilt weakened, and the internode length of the plants significantly decreased by 30.7% while the number of true leaves increased by 41.5%. qRT-PCR analysis indicated that GHHIT4_4 mainly enhanced cotton resistance to Verticillium wilt by indirectly regulating the PAL, 4CL, and CHI genes. The subcellular localization results revealed that GHHIT4_4 was predominantly distributed in the mitochondria and nucleus. This study offers preliminary evidence for the involvement of the GHHIT4_4 in cotton resistance to Verticillium wilt and lays the foundation for further research on the disease resistance mechanism of this gene in cotton.},
}
@article {pmid38534456,
year = {2024},
author = {Casey, W and Kumaran, T and Massey, SE and Mishra, B},
title = {How Mitochondrial Signaling Games May Shape and Stabilize the Nuclear-Mitochondrial Symbiosis.},
journal = {Biology},
volume = {13},
number = {3},
pages = {},
pmid = {38534456},
issn = {2079-7737},
abstract = {The eukaryotic lineage has enjoyed a long-term "stable" mutualism between nucleus and mitochondrion, since mitochondrial endosymbiosis began about 2 billion years ago. This mostly cooperative interaction has provided the basis for eukaryotic expansion and diversification, which has profoundly altered the forms of life on Earth. While we ignore the exact biochemical details of how the alpha-proteobacterial ancestor of mitochondria entered into endosymbiosis with a proto-eukaryote, in more general terms, we present a signaling games perspective of how the cooperative relationship became established, and has been maintained. While games are used to understand organismal evolution, information-asymmetric games at the molecular level promise novel insights into endosymbiosis. Using a previously devised biomolecular signaling games approach, we model a sender-receiver information asymmetric game, in which the informed mitochondrial sender signals and the uninformed nuclear receiver may take actions (involving for example apoptosis, senescence, regeneration and autophagy/mitophagy). The simulation shows that cellularization is a stabilizing mechanism for Pareto efficient sender/receiver strategic interaction. In stark contrast, the extracellular environment struggles to maintain efficient outcomes, as senders are indifferent to the effects of their signals upon the receiver. Our hypothesis has translational implications, such as in cellular therapy, as mitochondrial medicine matures. It also inspires speculative conjectures about how an analogous human-AI endosymbiosis may be engineered.},
}
@article {pmid38531492,
year = {2024},
author = {López-Hervas, K and Santos, JC and Ron, SR and Betancourth-Cundar, M and Cannatella, DC and Tarvin, RD},
title = {Deep divergences among inconspicuously colored clades of Epipedobates poison frogs.},
journal = {Molecular phylogenetics and evolution},
volume = {195},
number = {},
pages = {108065},
doi = {10.1016/j.ympev.2024.108065},
pmid = {38531492},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Poison Frogs ; *Anura/genetics ; Mitochondria ; Ecuador ; },
abstract = {Poison frogs (Dendrobatidae) are famous for their aposematic species, having a combination of diverse color patterns and defensive skin toxins, yet most species in this family are inconspicuously colored and considered non-aposematic. Epipedobates is among the youngest genus-level clades of Dendrobatidae that includes both aposematic and inconspicuous species. Using Sanger-sequenced mitochondrial and nuclear markers, we demonstrate deep genetic divergences among inconspicuous species of Epipedobates but relatively shallow genetic divergences among conspicuous species. Our phylogenetic analysis includes broad geographic sampling of the inconspicuous lineages typically identified as E. boulengeri and E. espinosai, which reveals two putative new species, one in west-central Colombia (E. sp. 1) and the other in north-central Ecuador (E. aff. espinosai). We conclude that E. darwinwallacei is a junior subjective synonym of E. espinosai. We also clarify the geographic distributions of inconspicuous Epipedobates species including the widespread E. boulengeri. We provide a qualitative assessment of the phenotypic diversity in each nominal species, with a focus on the color and pattern of inconspicuous species. We conclude that Epipedobates contains eight known valid species, six of which are inconspicuous. A relaxed molecular clock analysis suggests that the most recent common ancestor of Epipedobates is ∼11.1 million years old, which nearly doubles previous estimates. Last, genetic information points to a center of species diversity in the Chocó at the southwestern border of Colombia with Ecuador. A Spanish translation of this text is available in the supplementary materials.},
}
@article {pmid38525035,
year = {2024},
author = {Krasovec, G and Horkan, HR and Quéinnec, &#xc9; and Chambon, JP},
title = {Intrinsic apoptosis is evolutionarily divergent among metazoans.},
journal = {Evolution letters},
volume = {8},
number = {2},
pages = {267-282},
pmid = {38525035},
issn = {2056-3744},
abstract = {Apoptosis is regulated cell death that depends on caspases. A specific initiator caspase is involved upstream of each apoptotic signaling pathway. Characterized in nematode, fly, and mammals, intrinsic apoptosis is considered to be ancestral, conserved among animals, and depends on shared initiators: caspase-9, Apaf-1 and Bcl-2. However, the biochemical role of mitochondria, the pivotal function of cytochrome c and the modality of caspase activation remain highly heterogeneous and hide profound molecular divergence among apoptotic pathways in animals. Uncovering the phylogenetic history of apoptotic actors, especially caspases, is crucial to shed light on the evolutionary history of intrinsic apoptosis. Here, we demonstrate with phylogenetic analyses that caspase-9, the fundamental key of intrinsic apoptosis, is deuterostome-specific, while caspase-2 is ancestral to bilaterians. Our analysis of Bcl-2 and Apaf-1 confirms heterogeneity in functional organization of apoptotic pathways in animals. Our results support emergence of distinct intrinsic apoptotic pathways during metazoan evolution.},
}
@article {pmid38503840,
year = {2024},
author = {Duran, DP and Laroche, RA and Roman, SJ and Godwin, W and Herrmann, DP and Bull, E and Egan, SP},
title = {Species delimitation, discovery and conservation in a tiger beetle species complex despite discordant genetic data.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6617},
pmid = {38503840},
issn = {2045-2322},
mesh = {Animals ; Phylogeny ; *DNA, Mitochondrial/genetics ; Mitochondria ; Biodiversity ; *Coleoptera/genetics ; Species Specificity ; },
abstract = {In an age of species declines, delineating and discovering biodiversity is critical for both taxonomic accuracy and conservation. In recent years, there has been a movement away from using exclusively morphological characters to delineate and describe taxa and an increase in the use of molecular markers to describe diversity or through integrative taxonomy, which employs traditional morphological characters, as well as genetic or other data. Tiger beetles are charismatic, of conservation concern, and much work has been done on the morphological delineation of species and subspecies, but few of these taxa have been tested with genetic analyses. In this study, we tested morphologically based taxonomic hypotheses of polymorphic tiger beetles in the Eunota circumpicta (LaFerté-Sénectère, 1841) species complex using multilocus genomic and mtDNA analyses. We find multiple cryptic species within the previous taxonomic concept of Eunota circumpicta, some of which were historically recognized as subspecies. We found that the mtDNA and genomic datasets did not identify the same taxonomic units and that the mtDNA was most at odds with all other genetic and morphological patterns. Overall, we describe new cryptic diversity, which raises important conservation concerns, and provide a working example for testing species and subspecies validity despite discordant data.},
}
@article {pmid38503345,
year = {2024},
author = {Nuryadi, H and Mandagi, IF and Masengi, KWA and Kusumi, J and Inomata, N and Yamahira, K},
title = {Evidence for hybridization-driven heteroplasmy maintained across generations in a ricefish endemic to a Wallacean ancient lake.},
journal = {Biology letters},
volume = {20},
number = {3},
pages = {20230385},
pmid = {38503345},
issn = {1744-957X},
mesh = {Humans ; Animals ; *Heteroplasmy ; Lakes ; Phylogeny ; *Oryzias/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Heteroplasmy, the presence of multiple mitochondrial DNA (mtDNA) haplotypes within cells of an individual, is caused by mutation or paternal leakage. However, heteroplasmy is usually resolved to homoplasmy within a few generations because of germ-line bottlenecks; therefore, instances of heteroplasmy are limited in nature. Here, we report heteroplasmy in the ricefish species Oryzias matanensis, endemic to Lake Matano, an ancient lake in Sulawesi Island, in which one individual was known to have many heterozygous sites in the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. In this study, we cloned the ND2 gene for some additional individuals with heterozygous sites and demonstrated that they are truly heteroplasmic. Phylogenetic analysis revealed that the extra haplotype within the heteroplasmic O. matanensis individuals clustered with haplotypes of O. marmoratus, a congeneric species inhabiting adjacent lakes. This indicated that the heteroplasmy originated from paternal leakage due to interspecific hybridization. The extra haplotype was unique and contained two non-synonymous substitutions. These findings demonstrate that this hybridization-driven heteroplasmy was maintained across generations for a long time to the extent that the extra mitochondria evolved within the new host.},
}
@article {pmid38502499,
year = {2024},
author = {Kuntz, M and Dimnet, L and Pullara, S and Moyet, L and Rolland, N},
title = {The Main Functions of Plastids.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2776},
number = {},
pages = {89-106},
pmid = {38502499},
issn = {1940-6029},
mesh = {*Plastids/metabolism ; *Mitochondria/genetics ; },
abstract = {Plastids are semi-autonomous organelles like mitochondria and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.},
}
@article {pmid38502495,
year = {2024},
author = {Maréchal, E},
title = {How Did Thylakoids Emerge in Cyanobacteria, and How Were the Primary Chloroplast and Chromatophore Acquired?.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2776},
number = {},
pages = {3-20},
pmid = {38502495},
issn = {1940-6029},
mesh = {Thylakoids/metabolism ; Chloroplasts/genetics/metabolism ; Photosynthesis/genetics ; *Cyanobacteria/genetics/metabolism ; Eukaryota ; *Chromatophores ; Symbiosis/genetics ; },
abstract = {The emergence of thylakoid membranes in cyanobacteria is a key event in the evolution of all oxygenic photosynthetic cells, from prokaryotes to eukaryotes. Recent analyses show that they could originate from a unique lipid phase transition rather than from a supposed vesicular budding mechanism. Emergence of thylakoids coincided with the great oxygenation event, more than two billion years ago. The acquisition of semi-autonomous organelles, such as the mitochondrion, the chloroplast, and, more recently, the chromatophore, is a critical step in the evolution of eukaryotes. They resulted from primary endosymbiotic events that seem to share general features, i.e., an acquisition of a bacterium/cyanobacteria likely via a phagocytic membrane, a genome reduction coinciding with an escape of genes from the organelle to the nucleus, and, finally, the appearance of an active system translocating nuclear-encoded proteins back to the organelles. An intense mobilization of foreign genes of bacterial origin, via horizontal gene transfers, plays a critical role. Some third partners, like Chlamydia, might have facilitated the transition from cyanobacteria to the early chloroplast. This chapter further details our current understanding of primary endosymbiosis, focusing on primary chloroplasts, thought to have appeared over a billion years ago, and the chromatophore, which appeared around a hundred years ago.},
}
@article {pmid38500026,
year = {2024},
author = {Yang, Y and Duan, C},
title = {Mitochondrial genome features and systematic evolution of diospyros kaki thunb 'Taishuu'.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {285},
pmid = {38500026},
issn = {1471-2164},
support = {YCKJ-2021021//Modern Agriculture Project of Yuncheng/ ; YCKJ-2021021//Modern Agriculture Project of Yuncheng/ ; },
mesh = {*Diospyros/genetics ; *Genome, Mitochondrial ; Repetitive Sequences, Nucleic Acid ; Codon, Terminator ; RNA, Transfer/genetics ; Phylogeny ; },
abstract = {BACKGROUND: 'Taishuu' has a crisp texture, abundant juice, and sweet flavor with hints of cantaloupe. The availability of mitochondrial genome data of Diospyros species is far from the known number of species.<br><br>RESULTS: The sequencing data were assembled into a closed circular mitochondrial chromosome with a 421,308&#xa0;bp length and a 45.79% GC content. The mitochondrial genome comprised 40 protein-coding, 24 tRNA, and three rRNA genes. The most common codons for arginine (Arg), proline (Pro), glycine (Gly), tryptophan (Trp), valine (Val), alanine (Ala), and leucine (Leu) were AGA, CCA, GGA, UGG, GUA, GCA, and CUA, respectively. The start codon for cox1 and nad4L protein-coding genes was ACG (ATG), whereas the remaining protein-coding genes started with ATG. There are four types of stop codons: CGA, TAA, TAG, and TGA, with TAA being the most frequently used stop codon (45.24%). In the D. kaki Thunb. 'Taishuu' mitochondrial genome, a total of 645 repeat sequences were identified, including 125 SSRs, 7 tandem repeats, and 513 dispersed repeats. Collinearity analysis revealed a close relationship between D. kaki Thunb. 'Taishuu' and Diospyros oleifera, with conserved homologous gene fragments shared among these species in large regions of the mitochondrial genome. The protein-coding genes ccmB and nad4L were observed to undergo positive selection. Analysis of homologous sequences between chloroplasts and mitochondria identified 28 homologous segments, with a total length of 24,075&#xa0;bp, accounting for 5.71% of the mitochondrial genome. These homologous segments contain 8 annotated genes, including 6 tRNA genes and 2 protein-coding genes (rrn18 and ccmC). There are 23 homologous genes between chloroplasts and nuclei. Mitochondria, chloroplasts, and nuclei share two homologous genes, which are trnV-GAC and trnW-CCA.<br><br>CONCLUSION: In conclusion, a high-quality chromosome-level draft genome for D. kaki was generated in this study, which will contribute to further studies of major economic traits in the genus Diospyros.},
}
@article {pmid38493987,
year = {2024},
author = {Wang, S and Li, Y and Jiang, K and Zhou, J and Chen, J and Liang, J and Ndoni, A and Xue, H and Ye, Z and Bu, W},
title = {Identifying a potentially invasive population in the native range of a species: The enlightenment from the phylogeography of the yellow spotted stink bug, Erthesina fullo (Hemiptera: Pentatomidae).},
journal = {Molecular phylogenetics and evolution},
volume = {195},
number = {},
pages = {108056},
doi = {10.1016/j.ympev.2024.108056},
pmid = {38493987},
issn = {1095-9513},
mesh = {Animals ; Phylogeography ; Phylogeny ; *Heteroptera/genetics ; Biological Evolution ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Genetic Variation ; },
abstract = {The yellow spotted stink bug (YSSB), Erthesina fullo (Thunberg, 1783) is an important Asian pest that has recently successfully invaded Europe and an excellent material for research on the initial stage of biological invasion. Here, we reported the native evolutionary history, recent invasion history, and potential invasion threats of YSSB for the first time based on population genetic methods [using double digest restriction-site associated DNA (ddRAD) data and mitochondrial COI and CYTB] and ecological niche modelling. The results showed that four lineages (east, west, southwest, and Hainan Island) were established in the native range with a strong east-west differentiation phylogeographical structure, and the violent climate fluctuation might cause population divergence during the Middle and Upper Pleistocene. In addition, land bridges and monsoon promote dispersal and directional genetic exchanging between island populations and neighboring continental populations. The east lineage (EA) was identified as the source of invasion in Albania. EA had the widest geographical distribution among all other lineages, with a star-like haplotype network with the main haplotype as the core. It also had a rapid population expansion history, indicating that the source lineage might have stronger diffusion ability and adaptability. Our findings provided a significant biological basis for fine tracking of invasive source at the lineage or population level and promote early invasion warning of potential invasive species on a much subtler lineage level.},
}
@article {pmid38492251,
year = {2024},
author = {Keeling, PJ and Mtawali, M and Trznadel, M and Livingston, SJ and Wakeman, KC},
title = {Parallel functional reduction in the mitochondria of apicomplexan parasites.},
journal = {European journal of protistology},
volume = {94},
number = {},
pages = {126065},
doi = {10.1016/j.ejop.2024.126065},
pmid = {38492251},
issn = {1618-0429},
mesh = {*Apicomplexa/genetics/physiology/classification ; *Mitochondria/genetics ; Biological Evolution ; },
abstract = {Extreme functional reduction of mitochondria has taken place in parallel in many distantly related lineages of eukaryotes, leading to a number of recurring metabolic states with variously lost electron transport chain (ETC) complexes, loss of the tricarboxylic acid (TCA) cycle, and/or loss of the mitochondrial genome. The resulting mitochondria-related organelles (MROs) are generally structurally reduced and in the most extreme cases barely recognizable features of the cell with no role in energy metabolism whatsoever (e.g., mitosomes, which generally only make iron-sulfur clusters). Recently, a wide diversity of MROs were discovered to be hiding in plain sight: in gregarine apicomplexans. This diverse group of invertebrate parasites has been known and observed for centuries, but until recent applications of culture-free genomics, their mitochondria were unremarkable. The genomics, however, showed that mitochondrial function has reduced in parallel in multiple gregarine lineages to several different endpoints, including the most reduced mitosomes. Here we review this remarkable case of parallel evolution of MROs, and some of the interesting questions this work raises.},
}
@article {pmid38485499,
year = {2024},
author = {Li, CY and Liu, XC and Li, YZ and Wang, Y and Nie, YH and Xu, YT and Zhang, XT and Lu, Y and Sun, Q},
title = {Generation of mitochondrial replacement monkeys by female pronucleus transfer.},
journal = {Zoological research},
volume = {45},
number = {2},
pages = {292-298},
pmid = {38485499},
issn = {2095-8137},
mesh = {Mice ; Humans ; Female ; Animals ; *Mitochondrial Diseases/genetics/prevention &amp; control/veterinary ; Haplorhini/genetics ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Primates/genetics ; *Rodent Diseases ; },
abstract = {Mutations in mitochondrial DNA (mtDNA) are maternally inherited and have the potential to cause severe disorders. Mitochondrial replacement therapies, including spindle, polar body, and pronuclear transfers, are promising strategies for preventing the hereditary transmission of mtDNA diseases. While pronuclear transfer has been used to generate mitochondrial replacement mouse models and human embryos, its application in non-human primates has not been previously reported. In this study, we successfully generated four healthy cynomolgus monkeys (Macaca fascicularis) via female pronuclear transfer. These individuals all survived for more than two years and exhibited minimal mtDNA carryover (3.8%-6.7%), as well as relatively stable mtDNA heteroplasmy dynamics during development. The successful establishment of this non-human primate model highlights the considerable potential of pronuclear transfer in reducing the risk of inherited mtDNA diseases and provides a valuable preclinical research model for advancing mitochondrial replacement therapies in humans.},
}
@article {pmid38485105,
year = {2024},
author = {Na, I and Campos, C and Lax, G and Kwong, WK and Keeling, PJ},
title = {Phylogenomics reveals Adeleorina are an ancient and distinct subgroup of Apicomplexa.},
journal = {Molecular phylogenetics and evolution},
volume = {195},
number = {},
pages = {108060},
doi = {10.1016/j.ympev.2024.108060},
pmid = {38485105},
issn = {1095-9513},
mesh = {Animals ; Humans ; Phylogeny ; Plastids/genetics ; Genome ; *Apicomplexa/genetics ; *Genome, Plastid ; },
abstract = {Apicomplexans are a diverse phylum of unicellular eukaryotes that share obligate relationships with terrestrial and aquatic animal hosts. Many well-studied apicomplexans are responsible for several deadly zoonotic and human diseases, most notably malaria caused by Plasmodium. Interest in the evolutionary origin of apicomplexans has also spurred recent work on other more deeply-branching lineages, especially gregarines and sister groups like squirmids and chrompodellids. But a full picture of apicomplexan evolution is still lacking several lineages, and one major, diverse lineage that is notably absent is the adeleorinids. Adeleorina apicomplexans comprises hundreds of described species that infect invertebrate and vertebrate hosts across the globe. Although historically considered coccidians, phylogenetic trees based on limited data have shown conflicting branch positions for this subgroup, leaving this question unresolved. Phylogenomic trees and large-scale analyses comparing cellular functions and metabolism between major subgroups of apicomplexans have not incorporated Adeleorina because only a handful of molecular markers and a couple organellar genomes are available, ultimately excluding this group from contributing to our understanding of apicomplexan evolution and biology. To address this gap, we have generated complete genomes from mitochondria and plastids, as well as multiple deep-coverage single-cell transcriptomes of nuclear genes from two Adeleorina species, Klossia helicina and Legerella nova, and inferred a 206-protein phylogenomic tree of Apicomplexa. We observed distinct structures reported in species descriptions as remnant host structures surrounding adeleorinid oocysts. Klossia helicina and L. nova branched, as expected, with monoxenous adeleorinids within the Adeleorina and their mitochondrial and plastid genomes exhibited similarity to published organellar adeleorinid genomes. We show with a phylogeneomic tree and subsequent phylogenomic analyses that Adeleorina are not closely related to any of the currently sampled apicomplexan subgroups, and instead fall as a sister to a large clade encompassing Coccidia, Protococcidia, Hematozoa, and Nephromycida, collectively. This resolves Adeleorina as a key independently-branching group, separate from coccidians, on the tree of Apicomplexa, which now has all known major lineages sampled.},
}
@article {pmid38480360,
year = {2024},
author = {Ghamizi, M and Falniowski, A and Boudellah, A and Hofman, S and Rharras, AE and Assad, N and Moutaouakil, S and Jaszczyska, A},
title = {Two new genera and species of the valvatiform hydrobiid snails (Caenogastropoda: Truncatelloidea: Hydrobiidae) from Morocco.},
journal = {Zootaxa},
volume = {5418},
number = {3},
pages = {223-239},
doi = {10.11646/zootaxa.5418.3.2},
pmid = {38480360},
issn = {1175-5334},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; Morocco ; *Snails/genetics ; Phylogeny ; *Mitochondria/genetics ; },
abstract = {Stygobiont and crenobiont minute gastropods representing the family Hydrobiidae (Caenogastropoda: Truncatelloidea), characterized by the valvatoid low-spired shell, were collected from one spring and four wells in Bouregreg region, NW Morocco. The shells were photographed and measured; shell biometry is illustrated with principal component analysis. Penes were illustrated and described. Mitochondrial cytochrome oxidase subunit 1 (COI) and 16S rRNA, as well as nuclear 18S rRNA sequences were used to infer the phylogeny. The snails represented two genera, both new to science. Their closest relatives were taxa from the Iberian Peninsula, the rough molecular estimate of the time of divergence between these Moroccan and Iberian genera coincided with the Pliocene Flooding, which restored the Strait of Gibraltar to connect the Mediterranean Basin with Atlantic Ocean.},
}
@article {pmid38480282,
year = {2024},
author = {Gordon, DP and Quek, ZBR and Huang, D},
title = {Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa.},
journal = {Zootaxa},
volume = {5424},
number = {3},
pages = {323-357},
doi = {10.11646/zootaxa.5424.3.3},
pmid = {38480282},
issn = {1175-5334},
mesh = {Animals ; Phylogeny ; New Zealand ; RNA, Ribosomal, 18S/genetics ; Base Sequence ; *Mitochondria/genetics ; },
abstract = {All eight extant species ofRhabdopleuradescribed between 1869 and 2018 are provisionally accepted as valid based on a review of the literature and new data on two little-known species from the Azores. Additionally, four new species are described from the New Zealand region, increasing global diversity by 50%, and a dichotomous key to all 12 described species is provided based on morphological criteria. The distinction between colony morphologies based on erect-tube inception is regarded as particularly helpful in initial characterization of species. Erect ringed tubes are either produced directly from the surface of creeping-tubes or indirectly, i.e. a short adherent side branch from a creeping tube is interpolated between the creeping tube and an erect tube; such side branches are blind-ending. These two modes of erect-tube origination are here respectively termeddirectandindirect. Species with indirect erect-tube budding are predominant in the North Atlantic whereas species with direct erect-tube budding dominate in New Zealand waters. The only indirect-erect species from New Zealand, Rhabdopleura chathamica n. sp., was discovered on deepwater coral from 10081075 m, constituting the deepest record of the genus to date. Rhabdopleura emancipata n. sp., collected only in a detached state, constitutes a three-dimensional tangled growth that grew freely into the water columna unique morphology hitherto unknown among extant species. Owing to this growth mode, it provided a substratum for epibionts from several phyla. Rhabdopleura francesca n. sp. and Rhabdopleura decipula n. sp. are morphologically very similar but are distinguishable by their distinct placements in a phylogeny based on 16S mitochondrial and 18S nuclear rRNA genes. Phylogenetic reconstructions based on rRNA and mitochondrial genome data contribute to an updated phylogeny of all Rhabdopleura species sequenced thus far, some of which require more molecular sequences and morphological analyses for taxonomic determination.},
}
@article {pmid38480132,
year = {2024},
author = {Methou, P and Chen, C and Komai, T},
title = {Revision of the alvinocaridid shrimp genus Rimicaris Williams &amp; Rona, 1986 (Decapoda: Caridea) with description of a new species from the Mariana Arc hydrothermal vents.},
journal = {Zootaxa},
volume = {5406},
number = {4},
pages = {501-518},
doi = {10.11646/zootaxa.5406.4.1},
pmid = {38480132},
issn = {1175-5334},
mesh = {Animals ; Phylogeny ; *Hydrothermal Vents ; *Decapoda ; Mitochondria ; },
abstract = {A new species of alvinocaridid shrimp is reported, from the Northwest Eifuku hydrothermal vent field at 16191667 m depth on the Mariana Arc. A comprehensive phylogenetic reconstruction of Alvinocarididae based on the mitochondrial cytochrome c oxidase subunit I (COI) gene including this new species reveals the paraphyly of the genus Rimicaris Williams &amp; Rona, 1986 with four other generaAlvinocaridinides, Manuscaris, Opaepele, and Shinkaicarisnested within it. We re-examine material of these four problematic genera, and synonymise them under Rimicaris whose diagnosis has been amended, in order to maintain a monophyletic Rimicaris. Our new species, Rimicaris cambonae sp. nov. is genetically close to Rimicaris loihi (Williams &amp; Dobbs, 1995) comb. nov. (previously Opaepele loihi) with which it co-occurs, but can be morphologically distinguished by the less elevated dorsal surface of the rostrum, this being devoid of a median carina, a stronger pterygostomial tooth on the carapace, and a blunt rather than acuminate proximolateral process on the antennular stylocerite. Species previously assigned to the above listed, synonymized genera are also discussed, with new material examined for three key species: R. loihi, R. acuminata, and R. leurokolos. Further, Alvinocaridinides formosa Komai &amp; Chan, 2010 and Manuscaris liui Wang &amp; Sha, 2016 are synonymized under Rimicaris leurokolos (Kikuchi &amp; Hashimoto, 2000) comb. nov. and R. acuminata (Komai &amp; Tsuchida, 2015) comb. nov., respectively. Revised diagnoses are presented for R. loihi, R. acuminata, and R. leurokolos. After the present revision revision, Rimicaris now consists of 15 species.},
}
@article {pmid38475850,
year = {2024},
author = {Vesala, L and Basikhina, Y and Tuomela, T and Nurminen, A and Siukola, E and Vale, PF and Salminen, TS},
title = {Mitochondrial perturbation in immune cells enhances cell-mediated innate immunity in Drosophila.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {60},
pmid = {38475850},
issn = {1741-7007},
support = {RPG-2018-369//Leverhulme Trust/ ; 322732//Academy of Finland/ ; 328979//Academy of Finland/ ; 353367//Academy of Finland/ ; 3122800849//Sigrid Jus&#xe9;liuksen S&#xe4;&#xe4;ti&#xf6;/ ; },
mesh = {Animals ; Humans ; *Drosophila ; Drosophila melanogaster/metabolism ; *Wasps/genetics ; Mitochondria ; Immunity, Innate ; Hemocytes/metabolism ; },
abstract = {BACKGROUND: Mitochondria participate in various cellular processes including energy metabolism, apoptosis, autophagy, production of reactive oxygen species, stress responses, inflammation and immunity. However, the role of mitochondrial metabolism in immune cells and tissues shaping the innate immune responses are not yet fully understood. We investigated the effects of tissue-specific mitochondrial perturbation on the immune responses at the organismal level. Genes for oxidative phosphorylation (OXPHOS) complexes cI-cV were knocked down in the fruit fly Drosophila melanogaster, targeting the two main immune tissues, the fat body and the immune cells (hemocytes).<br><br>RESULTS: While OXPHOS perturbation in the fat body was detrimental, hemocyte-specific perturbation led to an enhanced immunocompetence. This was accompanied by the formation of melanized hemocyte aggregates (melanotic nodules), a sign of activation of cell-mediated innate immunity. Furthermore, the hemocyte-specific OXPHOS perturbation induced immune activation of hemocytes, resulting in an infection-like hemocyte profile and an enhanced immune response against parasitoid wasp infection. In addition, OXPHOS perturbation in hemocytes resulted in mitochondrial membrane depolarization and upregulation of genes associated with the mitochondrial unfolded protein response.<br><br>CONCLUSIONS: Overall, we show that while the effects of mitochondrial perturbation on immune responses are highly tissue-specific, mild mitochondrial dysfunction can be beneficial in immune-challenged individuals and contributes to variation in infection outcomes among individuals.},
}
@article {pmid38474079,
year = {2024},
author = {Mourokh, L and Friedman, J},
title = {Mitochondria at the Nanoscale: Physics Meets Biology-What Does It Mean for Medicine?.},
journal = {International journal of molecular sciences},
volume = {25},
number = {5},
pages = {},
pmid = {38474079},
issn = {1422-0067},
support = {Award # 66061-00 54//PSC-CUNY/ ; },
mesh = {Humans ; *Mitochondria/physiology ; *Mitochondrial Membranes/metabolism ; Proton Pumps/metabolism ; Physics ; Biology ; },
abstract = {Mitochondria are commonly perceived as "cellular power plants". Intriguingly, power conversion is not their only function. In the first part of this paper, we review the role of mitochondria in the evolution of eukaryotic organisms and in the regulation of the human body, specifically focusing on cancer and autism in relation to mitochondrial dysfunction. In the second part, we overview our previous works, revealing the physical principles of operation for proton-pumping complexes in the inner mitochondrial membrane. Our proposed simple models reveal the physical mechanisms of energy exchange. They can be further expanded to answer open questions about mitochondrial functions and the medical treatment of diseases associated with mitochondrial disorders.},
}
@article {pmid38468713,
year = {2024},
author = {Iverson, ENK},
title = {Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world.},
journal = {Evolutionary applications},
volume = {17},
number = {3},
pages = {e13642},
pmid = {38468713},
issn = {1752-4571},
abstract = {Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.},
}
@article {pmid38461774,
year = {2024},
author = {Diaz-Cuadros, M},
title = {Mitochondrial metabolism and the continuing search for ultimate regulators of developmental rate.},
journal = {Current opinion in genetics &amp; development},
volume = {86},
number = {},
pages = {102178},
doi = {10.1016/j.gde.2024.102178},
pmid = {38461774},
issn = {1879-0380},
mesh = {*Mitochondria/metabolism/genetics ; Animals ; *Embryonic Development/genetics ; *Gene Expression Regulation, Developmental/genetics ; Species Specificity ; Humans ; Protein Biosynthesis ; },
abstract = {The rate of embryonic development is a species-specific trait that depends on the properties of the intracellular environment, namely, the rate at which gene products flow through the central dogma of molecular biology. Although any given step in the production and degradation of gene products could theoretically be co-opted by evolution to modulate developmental speed, species are observed to accelerate or slow down all steps simultaneously. This suggests the rate of these molecular processes is jointly regulated by an upstream, ultimate factor. Mitochondrial metabolism was recently proposed to act as an ultimate regulator by controlling the pace of protein synthesis upstream of developmental tempo. Alternative candidates for ultimate regulators include species-specific gene expression levels of factors involved in the central dogma, as well as species-specific cell size. Overall, much work remains to be done before we can confidently identify the ultimate causes of species-specific developmental rates.},
}
@article {pmid38456969,
year = {2024},
author = {Ovciarikova, J and Shikha, S and Lacombe, A and Courjol, F and McCrone, R and Hussain, W and Maclean, A and Lemgruber, L and Martins-Duarte, ES and Gissot, M and Sheiner, L},
title = {Two ancient membrane pores mediate mitochondrial-nucleus membrane contact sites.},
journal = {The Journal of cell biology},
volume = {223},
number = {4},
pages = {},
pmid = {38456969},
issn = {1540-8140},
support = {/WT_/Wellcome Trust/United Kingdom ; 217173/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BB/N003675/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Eukaryotic Cells ; *Mitochondria/genetics/metabolism ; Mitochondria Associated Membranes ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/genetics/metabolism ; *Toxoplasma/cytology ; *Cell Nucleus/metabolism ; Nuclear Envelope/metabolism ; Nuclear Pore/metabolism ; Protozoan Proteins/metabolism ; },
abstract = {Coordination between nucleus and mitochondria is essential for cell survival, and thus numerous communication routes have been established between these two organelles over eukaryotic cell evolution. One route for organelle communication is via membrane contact sites, functional appositions formed by molecular tethers. We describe a novel nuclear-mitochondrial membrane contact site in the protozoan Toxoplasma gondii. We have identified specific contacts occurring at the nuclear pore and demonstrated an interaction between components of the nuclear pore and the mitochondrial protein translocon, highlighting them as molecular tethers. Genetic disruption of the nuclear pore or the TOM translocon components, TgNup503 or TgTom40, respectively, result in contact site reduction, supporting their potential involvement in this tether. TgNup503 depletion further leads to specific mitochondrial morphology and functional defects, supporting a role for nuclear-mitochondrial contacts in mediating their communication. The discovery of a contact formed through interaction between two ancient mitochondrial and nuclear complexes sets the ground for better understanding of mitochondrial-nuclear crosstalk in eukaryotes.},
}
@article {pmid38456649,
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 = {37},
number = {4},
pages = {442-450},
doi = {10.1093/jeb/voae027},
pmid = {38456649},
issn = {1420-9101},
support = {RPG-2018-369//Leverhulme Trust Research Project/ ; },
mesh = {Animals ; Female ; *Drosophila melanogaster/physiology ; *Mitochondria/genetics ; Longevity/genetics ; Genotype ; Fertility/genetics ; },
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 a sterile control and measured lifespan, fecundity, and locomotor activity. We observed mitotype-specific costs of immune stimulation and identified a positive genetic correlation between life span and the proportion of time cybrids spent moving while alive. Our results suggest 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 {pmid38449346,
year = {2024},
author = {Speijer, D},
title = {How mitochondrial cristae illuminate the important role of oxygen during eukaryogenesis.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {46},
number = {5},
pages = {e2300193},
doi = {10.1002/bies.202300193},
pmid = {38449346},
issn = {1521-1878},
mesh = {*Oxygen/metabolism ; *Mitochondria/metabolism/genetics ; *Mitochondrial Membranes/metabolism ; Animals ; Eukaryota/metabolism/genetics ; Adenosine Triphosphate/metabolism ; Biological Evolution ; Eukaryotic Cells/metabolism ; },
abstract = {Inner membranes of mitochondria are extensively folded, forming cristae. The observed overall correlation between efficient eukaryotic ATP generation and the area of internal mitochondrial inner membranes both in unicellular organisms and metazoan tissues seems to explain why they evolved. However, the crucial use of molecular oxygen (O2) as final acceptor of the electron transport chain is still not sufficiently appreciated. O2 was an essential prerequisite for cristae development during early eukaryogenesis and could be the factor allowing cristae retention upon loss of mitochondrial ATP generation. Here I analyze illuminating bacterial and unicellular eukaryotic examples. I also discuss formative influences of intracellular O2 consumption on the evolution of the last eukaryotic common ancestor (LECA). These considerations bring about an explanation for the many genes coming from other organisms than the archaeon and bacterium merging at the start of eukaryogenesis.},
}
@article {pmid38422090,
year = {2024},
author = {Yu, TS and Park, K and Han, KH and Kwak, IS},
title = {Morphological and genetic analysis for the diversity conservation of rare species, Thamnaconus multilineatus (Tetraodontiformes: Monacanthidae).},
journal = {PloS one},
volume = {19},
number = {2},
pages = {e0292916},
pmid = {38422090},
issn = {1932-6203},
mesh = {Animals ; *Tetraodontiformes ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria ; Biodiversity ; Endangered Species ; },
abstract = {Climate changes have altered biodiversity and ultimately induced community changes that have threatened the survival of certain aquatic organisms such as fish species. Obtaining biological and genetic information on endangered fish species is critical for ecological population management. Thamnaconus multilineatus, registered as an endangered species by the IUCN in 2019, is a Data Deficient (DD) species with a remarkably small number of habitats worldwide and no known information other than its habitat and external form. In this study, we characterized the external and osteological morphology of a T. multilineatus specimen collected from eastern Jeju Island, South Korea, in 2020. We also investigated the phylogenetic relationships among related fish species through complete mitochondrial DNA (mtDNA) analysis of the T. multilineatus specimen. The external and skeletal characteristics of T. multilineatus were similar to those of previous reports describing other fish of the genus Thamnaconus, making it difficult to classify T. multilineatus as a similar species based only on morphological characteristics. As a result of analyzing the complete mtDNA of T. multilineatus, the length of the mtDNA was determined to be 16,435 bp, and the mitochondrial genome was found to have 37 CDCs, including 13 PCGs, 22 tRNAs, and 2 rRNAs. In the phylogenetic analysis within the suborder Balistoidei, T. multilineatus mtDNA formed a cluster with fish of the genus Thamnaconus. This study is the first to report on the skeletal structure and complete mtDNA of T. multilineatus. Since the current research on T. multilineatus has only been reported on morphology, the results of this study will be utilized as important information for the management and restoration of T. multilineatus as an endangered species and significant fishery resource.},
}
@article {pmid38419371,
year = {2024},
author = {Chen, Z and Xie, X and Jia, C and Zhong, Q and Zhang, Q and Luo, D and Cao, Y and Mu, Y and Ren, C},
title = {Concentration-Driven Evolution of Adaptive Artificial Ion Channels or Nanopores with Specific Anticancer Activities.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {63},
number = {17},
pages = {e202318811},
doi = {10.1002/anie.202318811},
pmid = {38419371},
issn = {1521-3773},
support = {22271240//National Natural Science Foundation of China/ ; JCYJ20210324123411030//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; JCYJ20220530143206013//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; },
mesh = {Humans ; *Nanopores ; Ion Channels ; Organophosphorus Compounds/chemistry ; Doxorubicin/chemistry ; },
abstract = {In nature, ceramides are a class of sphingolipids possessing a unique ability to self-assemble into protein-permeable channels with intriguing concentration-dependent adaptive channel cavities. However, within the realm of artificial ion channels, this interesting phenomenon is scarcely represented. Herein, we report on a novel class of adaptive artificial channels, Pn-TPPs, based on PEGylated cholic acids bearing triphenylphosphonium (TPP) groups as anion binding motifs. Interestingly, the molecules self-assemble into chloride ion channels at low concentrations while transforming into small molecule-permeable nanopores at high concentrations. Moreover, the TPP groups endow the molecules with mitochondria-targeting properties, enabling them to selectively drill holes on the mitochondrial membrane of cancer cells and subsequently trigger the caspase 9 apoptotic pathway. The anticancer efficacies of Pn-TPPs correlate with their abilities to form nanopores. Significantly, the most active ensembles formed by P5-TPP exhibits impressive anticancer activity against human liver cancer cells, with an IC50 value of 3.8 μM. While demonstrating similar anticancer performance to doxorubicin, P5-TPP exhibits a selectivity index surpassing that of doxorubicin by a factor of 16.8.},
}
@article {pmid38413922,
year = {2024},
author = {Xu, L and Wang, J and Zhang, T and Xiao, H and Wang, H},
title = {Characterizing complete mitochondrial genome of Aquilegia amurensis and its evolutionary implications.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {142},
pmid = {38413922},
issn = {1471-2229},
support = {nos. 32070244//National Natural Science Foundation of China/ ; nos.32300187//National Natural Science Foundation of China/ ; },
mesh = {Phylogeny ; *Aquilegia/genetics ; *Genome, Mitochondrial/genetics ; Mitochondria/genetics ; RNA, Transfer/genetics ; },
abstract = {BACKGROUND: Aquilegia is a model system for studying the evolution of adaptive radiation. However, very few studies have been conducted on the Aquilegia mitochondrial genome. Since mitochondria play a key role in plant adaptation to abiotic stress, analyzing the mitochondrial genome may provide a new perspective for understanding adaptive evolution.<br><br>RESULTS: The Aquilegia amurensis mitochondrial genome was characterized by a circular chromosome and two linear chromosomes, with a total length of 538,736&#xa0;bp; the genes included 33 protein-coding genes, 24 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. We subsequently conducted a phylogenetic analysis based on single nucleotide polymorphisms (SNPs) in the mitochondrial genomes of 18 Aquilegia species, which were roughly divided into two clades: the European-Asian clade and the North American clade. Moreover, the genes mttB and rpl5 were shown to be positively selected in European-Asian species, and they may help European and Asian species adapt to environmental changes.<br><br>CONCLUSIONS: In this study, we assembled and annotated the first mitochondrial genome of the adaptive evolution model plant Aquilegia. The subsequent analysis provided us with a basis for further molecular studies on Aquilegia mitochondrial genomes and valuable information on adaptive evolution in Aquilegia.},
}
@article {pmid38411741,
year = {2024},
author = {Cardoso, DC and Baldez, BCL and Pereira, AH and Kalapothakis, E and Rosse, IC and Cristiano, MP},
title = {De novo assembly of the complete mitochondrial genome of Mycetophylax simplex Emery, 1888 through organelle targeting revels no substantial expansion of gene spacers, but rather some slightly shorter genes.},
journal = {Molecular genetics and genomics : MGG},
volume = {299},
number = {1},
pages = {16},
pmid = {38411741},
issn = {1617-4623},
support = {PPM199-18//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Animals ; *Genome, Mitochondrial/genetics ; Ecosystem ; Bayes Theorem ; Phylogeny ; Mitochondria/genetics ; *Ants/genetics ; },
abstract = {Mitochondria play a key role in cell biology and have their own genome, residing in a highly oxidative environment that induces faster changes than the nuclear genome. Because of this, mitochondrial markers have been exploited to reconstruct phylogenetic and phylogeographic relationships in studies of adaptation and molecular evolution. In this study, we determined the complete mitogenome of the fungus-farming ant Mycetophylax simplex (Hymenoptera, Formicidae) and conducted a comparative analysis among 29 myrmicine ant mitogenomes. Mycetophylax simplex is an endemic ant that inhabits sand dunes along the southern Atlantic coast. Specifically, the species occur in the ecosystem known as "restinga", within the Atlantic Forest biome. Due to habitat degradation, land use and decline of restinga habitats, the species is considered locally extinct in extremely urban beaches and is listed as vulnerable on the Brazilian Red List (ICMBio). We employed a mitochondrion-targeting approach to obtain the complete mitogenome through high-throughput DNA sequencing technology. This method allowed us to determine the mitogenome with high performance, coverage and low cost. The circular mitogenome has a length of 16,367 base pairs enclosing 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) along with one control region (CR). All the protein-coding genes begin with a typical ATN codon and end with the canonical stop codons. All tRNAs formed the fully paired acceptor stems and fold into the typical cloverleaf-shaped secondary structures. The gene order is consistent with the shared Myrmicinae structure, and the A + T content of the majority strand is 81.51%. Long intergenic spacers were not found but some gene are slightly shorter. The phylogenetic relationships based on concatenated nucleotide and amino acid sequences of the 13 protein-coding genes, using Maximum Likelihood and Bayesian Inference methods, indicated that mitogenome sequences were useful in resolving higher-level relationship within Formicidae.},
}
@article {pmid38411429,
year = {2024},
author = {Selosse, MA},
title = {[Mitochondria, organelles or bacteria?].},
journal = {Medecine sciences : M/S},
volume = {40},
number = {2},
pages = {197-198},
doi = {10.1051/medsci/2024001},
pmid = {38411429},
issn = {1958-5381},
mesh = {Humans ; *Mitochondria ; *Bacteria ; },
}
@article {pmid38402551,
year = {2024},
author = {Xu, R and Li, T and Luo, J and Zhang, X and Wang, T and Wang, Y and Ma, Y and Yang, B and Jia, J and Dmytriw, AA and Li, W and Jiao, L},
title = {PCSK9 increases vulnerability of carotid plaque by promoting mitochondrial dysfunction and apoptosis of vascular smooth muscle cells.},
journal = {CNS neuroscience &amp; therapeutics},
volume = {30},
number = {2},
pages = {e14640},
pmid = {38402551},
issn = {1755-5949},
support = {DFL20220702//Beijing Hospitals Authority's Ascent Plan/ ; 82171303//National Natural Science Foundation of China/ ; Z201100005520019//Beijing Scientific and Technologic Project/ ; Z201100005520020//Beijing Scientific and Technologic Project/ ; 7244353//Beijing Municipal Natural Science Foundation/ ; },
mesh = {Humans ; *Muscle, Smooth, Vascular ; Proprotein Convertase 9/genetics ; Apoptosis ; *Mitochondrial Diseases ; },
abstract = {BACKGROUND: Proprotein convertase subtilisin/kexin type 9 (PCSK9) has been recognized as a novel lipid-lowing target. Recent clinical studies suggested the value of inhibiting PCSK9 in decreasing the vulnerability of coronary plaques. However, the evidence of PCSK9-regulated evolution of unstable carotid plaques is unclear, which has limited the use of PCSK9 inhibitor in carotid plaques. This study aimed to determine the effect and molecular mechanisms of PCSK9 on vulnerability of carotid plaques, to provide potential therapeutic targets for stabilizing carotid plaques.<br><br>METHODS: The expression of PCSK9 in stable and unstable carotid plaques were examined in tissue and plasma. Human aortic vascular smooth muscle cells (VSMCs) and carotid VSMCs were employed to transfect lentivirus for overexpression and knockdown of PCSK9, respectively. Morphological and functional changes of mitochondria were observed by live-cell imaging. Cell apoptosis was evaluated by propidium iodide staining. RNA-sequencing and biological examinations were performed to explore and validate the underlying mechanisms. Truncated plasmids were employed to identify the functional domain of PCSK9 in regulation of VSMCs' mitochondrial morphology, function and apoptosis.<br><br>RESULTS: Clinically, PCSK9 was closely related with vulnerability of human carotid plaques. Increased expression of PCSK9 in human VSMCs was accompanied by higher level of apoptosis. At subcellular level of VSMCs, the morphology of mitochondria was shifted toward the fission state, followed by mitochondrial dysfunction. Inhibition of p38 MAPK activation partially rescued the above morphological and behavioral changes caused by PCSK9. Furthermore, inhibiting of dynamin-related protein 1 (DRP1) attenuated PCSK9-related mitochondrial dysfunction and cell apoptosis. The 1-149aa domain of PCSK9 protein was essential to achieve functional regulation to VSMCs.<br><br>CONCLUSION: Our findings demonstrated that PCSK9 induced morphology-related mitochondrial dysfunction and apoptosis of VSMCs, which may be related to increased vulnerability of carotid plaque.},
}
@article {pmid38402284,
year = {2024},
author = {Li, G and Zhang, H and Lin, Z and Li, H and Xu, G and Xu, Y and Ji, R and Luo, W and Qiu, Y and Qiu, S and Tang, H},
title = {Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {4547},
pmid = {38402284},
issn = {2045-2322},
mesh = {*Ipomoea batatas/genetics ; Phylogeny ; *Genome, Mitochondrial/genetics ; *Ipomoea/genetics ; *Genome, Chloroplast/genetics ; Chloroplasts/genetics ; Amino Acids/genetics ; RNA, Transfer/genetics ; },
abstract = {The increasing number of plant mitochondrial DNA genomes (mtDNA) sequenced reveals the extent of transfer from both chloroplast DNA genomes (cpDNA) and nuclear DNA genomes (nDNA). This study created a library and assembled the chloroplast and mitochondrial genomes of the leafy sweet potato better to understand the extent of mitochondrial and chloroplast gene transfer. The full-length chloroplast genome of the leafy sweet potato (OM808940) is 161,387 bp, with 132 genes annotated, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The mitochondrial genome (OM808941) was 269,578 bp in length and contained 69 functional genes, including 39 protein-coding genes, 6 rRNA genes, and 24 tRNA genes. 68 SSR loci were found in the leafy sweet potato organelle genome, including 54 in the chloroplast genome and 14 in the mitochondria genome. In the sweet potato mitochondrial genome, most genes have RNA editing sites, and the conversion ratio from hydrophilic amino acids to hydrophobic amino acids is the highest, reaching 47.12%. Horizontal transfer occurs in the sweet potato organelle genome and nuclear genome. 40 mitochondrial genome segments share high homology with 14 chloroplast genome segments, 33 of which may be derived from chloroplast genome horizontal transfer. 171 mitochondrial genome sequences come from the horizontal transfer of nuclear genome. The phylogenetic analysis of organelle genes revealed that the leafy sweet potato was closely related to the tetraploid wild species Ipomoea tabascana and the wild diploid species Ipomoea trifida.},
}
@article {pmid38391484,
year = {2024},
author = {Kan, S and Liao, X and Lan, L and Kong, J and Wang, J and Nie, L and Zou, J and An, H and Wu, Z},
title = {Cytonuclear Interactions and Subgenome Dominance Shape the Evolution of Organelle-Targeted Genes in the Brassica Triangle of U.},
journal = {Molecular biology and evolution},
volume = {41},
number = {3},
pages = {},
pmid = {38391484},
issn = {1537-1719},
mesh = {*Genome, Plant ; *Evolution, Molecular ; Mustard Plant/genetics ; Plastids/genetics ; Polyploidy ; },
abstract = {The interaction and coevolution between nuclear and cytoplasmic genomes are one of the fundamental hallmarks of eukaryotic genome evolution and, 2 billion yr later, are still major contributors to the formation of new species. Although many studies have investigated the role of cytonuclear interactions following allopolyploidization, the relative magnitude of the effect of subgenome dominance versus cytonuclear interaction on genome evolution remains unclear. The Brassica triangle of U features 3 diploid species that together have formed 3 separate allotetraploid species on similar evolutionary timescales, providing an ideal system for understanding the contribution of the cytoplasmic donor to hybrid polyploid. Here, we investigated the evolutionary pattern of organelle-targeted genes in Brassica carinata (BBCC) and 2 varieties of Brassica juncea (AABB) at the whole-genome level, with particular focus on cytonuclear enzyme complexes. We found partial evidence that plastid-targeted genes experience selection to match plastid genomes, but no obvious corresponding signal in mitochondria-targeted genes from these 2 separately formed allopolyploids. Interestingly, selection acting on plastid genomes always reduced the retention rate of plastid-targeted genes encoded by the B subgenome, regardless of whether the Brassica nigra (BB) subgenome was contributed by the paternal or maternal progenitor. More broadly, this study illustrates the distinct selective pressures experienced by plastid- and mitochondria-targeted genes, despite a shared pattern of inheritance and natural history. Our study also highlights an important role for subgenome dominance in allopolyploid genome evolution, even in genes whose function depends on separately inherited molecules.},
}
@article {pmid38381321,
year = {2024},
author = {Liu, T and Ji, D and Li, X and Liu, J and Xu, F and Miao, Z and Chang, Y and Tian, M and Xu, C},
title = {Population genetics reveals new introgression in the nucleus herd of min pigs.},
journal = {Genes &amp; genomics},
volume = {46},
number = {4},
pages = {389-398},
pmid = {38381321},
issn = {2092-9293},
support = {LH2019C017//Natural Science Foundation of Heilongjiang Province/ ; 2022ZX02B10-2//Heilongjiang Provincial Key R&amp;D Program/ ; },
mesh = {Swine/genetics ; Animals ; *Genetic Variation ; *Genetics, Population ; Polymorphism, Genetic ; Mitochondria/genetics ; Heterozygote ; },
abstract = {OBJECTIVE: Min pigs are a unique genetic resource among local pig breeds in China. They have more excellent characteristics in cold and stress resistance, good meat quality, and a high reproductive rate. However, the genetic structure and driving factors remain unclear in the nucleus herd. In this study, the genetic diversity of Min pigs was studied to reveal the formation mechanism of its unique genetic structure. We hope to protect and develop the genetic resources of Min pigs.<br><br>METHODS: We analyzed different types of genes to identify the genetic structure and gene introgression pattern of Min pigs. The nuclear DNA dataset includes information on 21 microsatellite loci and 6 Y-chromosome genes, and the mitochondrial D-loop gene is selected to represent maternal lineages. The above genes are all from the nucleus herd of Min pigs.<br><br>RESULTS: The results of genetic structure identification and analysis of potential exogenous gene introgression patterns indicate that the nucleus herd of Min pigs maintains a high level of genetic diversity (polymorphism information content&#x2009;=&#x2009;0.713, expected heterozygosity&#x2009;=&#x2009;0.662, observed heterozygosity&#x2009;=&#x2009;0.612). Compared with other Asian pig breeds, the formation of Min pig breeds is more special. Gene introgression from European pig breeds to Min pigs has occurred, which is characterized by complete introgression of paternal genes and incomplete introgression of maternal genes.<br><br>CONCLUSION: Gene introgression caused by cross-breeding is not the main factor leading to the formation of the current genetic structure of Min pigs, but this process has increased the level of genetic diversity in the nucleus herd. Compared with the influence of gene introgression, our research suggest that artificial selection and environmental adaptive evolution make Min pigs form unique genetic characteristics.},
}
@article {pmid38378784,
year = {2024},
author = {Li, H and Akella, S and Engstler, C and Omini, JJ and Rodriguez, M and Obata, T and Carrie, C and Cerutti, H and Mower, JP},
title = {Recurrent evolutionary switches of mitochondrial cytochrome c maturation systems in Archaeplastida.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1548},
pmid = {38378784},
issn = {2041-1723},
support = {MCB 2212075//National Science Foundation (NSF)/ ; },
mesh = {Amino Acid Sequence ; *Cytochromes c/genetics/metabolism ; *Mitochondria/genetics/metabolism ; },
abstract = {Mitochondrial cytochrome c maturation (CCM) requires heme attachment via distinct pathways termed systems I and III. The mosaic distribution of these systems in Archaeplastida raises questions about the genetic mechanisms and evolutionary forces promoting repeated evolution. Here, we show a recurrent shift from ancestral system I to the eukaryotic-specific holocytochrome c synthase (HCCS) of system III in 11 archaeplastid lineages. Archaeplastid HCCS is sufficient to rescue mutants of yeast system III and Arabidopsis system I. Algal HCCS mutants exhibit impaired growth and respiration, and altered biochemical and metabolic profiles, likely resulting from deficient CCM and reduced cytochrome c-dependent respiratory activity. Our findings demonstrate that archaeplastid HCCS homologs function as system III components in the absence of system I. These results elucidate the evolutionary trajectory and functional divergence of CCM pathways in Archaeplastida, providing insight into the causes, mechanisms, and consequences of repeated cooption of an entire biological pathway.},
}
@article {pmid38368456,
year = {2024},
author = {Széliová, D and Müller, S and Zanghellini, J},
title = {Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {196},
pmid = {38368456},
issn = {2399-3642},
mesh = {*Escherichia coli/metabolism ; *Ribosomes/genetics/metabolism ; RNA, Ribosomal/genetics/metabolism ; Ribosomal Proteins/genetics/metabolism ; RNA/metabolism ; },
abstract = {Ribosomes are key to cellular self-fabrication and limit growth rate. While most enzymes are proteins, ribosomes consist of 1/3 protein and 2/3 ribonucleic acid (RNA) (in E. coli).Here, we develop a mechanistic model of a self-fabricating cell, validated across diverse growth conditions. Through resource balance analysis (RBA), we explore the variation in maximum growth rate with ribosome composition, assuming constant kinetic parameters.Our model highlights the importance of RNA instability. If we neglect it, RNA synthesis is always cheaper than protein synthesis, leading to an RNA-only ribosome at maximum growth rate. Upon accounting for RNA turnover, we find that a mixed ribosome composed of RNA and proteins maximizes growth rate. To account for RNA turnover, we explore two scenarios regarding the activity of RNases. In (a) degradation is proportional to RNA content. In (b) ribosomal proteins cooperatively mitigate RNA instability by protecting it from misfolding and subsequent degradation. In both cases, higher protein content elevates protein synthesis costs and simultaneously lowers RNA turnover expenses, resulting in mixed RNA-protein ribosomes. Only scenario (b) aligns qualitatively with experimental data across varied growth conditions.Our research provides fresh insights into ribosome biogenesis and evolution, paving the way for understanding protein-rich ribosomes in archaea and mitochondria.},
}
@article {pmid38363119,
year = {2024},
author = {Tetzlaff, S and Hillebrand, A and Drakoulis, N and Gluhic, Z and Maschmann, S and Lyko, P and Wicke, S and Schmitz-Linneweber, C},
title = {Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {38363119},
issn = {2050-084X},
support = {IRTG2290-B01//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Genome, Mitochondrial ; Mitochondrial Ribosomes/metabolism ; Escherichia coli/genetics ; RNA, Ribosomal/metabolism ; RNA, Messenger/genetics ; *RNA, Small Untranslated/genetics/metabolism ; Recombination, Genetic ; },
abstract = {The mitochondrial genomes of apicomplexans comprise merely three protein-coding genes, alongside a set of thirty to forty genes encoding small RNAs (sRNAs), many of which exhibit homologies to rRNA from E. coli. The expression status and integration of these short RNAs into ribosomes remains unclear and direct evidence for active ribosomes within apicomplexan mitochondria is still lacking. In this study, we conducted small RNA sequencing on the apicomplexan Toxoplasma gondii to investigate the occurrence and function of mitochondrial sRNAs. To enhance the analysis of sRNA sequencing outcomes, we also re-sequenced the T. gondii mitochondrial genome using an improved organelle enrichment protocol and Nanopore sequencing. It has been established previously that the T. gondii genome comprises 21 sequence blocks that undergo recombination among themselves but that their order is not entirely random. The enhanced coverage of the mitochondrial genome allowed us to characterize block combinations at increased resolution. Employing this refined genome for sRNA mapping, we find that many small RNAs originated from the junction sites between protein-coding blocks and rRNA sequence blocks. Surprisingly, such block border sRNAs were incorporated into polysomes together with canonical rRNA fragments and mRNAs. In conclusion, apicomplexan ribosomes are active within polysomes and are indeed assembled through the integration of sRNAs, including previously undetected sRNAs with merged mRNA-rRNA sequences. Our findings lead to the hypothesis that T. gondii's block-based genome organization enables the dual utilization of mitochondrial sequences as both messenger RNAs and ribosomal RNAs, potentially establishing a link between the regulation of rRNA and mRNA expression.},
}
@article {pmid38361280,
year = {2024},
author = {Degli Esposti, M},
title = {Did mitophagy follow the origin of mitochondria?.},
journal = {Autophagy},
volume = {20},
number = {5},
pages = {985-993},
pmid = {38361280},
issn = {1554-8635},
mesh = {*Mitophagy/physiology ; *Mitochondria/metabolism ; Humans ; Animals ; Prohibitins ; Mitochondrial Membranes/metabolism ; Signal Transduction ; },
abstract = {Mitophagy is the process of selective autophagy that removes superfluous and dysfunctional mitochondria. Mitophagy was first characterized in mammalian cells and is now recognized to follow several pathways including basal forms in specific organs. Mitophagy pathways are regulated by multiple, often interconnected factors. The present review aims to streamline this complexity and evaluate common elements that may define the evolutionary origin of mitophagy. Key issues surrounding mitophagy signaling at the mitochondrial surface may fundamentally derive from mitochondrial membrane dynamics. Elements of such membrane dynamics likely originated during the endosymbiosis of the alphaproteobacterial ancestor of our mitochondria but underwent an evolutionary leap forward in basal metazoa that determined the currently known variations in mitophagy signaling.Abbreviations: AGPAT, 1-acylglycerol-3-phosphate O-acyltransferase; ATG, autophagy related; BCL2L13, BCL2 like 13; BNIP3, BCL2 interacting protein 3; BNIP3L, BCL2 interacting protein 3 like; CALCOCO, calcium binding and coiled-coil domain; CL, cardiolipin; ER, endoplasmic reticulum; ERMES, ER-mitochondria encounter structure; FBXL4, F-box and leucine rich repeat protein 4; FUNDC1, FUN14 domain containing 1; GABARAPL1, GABA type A receptor associated protein like 1; HIF, hypoxia inducible factor; IMM, inner mitochondrial membrane; LBPA/BMP, lysobisphosphatidic acid; LIR, LC3-interacting region; LPA, lysophosphatidic acid; MAM, mitochondria-associated membranes; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MCL, monolysocardiolipin; ML, maximum likelihood; NBR1, NBR1 autophagy cargo receptor; OMM, outer mitochondrial membrane; PA, phosphatidic acid; PACS2, phosphofurin acidic cluster sorting protein 2; PC/PLC, phosphatidylcholine; PE, phosphatidylethanolamine; PHB2, prohibitin 2; PINK1, PTEN induced kinase 1; PtdIns, phosphatidylinositol; SAR, Stramenopiles, Apicomplexa and Rhizaria; TAX1BP1, Tax1 binding protein 1; ULK1, unc-51 like autophagy activating kinase 1; VDAC/porin, voltage dependent anion channel.},
}
@article {pmid38361161,
year = {2024},
author = {Serrano, IM and Hirose, M and Valentine, CC and Roesner, S and Schmidt, E and Pratt, G and Williams, L and Salk, J and Ibrahim, S and Sudmant, PH},
title = {Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout ageing.},
journal = {Nature ecology &amp; evolution},
volume = {8},
number = {5},
pages = {1021-1034},
pmid = {38361161},
issn = {2397-334X},
support = {R35GM142916//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; N/A//Vallee Foundation (Bert L. &amp; N. Kuggie Vallee Foundation)/ ; R35 GM142916/GM/NIGMS NIH HHS/United States ; 2146752//NSF | Directorate for Education &amp; Human Resources | Division of Graduate Education (DGE)/ ; N/A//Ford Foundation/ ; 1752814//NSF | Directorate for Education &amp; Human Resources | Division of Graduate Education (DGE)/ ; },
mesh = {Animals ; *Haplotypes ; *Aging/genetics ; *Mutation ; *Selection, Genetic ; Mice ; *Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; Cell Nucleus/genetics ; Female ; Mitochondria/genetics ; Mice, Inbred C57BL ; Male ; },
abstract = {Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in the female germline. Here we investigate how mismatching between nuclear and mitochondrial ancestry impacts the somatic evolution of the mitochondrial genome in different tissues throughout ageing. We used ultrasensitive duplex sequencing to profile ~2.5 million mitochondrial genomes across five mitochondrial haplotypes and three tissues in young and aged mice, cataloguing ~1.2 million mitochondrial somatic and ultralow-frequency inherited mutations, of which 81,097 are unique. We identify haplotype-specific mutational patterns and several mutational hotspots, including at the light strand origin of replication, which consistently exhibits the highest mutation frequency. We show that rodents exhibit a distinct mitochondrial somatic mutational spectrum compared with primates with a surfeit of reactive oxygen species-associated G > T/C > A mutations, and that somatic mutations in protein-coding genes exhibit signatures of negative selection. Lastly, we identify an extensive enrichment in somatic reversion mutations that 're-align' mito-nuclear ancestry within an organism's lifespan. Together, our findings demonstrate that mitochondrial genomes are a dynamically evolving subcellular population shaped by somatic mutation and selection throughout organismal lifetimes.},
}
@article {pmid38351074,
year = {2024},
author = {Choudhury, C and Gill, MK and McAleese, CE and Butcher, NJ and Ngo, ST and Steyn, FJ and Minchin, RF},
title = {The Arylamine N-Acetyltransferases as Therapeutic Targets in Metabolic Diseases Associated with Mitochondrial Dysfunction.},
journal = {Pharmacological reviews},
volume = {76},
number = {2},
pages = {300-320},
doi = {10.1124/pharmrev.123.000835},
pmid = {38351074},
issn = {1521-0081},
mesh = {Humans ; *Arylamine N-Acetyltransferase/genetics/metabolism ; Acetyltransferases/genetics/metabolism ; Substrate Specificity ; *Metabolic Diseases/drug therapy ; *Mitochondrial Diseases/drug therapy ; },
abstract = {In humans, there are two arylamine N-acetyltransferase genes that encode functional enzymes (NAT1 and NAT2) as well as one pseudogene, all of which are located together on chromosome 8. Although they were first identified by their role in the acetylation of drugs and other xenobiotics, recent studies have shown strong associations for both enzymes in a variety of diseases, including cancer, cardiovascular disease, and diabetes. There is growing evidence that this association may be causal. Consistently, NAT1 and NAT2 are shown to be required for healthy mitochondria. This review discusses the current literature on the role of both NAT1 and NAT2 in mitochondrial bioenergetics. It will attempt to relate our understanding of the evolution of the two genes with biologic function and then present evidence that several major metabolic diseases are influenced by NAT1 and NAT2. Finally, it will discuss current and future approaches to inhibit or enhance NAT1 and NAT2 activity/expression using small-molecule drugs. SIGNIFICANCE STATEMENT: The arylamine N-acetyltransferases (NATs) NAT1 and NAT2 share common features in their associations with mitochondrial bioenergetics. This review discusses mitochondrial function as it relates to health and disease, and the importance of NAT in mitochondrial function and dysfunction. It also compares NAT1 and NAT2 to highlight their functional similarities and differences. Both NAT1 and NAT2 are potential drug targets for diseases where mitochondrial dysfunction is a hallmark of onset and progression.},
}
@article {pmid38349189,
year = {2024},
author = {Lanza, A and Kimura, S and Hirono, I and Yoshitake, K and Kinoshita, S and Asakawa, S},
title = {Transcriptome analysis of Edwardsiella piscicida during intracellular infection reveals excludons are involved with the activation of a mitochondrion-like energy generation program.},
journal = {mBio},
volume = {15},
number = {3},
pages = {e0352623},
pmid = {38349189},
issn = {2150-7511},
support = {20H00429//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; //Toagosei (Toagosei Co., Ltd.)/ ; },
mesh = {Animals ; Zebrafish ; Phylogeny ; *Edwardsiella/genetics ; Gene Expression Profiling ; *Enterobacteriaceae Infections/microbiology ; *Fish Diseases/microbiology ; },
abstract = {Phylogenetic evidence suggests a shared ancestry between mitochondria and modern Proteobacteria, a phylum including several genera of intracellular pathogens. Studying these diverse pathogens, particularly during intracellular infection of their hosts, can reveal characteristics potentially representative of the mitochondrial-Proteobacterial ancestor by identifying traits shared with mitochondria. While transcriptomic approaches can provide global insights into intracellular acclimatization by pathogens, they are often limited by excess host RNAs in extracts. Here, we developed a method employing magnetic nanoparticles to enrich RNA from an intracellular Gammaproteobacterium, Edwardsiella piscicida, within zebrafish, Danio rerio, fin fibroblasts, enabling comprehensive exploration of the bacterial transcriptome. Our findings revealed that the intracellular E. piscicida transcriptome reflects a mitochondrion-like energy generation program characterized by the suppression of glycolysis and sugar transport, coupled with upregulation of the tricarboxylic acid (TCA) cycle and alternative import of simple organic acids that directly flux into TCA cycle intermediates or electron transport chain donors. Additionally, genes predicted to be members of excludons, loci of gene pairs antagonistically co-regulated by overlapping antisense transcription, are significantly enriched in the set of all genes with perturbed sense and antisense transcription, suggesting a general but important involvement of excludons with intracellular acclimatization. Notably, genes involved with the activation of the mitochondrion-like energy generation program, specifically with metabolite import and glycolysis, are also members of predicted excludons. Other intracellular Proteobacterial pathogens appear to employ a similar mitochondrion-like energy generation program, suggesting a potentially conserved mechanism for optimized energy acquisition from hosts centered around the TCA cycle.IMPORTANCEPhylogenetic evidence suggests that mitochondria and Proteobacteria, a phylum encompassing various intracellular pathogens, share a common ancestral lineage. In this study, we developed a novel method employing magnetic nanoparticles to explore the transcriptome of an aquatic Gammaproteobacterium, Edwardsiella piscicida, during intracellular infection of host cells. We show that the strategy E. piscicida uses to generate energy strikingly mirrors the function of mitochondria-energy generators devoid of glycolytic processes. Notably, several implicated genes are members of excludons-gene pairs antagonistically co-regulated by overlapping antisense transcription. Other intracellular Proteobacterial pathogens appear to adopt a similar mitochondrion-like energy generation program, indicating a possibly conserved strategy for optimized energy acquisition from hosts centered around the tricarboxylic acid cycle.},
}
@article {pmid38346534,
year = {2024},
author = {Fehsenfeld, S and Yoon, GR and Quijada-Rodriguez, AR and Kandachi-Toujas, H and Calosi, P and Breton, S and Weihrauch, D},
title = {Short-term exposure to high pCO2 leads to decreased branchial cytochrome C oxidase activity in the presence of octopamine in a decapod.},
journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology},
volume = {291},
number = {},
pages = {111603},
doi = {10.1016/j.cbpa.2024.111603},
pmid = {38346534},
issn = {1531-4332},
mesh = {Animals ; Hypercapnia/metabolism ; Electron Transport Complex IV/metabolism ; Octopamine/metabolism ; *Acidosis, Respiratory/metabolism ; *Decapoda ; *Brachyura/physiology ; Gills/metabolism ; },
abstract = {In a recent mechanistic study, octopamine was shown to promote proton transport over the branchial epithelium in green crabs, Carcinus maenas. Here, we follow up on this finding by investigating the involvement of octopamine in an environmental and physiological context that challenges acid-base homeostasis, the response to short-term high pCO2 exposure (400 Pa) in a brackish water environment. We show that hyperregulating green crabs experienced a respiratory acidosis as early as 6 h of exposure to hypercapnia, with a rise in hemolymph pCO2 accompanied by a simultaneous drop of hemolymph pH. The slightly delayed increase in hemolymph HCO3[-] observed after 24 h helped to restore hemolymph pH to initial values by 48 h. Circulating levels of the biogenic amine octopamine were significantly higher in short-term high pCO2 exposed crabs compared to control crabs after 48 h. Whole animal metabolic rates, intracellular levels of octopamine and cAMP, as well as branchial mitochondrial enzyme activities for complex I + III and citrate synthase were unchanged in posterior gill #7 after 48 h of hypercapnia. However, application of octopamine in gill respirometry experiments suppressed branchial metabolic rate in posterior gills of short-term high pCO2 exposed animals. Furthermore, branchial enzyme activity of cytochrome C oxidase decreased in high pCO2 exposed crabs after 48 h. Our results indicate that hyperregulating green crabs are capable of quickly counteracting a hypercapnia-induced respiratory acidosis. The role of octopamine in the acclimation of green crabs to short-term hypercapnia seems to entail the alteration of branchial metabolic pathways, possibly targeting mitochondrial cytochrome C in the gill. Our findings help advancing our current limited understanding of endocrine components in hypercapnia acclimation. SUMMARY STATEMENT: Acid-base compensation upon short-term high pCO2 exposure in hyperregulating green crabs started after 6 h and was accomplished by 48 h with the involvement of the biogenic amine octopamine, accumulation of hemolymph HCO3[-], and regulation of mitochondrial complex IV (cytochrome C oxidase).},
}
@article {pmid38337951,
year = {2024},
author = {Guan, J and Zhang, Z and Shi, G},
title = {Genome-Wide Identification of the Ferric Chelate Reductase (FRO) Gene Family in Peanut and Its Diploid Progenitors: Structure, Evolution, and Expression Profiles.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
pmid = {38337951},
issn = {2223-7747},
abstract = {The ferric chelate reductase (FRO) family plays a vital role in metal ion homeostasis in a variety of locations in the plants. However, little is known about this family in peanut (Arachis hypogaea). This study aimed to identify FRO genes from the genomes of peanut and the two diploid progenitors (A. duranensis and A. ipaensis) and to analyze their gene/protein structures and evolution. In addition, transcriptional responses of AhFRO genes to Fe deficiency and/or Cu exposure were investigated in two peanut cultivars with different Fe deficiency tolerance (Silihong and Fenghua 1). A total of nine, four, and three FRO genes were identified in peanut, A. duranensis, and A. ipaensis, respectively, which were divided into three groups. Most AhFRO genes underwent WGD/segmental duplication, leading to the expansion of the AhFRO gene family. In general, clustered members share similar gene/protein structures. However, significant divergences occurred in AhFRO2 genes. Three out of five AhFRO2 genes were lowly expressed in all tissues under normal conditions, which may be beneficial for avoiding gene loss. Transcription analysis revealed that AhFRO2 and AhFRO7 genes might be involved in the reduction of Fe/Cu in plasma membranes and plastids, respectively. AhFRO8 genes appear to confer Fe reduction in the mitochondria. Moreover, Fe deficiency induced an increase of Cu accumulation in peanut plants in which AhFRO2.2/2.4/2.5 and FRO7.1/7.2 might be involved. Our findings provided new clues for further understanding the roles of AhFRO genes in the Fe/Cu interaction in peanut.},
}
@article {pmid38332473,
year = {2024},
author = {Wang, Y and Li, H and Niu, G and Li, Y and Huang, Z and Cheng, S and Zhang, K and Li, H and Fu, Q and Jiang, Y},
title = {Boosting Sono-immunotherapy of Prostate Carcinoma through Amplifying Domino-Effect of Mitochondrial Oxidative Stress Using Biodegradable Cascade-Targeting Nanocomposites.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.3c12511},
pmid = {38332473},
issn = {1936-086X},
abstract = {Sono-immunotherapy faces challenges from poor immunogenicity and low response rate due to complex biological barriers. Herein, we prepared MCTH nanocomposites (NCs) consisting of disulfide bonds (S-S) doped mesoporous organosilica (MONs), Cu-modified protoporphyrin (CuPpIX), mitochondria-targeting triphenylphosphine (TPP), and CD44-targeting hyaluronic acid (HA). MCTH NCs efficiently accumulate at the tumor site due to the overexpressed CD44 receptors on the membrane of the cancer cells. Under the function of HAase and glutathione (GSH), MCTH degrades and exposes TPP to deliver CuPpIX to the mitochondrial site and induce a reactive oxygen species (ROS) burst in situ under ultrasound irradiations, thereby causing severe mitochondria dysfunction. This cascade-targeting ability of MCTH NCs not only reinforces oxidative stress in cancer cells but also amplifies immunogenic cell death (ICD) to stimulate the body's immune response and alleviate the tumor immunosuppressive microenvironment. These NCs significantly enhance the infiltration of immune cells into the tumor, particularly CD8[+] T cells, for a powerful antitumor sono-immunotherapy. The proposed cascade-targeting strategy holds promise for strengthening sono-immunotherapy for prostate cancer treatment and overcoming the limitations of traditional immunotherapy.},
}
@article {pmid38328137,
year = {2024},
author = {Iverson, ENK and Criswell, A and Havird, JC},
title = {Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38328137},
issn = {2692-8205},
support = {R35 GM142836/GM/NIGMS NIH HHS/United States ; },
abstract = {Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.},
}
@article {pmid38326590,
year = {2024},
author = {Murphy, MP and O'Neill, LAJ},
title = {A break in mitochondrial endosymbiosis as a basis for inflammatory diseases.},
journal = {Nature},
volume = {626},
number = {7998},
pages = {271-279},
pmid = {38326590},
issn = {1476-4687},
mesh = {Humans ; Autoimmune Diseases/etiology/metabolism/pathology ; Diet/adverse effects ; Homeostasis ; *Inflammation/etiology/metabolism/pathology ; *Mitochondria/metabolism/pathology/physiology ; Mitochondrial Proteins/metabolism ; *Models, Biological ; Nucleic Acids/metabolism ; Obesity/complications/metabolism/pathology ; Phospholipids/metabolism ; Reactive Oxygen Species/metabolism ; *Symbiosis/physiology ; Animals ; },
abstract = {Mitochondria retain bacterial traits due to their endosymbiotic origin, but host cells do not recognize them as foreign because the organelles are sequestered. However, the regulated release of mitochondrial factors into the cytosol can trigger cell death, innate immunity and inflammation. This selective breakdown in the 2-billion-year-old endosymbiotic relationship enables mitochondria to act as intracellular signalling hubs. Mitochondrial signals include proteins, nucleic acids, phospholipids, metabolites and reactive oxygen species, which have many modes of release from mitochondria, and of decoding in the cytosol and nucleus. Because these mitochondrial signals probably contribute to the homeostatic role of inflammation, dysregulation of these processes may lead to autoimmune and inflammatory diseases. A potential reason for the increased incidence of these diseases may be changes in mitochondrial function and signalling in response to such recent phenomena as obesity, dietary changes and other environmental factors. Focusing on the mixed heritage of mitochondria therefore leads to predictions for future insights, research paths and therapeutic opportunities. Thus, whereas mitochondria can be considered 'the enemy within' the cell, evolution has used this strained relationship in intriguing ways, with increasing evidence pointing to the recent failure of endosymbiosis being critical for the pathogenesis of inflammatory diseases.},
}
@article {pmid38325701,
year = {2024},
author = {Wang, C and Yu, X and Wang, J and Zhao, Z and Wan, J},
title = {Genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {51},
number = {6},
pages = {583-593},
doi = {10.1016/j.jgg.2024.01.007},
pmid = {38325701},
issn = {1673-8527},
mesh = {*Oryza/genetics ; *Hybrid Vigor/genetics ; *Reproductive Isolation ; *Plant Breeding/methods ; *Hybridization, Genetic ; Mitochondria/genetics ; },
abstract = {Heterosis, also known as hybrid vigor, is commonly observed in rice crosses. The hybridization of rice species or subspecies exhibits robust hybrid vigor, however, the direct harnessing of this vigor is hindered by reproductive isolation. Here, we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific hybrids. This review encompasses the genetic model of reproductive isolation within and among Oryza sativa species, emphasizing the essential role of mitochondria in this process. Additionally, we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes, elucidating their significant contribution to reproductive isolation. Furthermore, our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in rice. Building on these advances, we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.},
}
@article {pmid38316513,
year = {2024},
author = {Liu, X and You, Q and Liu, M and Bo, C and Zhu, Y and Duan, Y and Xue, J and Wang, D and Xue, T},
title = {Assembly and comparative analysis of the complete mitochondrial genome of Pinellia ternata.},
journal = {Functional plant biology : FPB},
volume = {51},
number = {},
pages = {},
doi = {10.1071/FP23256},
pmid = {38316513},
issn = {1445-4416},
mesh = {*Pinellia/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; *Plants, Medicinal/genetics ; Plant Tubers ; },
abstract = {Pinellia ternata is an important natural medicinal herb in China. However, it is susceptible to withering when exposed to high temperatures during growth, which limits its tuber production. Mitochondria usually function in stress response. The P . ternata mitochondrial (mt) genome has yet to be explored. Therefore, we integrated PacBio and Illumina sequencing reads to assemble and annotate the mt genome of P . ternata . The circular mt genome of P . ternata is 876 608bp in length and contains 38 protein-coding genes (PCGs), 20 tRNA genes and three rRNA genes. Codon usage, sequence repeats, RNA editing and gene migration from chloroplast (cp) to mt were also examined. Phylogenetic analysis based on the mt genomes of P . ternata and 36 other taxa revealed the taxonomic and evolutionary status of P . ternata . Furthermore, we investigated the mt genome size and GC content by comparing P . ternata with the other 35 species. An evaluation of non-synonymous substitutions and synonymous substitutions indicated that most PCGs in the mt genome underwent negative selection. Our results provide comprehensive information on the P . ternata mt genome, which may facilitate future research on the high-temperature response of P . ternata and provide new molecular insights on the Araceae family.},
}
@article {pmid38309455,
year = {2024},
author = {Miyakawa, Y and Otsuka, M and Shibata, C and Seimiya, T and Yamamoto, K and Ishibashi, R and Kishikawa, T and Tanaka, E and Isagawa, T and Takeda, N and Kamio, N and Imai, K and Fujishiro, M},
title = {Gut Bacteria-derived Membrane Vesicles Induce Colonic Dysplasia by Inducing DNA Damage in Colon Epithelial Cells.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {17},
number = {5},
pages = {745-767},
pmid = {38309455},
issn = {2352-345X},
mesh = {Mice ; Animals ; Humans ; *Colon/microbiology ; Reactive Oxygen Species ; Base Composition ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Induced Pluripotent Stem Cells ; Epithelial Cells ; Bacteria/genetics ; },
abstract = {BACKGROUND &amp; AIMS: Colorectal cancer (CRC) is the third most common cancer in the world. Gut microbiota has recently been implicated in the development of CRC. Actinomyces odontolyticus is one of the most abundant bacteria in the gut of patients with very early stages of CRC. A odontolyticus is an anaerobic bacterium existing principally in the oral cavity, similar to Fusobacterium nucleatum, which is known as a colon carcinogenic bacterium. Here we newly determined the biological functions of A odontolyticus on colonic oncogenesis.<br><br>METHODS: We examined the induction of intracellular signaling by A odontolyticus in human colonic epithelial cells (CECs). DNA damage levels in CECs were confirmed using the human induced pluripotent stem cell-derived gut organoid model and mouse colon tissues in&#xa0;vivo.<br><br>RESULTS: A odontolyticus secretes membrane vesicles (MVs), which induce nuclear factor kappa B signaling and also produce excessive reactive oxygen species (ROS) in colon epithelial cells. We found that A odontolyticus secretes lipoteichoic acid-rich MVs, promoting inflammatory signaling via TLR2. Simultaneously, those MVs are internalized into the colon epithelial cells, co-localize with the mitochondria, and cause mitochondrial dysfunction, resulting in excessive ROS production and DNA damage. Induction of excessive DNA damage in colonic cells by A odontolyticus-derived MVs was confirmed in the gut organoid model and also in mouse colon tissues.<br><br>CONCLUSIONS: A odontolyticus secretes MVs, which cause&#xa0;chronic inflammation and ROS production in colonic epithelial cells, leading to the initiation of CRC.},
}
@article {pmid38307786,
year = {2024},
author = {Muñoz-Gómez, SA},
title = {The energetic costs of cellular complexity in evolution.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.01.003},
pmid = {38307786},
issn = {1878-4380},
abstract = {The evolutionary history of cells has been marked by drastic increases in complexity. Some hypothesize that such cellular complexification requires a massive energy flux as the origin of new features is hypothetically more energetically costly than their evolutionary maintenance. However, it remains unclear how increases in cellular complexity demand more energy. I propose that the early evolution of new genes with weak functions imposes higher energetic costs by overexpression before their functions are evolutionarily refined. In the long term, the accumulation of new genes deviates resources away from growth and reproduction. Accrued cellular complexity further requires additional infrastructure for its maintenance. Altogether, this suggests that larger and more complex cells are defined by increased survival but lower reproductive capacity.},
}
@article {pmid38305563,
year = {2024},
author = {McCallum, Q and Askelson, K and Fogarty, FF and Natola, L and Nikelski, E and Huang, A and Irwin, D},
title = {Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation.},
journal = {Journal of evolutionary biology},
volume = {37},
number = {2},
pages = {171-188},
doi = {10.1093/jeb/voae004},
pmid = {38305563},
issn = {1420-9101},
support = {RGPIN-2017-03919//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Sparrows/genetics ; Genetics, Population ; Genetic Speciation ; Sex Chromosomes/genetics ; Gene Flow ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome-for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA-show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (Zonotrichia atricapilla) and the white-crowned sparrow (Zonotrichia leucophrys) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of Z. leucophrys. The two Z. leucophrys subspecies show moderate levels of relative differentiation and patterns consistent with a history of recurrent selection in both ancestral and daughter populations, with much of the sex chromosome Z and a large region on the autosome 1A showing increased differentiation compared to the rest of the genome. The two species Z. leucophrys and Z. atricapilla show high relative differentiation and strong heterogeneity in the level of differentiation among various chromosomal regions, with a large portion of the sex chromosome (Z) showing highly divergent haplotypes between these species. Studies of speciation often emphasize mitochondrial DNA differentiation, but speciation between Z. atricapilla and Z. leucophrys appears primarily associated with Z chromosome divergence and more moderately associated with autosomal differentiation, whereas mitochondria are highly similar due apparently to recent introgression. These results add to the growing body of evidence for highly heterogeneous patterns of genomic differentiation during speciation, with some genomic regions showing a lack of gene flow between populations many hundreds of thousands of years before other genomic regions.},
}
@article {pmid38291287,
year = {2024},
author = {Li, X and Zhu, Y and Ruiz-Lozano, P and Wei, K},
title = {Mitochondrial-to-nuclear communications through multiple routes regulate cardiomyocyte proliferation.},
journal = {Cell regeneration (London, England)},
volume = {13},
number = {1},
pages = {2},
pmid = {38291287},
issn = {2045-9769},
support = {2018YFA0800104//Ministry of Science and Technology of the People's Republic of China/ ; 92168205//National Natural Science Foundation of China/ ; 32070823//National Natural Science Foundation of China/ ; 22120230471//Fundamental Research Funds for the Central Universities/ ; },
abstract = {The regenerative capacity of the adult mammalian heart remains a formidable challenge in biological research. Despite extensive investigations into the loss of regenerative potential during evolution and development, unlocking the mechanisms governing cardiomyocyte proliferation remains elusive. Two recent groundbreaking studies have provided fresh perspectives on mitochondrial-to-nuclear communication, shedding light on novel factors that regulate cardiomyocyte proliferation. The studies identified two mitochondrial processes, fatty acid oxidation and protein translation, as key players in restricting cardiomyocyte proliferation. Inhibition of these processes led to increased cell cycle activity in cardiomyocytes, mediated by reduction in H3k4me3 levels through accumulated α-ketoglutarate (αKG), and activation of the mitochondrial unfolded protein response (UPR[mt]), respectively. In this research highlight, we discuss the novel insights into mitochondrial-to-nuclear communication presented in these studies, the broad implications in cardiomyocyte biology and cardiovascular diseases, as well as the intriguing scientific questions inspired by the studies that may facilitate future investigations into the detailed molecular mechanisms of cardiomyocyte metabolism, proliferation, and mitochondrial-to-nuclear communications.},
}
@article {pmid38290047,
year = {2024},
author = {Cao, J and Luo, Y and Chen, Y and Wu, Z and Zhang, J and Wu, Y and Hu, W},
title = {Maternal mitochondrial function affects paternal mitochondrial inheritance in Drosophila.},
journal = {Genetics},
volume = {226},
number = {4},
pages = {},
pmid = {38290047},
issn = {1943-2631},
support = {32160177//National Natural Science Foundation of China/ ; },
mesh = {Male ; Animals ; *DNA, Mitochondrial/genetics ; *Drosophila/genetics ; Genes, Mitochondrial ; Drosophila melanogaster/genetics ; Mitochondria/genetics ; },
abstract = {The maternal inheritance of mitochondria is a widely accepted paradigm, and mechanisms that prevent paternal mitochondria transmission to offspring during spermatogenesis and postfertilization have been described. Although certain species do retain paternal mitochondria, the factors affecting paternal mitochondria inheritance in these cases are unclear. More importantly, the evolutionary benefit of retaining paternal mitochondria and their ultimate fate are unknown. Here we show that transplanted exogenous paternal D. yakuba mitochondria can be transmitted to offspring when maternal mitochondria are dysfunctional in D. melanogaster. Furthermore, we show that the preserved paternal mitochondria are functional, and can be stably inherited, such that the proportion of paternal mitochondria increases gradually in subsequent generations. Our work has important implications that paternal mitochondria inheritance should not be overlooked as a genetic phenomenon in evolution, especially when paternal mitochondria are of significant differences from the maternal mitochondria or the maternal mitochondria are functionally abnormal. Our results improve the understanding of mitochondrial inheritance and provide a new model system for its study.},
}
@article {pmid38288498,
year = {2024},
author = {Meng, X and Wang, D and Pang, Q and Wang, H and Zhou, H},
title = {Multiple independent origins of duplicated mitochondrial control regions indicate an apomorphy in the Thysanoptera (Insecta).},
journal = {Archives of insect biochemistry and physiology},
volume = {115},
number = {1},
pages = {e22087},
doi = {10.1002/arch.22087},
pmid = {38288498},
issn = {1520-6327},
support = {2021YFD1400200//National Key R&amp;D program of China/ ; },
mesh = {Animals ; *Thysanoptera/genetics ; Evolution, Molecular ; Phylogeny ; Mitochondria/genetics ; Gene Rearrangement ; DNA, Mitochondrial/genetics ; },
abstract = {The mitochondrial genome (mitogenome) of thrips is characterized by the presence of control region (CR) duplication. However, the evolution pattern of duplicated CRs in thrips is still unclear. In this study, the multiple independent origins of duplicated CR indicated that the CR duplication was not an ancestral state for Thysanoptera. The macroevolutionary pattern suggested that the earliest CR duplication event occurred in the middle Cretaceous (94.85 Ma) coincided with rearrangement events forming the ancestors of Aeolothripidae, but much later than that forming the ancestors of the suborder Terebrantia. The mitogenome with duplicated CRs showed a higher rate of gene rearrangement. The sequence similarity of the CR copies and divergence time were negatively correlated, indicating age-related deterioration of mitochondrial function. No significant differences were found in the mitochondrial DNA, the P123 and P4FD between the single and multiple-CR charactered mitogenomes, which suggested that the duplicated CRs may not affect the replication process in thrip mitogenome. The mitogenomes with duplicated CRs (mean: 0.0088 subs/s/my) show a significantly increased evolutionary rate than that with a single one (mean: 0.0058 subs/s/my). However, it seems that this higher evolutionary rate did not have adaptive mechanisms in Terebrantia. We speculated that the duplicated CRs may cause a more intense production of energy by mitochondria, and an accelerated mutation and substitution rate is expected in such mitogenomes. Our study provided new insights into the presence of CR duplications and their evolution in the mitogenomes of thrips.},
}
@article {pmid38275595,
year = {2023},
author = {Li, K and Yu, SW and Hu, H and Feng, YF and Storey, KB and Ma, Y and Zhang, JY and Yu, DN},
title = {The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes.},
journal = {Genes},
volume = {15},
number = {1},
pages = {},
pmid = {38275595},
issn = {2073-4425},
support = {LY23C040002//the Natural Science Foundation of Zhejiang Province/ ; },
mesh = {Animals ; Phylogeny ; *Genome, Mitochondrial ; *Coleoptera/genetics ; Bayes Theorem ; Mitochondria/genetics ; },
abstract = {Lamiinae is the largest subfamily of the Cerambycidae (longhorn beetles), with approximately 21,863 described species. Previous phylogenetic studies of Lamiinae showed that this subfamily was monophyletic, but the relationship between the tribes of Lamiinae is still controversial. Partial molecular data and species morphological characteristics are not sufficient to resolve species phylogenetic studies perfectly. At the same time, the full mitochondrial genome contains more comprehensive genetic data. Benefiting from the development of next-generation sequencing (NGS), mitochondrial genomes can be easily acquired and used as reliable molecular markers to investigate phylogenetic relationships within Cerambycidae. Using NGS technology, we obtained 11 mitochondrial genome sequences of Lamiinae species. Based on this newly generated mitochondrial genome dataset matrix, we reconstructed the phylogeny of Lamiinae. The Bayesian Inference and Maximum Likelihood analyses strongly support the monophyly of four tribes (Lamiini, Batocerini, Mesosini, and Saperdini), whereas the tribe Acanthocinini was identified as paraphyletic. Other mitochondrial structural features were also observed: the start codon in the nad1 gene of all 11 mitochondrial genomes is TTG; 17-22 bp intergenic spacers (IGS) with a 'TACTA' motif were found between trnS2 and nad1. Moreover, two long IGS were found in Mesosa myops and Batocera sp. Tandem repeats were found in the IGS of Batocera sp.},
}
@article {pmid38273274,
year = {2024},
author = {Butenko, A and Lukeš, J and Speijer, D and Wideman, JG},
title = {Mitochondrial genomes revisited: why do different lineages retain different genes?.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {15},
pmid = {38273274},
issn = {1741-7007},
support = {DBI-2119963//Division of Biological Infrastructure/ ; 23-07695S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 23-06479X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; },
mesh = {*Genome, Mitochondrial ; Evolution, Molecular ; Eukaryota/genetics ; Mitochondria/genetics ; Base Sequence ; Phylogeny ; },
abstract = {The mitochondria contain their own genome derived from an alphaproteobacterial endosymbiont. From thousands of protein-coding genes originally encoded by their ancestor, only between 1 and about 70 are encoded on extant mitochondrial genomes (mitogenomes). Thanks to a dramatically increasing number of sequenced and annotated mitogenomes a coherent picture of why some genes were lost, or relocated to the nucleus, is emerging. In this review, we describe the characteristics of mitochondria-to-nucleus gene transfer and the resulting varied content of mitogenomes across eukaryotes. We introduce a 'burst-upon-drift' model to best explain nuclear-mitochondrial population genetics with flares of transfer due to genetic drift.},
}
@article {pmid38271822,
year = {2024},
author = {Alcantara da Silva, JV and Ispada, J and Nociti, RP and da Fonseca Junior, AM and de Lima, CB and Dos Santos, EC and Chiaratti, MR and Milazzotto, MP},
title = {The central role of pyruvate metabolism on the epigenetic maturation and transcriptional profile of bovine oocytes.},
journal = {Reproduction (Cambridge, England)},
volume = {167},
number = {4},
pages = {},
doi = {10.1530/REP-23-0181},
pmid = {38271822},
issn = {1741-7899},
mesh = {Animals ; Cattle ; Female ; *In Vitro Oocyte Maturation Techniques/veterinary/methods ; Acetyl Coenzyme A/metabolism ; *Histones/metabolism ; Oocytes/metabolism ; Pyruvic Acid/pharmacology/metabolism ; Epigenesis, Genetic ; Cumulus Cells ; },
abstract = {IN BRIEF: Pyruvate metabolism is one of the main metabolic pathways during oocyte maturation. This study demonstrates that pyruvate metabolism also regulates the epigenetic and molecular maturation in bovine oocytes.<br><br>ABSTRACT: Pyruvate, the final product of glycolysis, undergoes conversion into acetyl-CoA within the mitochondria of oocytes, serving as a primary fuel source for the tricarboxylic acid (TCA) cycle. The citrate generated in the TCA cycle can be transported to the cytoplasm and converted back into acetyl-CoA. This acetyl-CoA can either fuel lipid synthesis or act as a substrate for histone acetylation. This study aimed to investigate how pyruvate metabolism influences lysine 9 histone 3 acetylation (H3K9ac) dynamics and RNA transcription in bovine oocytes during in vitro maturation (IVM). Bovine cumulus-oocyte complexes were cultured in vitro for 24 h, considering three experimental groups: Control (IVM medium only), DCA (IVM supplemented with sodium dichloroacetate, a stimulant of pyruvate oxidation into acetyl-CoA), or IA (IVM supplemented with sodium iodoacetate, a glycolysis inhibitor). The results revealed significant alterations in oocyte metabolism in both treatments, promoting the utilization of lipids as an energy source. These changes during IVM affected the dynamics of H3K9ac, subsequently influencing the oocyte's transcriptional activity. In the DCA and IA groups, a total of 148 and 356 differentially expressed genes were identified, respectively, compared to the control group. These findings suggest that modifications in pyruvate metabolism trigger the activation of metabolic pathways, particularly lipid metabolism, changing acetyl-CoA availability and H3K9ac levels, ultimately impacting the mRNA content of in vitro matured bovine oocytes.},
}
@article {pmid38271341,
year = {2024},
author = {Serrano, MJ and Goudet, J and Cumer, T},
title = {Characterization of the diversity of barn owl's mitochondrial genome reveals high copy number variations in the control region.},
journal = {PloS one},
volume = {19},
number = {1},
pages = {e0295595},
pmid = {38271341},
issn = {1932-6203},
mesh = {Animals ; Humans ; DNA Copy Number Variations ; *Strigiformes/genetics ; *Genome, Mitochondrial ; Base Sequence ; Tandem Repeat Sequences/genetics ; },
abstract = {Mitochondria are known to play an essential role in the cell. These organelles contain their own DNA, which is divided in a coding and non-coding region (NCR). While much of the NCR's function is unknown, tandem repeats have been observed in several vertebrates, with extreme intra-individual, intraspecific and interspecific variation. Taking advantage of a new complete reference for the mitochondrial genome of the Afro-European Barn Owl (Tyto alba), as well as 172 whole genome-resequencing; we (i) describe the reference mitochondrial genome with a special focus on the repeats in the NCR, (ii) quantify the variation in number of copies between individuals, and (iii) explore the possible factors associated with the variation in the number of repetitions. The reference mitochondrial genome revealed a long (256bp) and a short (80bp) tandem repeat in the NCR region. The re-sequenced genomes showed a great variation in number of copies between individuals, with 4 to 38 copies of the Long and 6 to 135 copies of the short repeat. Among the factors associated with this variation between individuals, the tissue used for extraction was the most significant. The exact mechanisms of the formations of these repeats are still to be discovered and understanding them will help explain the maintenance of the polymorphism in the number of copies, as well as their interactions with the metabolism, the aging and health of the individuals.},
}
@article {pmid38271287,
year = {2024},
author = {Harada, R and Hirakawa, Y and Yabuki, A and Kim, E and Yazaki, E and Kamikawa, R and Nakano, K and Eliáš, M and Inagaki, Y},
title = {Encyclopedia of Family A DNA Polymerases Localized in Organelles: Evolutionary Contribution of Bacteria Including the Proto-Mitochondrion.},
journal = {Molecular biology and evolution},
volume = {41},
number = {2},
pages = {},
pmid = {38271287},
issn = {1537-1719},
support = {18KK0203//Japan Society for Promotion of Sciences projects/ ; 21-19664S//Czech Science Foundation/ ; //National Institute for Environmental Studies/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; //National Institute of Genetics/ ; //University of Tsukuba/ ; },
mesh = {*Organelles/genetics ; Phylogeny ; DNA-Directed DNA Polymerase/genetics ; Plastids/genetics ; Mitochondria ; *Cyanobacteria/genetics ; Symbiosis ; },
abstract = {DNA polymerases synthesize DNA from deoxyribonucleotides in a semiconservative manner and serve as the core of DNA replication and repair machinery. In eukaryotic cells, there are 2 genome-containing organelles, mitochondria, and plastids, which were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNA polymerases that localize and work in them to maintain their genomes. The evolution of organellar DNA polymerases has yet to be fully understood because of 2 unsettled issues. First, the diversity of organellar DNA polymerases has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNA polymerases that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNA polymerases known to date show no phylogenetic affinity to those of the extant alphaproteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNA polymerase sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNA polymerases were further examined experimentally. The results presented here suggest that the diversity of organellar DNA polymerases has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed 2 mitochondrial DNA polymerases, POP, and a candidate of the direct descendant of the proto-mitochondrial DNA polymerase I, rdxPolA, identified in this study.},
}
@article {pmid38267606,
year = {2024},
author = {Sloan, DB and Conover, JL and Grover, CE and Wendel, JF and Sharbrough, J},
title = {Polyploid plants take cytonuclear perturbations in stride.},
journal = {The Plant cell},
volume = {36},
number = {4},
pages = {829-839},
pmid = {38267606},
issn = {1532-298X},
support = {IOS-1829176//National Science Foundation/ ; IOS-2209085//Postdoctoral Research Fellowship in Biology/ ; },
mesh = {*Cell Nucleus/genetics/metabolism ; *Polyploidy ; Plastids/genetics/metabolism ; Mitochondria/genetics ; Hybridization, Genetic ; Genome, Plant/genetics ; Evolution, Molecular ; },
abstract = {Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between nuclear and organellar (mitochondrial and plastid) genomes by creating imbalances in the relative copy number of these genomes and producing genetic incompatibilities between maternally derived organellar genomes and the half of the allopolyploid nuclear genome from the paternal progenitor. Several evolutionary responses have been predicted to ameliorate these effects, including selection for changes in protein sequences that restore cytonuclear interactions; biased gene retention/expression/conversion favoring maternal nuclear gene copies; and fine-tuning of relative cytonuclear genome copy numbers and expression levels. Numerous recent studies, however, have found that evolutionary responses are inconsistent and rarely scale to genome-wide generalities. The apparent robustness of plant cytonuclear interactions to allopolyploidy may reflect features that are general to allopolyploids such as the lack of F2 hybrid breakdown under disomic inheritance, and others that are more plant-specific, including slow sequence divergence in organellar genomes and preexisting regulatory responses to changes in cell size and endopolyploidy during development. Thus, cytonuclear interactions may only rarely act as the main barrier to establishment of allopolyploid lineages, perhaps helping to explain why allopolyploidy is so pervasive in plant evolution.},
}
@article {pmid38267054,
year = {2024},
author = {Takusagawa, M and Misumi, O and Nozaki, H and Kato, S and Maruyama, S and Tsujimoto-Inui, Y and Yagisawa, F and Ohnuma, M and Kuroiwa, H and Kuroiwa, T and Matsunaga, S},
title = {Complete mitochondrial and chloroplast DNA sequences of the freshwater green microalga Medakamo hakoo.},
journal = {Genes &amp; genetic systems},
volume = {98},
number = {6},
pages = {353-360},
doi = {10.1266/ggs.23-00275},
pmid = {38267054},
issn = {1880-5779},
mesh = {DNA, Chloroplast/genetics ; *Microalgae ; Mitochondria/genetics ; *Genome, Mitochondrial ; Chloroplasts/genetics ; *Chlorophyta/genetics ; Fresh Water ; Phylogeny ; DNA, Mitochondrial/genetics ; },
abstract = {We report the complete organellar genome sequences of an ultrasmall green alga, Medakamo hakoo strain M-hakoo 311, which has the smallest known nuclear genome in freshwater green algae. Medakamo hakoo has 90.8-kb chloroplast and 36.5-kb mitochondrial genomes containing 80 and 33 putative protein-coding genes, respectively. The mitochondrial genome is the smallest in the Trebouxiophyceae algae studied so far. The GC content of the nuclear genome is 73%, but those of chloroplast and mitochondrial genomes are 41% and 35%, respectively. Codon usages in the organellar genomes have a different tendency from that in the nuclear genome. The organellar genomes have unique characteristics, such as the biased encoding of mitochondrial genes on a single strand and the absence of operon structures in chloroplast ribosomal genes. Medakamo hakoo will be helpful for understanding the evolution of the organellar genome and the regulation of gene expression in chloroplasts and mitochondria.},
}
@article {pmid38262350,
year = {2024},
author = {Eglit, Y and Shiratori, T and Jerlström-Hultqvist, J and Williamson, K and Roger, AJ and Ishida, KI and Simpson, AGB},
title = {Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora.},
journal = {Current biology : CB},
volume = {34},
number = {2},
pages = {451-459.e6},
doi = {10.1016/j.cub.2023.12.032},
pmid = {38262350},
issn = {1879-0445},
mesh = {Phylogeny ; *Eukaryota ; *Eukaryotic Cells ; Flagella ; Microscopy, Electron, Transmission ; },
abstract = {"Kingdom-level" branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down.[1][,][2][,][3][,][4] Some are completely new discoveries, whereas others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19[th] century but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted.[2]Meteora sporadica[5] is a protist with a unique morphology; cells glide over substrates along a long axis of anterior and posterior projections while a pair of lateral "arms" swing back and forth, a motility system without any obvious parallels. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved.[6] Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that both the anterior-posterior projections and the arms are supported by microtubules originating from a cluster of subnuclear microtubule organizing centers (MTOCs). Neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be among the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse "supergroup" and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.},
}
@article {pmid38262211,
year = {2024},
author = {Tang, W and Li, X and Ye, B and Shi, B and Zhang, H and Dang, Z and Sun, Y and Danqu, L and Xia, C and Quzhen, D and Zhao, X and Chui, W and Huang, F},
title = {Characterization of the complete mitochondrial genome and phylogenetic analyses of Haemaphysalis tibetensis Hoogstraal, 1965 (Acari: Ixodidae).},
journal = {Ticks and tick-borne diseases},
volume = {15},
number = {2},
pages = {102311},
doi = {10.1016/j.ttbdis.2024.102311},
pmid = {38262211},
issn = {1877-9603},
mesh = {Animals ; Humans ; Phylogeny ; *Ixodidae ; *Genome, Mitochondrial ; RNA, Ribosomal/genetics ; Tibet ; },
abstract = {Ticks are specialized ectoparasites that feed on blood, causing physical harm to the host and facilitating pathogen transmission. The genus Haemaphysalis contains vectors for numerous infectious agents. These agents cause various diseases in humans and animals. Mitochondrial genome sequences serve as reliable molecular markers, forming a crucial basis for evolutionary analyses, studying species origins, and exploring molecular phylogeny. We extracted mitochondrial genome from the enriched mitochondria of Haemaphysalis tibetensis and obtained a 14,714-bp sequence. The mitochondrial genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNAs (tRNAs), and two control regions. The nucleotide composition of H. tibetensis mitochondrial genome was 38.38 % for A, 9.61 % for G, 39.32 % for T, and 12.69 % for C. The A + T content of H. tibetensis mitochondrial genome was 77.7 %, significantly higher than the G + C content. The repeat units of H. tibetensis exhibited two identical repeat units of 33 bp in length, positioned downstream of nad1 and rrnL genes. Furthermore, phylogenetic analyses based on the 13 PCGs indicated that Haemaphysalis tibetensis (subgenus Allophysalis) formed a monophyletic clade with Haemaphysalis nepalensis (subgenus Herpetobia) and Haemaphysalis danieli (subgenus Allophysalis). Although the species Haemaphysalis inermis, Haemaphysalis kitaokai, Haemaphysalis kolonini, and Haemaphysalis colasbelcouri belong to the subgenus Alloceraea, which were morphologically primitive hemaphysalines just like H. tibetensis, these four tick species cannot form a single clade with H. tibetensis. In this study, the whole mitochondrial genome sequence of H. tibetensis from Tibet was obtained, which enriched the mitochondrial genome data of ticks and provided genetic markers to study the population heredity and molecular evolution of the genus Haemaphysalis.},
}
@article {pmid38261394,
year = {2024},
author = {Sequeira, AN and O'Keefe, IP and Katju, V and Bergthorsson, U},
title = {Friend turned foe: selfish behavior of a spontaneously arising mitochondrial deletion in an experimentally evolved Caenorhabditis elegans population.},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {4},
pages = {},
pmid = {38261394},
issn = {2160-1836},
support = {MCB-1817762//National Science Foundation/ ; //Department of Veterinary Integrative Biosciences/ ; //College of Veterinary Medicine and Biomedical Sciences, Texas A and M University/ ; },
mesh = {Animals ; Humans ; *Caenorhabditis elegans/genetics ; Friends ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Mutation ; *Genome, Mitochondrial ; },
abstract = {Selfish mitochondrial DNA (mtDNA) mutations are variants that can proliferate within cells and enjoy a replication or transmission bias without fitness benefits for the host. mtDNA deletions in Caenorhabditis elegans can reach high heteroplasmic frequencies despite significantly reducing fitness, illustrating how new mtDNA variants can give rise to genetic conflict between different levels of selection and between the nuclear and mitochondrial genomes. During a mutation accumulation experiment in C. elegans, a 1,034-bp deletion originated spontaneously and reached an 81.7% frequency within an experimental evolution line. This heteroplasmic mtDNA deletion, designated as meuDf1, eliminated portions of 2 protein-coding genes (coxIII and nd4) and tRNA-thr in entirety. mtDNA copy number in meuDf1 heteroplasmic individuals was 35% higher than in individuals with wild-type mitochondria. After backcrossing into a common genetic background, the meuDf1 mitotype was associated with reduction in several fitness traits and independent competition experiments found a 40% reduction in composite fitness. Experiments that relaxed individual selection by single individual bottlenecks demonstrated that the deletion-bearing mtDNA possessed a strong transmission bias, thereby qualifying it as a novel selfish mitotype.},
}
@article {pmid38259100,
year = {2024},
author = {Zhang, Y and Li, H and Wang, Y and Nie, M and Zhang, K and Pan, J and Zhang, Y and Ye, Z and Zufall, RA and Lynch, M and Long, H},
title = {Mitogenomic architecture and evolution of the soil ciliates Colpoda.},
journal = {mSystems},
volume = {9},
number = {2},
pages = {e0116123},
pmid = {38259100},
issn = {2379-5077},
support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; },
mesh = {Evolution, Molecular ; Soil ; Phylogeny ; Genomics ; *Genome, Mitochondrial/genetics ; *Ciliophora/genetics ; },
abstract = {Colpoda are cosmopolitan unicellular eukaryotes primarily inhabiting soil and benefiting plant growth, but they remain one of the least understood taxa in genetics and genomics within the realm of ciliated protozoa. Here, we investigate the architecture of de novo assembled mitogenomes of six Colpoda species, using long-read sequencing and involving 36 newly isolated natural strains in total. The mitogenome sizes span from 43 to 63 kbp and typically contain 28-33 protein-coding genes. They possess a linear structure with variable telomeres and central repeats, with one Colpoda elliotti strain isolated from Tibet harboring the longest telomeres among all studied ciliates. Phylogenomic analyses reveal that Colpoda species started to diverge more than 326 million years ago, eventually evolving into two distinct groups. Collinearity analyses also reveal significant genomic divergences and a lack of long collinear blocks. One of the most notable features is the exceptionally high level of gene rearrangements between mitochondrial genomes of different Colpoda species, dominated by gene loss events. Population-level mitogenomic analysis on natural strains also demonstrates high sequence divergence, regardless of geographic distance, but the gene order remains highly conserved within species, offering a new species identification criterion for Colpoda species. Furthermore, we identified underlying heteroplasmic sites in the majority of strains of three Colpoda species, albeit without a discernible recombination signal to account for this heteroplasmy. This comprehensive study systematically unveils the mitogenomic structure and evolution of these ancient and ecologically significant Colpoda ciliates, thus laying the groundwork for a deeper understanding of the evolution of unicellular eukaryotes.IMPORTANCEColpoda, one of the most widespread ciliated protozoa in soil, are poorly understood in regard to their genetics and evolution. Our research revealed extreme mitochondrial gene rearrangements dominated by gene loss events, potentially leading to the streamlining of Colpoda mitogenomes. Surprisingly, while interspecific rearrangements abound, our population-level mitogenomic study revealed a conserved gene order within species, offering a potential new identification criterion. Phylogenomic analysis traced their lineage over 326 million years, revealing two distinct groups. Substantial genomic divergence might be associated with the lack of extended collinear blocks and relaxed purifying selection. This study systematically reveals Colpoda ciliate mitogenome structures and evolution, providing insights into the survival and evolution of these vital soil microorganisms.},
}
@article {pmid38258637,
year = {2024},
author = {Li, X and Li, W and Huo, J and Li, L and Chen, B and Guo, Z and Ma, Z},
title = {[Identification and expression analysis of citrate synthase 3 gene family members in apple].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {40},
number = {1},
pages = {137-149},
doi = {10.13345/j.cjb.230166},
pmid = {38258637},
issn = {1872-2075},
mesh = {*Citric Acid ; *Malus/genetics ; Citrate (si)-Synthase ; Phylogeny ; Citrates ; },
abstract = {As one of the key enzymes in cell metabolism, the activity of citrate synthase 3 (CS3) regulates the substance and energy metabolism of organisms. The protein members of CS3 family were identified from the whole genome of apple, and bioinformatics analysis was performed and expression patterns were analyzed to provide a theoretical basis for studying the potential function of CS3 gene in apple. BLASTp was used to identify members of the apple CS3 family based on the GDR database, and the basic information of CS3 protein sequence, subcellular localization, domain composition, phylogenetic relationship and chromosome localization were analyzed by Pfam, SMART, MEGA5.0, clustalx.exe, ExPASy Proteomics Server, MEGAX, SOPMA, MEME, WoLF PSORT and other software. The tissue expression and inducible expression characteristics of 6 CS3 genes in apple were determined by acid content and real-time fluorescence quantitative polymerase chain reaction (qRT-PCR). Apple CS3 gene family contains 6 members, and these CS3 proteins contain 473-608 amino acid residues, with isoelectric point distribution between 7.21 and 8.82. Subcellular localization results showed that CS3 protein was located in mitochondria and chloroplasts, respectively. Phylogenetic analysis divided them into 3 categories, and the number of genes in each subfamily was 2. Chromosome localization analysis showed that CS3 gene was distributed on different chromosomes of apple. The secondary structure of protein is mainly α-helix, followed by random curling, and the proportion of β-angle is the smallest. The 6 members were all expressed in different apple tissues. The overall expression trend from high to low was the highest relative expression content of MdCS3.4, followed by MdCS3.6, and the relative expression level of other members was in the order of MdCS3.3 > MdCS3.2 > MdCS3.1 > MdCS3.5. qRT-PCR results showed that MdCS3.1 and MdCS3.3 genes had the highest relative expression in the pulp of 'Chengji No. 1' with low acid content, and MdCS3.2 and MdCS3.3 genes in the pulp of 'Asda' with higher acid content had the highest relative expression. Therefore, in this study, the relative expression of CS3 gene in apple cultivars with different acid content in different apple varieties was detected, and its role in apple fruit acid synthesis was analyzed. The experimental results showed that the relative expression of CS3 gene in different apple varieties was different, which provided a reference for the subsequent study of the quality formation mechanism of apple.},
}
@article {pmid38255908,
year = {2024},
author = {Mirra, S and Marfany, G},
title = {From Beach to the Bedside: Harnessing Mitochondrial Function in Human Diseases Using New Marine-Derived Strategies.},
journal = {International journal of molecular sciences},
volume = {25},
number = {2},
pages = {},
pmid = {38255908},
issn = {1422-0067},
support = {PID2022-140957OB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 2021SGR-01093//Government of Catalonia/ ; },
mesh = {Humans ; *Ecosystem ; *Mitochondria ; Cell Death ; Eukaryotic Cells ; Oxidative Stress ; },
abstract = {Mitochondria are double-membrane organelles within eukaryotic cells that act as cellular power houses owing to their ability to efficiently generate the ATP required to sustain normal cell function. Also, they represent a "hub" for the regulation of a plethora of processes, including cellular homeostasis, metabolism, the defense against oxidative stress, and cell death. Mitochondrial dysfunctions are associated with a wide range of human diseases with complex pathologies, including metabolic diseases, neurodegenerative disorders, and cancer. Therefore, regulating dysfunctional mitochondria represents a pivotal therapeutic opportunity in biomedicine. Marine ecosystems are biologically very diversified and harbor a broad range of organisms, providing both novel bioactive substances and molecules with meaningful biomedical and pharmacological applications. Recently, many mitochondria-targeting marine-derived molecules have been described to regulate mitochondrial biology, thus exerting therapeutic effects by inhibiting mitochondrial abnormalities, both in vitro and in vivo, through different mechanisms of action. Here, we review different strategies that are derived from marine organisms which modulate specific mitochondrial processes or mitochondrial molecular pathways and ultimately aim to find key molecules to treat a wide range of human diseases characterized by impaired mitochondrial function.},
}
@article {pmid38243701,
year = {2024},
author = {Gangavarapu, K and Ji, X and Baele, G and Fourment, M and Lemey, P and Matsen, FA and Suchard, MA},
title = {Many-core algorithms for high-dimensional gradients on phylogenetic trees.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {2},
pages = {},
pmid = {38243701},
issn = {1367-4811},
support = {R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; R01 AI153044/NH/NIH HHS/United States ; },
mesh = {Phylogeny ; *Software ; Bayes Theorem ; *Algorithms ; Codon ; Nucleotides ; },
abstract = {MOTIVATION: Advancements in high-throughput genomic sequencing are delivering genomic pathogen data at an unprecedented rate, positioning statistical phylogenetics as a critical tool to monitor infectious diseases globally. This rapid growth spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters of these phylogenetic models where the dimensions of the parameters increase with the number of sequences N. HMC requires repeated calculation of the gradient of the data log-likelihood with respect to (wrt) all branch-length-specific (BLS) parameters that traditionally takes O(N2) operations using the standard pruning algorithm. A recent study proposes an approach to calculate this gradient in O(N), enabling researchers to take advantage of gradient-based samplers such as HMC. The CPU implementation of this approach makes the calculation of the gradient computationally tractable for nucleotide-based models but falls short in performance for larger state-space size models, such as Markov-modulated and codon models. Here, we describe novel massively parallel algorithms to calculate the gradient of the log-likelihood wrt all BLS parameters that take advantage of graphics processing units (GPUs) and result in many fold higher speedups over previous CPU implementations.<br><br>RESULTS: We benchmark these GPU algorithms on three computing systems using three evolutionary inference examples exploring complete genomes from 997 dengue viruses, 62 carnivore mitochondria and 49 yeasts, and observe a >128-fold speedup over the CPU implementation for codon-based models and >8-fold speedup for nucleotide-based models. As a practical demonstration, we also estimate the timing of the first introduction of West Nile virus into the continental Unites States under a codon model with a relaxed molecular clock from 104 full viral genomes, an inference task previously intractable.<br><br>We provide an implementation of our GPU algorithms in BEAGLE v4.0.0 (https://github.com/beagle-dev/beagle-lib), an open-source library for statistical phylogenetics that enables parallel calculations on multi-core CPUs and GPUs. We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (https://github.com/beast-dev/beast-mcmc).},
}
@article {pmid38243053,
year = {2024},
author = {Seesamut, T and Oba, Y and Jirapatrasilp, P and Martinsson, S and Lindström, M and Erséus, C and Panha, S},
title = {Global species delimitation of the cosmopolitan marine littoral earthworm Pontodrilus litoralis (Grube, 1855).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {1753},
pmid = {38243053},
issn = {2045-2322},
support = {TRF-DPG628001//Thailand Research Fund/ ; BDC-PG2-161002//Center of Excellence on Biodiversity/ ; N35E660138//National Research Council of Thailand/ ; },
mesh = {Animals ; Phylogeny ; *Oligochaeta/genetics ; Mitochondria ; Asia ; Australia ; },
abstract = {The marine littoral earthworm Pontodrilus litoralis (Grube, 1855) is widely distributed and is reported as a single species. This study utilized an integrative taxonomic approach based upon morphological examination, phylogenetic reconstruction, and molecular species delimitation, to test whether the taxon is a single species or a species complex. For this, a total of 114 P. litoralis specimens collected from North America, Africa, Australia and Oceania, Europe and Asia were used. The phylogenetic analyses revealed deeply divergent mitochondrial lineages and a high level of genetic diversity among P. litoralis populations. Both single and multi-locus species delimitation analyses yielded several molecular operational taxonomic units. Therefore, due to the homogeneity of morphological characteristics, it is likely that the morphospecies P. litoralis is a complex of four or more cryptic species, suggesting that more sampling is required and that the population structure genetic data and gene flow need to be investigated.},
}
@article {pmid38241813,
year = {2024},
author = {Satoh, S and Miyake, K and Adachi, Y and Masuhiro, K and Futami, S and Naito, Y and Shiroyama, T and Koyama, S and Yamaguchi, Y and Konaka, H and Takamatsu, H and Okuzaki, D and Nagatomo, I and Takeda, Y and Kumanogoh, A},
title = {Cancer-associated SNRPD3 mutation confers resistance to hypoxia, which is attenuated by DRP1 inhibition.},
journal = {Biochemical and biophysical research communications},
volume = {696},
number = {},
pages = {149511},
doi = {10.1016/j.bbrc.2024.149511},
pmid = {38241813},
issn = {1090-2104},
mesh = {Humans ; Dynamins/genetics/metabolism ; *GTP Phosphohydrolases/metabolism ; Hypoxia/metabolism ; Mitochondria/metabolism ; Mitochondrial Dynamics/genetics ; Mutation ; *Neoplasms/genetics/metabolism ; },
abstract = {RNA splicing is a fundamental cellular mechanism performed by spliceosomes that synthesise multiple mature RNA isoforms from a single gene. The association between spliceosome abnormality and solid cancers remains largely unknown. Here, we demonstrated that Sm proteins, which are common components of the spliceosomes and constitute the Sm ring, were overexpressed in multiple cancers and their expression levels were correlated with clinical prognosis. In a pan-cancer mutational hotspot in the Sm ring at SNRPD3 G96V, we found that the G96V substitution confers resistance to hypoxia. RNA-seq detected numerous differentially spliced events between the wild-type and mutation-carrying cells cultured under hypoxia, wherein skipping exons and mutually exclusive exons were frequently observed. This was observed in DNM1L mRNA, which encodes the DRP1 protein that regulates mitochondrial fission. The mitochondria of cells carrying this mutation were excessively fragmented compared with those of wild-type cells. Furthermore, treatment with a DRP1 inhibitor (Mdivi-1) recovered the over-fragmented mitochondria, leading to the attenuation of hypoxia resistance in the mutant cells. These results propose a novel correlation between the cancer-related spliceosome abnormality and mitochondrial fission. Thus, targeting SNRPD3 G96V with a DRP1 inhibitor is a potential treatment strategy for cancers with spliceosome abnormalities.},
}
@article {pmid38238104,
year = {2024},
author = {Ali, NA and Song, W and Huang, J and Wu, D and Zhao, X},
title = {Recent advances and biotechnological applications of RNA metabolism in plant chloroplasts and mitochondria.},
journal = {Critical reviews in biotechnology},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/07388551.2023.2299789},
pmid = {38238104},
issn = {1549-7801},
abstract = {The chloroplast and mitochondrion are semi-autonomous organelles that play essential roles in cell function. These two organelles are embellished with prokaryotic remnants and contain many new features emerging from the co-evolution of organelles and the nucleus. A typical plant chloroplast or mitochondrion genome encodes less than 100 genes, and the regulation of these genes' expression is remarkably complex. The regulation of chloroplast and mitochondrion gene expression can be achieved at multiple levels during development and in response to environmental cues, in which, RNA metabolism, including: RNA transcription, processing, translation, and degradation, plays an important role. RNA metabolism in plant chloroplasts and mitochondria combines bacterial-like traits with novel features evolved in the host cell and is regulated by a large number of nucleus-encoded proteins. Among these, pentatricopeptide repeat (PPR) proteins are deeply involved in multiple aspects of the RNA metabolism of organellar genes. Research over the past decades has revealed new insights into different RNA metabolic events in plant organelles, such as the composition of chloroplast and mitochondrion RNA editosomes. We summarize and discuss the most recent knowledge and biotechnological implications of various RNA metabolism processes in plant chloroplasts and mitochondria, with a focus on the nucleus-encoded factors supporting them, to gain a deeper understanding of the function and evolution of these two organelles in plant cells. Furthermore, a better understanding of the role of nucleus-encoded factors in chloroplast and mitochondrion RNA metabolism will motivate future studies on manipulating the plant gene expression machinery with engineered nucleus-encoded factors.},
}
@article {pmid38235059,
year = {2023},
author = {Bayazit, MB and Francois, A and McGrail, E and Accornero, F and Stratton, MS},
title = {mt-tRNAs in the polymerase gamma mutant heart.},
journal = {The journal of cardiovascular aging},
volume = {3},
number = {4},
pages = {},
pmid = {38235059},
issn = {2768-5993},
support = {K01 AG056848/AG/NIA NIH HHS/United States ; R01 HL154001/HL/NHLBI NIH HHS/United States ; R01 HL136951/HL/NHLBI NIH HHS/United States ; R01 HL158971/HL/NHLBI NIH HHS/United States ; F31 HL162513/HL/NHLBI NIH HHS/United States ; },
abstract = {INTRODUCTION: Mice harboring a D257A mutation in the proofreading domain of the mitochondrial DNA polymerase, Polymerase Gamma (POLG), experience severe metabolic dysfunction and display hallmarks of accelerated aging. We previously reported a mitochondrial unfolded protein response (UPT[mt]) - like (UPR[mt]-like) gene and protein expression pattern in the right ventricular tissue of POLG mutant mice.<br><br>AIM: We sought to determine if POLG mutation altered the expression of genes encoded by the mitochondria in a way that might also reduce proteotoxic stress.<br><br>METHODS AND RESULTS: The expression of genes encoded by the mitochondrial DNA was interrogated via RNA-seq and northern blot analysis. A striking, location-dependent effect was seen in the expression of mitochondrial-encoded tRNAs in the POLG mutant as assayed by RNA-seq. These expression changes were negatively correlated with the tRNA partner amino acid's amyloidogenic potential. Direct measurement by northern blot was conducted on candidate mt-tRNAs identified from the RNA-seq. This analysis confirmed reduced expression of MT-TY in the POLG mutant but failed to show increased expression of MT-TP, which was dramatically increased in the RNA-seq data.<br><br>CONCLUSION: We conclude that reduced expression of amyloid-associated mt-tRNAs is another indication of adaptive response to severe mitochondrial dysfunction in the POLG mutant. Incongruence between RNA-seq and northern blot measurement of MT-TP expression points towards the existence of mt-tRNA post-transcriptional modification regulation in the POLG mutant that alters either polyA capture or cDNA synthesis in RNA-seq library generation. Together, these data suggest that 1) evolution has distributed mt-tRNAs across the circular mitochondrial genome to allow chromosomal location-dependent mt-tRNA regulation (either by expression or PTM) and 2) this regulation is cognizant of the tRNA partner amino acid's amyloidogenic properties.},
}
@article {pmid38231368,
year = {2024},
author = {Nevarez-Lopez, CA and Muhlia-Almazan, A and Gamero-Mora, E and Sanchez-Paz, A and Sastre-Velasquez, CD and Lopez-Martinez, J},
title = {The branched mitochondrial respiratory chain from the jellyfish Stomolophus sp2 as a probable adaptive response to environmental changes.},
journal = {Journal of bioenergetics and biomembranes},
volume = {56},
number = {2},
pages = {101-115},
pmid = {38231368},
issn = {1573-6881},
support = {171862//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; },
mesh = {Animals ; Electron Transport ; Phylogeny ; *Mitochondrial Membranes/metabolism ; *Scyphozoa/chemistry/metabolism ; Mitochondria/metabolism ; Electron Transport Complex IV ; },
abstract = {During their long evolutionary history, jellyfish have faced changes in multiple environmental factors, to which they may selectively fix adaptations, allowing some species to survive and inhabit diverse environments. Previous findings have confirmed the jellyfish's ability to synthesize large ATP amounts, mainly produced by mitochondria, in response to environmental challenges. This study characterized the respiratory chain from the mitochondria of the jellyfish Stomolophus sp2 (previously misidentified as Stomolophus meleagris). The in-gel activity from isolated jellyfish mitochondria confirmed that the mitochondrial respiratory chain contains the four canonical complexes I to IV and F0F1-ATP synthase. Specific additional activity bands, immunodetection, and mass spectrometry identification confirmed the occurrence of four alternative enzymes integrated into a branched mitochondrial respiratory chain of Stomolophus sp2: an alternative oxidase and three dehydrogenases (two NADH type II enzymes and a mitochondrial glycerol-3-phosphate dehydrogenase). The analysis of each transcript sequence, their phylogenetic relationships, and each protein's predicted models confirmed the mitochondrial alternative enzymes' identity and specific characteristics. Although no statistical differences were found among the mean values of transcript abundance of each enzyme in the transcriptomes of jellyfish exposed to three different temperatures, it was confirmed that each gene was expressed at all tested conditions. These first-time reported enzymes in cnidarians suggest the adaptative ability of jellyfish's mitochondria to display rapid metabolic responses, as previously described, to maintain energetic homeostasis and face temperature variations due to climate change.},
}
@article {pmid38228651,
year = {2024},
author = {Krishnan, N and Csiszár, V and Móri, TF and Garay, J},
title = {Genesis of ectosymbiotic features based on commensalistic syntrophy.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {1366},
pmid = {38228651},
issn = {2045-2322},
support = {955708//Horizon 2020/ ; 125569//NKFIH/ ; },
mesh = {Humans ; Phylogeny ; *Symbiosis ; *Eukaryota ; Mitochondria ; Biological Evolution ; },
abstract = {The symbiogenetic origin of eukaryotes with mitochondria is considered a major evolutionary transition. The initial interactions and conditions of symbiosis, along with the phylogenetic affinity of the host, are widely debated. Here, we focus on a possible evolutionary path toward an association of individuals of two species based on unidirectional syntrophy. With the backing of a theoretical model, we hypothesize that the first step in the evolution of such symbiosis could be the appearance of a linking structure on the symbiont's membrane, using which it forms an ectocommensalism with its host. We consider a commensalistic model based on the syntrophy hypothesis in the framework of coevolutionary dynamics and mutant invasion into a monomorphic resident system (evolutionary substitution). We investigate the ecological and evolutionary stability of the consortium (or symbiotic merger), with vertical transmissions playing a crucial role. The impact of the 'effectiveness of vertical transmission' on the dynamics is also analyzed. We find that the transmission of symbionts and the additional costs incurred by the mutant determine the conditions of fixation of the consortia. Additionally, we observe that small and highly metabolically active symbionts are likely to form the consortia.},
}
@article {pmid38221380,
year = {2023},
author = {Doniol-Valcroze, P and Coiffard, P and Alstrm, P and Robb, M and Dufour, P and Crochet, PA},
title = {Molecular and acoustic evidence support the species status of Anthus rubescens rubescens and Anthus [rubescens] japonicus (Passeriformes: Motacillidae).},
journal = {Zootaxa},
volume = {5343},
number = {2},
pages = {173-192},
doi = {10.11646/zootaxa.5343.2.4},
pmid = {38221380},
issn = {1175-5334},
mesh = {Animals ; *Passeriformes/genetics ; Plant Breeding ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {The Buff-bellied Pipit Anthus rubescens comprises two allopatric subspecies groups: A. r. rubescens and A. r. alticola in North America and A. [r.] japonicus in north-east Asia. Despite their great morphological resemblance in breeding plumage, most individuals can be assigned to one or the other subspecies group in non-breeding plumage. Allopatric distributions, morphological differentiation and previously reported molecular divergence suggested the need for additional taxonomic study to assess the rank of these two populations. To resolve the taxonomy of the Buff-bellied Pipit species complex we analysed i) two mitochondrial DNA (mtDNA) loci and ii) nine bioacoustic parameters across 69 sound recordings (338 flight calls) recovered from public databases using principal component analysis and Euclidean distance measures. By comparing our mtDNA and call divergence measures with similar values measured between long-recognised species pairs of the genus, we show that the level of mitochondrial and acoustic divergence between the two Buff-bellied Pipit subspecies groups is typical of species-level divergence in the genus Anthus. Therefore, we recommend splitting the Buff-bellied Pipit species complex into two species: Anthus rubescens (American Pipit) and Anthus japonicus (Siberian Pipit). Our results also suggest that the Water Pipit A. spinoletta deserves taxonomic reassessment as its lineages are highly divergent in acoustics and mtDNA, while mtDNA relationships suggest paraphyly relative to the Rock Pipit A. petrosus. Our work highlights the crucial importance of integrative approaches in taxonomy and the usefulness of bioacoustics in studying cryptic diversity.},
}
@article {pmid38221354,
year = {2023},
author = {Hoare, RJB and Patrick, BH and Buckley, TR and Brav-Cubitt, T},
title = {Wing pattern variation and DNA barcodes defy taxonomic splitting in the New Zealand Pimelea Looper Notoreas perornata (Walker) (Lepidoptera: Geometridae: Larentiinae): the importance of populations as conservation units.},
journal = {Zootaxa},
volume = {5346},
number = {1},
pages = {1-27},
doi = {10.11646/zootaxa.5346.1.1},
pmid = {38221354},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera/genetics ; DNA Barcoding, Taxonomic ; New Zealand ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; *Moths/genetics/anatomy &amp; histology ; Phylogeny ; },
abstract = {The endemic Notoreas perornata (Walker, 1863) complex (Lepidoptera: Geometridae: Larentiinae) from the North Island and northern South Island of New Zealand is reviewed. Larvae feed on Pimelea spp. (Thymelaeaceae), frequently in highly fragmented and threatened shrubland habitats. Allopatric populations tend to differ in size and wing pattern characteristics, but not in genitalia; moreover extensive variation renders recognition of subspecies / allopatric species based on any species concept problematic. A mitochondrial DNA gene tree is not congruent with morphology and indicates rapid recent divergence that has not settled into diagnosable lineages. Based on our results, we synonymise Notoreas simplex Hudson, 1898 with N. perornata (Walker, 1863), and retain N. perornata as a single, highly diverse but monotypic species. All known populations are illustrated to display variation. For conservation purposes, we recommend the continued recognition within the species of 10 populations or groups of populations that appear to be on the way to diverging at subspecific level based on morphological and/or DNA data. The conservation status of all these populations is reviewed. One conservation unit, comprising the populations from Westland, has not been seen since 1998 and is feared possibly extinct.},
}
@article {pmid38221179,
year = {2024},
author = {Antoniolli, HRM and Carvalho, TL and Gottschalk, MS and Loreto, ELS and Robe, LJ and Depr, M},
title = {Systematics and spatio-temporal evolutionary patterns of the flavopilosa group of Drosophila (Diptera, Drosophilidae).},
journal = {Zootaxa},
volume = {5399},
number = {1},
pages = {1-18},
doi = {10.11646/zootaxa.5399.1.1},
pmid = {38221179},
issn = {1175-5334},
mesh = {Animals ; *Drosophila/genetics ; Phylogeny ; *Plant Breeding ; Biological Evolution ; Mitochondria/genetics ; },
abstract = {The Drosophila flavopilosa group comprises morphologically cryptic species that are ecologically restricted to feeding, breeding and ovipositing on flowers of Cestrum and Sessea (Solanaceae). Previous studies confirmed the monophyly of the group and the success of DNA barcoding in identifying a subset of its species, but several others remain yet to be evaluated. Furthemore, the taxonomy of the group remains incomplete, with only nine of the 17 species assigned to subgroups. Here, we accessed the phylogenetic relationships and spatio-temporal evolutionary patterns of the flavopilosa group based on a mitochondrial and two nuclear genes, providing the first molecular support to the subdivision of the group and suggesting a new taxonomic scheme for its species. Barcoding proved to be an effective tool, as all species were reciprocally monophyletic and different analyses of species delimitation yielded congruent results. The close relationship of D. flavopilosa with D. cestri and D. cordeiroi was strongly supported, suggesting that the latter should be placed in the flavopilosa subgroup together with the first. Furthermore, D. mariaehelenae was positioned as sister to D. incompta, supporting its inclusion in the nesiota subgroup. Despite new taxonomic assignments, the synapomorphic status of the diagnostic characters proposed for both subgroups was supported. Based on them, each of the remaining species were placed into one of both subgroups. Divergence time estimates suggest that their diversification coincided with the divergence of Sessea and Cestrum, providing an interesting case of coevolution.},
}
@article {pmid38220520,
year = {2024},
author = {Wang, J and Kan, S and Liao, X and Zhou, J and Tembrock, LR and Daniell, H and Jin, S and Wu, Z},
title = {Plant organellar genomes: much done, much more to do.},
journal = {Trends in plant science},
volume = {29},
number = {7},
pages = {754-769},
doi = {10.1016/j.tplants.2023.12.014},
pmid = {38220520},
issn = {1878-4372},
mesh = {*Genome, Plant/genetics ; Gene Editing/methods ; Plants/genetics ; Organelles/genetics ; Plastids/genetics ; Mitochondria/genetics ; Evolution, Molecular ; CRISPR-Cas Systems ; },
abstract = {Plastids and mitochondria are the only organelles that possess genomes of endosymbiotic origin. In recent decades, advances in sequencing technologies have contributed to a meteoric rise in the number of published organellar genomes, and have revealed greatly divergent evolutionary trajectories. In this review, we quantify the abundance and distribution of sequenced plant organellar genomes across the plant tree of life. We compare numerous genomic features between the two organellar genomes, with an emphasis on evolutionary trajectories, transfers, the current state of organellar genome editing by transcriptional activator-like effector nucleases (TALENs), transcription activator-like effector (TALE)-mediated deaminase, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas), as well as genetic transformation. Finally, we propose future research to understand these different evolutionary trajectories, and genome-editing strategies to promote functional studies and eventually improve organellar genomes.},
}
@article {pmid38216865,
year = {2024},
author = {Cao, L and Chen, P and Hou, X and Ma, J and Yang, N and Lu, Y and Huang, H},
title = {rDNA and mtDNA analysis for the identification of genetic characters in the hybrid grouper derived from hybridization of Cromileptes altivelis (female) × Epinephelus lanceolatus (male).},
journal = {BMC genomic data},
volume = {25},
number = {1},
pages = {5},
pmid = {38216865},
issn = {2730-6844},
support = {YSPTZX202103//The Innovation Platform for Academicians of Hainan Province/ ; RHDRC202010//Scientific Research Foundation of Hainan Tropical Ocean University/ ; 321QN263//Hainan Provincial Natural Science Foundation of China/ ; 32160861//National Natural Science Foundation of China/ ; ZDKJ2021017//The Major Science and Technology plan of Hainan Province/ ; 2020KF001//State Key Laboratory of Developmental Biology of Freshwater Fish/ ; },
mesh = {Animals ; *Bass/genetics/anatomy &amp; histology ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Phylogeny ; Mitochondria/genetics ; },
abstract = {BACKGROUND: Hybridization is a useful strategy to produce offspring with more desirable phenotypic characteristics than those of parents. The hybrid grouper derived from the cross of Cromileptes altivelis (♀, 2n = 48) with Epinephelus lanceolatus (♂, 2n = 48) exhibits improved growth compared with its female parent, which makes it valuable to aquaculture. However, the genetic traits of the hybrid grouper are poorly understood.<br><br>RESULTS: The observations showed that the hybrid grouper was diploid (2n&#x2009;=&#x2009;48) and displayed intermediate morphology with the parent's measurable characteristics. The ribosomal DNA (rDNA) and mitochondria DNA (mtDNA) were characterized at molecular and phylogenetic level. High similarity and low genetic distance of 5S rDNA and mtDNA sequences between the hybrid grouper and C. altivelis showed that the hybrid grouper had a closer genetic relationship with female parents. The reconstructed phylogenetic tree based on COI gene and D-loop region of mtDNA recovered that mtDNA was maternally inherited in the hybrid grouper. Additionally, the DNA methylation level of 5S rDNA intergenic spacers (IGS) sequence was tested in here. The results showed that the DNA methylation status of the hybrid grouper was significantly lower than that of C. altivelis.<br><br>CONCLUSION: Results of this study provide important data on the genetic characteristics of the hybrid derived from the cross of C. altivelis and E. lanceolatus, and contribute the knowledge of both evolution and marine fish breeding.},
}
@article {pmid38206324,
year = {2024},
author = {Crino, OL and Head, ML and Jennions, MD and Noble, DWA},
title = {Mitochondrial function and sexual selection: can physiology resolve the 'lek paradox'?.},
journal = {The Journal of experimental biology},
volume = {227},
number = {2},
pages = {},
doi = {10.1242/jeb.245569},
pmid = {38206324},
issn = {1477-9145},
support = {DP210101152//Australian Research Council/ ; },
mesh = {Female ; Male ; Humans ; *Reproduction ; *Biological Evolution ; Exercise ; Food ; Mitochondria/genetics ; },
abstract = {Across many taxa, males use elaborate ornaments or complex displays to attract potential mates. Such sexually selected traits are thought to signal important aspects of male 'quality'. Female mating preferences based on sexual traits are thought to have evolved because choosy females gain direct benefits that enhance their lifetime reproductive success (e.g. greater access to food) and/or indirect benefits because high-quality males contribute genes that increase offspring fitness. However, it is difficult to explain the persistence of female preferences when males only provide genetic benefits, because female preferences should erode the heritable genetic variation in fitness that sexually selected traits signal. This 'paradox of the lek' has puzzled evolutionary biologists for decades, and inspired many hypotheses to explain how heritable variation in sexually selected traits is maintained. Here, we discuss how factors that affect mitochondrial function can maintain variation in sexually selected traits despite strong female preferences. We discuss how mitochondrial function can influence the expression of sexually selected traits, and we describe empirical studies that link the expression of sexually selected traits to mitochondrial function. We explain how mothers can affect mitochondrial function in their offspring by (a) influencing their developmental environment through maternal effects and (b) choosing a mate to increase the compatibility of mitochondrial and nuclear genes (i.e. the 'mitonuclear compatibility model of sexual selection'). Finally, we discuss how incorporating mitochondrial function into models of sexual selection might help to resolve the paradox of the lek, and we suggest avenues for future research.},
}
@article {pmid38203264,
year = {2023},
author = {Baleva, MV and Piunova, U and Chicherin, I and Vasilev, R and Levitskii, S and Kamenski, P},
title = {Mitochondrial Protein SLIRP Affects Biosynthesis of Cytochrome c Oxidase Subunits in HEK293T Cells.},
journal = {International journal of molecular sciences},
volume = {25},
number = {1},
pages = {},
pmid = {38203264},
issn = {1422-0067},
support = {21-14-00008//Russian Science Foundation/ ; 24-2-21//Moscow University State Assignment/ ; },
mesh = {Humans ; *Electron Transport Complex IV/genetics ; *Mitochondrial Proteins/genetics ; HEK293 Cells ; Mitochondria/genetics ; Eukaryotic Cells ; RNA-Binding Proteins ; },
abstract = {Mitochondria carry out various vital roles in eukaryotic cells, including ATP energy synthesis, the regulation of apoptosis, Fe-S cluster formation, and the metabolism of fatty acids, amino acids, and nucleotides. Throughout evolution, mitochondria lost most of their ancestor's genome but kept the replication, transcription, and translation machinery. Protein biosynthesis in mitochondria is specialized in the production of highly hydrophobic proteins encoded by mitochondria. These proteins are components of oxidative phosphorylation chain complexes. The coordination of protein synthesis must be precise to ensure the correct assembly of nuclear-encoded subunits for these complexes. However, the regulatory mechanisms of mitochondrial translation in human cells are not yet fully understood. In this study, we examined the contribution of the SLIRP protein in regulating protein biosynthesis in mitochondria. Using a click-chemistry approach, we discovered that deletion of the SLIRP gene disturbs mitochondrial translation, leading to the dysfunction of complexes I and IV, but it has no significant effect on complexes III and V. We have shown that this protein interacts only with the small subunit of the mitochondrial ribosome, which may indicate its involvement in the regulation of the mitochondrial translation initiation stage.},
}
@article {pmid38200446,
year = {2024},
author = {Korolija, M and Sukser, V and Vlahoviček, K},
title = {Mitochondrial point heteroplasmy: insights from deep-sequencing of human replicate samples.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {48},
pmid = {38200446},
issn = {1471-2164},
mesh = {Humans ; *Heteroplasmy ; Phylogeny ; *Mitochondria/genetics ; High-Throughput Nucleotide Sequencing ; DNA, Mitochondrial/genetics ; },
abstract = {BACKGROUND: Human mitochondrial heteroplasmy is an extensively investigated phenomenon in the context of medical diagnostics, forensic identification and molecular evolution. However, technical limitations of high-throughput sequencing hinder reliable determination of point heteroplasmies (PHPs) with minor allele frequencies (MAFs) within the noise threshold.<br><br>RESULTS: To investigate the PHP landscape at an MAF threshold down to 0.1%, we sequenced whole mitochondrial genomes at approximately 7.700x coverage, in multiple technical and biological replicates of longitudinal blood and buccal swab samples from 11 human donors (159 libraries in total). The results obtained by two independent sequencing platforms and bioinformatics pipelines indicate distinctive PHP patterns below and above the 1% MAF cut-off. We found a high inter-individual prevalence of low-level PHPs (MAF&#x2009;<&#x2009;1%) at polymorphic positions of the mitochondrial DNA control region (CR), their tissue preference, and a tissue-specific minor allele linkage. We also established the position-dependent potential of minor allele expansion in PHPs, and short-term PHP instability in a mitotically active tissue. We demonstrate that the increase in sensitivity of PHP detection to minor allele frequencies below 1% within a robust experimental and analytical pipeline, provides new information with potential applicative value.<br><br>CONCLUSIONS: Our findings reliably show different mutational loads between tissues at sub-1% allele frequencies, which may serve as an informative medical biomarker of time-dependent, tissue-specific mutational burden, or help discriminate forensically relevant tissues in a single person, close maternal relatives or unrelated individuals of similar phylogenetic background.},
}
@article {pmid38200362,
year = {2024},
author = {Liu, J and Hu, JY and Li, DZ},
title = {Remarkable mitochondrial genome heterogeneity in Meniocus linifolius (Brassicaceae).},
journal = {Plant cell reports},
volume = {43},
number = {2},
pages = {36},
pmid = {38200362},
issn = {1432-203X},
support = {XDB31000000//Strategic Priority Research Program (Type-B), Chinese Academy of Science/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Brassicaceae/genetics ; Phylogeny ; Biological Evolution ; DNA, Mitochondrial/genetics ; },
abstract = {Detailed analyses of 16 genomes identified a remarkable acceleration of mutation rate, hence mitochondrial sequence and structural heterogeneity, in Meniocus linifolius (Brassicaceae). The powerhouse, mitochondria, in plants feature high levels of structural variation, while the encoded genes are normally conserved. However, the substitution rates and spectra of mitochondria DNA within the Brassicaceae, a family with substantial scientific and economic importance, have not been adequately deciphered. Here, by analyzing three newly assembled and 13 known mitochondrial genomes (mitogenomes), we report the highly variable genome structure and mutation rates in Brassicaceae. The genome sizes and GC contents are 196,604 bp and 46.83%, 288,122 bp and 44.79%, and 287,054 bp and 44.93%, for Meniocus linifolius (Mli), Crucihimalaya lasiocarpa (Cla), and Lepidium sativum (Lsa), respectively. In total, 29, 33, and 34 protein-coding genes (PCGs) and 14, 18, and 18 tRNAs are annotated for Mli, Cla, and Lsa, respectively, while all mitogenomes contain one complete circular molecule with three rRNAs and abundant RNA editing sites. The Mli mitogenome features four conformations likely mediated by the two pairs of long repeats, while at the same time seems to have an unusual evolutionary history due to higher GC content, loss of more genes and sequences, but having more repeats and plastid DNA insertions. Corroborating with these, an ambiguous phylogenetic position with long branch length and elevated synonymous substitution rate in nearly all PCGs are observed for Mli. Taken together, our results reveal a high level of mitogenome heterogeneity at the family level and provide valuable resources for further understanding the evolutionary pattern of organelle genomes in Brassicaceae.},
}
@article {pmid38189676,
year = {2024},
author = {Huttner, WB and Heide, M and Mora-Bermúdez, F and Namba, T},
title = {Neocortical neurogenesis in development and evolution-Human-specific features.},
journal = {The Journal of comparative neurology},
volume = {532},
number = {2},
pages = {e25576},
doi = {10.1002/cne.25576},
pmid = {38189676},
issn = {1096-9861},
support = {//Max Planck Society/ ; },
mesh = {Animals ; Humans ; *Neural Stem Cells/metabolism ; *Neanderthals/metabolism ; Ependymoglial Cells/metabolism ; *Neocortex/metabolism ; Neurogenesis/physiology ; Transketolase/metabolism ; GTPase-Activating Proteins/metabolism ; },
abstract = {In this review, we focus on human-specific features of neocortical neurogenesis in development and evolution. Two distinct topics will be addressed. In the first section, we discuss the expansion of the neocortex during human evolution and concentrate on the human-specific gene ARHGAP11B. We review the ability of ARHGAP11B to amplify basal progenitors and to expand a primate neocortex. We discuss the contribution of ARHGAP11B to neocortex expansion during human evolution and its potential implications for neurodevelopmental disorders and brain tumors. We then review the action of ARHGAP11B in mitochondria as a regulator of basal progenitor metabolism, and how it promotes glutaminolysis and basal progenitor proliferation. Finally, we discuss the increase in cognitive performance due to the ARHGAP11B-induced neocortical expansion. In the second section, we focus on neocortical development in modern humans versus Neanderthals. Specifically, we discuss two recent findings pointing to differences in neocortical neurogenesis between these two hominins that are due to a small number of amino acid substitutions in certain key proteins. One set of such proteins are the kinetochore-associated proteins KIF18a and KNL1, where three modern human-specific amino acid substitutions underlie the prolongation of metaphase during apical progenitor mitosis. This prolongation in turn is associated with an increased fidelity of chromosome segregation to the apical progenitor progeny during modern human neocortical development, with implications for the proper formation of radial units. Another such key protein is transketolase-like 1 (TKTL1), where a single modern human-specific amino acid substitution endows TKTL1 with the ability to amplify basal radial glia, resulting in an increase in upper-layer neuron generation. TKTL1's ability is based on its action in the pentose phosphate pathway, resulting in increased fatty acid synthesis. The data imply greater neurogenesis during neocortical development in modern humans than Neanderthals due to TKTL1, in particular in the developing frontal lobe.},
}
@article {pmid38188667,
year = {2023},
author = {Riew, TR and Hwang, JW and Jin, X and Kim, HL and Jung, SJ and Lee, MY},
title = {Astrocytes are involved in the formation of corpora amylacea-like structures from neuronal debris in the CA1 region of the rat hippocampus after ischemia.},
journal = {Frontiers in cellular neuroscience},
volume = {17},
number = {},
pages = {1308247},
pmid = {38188667},
issn = {1662-5102},
abstract = {Recently, we demonstrated that the corpora amylacea (CA), a glycoprotein-rich aggregate frequently found in aged brains, accumulates in the ischemic hippocampus and that osteopontin (OPN) mediates the entire process of CA formation. Therefore, this study aimed to elucidate the mechanisms by which astrocytes and microglia participate in CA formation during the late phase (4-12 weeks) of brain ischemia. Based on various morphological analyses, including immunohistochemistry, in situ hybridization, immunoelectron microscopy, and correlative light and electron microscopy, we propose that astrocytes are the primary cells responsible for CA formation after ischemia. During the subacute phase after ischemia, astrocytes, rather than microglia, express Opn messenger ribonucleic acid and OPN protein, a surrogate marker and key component of CA. Furthermore, the specific localization of OPN in the Golgi complex suggests that it is synthesized and secreted by astrocytes. Astrocytes were in close proximity to type I OPN deposits, which accumulated in the mitochondria of degenerating neurons before fully forming the CA (type III OPN deposits). Throughout CA formation, astrocytes remained closely attached to OPN deposits, with their processes exhibiting well-developed gap junctions. Astrocytic cytoplasmic protein S100β, a calcium-binding protein, was detected within the fully formed CA. Additionally, ultrastructural analysis revealed direct contact between astroglial fibrils and the forming facets of the CA. Overall, we demonstrated that astrocytes play a central role in mediating CA formation from the initial stages of OPN deposit accumulation to the evolution of fully formed CA following transient ischemia in the hippocampus.},
}
@article {pmid38187609,
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 = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.12.18.572194},
pmid = {38187609},
issn = {2692-8205},
abstract = {UNLABELLED: 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 the 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.<br><br>HIGHLIGHTS: Boolean regulatory network model reproduces mitochondrial dynamics during cell cycle progression, apoptosis, and glucose starvation. Model offers a mechanistic explanation for the positive feedback loop that locks in Mitochondrial Dysfunction-Associated Senescence (MiDAS), involving autophagy-resistant, hyperfused, dysfunctional mitochondria. Model reproduces ROS-mediated mitochondrial dysfunction and suggests that MiDAS is part of the early phase of damage-induced senescence. Model predicts that cancer-driving mutations that bypass the G1/S checkpoint generally increase the incidence of MiDAS, except for p53 loss.},
}
@article {pmid38186275,
year = {2024},
author = {Prokkola, JM and Chew, KK and Anttila, K and Maamela, KS and Yildiz, A and Åsheim, ER and Primmer, CR and Aykanat, T},
title = {Tissue-specific metabolic enzyme levels covary with whole-animal metabolic rates and life-history loci via epistatic effects.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1896},
pages = {20220482},
pmid = {38186275},
issn = {1471-2970},
mesh = {Animals ; Humans ; Anaerobiosis ; Biological Evolution ; Genotype ; Heart ; *Muscles ; *Salmo salar ; Transcription Factors ; Energy Metabolism/physiology ; },
abstract = {Metabolic rates, including standard (SMR) and maximum (MMR) metabolic rate have often been linked with life-history strategies. Variation in context- and tissue-level metabolism underlying SMR and MMR may thus provide a physiological basis for life-history variation. This raises a hypothesis that tissue-specific metabolism covaries with whole-animal metabolic rates and is genetically linked to life history. In Atlantic salmon (Salmo salar), variation in two loci, vgll3 and six6, affects life history via age-at-maturity as well as MMR. Here, using individuals with known SMR and MMR with different vgll3 and six6 genotype combinations, we measured proxies of mitochondrial density and anaerobic metabolism, i.e. maximal activities of the mitochondrial citrate synthase (CS) and lactate dehydrogenase (LDH) enzymes, in four tissues (heart, intestine, liver, white muscle) across low- and high-food regimes. We found enzymatic activities were related to metabolic rates, mainly SMR, in the intestine and heart. Individual loci were not associated with the enzymatic activities, but we found epistatic effects and genotype-by-environment interactions in CS activity in the heart and epistasis in LDH activity in the intestine. These effects suggest that mitochondrial density and anaerobic capacity in the heart and intestine may partly mediate variation in metabolic rates and life history via age-at-maturity. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.},
}
@article {pmid38186271,
year = {2024},
author = {Thoral, E and Dargère, L and Medina-Suárez, I and Clair, A and Averty, L and Sigaud, J and Morales, A and Salin, K and Teulier, L},
title = {Non-lethal sampling for assessment of mitochondrial function does not affect metabolic rate and swimming performance.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1896},
pages = {20220483},
pmid = {38186271},
issn = {1471-2970},
mesh = {Animals ; *Swimming ; *Biological Evolution ; Mitochondria ; Muscles ; Oxygen Consumption ; },
abstract = {A fundamental issue in the metabolic field is whether it is possible to understand underlying mechanisms that characterize individual variation. Whole-animal performance relies on mitochondrial function as it produces energy for cellular processes. However, our lack of longitudinal measures to evaluate how mitochondrial function can change within and among individuals and with environmental context makes it difficult to assess individual variation in mitochondrial traits. The aims of this study were to test the repeatability of muscle mitochondrial metabolism by performing two biopsies of red muscle, and to evaluate the effects of biopsies on whole-animal performance in goldfish Carassius auratus. Our results show that basal mitochondrial respiration and net phosphorylation efficiency are repeatable at 14-day intervals. We also show that swimming performance (optimal cost of transport and critical swimming speed) was repeatable in biopsied fish, whereas the repeatability of individual oxygen consumption (standard and maximal metabolic rates) seemed unstable over time. However, we noted that the means of individual and mitochondrial traits did not change over time in biopsied fish. This study shows that muscle biopsies allow the measurement of mitochondrial metabolism without sacrificing animals and that two muscle biopsies 14 days apart affect the intraspecific variation in fish performance without affecting average performance of individuals. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.},
}
@article {pmid38185351,
year = {2024},
author = {Zhang, D and Jakovlić, I and Zou, H and Liu, F and Xiang, CY and Gusang, Q and Tso, S and Xue, S and Zhu, WJ and Li, Z and Wu, J and Wang, GT},
title = {Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea.},
journal = {International journal for parasitology},
volume = {54},
number = {5},
pages = {213-223},
doi = {10.1016/j.ijpara.2024.01.001},
pmid = {38185351},
issn = {1879-0135},
mesh = {Animals ; Phylogeny ; RNA, Ribosomal, 16S ; *Trematoda/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; *Genome, Mitochondrial ; },
abstract = {The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3'-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery.},
}
@article {pmid38185291,
year = {2024},
author = {Bian, C and Ji, S and Xue, R and Zhou, L and Sun, J and Ji, H},
title = {Molecular cloning and characterization of BNIP3 and NIX1/2 and their role in DHA-induced mitophagy and apoptosis in grass carp (Ctenopharyngodon idellus) adipocytes.},
journal = {Gene},
volume = {899},
number = {},
pages = {148140},
doi = {10.1016/j.gene.2024.148140},
pmid = {38185291},
issn = {1879-0038},
mesh = {Animals ; *Mitophagy/genetics ; *Carps/genetics ; Phylogeny ; Apoptosis/genetics ; Adipocytes/metabolism ; Cloning, Molecular ; Mammals/genetics ; },
abstract = {B-cell lymphoma-2 and adenovirus E1B 19-kDa-interacting protein 3 (BNIP3) and BNIP3 like (BNIP3L or NIX) play a vital role in regulating mitophagy and the intrinsic apoptosis in mammals, but their gene characterizations remain unclear in fish. Herein, bnip3, nix1 and nix2 were isolated and characterized from grass carp (Ctenopharyngodon idellus), which encode peptides of 194, 233 and 222 amino acids, respectively. As typical BH3-only proteins, grass carp BNIP3, NIX1 and NIX2 proteins contain BH3 and C-terminal transmembrane domains for inducing apoptosis. Moreover, the LC3-interacting region motif of BNIP3, NIX1 and NIX2 is also conserved in grass carp. Phylogenetic analyses also demonstrated that nix1 and nix2 may have originated from the genome duplication event. Expression pattern analysis indicated that bnip3, nix1 and nix2 were highest expressed in brain, followed by eye (bnip3) and liver (nix1 and nix2). BNIP3, NIX1 and NIX2 localized to the nucleus and the cytoplasm, with a predominant localization to mitochondria within the cytoplasm. In the present study, we found that 200 μM DHA impaired the mitochondrial function, manifested as the decreased antioxidant ability, cellular ATP content and mitochondrial membrane potential in grass carp adipocytes. In addition, the gene expression and enzyme activities of caspase family were significantly increased in 200 μM DHA group, indicating that adipocyte apoptosis was induced. Meanwhile, DHA increased the gene expression of bnip3, nix1 and nix2 in a dose-dependent manner in grass carp adipocytes. The colocalization of mitochondria and lysosomes was promoted by 200 μM DHA treatment, implying that BNIP3/NIX-related mitophagy was activated in adipocytes. Based on these findings, it can be inferred that BNIP3/NIX-related mitophagy may be involved in the adipocyte apoptosis induced by DHA in grass carp.},
}
@article {pmid38177203,
year = {2024},
author = {Yonezawa, T and Mannen, H and Honma, K and Matsunaga, M and Rakotondraparany, F and Ratsoavina, FM and Wu, J and Nishibori, M and Yamamoto, Y},
title = {Origin and spatial population structure of Malagasy native chickens based on mitochondrial DNA.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {569},
pmid = {38177203},
issn = {2045-2322},
support = {21KK0122//JSPS KAKENHI/ ; 21KK0122//JSPS KAKENHI/ ; 21KK0122//JSPS KAKENHI/ ; 21KK0122//JSPS KAKENHI/ ; },
mesh = {Animals ; Africa ; *Chickens/genetics ; *DNA, Mitochondrial/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Madagascar ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Since Malagasy human culture became established in a multi-layered way by genetic admixture of Austronesian (Indonesia), Bantu (East Africa) and West Asian populations, the Malagasy native livestock should also have originated from these regions. While recent genetic studies revealed that Malagasy native dogs and goats were propagated from Africa, the origin of Malagasy native chickens is still controversial. Here, we conducted a phylogeographic analysis of the native chickens, focusing on the historical relationships among the Indian Ocean rim countries and based on mitochondrial D-loop sequences. Although previous work suggested that the rare Haplogroup D occurs with high frequencies in Island Southeast Asia-Pacific, East Africa and Madagascar, the major mitochondrial lineage in Malagasy populations is actually not Haplogroup D but the Sub-haplogroup C2, which is also observed in East Africa, North Africa, India and West Asia. We demonstrate that the Malagasy native chickens were propagated directly from West Asia (including India and North Africa), and not via East Africa. Furthermore, they display clear genetic differentiation within Madagascar, separated into the Highland and Lowland regions as seen in the human genomic landscape on this island. Our findings provide new insights for better understanding the intercommunion of material/non-material cultures within and around Madagascar.},
}
@article {pmid38174367,
year = {2024},
author = {Chi, HM and Davies, MR and Garcia, SM and Montenegro, C and Sharma, S and Lizarraga, M and Wang, Z and Nuthalapati, P and Kim, HT and Liu, X and Feeley, BT},
title = {Defining Endogenous Mitochondrial Transfer in Muscle After Rotator Cuff Injury.},
journal = {The American journal of sports medicine},
volume = {52},
number = {2},
pages = {451-460},
doi = {10.1177/03635465231214225},
pmid = {38174367},
issn = {1552-3365},
mesh = {Humans ; Mice ; Animals ; *Rotator Cuff Injuries/surgery ; Rotator Cuff/surgery ; Mice, Transgenic ; Muscular Atrophy/pathology ; Mitochondria ; *Red Fluorescent Protein ; },
abstract = {BACKGROUND: Rotator cuff muscle degeneration leads to poor clinical outcomes for patients with rotator cuff tears. Fibroadipogenic progenitors (FAPs) are resident muscle stem cells with the ability to differentiate into fibroblasts as well as white and beige adipose tissue. Induction of the beige adipose phenotype in FAPs has been shown to improve muscle quality after rotator cuff tears, but the mechanisms of how FAPs exert their beneficial effects have not been fully elucidated.<br><br>PURPOSE: To study the horizontal transfer of mitochondria from FAPs to myogenic cells and examine the effects of &#x3b2;-agonism on this novel process.<br><br>STUDY DESIGN: Controlled laboratory study.<br><br>METHODS: In mice that had undergone a massive rotator cuff tear, single-cell RNA sequencing was performed on isolated FAPs for genes associated with mitochondrial biogenesis and transfer. Murine FAPs were isolated by fluorescence-activated cell sorting and treated with a &#x3b2;-agonist versus control. FAPs were stained with mitochondrial dyes and cocultured with recipient C2C12 myoblasts, and the rate of transfer was measured after 24 hours by flow cytometry. PdgfraCre[ERT]/MitoTag mice were generated to study the effects of a rotator cuff injury on mitochondrial transfer. PdgfraCre[ERT]/tdTomato mice were likewise generated to perform lineage tracing of PDGFRA[+] cells in this injury model. Both populations of transgenic mice underwent tendon transection and denervation surgery, and MitoTag-labeled mitochondria from Pdgfra[+] FAPs were visualized by fluorescent microscopy, spinning disk confocal microscopy, and 2-photon microscopy; overall mitochondrial quantity was compared between mice treated with &#x3b2;-agonists and dimethyl sulfoxide.<br><br>RESULTS: Single-cell RNA sequencing in mice that underwent rotator cuff tear demonstrated an association between transcriptional markers of adipogenic differentiation and genes associated with mitochondrial biogenesis. In vitro cocultures of murine FAPs with C2C12 cells revealed that treatment of cells with a &#x3b2;-agonist increased mitochondrial transfer compared to control conditions (17.8% &#xb1; 9.9% to 99.6% &#xb1; 0.13% P < .0001). Rotator cuff injury in PdgfraCre[ERT]/MitoTag mice resulted in a robust increase in MitoTag signal in adjacent myofibers compared with uninjured mice. No accumulation of tdTomato signal from PDGFRA[+] cells was seen in injured fibers at 6 weeks after injury, suggesting that FAPs do not fuse with injured muscle fibers but rather contribute their mitochondria.<br><br>CONCLUSION: The authors have described a novel process of endogenous mitochondrial transfer that can occur within the injured rotator cuff between FAPs and myogenic cells. This process may be leveraged therapeutically with &#x3b2;-agonist treatment and represents an exciting target for improving translational therapies available for rotator cuff muscle degeneration.<br><br>CLINICAL RELEVANCE: Promoting endogenous mitochondrial transfer may represent a novel translational strategy to address muscle degeneration after rotator cuff tears.},
}
@article {pmid38170752,
year = {2024},
author = {Cui, M and Yamano, K and Yamamoto, K and Yamamoto-Imoto, H and Minami, S and Yamamoto, T and Matsui, S and Kaminishi, T and Shima, T and Ogura, M and Tsuchiya, M and Nishino, K and Layden, BT and Kato, H and Ogawa, H and Oki, S and Okada, Y and Isaka, Y and Kosako, H and Matsuda, N and Yoshimori, T and Nakamura, S},
title = {HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {2},
pages = {e2306454120},
pmid = {38170752},
issn = {1091-6490},
support = {N/A//China Scholarship Council (CSC)/ ; JPMJCR17H6//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; JP22gm1410014//Japan Agency for Medical Research and Development (AMED)/ ; N/A//Takeda Science Foundation (TSF)/ ; 21H05145//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 21H02428//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; N/A//Astellas Foundation for Research on Metabolic Disorders/ ; N/A//Mochida Memorial Foundation for Medical and Pharmaceutical Research ()/ ; N/A//Mitsubishi Foundation (The Mitsubishi Foundation)/ ; N/A//NOVARTIS Foundation (Japan) for the Promotion of Science (NOVARTIS Foundation (Japan))/ ; 22H04982//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K18140//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23jm0610091h0001//Japan Agency for Medical Research and Development (AMED)/ ; },
mesh = {*Hexokinase/genetics/metabolism ; Prospective Studies ; *Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics/metabolism ; Mitochondria/metabolism ; Lysosomes/metabolism ; Protein Kinases/metabolism ; Cellular Senescence/genetics ; Homeostasis ; Autophagy/genetics ; },
abstract = {Mitochondrial and lysosomal functions are intimately linked and are critical for cellular homeostasis, as evidenced by the fact that cellular senescence, aging, and multiple prominent diseases are associated with concomitant dysfunction of both organelles. However, it is not well understood how the two important organelles are regulated. Transcription factor EB (TFEB) is the master regulator of lysosomal function and is also implicated in regulating mitochondrial function; however, the mechanism underlying the maintenance of both organelles remains to be fully elucidated. Here, by comprehensive transcriptome analysis and subsequent chromatin immunoprecipitation-qPCR, we identified hexokinase domain containing 1 (HKDC1), which is known to function in the glycolysis pathway as a direct TFEB target. Moreover, HKDC1 was upregulated in both mitochondrial and lysosomal stress in a TFEB-dependent manner, and its function was critical for the maintenance of both organelles under stress conditions. Mechanistically, the TFEB-HKDC1 axis was essential for PINK1 (PTEN-induced kinase 1)/Parkin-dependent mitophagy via its initial step, PINK1 stabilization. In addition, the functions of HKDC1 and voltage-dependent anion channels, with which HKDC1 interacts, were essential for the clearance of damaged lysosomes and maintaining mitochondria-lysosome contact. Interestingly, HKDC1 regulated mitophagy and lysosomal repair independently of its prospective function in glycolysis. Furthermore, loss function of HKDC1 accelerated DNA damage-induced cellular senescence with the accumulation of hyperfused mitochondria and damaged lysosomes. Our results show that HKDC1, a factor downstream of TFEB, maintains both mitochondrial and lysosomal homeostasis, which is critical to prevent cellular senescence.},
}
@article {pmid38170710,
year = {2024},
author = {Graham, AM and Lavretsky, P and Wilson, RE and McCracken, KG},
title = {High-altitude adaptation is accompanied by strong signatures of purifying selection in the mitochondrial genomes of three Andean waterfowl.},
journal = {PloS one},
volume = {19},
number = {1},
pages = {e0294842},
pmid = {38170710},
issn = {1932-6203},
mesh = {*Genome, Mitochondrial/genetics ; Altitude ; Genetic Drift ; Mitochondria/genetics ; Environment ; Adaptation, Physiological/genetics ; Selection, Genetic ; },
abstract = {Evidence from a variety of organisms points to convergent evolution on the mitochondria associated with a physiological response to oxygen deprivation or temperature stress, including mechanisms for high-altitude adaptation. Here, we examine whether demography and/or selection explains standing mitogenome nucleotide diversity in high-altitude adapted populations of three Andean waterfowl species: yellow-billed pintail (Anas georgica), speckled teal (Anas flavirostris), and cinnamon teal (Spatula cyanoptera). We compared a total of 60 mitogenomes from each of these three duck species (n = 20 per species) across low and high altitudes and tested whether part(s) or all of the mitogenome exhibited expected signatures of purifying selection within the high-altitude populations of these species. Historical effective population sizes (Ne) were inferred to be similar between high- and low-altitude populations of each species, suggesting that selection rather than genetic drift best explains the reduced genetic variation found in mitochondrial genes of high-altitude populations compared to low-altitude populations of the same species. Specifically, we provide evidence that establishment of these three Andean waterfowl species in the high-altitude environment, coincided at least in part with a persistent pattern of negative purifying selection acting on oxidative phosphorylation (OXPHOS) function of the mitochondria. Our results further reveal that the extent of gene-specific purifying selection has been greatest in the speckled teal, the species with the longest history of high-altitude occupancy.},
}
@article {pmid38164224,
year = {2023},
author = {Labbadia, J},
title = {Potential roles for mitochondria-to-HSF1 signaling in health and disease.},
journal = {Frontiers in molecular biosciences},
volume = {10},
number = {},
pages = {1332658},
pmid = {38164224},
issn = {2296-889X},
abstract = {The ability to respond rapidly and efficiently to protein misfolding is crucial for development, reproduction and long-term health. Cells respond to imbalances in cytosolic/nuclear protein homeostasis through the Heat Shock Response, a tightly regulated transcriptional program that enhances protein homeostasis capacity by increasing levels of protein quality control factors. The Heat Shock Response is driven by Heat Shock Factor 1, which is rapidly activated by the appearance of misfolded proteins and drives the expression of genes encoding molecular chaperones and protein degradation factors, thereby restoring proteome integrity. HSF1 is critical for organismal health, and this has largely been attributed to the preservation of cytosolic and nuclear protein homeostasis. However, evidence is now emerging that HSF1 is also a key mediator of mitochondrial function, raising the possibility that many of the health benefits conferred by HSF1 may be due to the maintenance of mitochondrial homeostasis. In this review, I will discuss our current understanding of the interplay between HSF1 and mitochondria and consider how mitochondria-to-HSF1 signaling may influence health and disease susceptibility.},
}
@article {pmid38161329,
year = {2023},
author = {Hambardikar, V and Akosah, YA and Scoma, ER and Guitart-Mampel, M and Urquiza, P and Da Costa, RT and Perez, MM and Riggs, LM and Patel, R and Solesio, ME},
title = {Toolkit for cellular studies of mammalian mitochondrial inorganic polyphosphate.},
journal = {Frontiers in cell and developmental biology},
volume = {11},
number = {},
pages = {1302585},
pmid = {38161329},
issn = {2296-634X},
support = {R00 AG055701/AG/NIA NIH HHS/United States ; },
abstract = {Introduction: Inorganic polyphosphate (polyP) is an ancient polymer which is extremely well-conserved throughout evolution, and found in every studied organism. PolyP is composed of orthophosphates linked together by high-energy bonds, similar to those found in ATP. The metabolism and the functions of polyP in prokaryotes and simple eukaryotes are well understood. However, little is known about its physiological roles in mammalian cells, mostly due to its unknown metabolism and lack of systematic methods and effective models for the study of polyP in these organisms. Methods: Here, we present a comprehensive set of genetically modified cellular models to study mammalian polyP. Specifically, we focus our studies on mitochondrial polyP, as previous studies have shown the potent regulatory role of mammalian polyP in the organelle, including bioenergetics, via mechanisms that are not yet fully understood. Results: Using SH-SY5Y cells, our results show that the enzymatic depletion of mitochondrial polyP affects the expression of genes involved in the maintenance of mitochondrial physiology, as well as the structure of the organelle. Furthermore, this depletion has deleterious effects on mitochondrial respiration, an effect that is dependent on the length of polyP. Our results also show that the depletion of mammalian polyP in other subcellular locations induces significant changes in gene expression and bioenergetics; as well as that SH-SY5Y cells are not viable when the amount and/or the length of polyP are increased in mitochondria. Discussion: Our findings expand on the crucial role of polyP in mammalian mitochondrial physiology and place our cell lines as a valid model to increase our knowledge of both mammalian polyP and mitochondrial physiology.},
}
@article {pmid38157451,
year = {2024},
author = {Yang, X and Li, G and Lou, P and Zhang, M and Yao, K and Xiao, J and Chen, Y and Xu, J and Tian, S and Deng, M and Pan, Y and Li, M and Wu, X and Liu, R and Shi, X and Tian, Y and Yu, L and Ke, H and Jiao, B and Cong, Y and Plikus, MV and Liu, X and Yu, Z and Lv, C},
title = {Excessive nucleic acid R-loops induce mitochondria-dependent epithelial cell necroptosis and drive spontaneous intestinal inflammation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {1},
pages = {e2307395120},
pmid = {38157451},
issn = {1091-6490},
support = {82025006//MOST | National Natural Science Foundation of China (NSFC)/ ; 82230017//MOST | National Natural Science Foundation of China (NSFC)/ ; 82000498//MOST | National Natural Science Foundation of China (NSFC)/ ; 82270588//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022YFA1104001//National Basic Research Program of China/ ; 2022YFC3602102//National Basic Research Program of China/ ; 2022YFD1300403//National Basic Research Program of China/ ; 2021YFF1000603//National Basic Research Program of China/ ; 82300635//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022M723412//Postdoctoral Science Foundation of China/ ; 88220019//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Humans ; Animals ; Mice ; *Necroptosis ; NAD/metabolism ; R-Loop Structures ; *Inflammatory Bowel Diseases/metabolism ; Epithelial Cells/metabolism ; Intestinal Mucosa/metabolism ; Inflammation/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Mitochondria/metabolism ; },
abstract = {Oxidative stress, which can be activated by a variety of environmental risk factors, has been implicated as an important pathogenic factor for inflammatory bowel disease (IBD). However, how oxidative stress drives IBD onset remains elusive. Here, we found that oxidative stress was strongly activated in inflamed tissues from both ulcerative colitis patients and Crohn's disease patients, and it caused nuclear-to-cytosolic TDP-43 transport and a reduction in the TDP-43 protein level. To investigate the function of TDP-43 in IBD, we inducibly deleted exons 2 to 3 of Tardbp (encoding Tdp-43) in mouse intestinal epithelium, which disrupted its nuclear localization and RNA-processing function. The deletion gave rise to spontaneous intestinal inflammation by inducing epithelial cell necroptosis. Suppression of the necroptotic pathway with deletion of Mlkl or the RIP1 inhibitor Nec-1 rescued colitis phenotypes. Mechanistically, disruption of nuclear TDP-43 caused excessive R-loop accumulation, which triggered DNA damage and genome instability and thereby induced PARP1 hyperactivation, leading to subsequent NAD[+] depletion and ATP loss, consequently activating mitochondrion-dependent necroptosis in intestinal epithelial cells. Importantly, restoration of cellular NAD[+] levels with NAD[+] or NMN supplementation, as well as suppression of ALKBH7, an α-ketoglutarate dioxygenase in mitochondria, rescued TDP-43 deficiency-induced cell death and intestinal inflammation. Furthermore, TDP-43 protein levels were significantly inversely correlated with γ-H2A.X and p-MLKL levels in clinical IBD samples, suggesting the clinical relevance of TDP-43 deficiency-induced mitochondrion-dependent necroptosis. Taken together, these findings identify a unique pathogenic mechanism that links oxidative stress to intestinal inflammation and provide a potent and valid strategy for IBD intervention.},
}
@article {pmid38157080,
year = {2023},
author = {Kuprina, K and Smorkatcheva, A and Rudyk, A and Galkina, S},
title = {Numerous insertions of mitochondrial DNA in the genome of the northern mole vole, Ellobius talpinus.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {36},
pmid = {38157080},
issn = {1573-4978},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; Phylogeny ; Genome ; Mitochondria/genetics ; Arvicolinae/genetics ; Sequence Analysis, DNA ; *Genome, Mitochondrial/genetics ; },
abstract = {BACKGROUND: Ellobius talpinus is a subterranean rodent representing an attractive model in population ecology studies due to its highly special lifestyle and sociality. In such studies, mitochondrial DNA (mtDNA) is widely used. However, if nuclear copies of mtDNA, aka NUMTs, are present, they may co-amplify with the target mtDNA fragment, generating misleading results. The aim of this study was to determine whether NUMTs are present in E. talpinus.<br><br>METHODS AND RESULTS: PCR amplification of the putative mtDNA CytB-D-loop fragment using 'universal' primers from 56 E. talpinus samples produced multiple double peaks in 90% of the sequencing chromatograms. To reveal NUMTs, molecular cloning and sequencing of PCR products of three specimens was conducted, followed by phylogenetic analysis. The pseudogene nature of three out of the seven detected haplotypes was confirmed by their basal positions in relation to other Ellobius haplotypes in the phylogenetic tree. Additionally, 'haplotype B' was basal in relation to other E. talpinus haplotypes and found present in very distant sampling sites. BLASTN search revealed 195 NUMTs in the E. talpinus nuclear genome, including fragments of all four PCR amplified pseudogenes. Although the majority of the NUMTs studied were short, the entire mtDNA had copies in the nuclear genome. The most numerous NUMTs were found for rrnL, COXI, and D-loop.<br><br>CONCLUSIONS: Numerous NUMTs are present in E. talpinus and can be difficult to discriminate against mtDNA sequences. Thus, in future population or phylogenetic studies in E. talpinus, the possibility of cryptic NUMTs amplification should always be taken into account.},
}
@article {pmid38149397,
year = {2023},
author = {Shen, Q and Yuan, Y and Jin, J},
title = {[Relationship between Notch signaling pathway and mitochondrial energy metabolism].},
journal = {Zhonghua wei zhong bing ji jiu yi xue},
volume = {35},
number = {12},
pages = {1321-1326},
doi = {10.3760/cma.j.cn121430-20230719-00532},
pmid = {38149397},
issn = {2095-4352},
mesh = {*Signal Transduction/physiology ; *Mitochondria ; Receptors, Notch/metabolism ; Cell Differentiation/physiology ; Energy Metabolism ; },
abstract = {Notch signaling pathway is a highly conserved signaling pathway in the process of evolution. It is composed of three parts: Notch receptor, ligand and effector molecules responsible for intracellular signal transduction. It plays an important role in cell proliferation, differentiation, development, migration, apoptosis and other processes, and has a regulatory effect on tissue homeostasis and homeostasis. Mitochondria are the sites of oxidative metabolism in eukaryotes, where sugars, fats and proteins are finally oxidized to release energy. In recent years, the regulation of Notch signaling pathway on mitochondrial energy metabolism has attracted more and more attention. A large number of data have shown that Notch signaling pathway has a significant effect on mitochondrial energy metabolism, but the relationship between Notch signaling pathway and mitochondrial energy metabolism needs to be specifically and systematically discussed. In this paper, the relationship between Notch signaling pathway and mitochondrial energy metabolism is reviewed, in order to improve the understanding of them and provide new ideas for the treatment of related diseases.},
}
@article {pmid38147995,
year = {2023},
author = {Yang, J and Gao, J and Li, W and Liu, J and Huo, J and Ren, Z and Li, L and Chen, B and Mao, J and Ma, Z},
title = {[Identification and expression analysis of apple PDHB-1 gene family].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {39},
number = {12},
pages = {4965-4981},
doi = {10.13345/j.cjb.230011},
pmid = {38147995},
issn = {1872-2075},
mesh = {*Malus/genetics/chemistry/metabolism ; Fruit/genetics ; Protein Structure, Secondary ; },
abstract = {Pyruvate dehydrogenase E1 component subunit beta-1 (PDHB-1) is a gene encoding the β-subunit of pyruvate dehydrogenase complex, which plays an important role in fruit acid accumulation. The aim of this study was to investigate the evolution characteristics of apple PDHB-1 family and its expression in apples with different acid contents. Bioinformatics analysis was performed using databases including NCBI, Pfam and software including ClustalX, MEGA, and TBtools. By combining titratable acid content determination and quantitative real-time PCR (qRT-PCR), the expression of this family genes in the peel and pulp of apple 'Asda' and 'Chengji No.1' with different acid content were obtained, respectively. The family members were mainly located in chloroplast, cytoplasm and mitochondria. α-helix and random coil were the main factors for the formation of secondary structure in this family. Tissue-specific expression profiles showed that the expression of most members were higher in fruit than in other tissues. qRT-PCR results showed that the expression profile of most members was consistent with the profile of titratable acid contents. In the peel, the expression levels of 14 members in 'Asda' apples with high acid content were significantly higher than that in 'Chengji No.1' apples with low acid content, where the expression difference of MdPDHB1-15 was the most significant. In the pulp, the expression levels of 17 members in 'Asda' apples were significantly higher than that in 'Chengji No.1' apples, where MdPDHB1-01 was the most highly expressed. It was predicted that PDHB-1 gene family in apple plays an important role in the regulation of fruit acidity.},
}
@article {pmid38142841,
year = {2024},
author = {Buonvicino, D and Pratesi, S and Ranieri, G and Pistolesi, A and Guasti, D and Chiarugi, A},
title = {The mitochondriogenic but not the immunosuppressant effects of mTOR inhibitors prompt neuroprotection and delay disease evolution in a mouse model of progressive multiple sclerosis.},
journal = {Neurobiology of disease},
volume = {191},
number = {},
pages = {106387},
doi = {10.1016/j.nbd.2023.106387},
pmid = {38142841},
issn = {1095-953X},
mesh = {Female ; Animals ; Mice ; *Multiple Sclerosis/pathology ; MTOR Inhibitors ; Fingolimod Hydrochloride/pharmacology/therapeutic use ; Neuroprotection ; Everolimus/pharmacology/therapeutic use ; Mice, Inbred NOD ; Immunosuppressive Agents/pharmacology/therapeutic use ; Sirolimus/pharmacology/therapeutic use ; Dexamethasone/pharmacology ; *Encephalomyelitis, Autoimmune, Experimental/pathology ; Mice, Inbred C57BL ; },
abstract = {INTRODUCTION: Purportedly, the progression of multiple sclerosis (MS) occurs when neurodegenerative processes due to derangement of axonal bioenergetics take over the autoimmune response. However, a clear picture of the causative interrelationship between autoimmunity and axonal mitochondrial dysfunction in progressive MS (PMS) pathogenesis waits to be provided.<br><br>METHODS: In the present study, by adopting the NOD mouse model of PMS, we compared the pharmacological effects of the immunosuppressants dexamethasone and fingolimod with those of mTOR inhibitors rapamycin and everolimus that, in addition to immunosuppression, also regulate mitochondrial functioning. Female Non-Obese Diabetic (NOD) mice were immunized with MOG35-55 and treated with drugs to evaluate functional, immune and mitochondrial parameters during disease evolution.<br><br>RESULTS: We found that dexamethasone and fingolimod did not affect the pattern of progression as well as survival. Conversely, mTOR inhibitors rapamycin and everolimus delayed disease progression and robustly extended survival of immunized mice. The same effects were obtained when treatment was delayed by 30&#xa0;days after immunization. Remarkably, dexamethasone and fingolimod prompted the same degree of immunosuppression of rapamycin within both spleen and spinal cord of mice. However, only rapamycin prompted mitochondriogenesis by increasing mitochondrial content, and expression of several mitochondrial respiratory complex subunits, thereby preventing mtDNA reduction in the spinal cords of immunized mice. These pharmacodynamic effects were not reproduced in healthy NOD mice, suggesting a disease context-dependent pharmacodynamic effect.<br><br>DISCUSSION: Data corroborate the key role of mitochondriogenesis to treatment of MS progression, and for the first time disclose the translational potential of mTOR inhibitors in PMS therapy.},
}
@article {pmid38142270,
year = {2024},
author = {Khan, MM and Suhail, SM and Majid, HA and Ahmad, I and Sadique, U and Khan, R and Ahmad, I and Ijaz, A and Khan, K and Ali, F and Khan, MS and El-Mansi, AA},
title = {Morpometric and molecular characterization of Surguli goat through CO1 gene in district Kohat.},
journal = {Animal biotechnology},
volume = {35},
number = {1},
pages = {2290528},
doi = {10.1080/10495398.2023.2290528},
pmid = {38142270},
issn = {1532-2378},
mesh = {Animals ; *Goats/genetics ; Phylogeny ; Base Sequence ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {The present study was designed with the aim to study morphometric characterization as well as phylogeny and diversity of the local Surguli goat at their breeding tract district Kohat through mitochondrial DNA region, i.e., Cytochrome C Oxidase Subunit One (CO1) gene. Morphometric data and blood samples were collected from thirty (30) pure goats. Morphometric analysis showed that sex had significant effect (p < 0.05) on body weight, body length, hearth girth and horn length while no significant effect (p > 0.05) was observed for other characteristics. The results also indicated that age had significant effect (p < 0.05) on height at rump, ear length, horn length and tail length while no significant effect (p > 0.05) was observed for other characteristics. The phylogenetic analysis through CO1 nucleotide sequences within nucleotide range 1-767 showed nine polymorphic sites segregating into eight haplotypes. The mean intraspecific diversity and mean interspecific diversity were calculated as 0.23 and 2.36%, respectively. Phylogenetic tree revealed that Capra Ibex and native Surguli goat have common ancestors. The morphometric and molecular results obtained from the present study can be exploited as a selection tool for breeding and overall improvement.},
}
@article {pmid38140813,
year = {2024},
author = {Griseti, E and Bello, AA and Bieth, E and Sabbagh, B and Iacovoni, JS and Bigay, J and Laurell, H and Čopič, A},
title = {Molecular mechanisms of perilipin protein function in lipid droplet metabolism.},
journal = {FEBS letters},
volume = {598},
number = {10},
pages = {1170-1198},
doi = {10.1002/1873-3468.14792},
pmid = {38140813},
issn = {1873-3468},
support = {856404/ERC_/European Research Council/International ; },
mesh = {Humans ; *Lipid Droplets/metabolism ; Animals ; *Perilipins/metabolism/genetics ; Lipid Metabolism ; Lipolysis ; Perilipin-1/metabolism/genetics ; },
abstract = {Perilipins are abundant lipid droplet (LD) proteins present in all metazoans and also in Amoebozoa and fungi. Humans express five perilipins, which share a similar domain organization: an amino-terminal PAT domain and an 11-mer repeat region, which can fold into amphipathic helices that interact with LDs, followed by a structured carboxy-terminal domain. Variations of this organization that arose during vertebrate evolution allow for functional specialization between perilipins in relation to the metabolic needs of different tissues. We discuss how different features of perilipins influence their interaction with LDs and their cellular targeting. PLIN1 and PLIN5 play a direct role in lipolysis by regulating the recruitment of lipases to LDs and LD interaction with mitochondria. Other perilipins, particularly PLIN2, appear to protect LDs from lipolysis, but the molecular mechanism is not clear. PLIN4 stands out with its long repetitive region, whereas PLIN3 is most widely expressed and is used as a nascent LD marker. Finally, we discuss the genetic variability in perilipins in connection with metabolic disease, prominent for PLIN1 and PLIN4, underlying the importance of understanding the molecular function of perilipins.},
}
@article {pmid38139163,
year = {2023},
author = {He, X and Zhang, X and Deng, Y and Yang, R and Yu, LX and Jia, S and Zhang, T},
title = {Structural Reorganization in Two Alfalfa Mitochondrial Genome Assemblies and Mitochondrial Evolution in Medicago Species.},
journal = {International journal of molecular sciences},
volume = {24},
number = {24},
pages = {},
pmid = {38139163},
issn = {1422-0067},
support = {SJCZFY2022-3//Breeding of New Alfalfa Varieties/ ; 2022JBGS0020//Breeding and Industrialization Demonstration of New High-quality Alfalfa Varieties/ ; },
mesh = {*Genome, Mitochondrial ; Medicago sativa/genetics ; DNA, Mitochondrial/genetics ; Medicago/genetics ; Mitochondria/genetics ; },
abstract = {Plant mitochondria are crucial for species evolution, phylogenetics, classification, and identification as maternal genetic material. However, the presence of numerous repetitive sequences, complex structures, and a low number of genes in the mitochondrial genome has hindered its complete assembly and related research endeavors. In this study, we assembled two mitochondrial genomes of alfalfa varieties of Zhongmu No.1 (299,123 bp) and Zhongmu No.4 (306,983 bp), based on a combination of PacBio, Illumina, and Hi-C sequences. The comparison of genome assemblies revealed that the same number of mitochondrial genes, including thirty-three protein-coding genes, sixteen tRNA genes, and three rRNA genes existed in the two varieties. Additionally, large fragments of repetitive sequences were found underlying frequent mitochondrial recombination events. We observed extensive transfer of mitochondrial fragments into the nuclear genome of Zhongmu No.4. Analysis of the cox1 and rrn18s genes in 35 Medicago accessions revealed the presence of population-level deletions and substitutions in the rrn18s gene. We propose that mitochondrial structural reorganizations may contribute to alfalfa evolution.},
}
@article {pmid38135240,
year = {2024},
author = {Bľandová, G and Janoštiaková, N and Kodada, D and Pastorek, M and Lipták, R and Hodosy, J and Šebeková, K and Celec, P and Krasňanská, G and Eliaš, V and Wachsmannová, L and Konečný, M and Repiská, V and Baldovič, M},
title = {Mitochondrial DNA variability and Covid-19 in the Slovak population.},
journal = {Mitochondrion},
volume = {75},
number = {},
pages = {101827},
doi = {10.1016/j.mito.2023.101827},
pmid = {38135240},
issn = {1872-8278},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; Phylogeny ; Slovakia/epidemiology ; Haplotypes ; *COVID-19/genetics ; Mitochondria/genetics ; },
abstract = {Recent studies have shown that mitochondria are involved in the pathogenesis of Covid-19. Mitochondria play a role in production of reactive oxygen species and induction of an innate immune response, both important during infections. Common variability of mitochondrial DNA (mtDNA) can affect oxidative phosphorylation and the risk or lethality of cardiovascular, neurodegenerative diseases and sepsis. However, it is unclear whether susceptibility of severe Covid-19 might be affected by mtDNA variation. Thus, we have analyzed mtDNA in a sample of 446 Slovak patients hospitalized due to Covid-19 and a control population group consisting of 1874 individuals. MtDNA variants in the HVRI region have been analyzed and classified into haplogroups at various phylogenetic levels. Binary logistic regression was used to assess the risk of Covid-19. Haplogroups T1, H11, K and variants 16256C > T, 16265A > C, 16293A > G, 16311 T > C and 16399A > G were associated with an increased Covid-19 risk. On contrary, Haplogroup J1, haplogroup clusters H + U5b and T2b + U5b, and the mtDNA variant 16189 T > C were associated with decreased risk of Covid-19. Following the application of the Bonferroni correction, statistical significance was observed exclusively for the cluster of haplogroups H + U5b. Unsurprisingly, the most significant factor contributing to the mortality of patients with Covid-19 is the age of patients. Our findings suggest that mtDNA haplogroups can play a role in Covid-19 pathogenesis, thus potentially useful in identifying susceptibility to its severe form. To confirm these associations, further studies taking into account the nuclear genome or other non-biological influences are needed.},
}
@article {pmid38124445,
year = {2024},
author = {Uvizl, M and Puechmaille, SJ and Power, S and Pippel, M and Carthy, S and Haerty, W and Myers, EW and Teeling, EC and Huang, Z},
title = {Comparative Genome Microsynteny Illuminates the Fast Evolution of Nuclear Mitochondrial Segments (NUMTs) in Mammals.},
journal = {Molecular biology and evolution},
volume = {41},
number = {1},
pages = {},
pmid = {38124445},
issn = {1537-1719},
mesh = {Animals ; Phylogeny ; *Genomics ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Mammals/genetics ; Sequence Analysis, DNA ; Cell Nucleus/genetics ; *Genome, Mitochondrial ; Evolution, Molecular ; },
abstract = {The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-and-absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference.},
}
@article {pmid38123538,
year = {2023},
author = {Cui, Z and Zhong, Y and Sun, Z and Jiang, Z and Deng, J and Wang, Q and Nielsen, J and Hou, J and Qi, Q},
title = {Reconfiguration of the reductive TCA cycle enables high-level succinic acid production by Yarrowia lipolytica.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {8480},
pmid = {38123538},
issn = {2041-1723},
support = {22208192//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Yarrowia/genetics/metabolism ; Succinic Acid/metabolism ; NAD/metabolism ; Citric Acid Cycle ; Fermentation ; Glucose/metabolism ; Metabolic Engineering ; },
abstract = {Succinic acid (SA) is an important C4-dicarboxylic acid. Microbial production of SA at low pH results in low purification costs and hence good overall process economics. However, redox imbalances limited SA biosynthesis from glucose via the reductive tricarboxylic acid (TCA) cycle in yeast. Here, we engineer the strictly aerobic yeast Yarrowia lipolytica for efficient SA production without pH control. Introduction of the reductive TCA cycle into the cytosol of a succinate dehydrogenase-disrupted yeast strain causes arrested cell growth. Although adaptive laboratory evolution restores cell growth, limited NADH supply restricts SA production. Reconfiguration of the reductive SA biosynthesis pathway in the mitochondria through coupling the oxidative and reductive TCA cycle for NADH regeneration results in improved SA production. In pilot-scale fermentation, the engineered strain produces 111.9 g/L SA with a yield of 0.79 g/g glucose within 62 h. This study paves the way for industrial production of biobased SA.},
}
@article {pmid38112480,
year = {2023},
author = {He, Z and Fang, Y and Zhang, F and Liu, Y and Cheng, X and Wang, J and Li, D and Chen, D and Wu, F},
title = {Adenine nucleotide translocase 2 (Ant2) is required for individualization of spermatogenesis of Drosophila melanogaster.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.13309},
pmid = {38112480},
issn = {1744-7917},
support = {CARS-18-SYZ10//China Agricultural Research System of MOF and MARA/ ; 2021-620-000-001-009//Hubei Province Agricultural Science and Technology Innovation Center Project/ ; 2022BBA0079//Hubei Province key Research and Development Project/ ; },
abstract = {Successful completion of spermatogenesis is crucial for the perpetuation of the species. In Drosophila, spermatid individualization, a process involving changes in mitochondrial structure and function is critical to produce functional mature sperm. Ant2, encoding a mitochondrial adenine nucleotide translocase, is highly expressed in male testes and plays a role in energy metabolism in the mitochondria. However, its molecular function remains unclear. Here, we identified an important role of Ant2 in spermatid individualization. In Ant2 knockdown testes, spermatid individualization complexes composed of F-actin cones exhibited a diffuse distribution, and mature sperms were absent in the seminal vesicle, thus leading to male sterility. The most striking effects in Ant2-knockdown spermatids were decrease in tubulin polyglycylation and disruption of proper mitochondria derivatives function. Excessive apoptotic cells were also observed in Ant2-knockdown testes. To further investigate the phenotype of Ant2 knockdown in testes at the molecular level, complementary transcriptome and proteome analyses were performed. At the mRNA level, 868 differentially expressed genes were identified, of which 229 genes were upregulated and 639 were downregulated induced via Ant2 knockdown. iTRAQ-labeling proteome analysis revealed 350 differentially expressed proteins, of which 117 proteins were upregulated and 233 were downregulated. The expression of glutathione transferase (GstD5, GstE5, GstE8, and GstD3), proteins involved in reproduction were significantly regulated at both the mRNA and protein levels. These results indicate that Ant2 is crucial for spermatid maturation by affecting mitochondrial morphogenesis.},
}
@article {pmid38105202,
year = {2023},
author = {Baleva, MV and Piunova, UE and Chicherin, IV and Levitskii, SA and Kamenski, PA},
title = {Diversity and Evolution of Mitochondrial Translation Apparatus.},
journal = {Biochemistry. Biokhimiia},
volume = {88},
number = {11},
pages = {1832-1843},
doi = {10.1134/S0006297923110135},
pmid = {38105202},
issn = {1608-3040},
mesh = {*Mitochondria/genetics/metabolism ; Protein Biosynthesis ; *Genome, Mitochondrial ; Mitochondrial Proteins/genetics/metabolism ; },
abstract = {The evolution of mitochondria has proceeded independently in different eukaryotic lines, which is reflected in the diversity of mitochondrial genomes and mechanisms of their expression in eukaryotic species. Mitochondria have lost most of bacterial ancestor genes by transferring them to the nucleus or eliminating them. However, mitochondria of almost all eukaryotic cells still retain relatively small genomes, as well as their replication, transcription, and translation apparatuses. The dependence on the nuclear genome, specific features of mitochondrial transcripts, and synthesis of highly hydrophobic membrane proteins in the mitochondria have led to significant changes in the translation apparatus inherited from the bacterial ancestor, which retained the basic structure necessary for protein synthesis but became more specialized and labile. In this review, we discuss specific properties of translation initiation in the mitochondria and how the evolution of mitochondria affected the functions of main factors initiating protein biosynthesis in these organelles.},
}
@article {pmid38103995,
year = {2024},
author = {Yu, Y and Li, YP and Ren, K and Hao, X and Fru, EC and Rønn, R and Rivera, WL and Becker, K and Feng, R and Yang, J and Rensing, C},
title = {A brief history of metal recruitment in protozoan predation.},
journal = {Trends in microbiology},
volume = {32},
number = {5},
pages = {465-476},
doi = {10.1016/j.tim.2023.11.008},
pmid = {38103995},
issn = {1878-4380},
mesh = {*Metals/metabolism ; *Phagocytosis ; *Dictyostelium/metabolism/physiology ; Biological Evolution ; Acanthamoeba ; Animals ; Phagosomes/metabolism ; Zinc/metabolism ; Metalloids/metabolism ; Copper/metabolism ; Biological Availability ; Mitochondria/metabolism ; },
abstract = {Metals and metalloids are used as weapons for predatory feeding by unicellular eukaryotes on prokaryotes. This review emphasizes the role of metal(loid) bioavailability over the course of Earth's history, coupled with eukaryogenesis and the evolution of the mitochondrion to trace the emergence and use of the metal(loid) prey-killing phagosome as a feeding strategy. Members of the genera Acanthamoeba and Dictyostelium use metals such as zinc (Zn) and copper (Cu), and possibly metalloids, to kill their bacterial prey after phagocytosis. We provide a potential timeline on when these capacities first evolved and how they correlate with perceived changes in metal(loid) bioavailability through Earth's history. The origin of phagotrophic eukaryotes must have postdated the Great Oxidation Event (GOE) in agreement with redox-dependent modification of metal(loid) bioavailability for phagotrophic poisoning. However, this predatory mechanism is predicted to have evolved much later - closer to the origin of the multicellular metazoans and the evolutionary development of the immune systems.},
}
@article {pmid38103543,
year = {2024},
author = {Wang, S and He, B and Wu, H and Cai, Q and Ramírez-Sánchez, O and Abreu-Goodger, C and Birch, PRJ and Jin, H},
title = {Plant mRNAs move into a fungal pathogen via extracellular vesicles to reduce infection.},
journal = {Cell host &amp; microbe},
volume = {32},
number = {1},
pages = {93-105.e6},
pmid = {38103543},
issn = {1934-6069},
support = {R35 GM136379/GM/NIGMS NIH HHS/United States ; },
mesh = {RNA, Messenger/genetics/metabolism ; RNA ; *Arabidopsis/genetics/microbiology ; Plants/genetics ; *Extracellular Vesicles ; Plant Diseases/microbiology ; },
abstract = {Cross-kingdom small RNA trafficking between hosts and microbes modulates gene expression in the interacting partners during infection. However, whether other RNAs are also transferred is unclear. Here, we discover that host plant Arabidopsis thaliana delivers mRNAs via extracellular vesicles (EVs) into the fungal pathogen Botrytis cinerea. A fluorescent RNA aptamer reporter Broccoli system reveals host mRNAs in EVs and recipient fungal cells. Using translating ribosome affinity purification profiling and polysome analysis, we observe that delivered host mRNAs are translated in fungal cells. Ectopic expression of two transferred host mRNAs in B. cinerea shows that their proteins are detrimental to infection. Arabidopsis knockout mutants of the genes corresponding to these transferred mRNAs are more susceptible. Thus, plants have a strategy to reduce infection by transporting mRNAs into fungal cells. mRNAs transferred from plants to pathogenic fungi are translated to compromise infection, providing knowledge that helps combat crop diseases.},
}
@article {pmid38100746,
year = {2024},
author = {Araujo, TQ and King-Trudeau, S and VanDyke, J and Hochberg, R},
title = {First ultrastructural description of an apomictic opsiblastic egg in freshwater Gastrotricha.},
journal = {Journal of morphology},
volume = {285},
number = {1},
pages = {e21659},
doi = {10.1002/jmor.21659},
pmid = {38100746},
issn = {1097-4687},
support = {//National Science Foundation/ ; },
mesh = {Animals ; Phylogeny ; *Oocytes/ultrastructure ; *Oogenesis ; Endoplasmic Reticulum ; Fresh Water ; },
abstract = {Freshwater gastrotrichs have a biphasic lifecycle that reputedly involves the production of three types of eggs: apomictic and fast hatching (tachyblastic ova), apomictic and delayed hatching (opsiblastic ova), and plaque-bearing eggs (potentially derived from mixis). While some details of oogenesis and eggshell structure are known for tachyblastic ova, there are few details on other egg types. Here, we provide the first ultrastructural description of the oviposited opsiblastic eggs of the freshwater gastrotrich, Lepidodermella squamata. Scanning electron microscopy revealed the eggshell surface to be ornamented with long flattened pillar-like structures centered on polygonal plates that are pitted along their periphery. Transmission electron microscopy showed the pits to lead to a vast labyrinth of tubular spaces and larger cavities throughout the thick apical layer of the shell. The basal layer of the shell is amorphous and connected to a network of fine fibers that traverse an extra-oocyte space and forms a protective sheet around the uncleaved oocyte. The uncleaved oocyte has a dense layer of peripheral ooplasm surrounding a core of organelles including mitochondria, membrane-bound secretion granules, endoplasmic reticulum, and a single nucleus in a granular, ribosome-rich cytoplasm. Secretion granules are the most abundant organelles and presumably contain lipid-rich yolk that will be used as energy for delayed cleavage, thus functioning in temporal dispersal. These data are compared to the fine structure of invertebrate resting eggs across the phylogenetic spectrum to determine the novelty of opsiblastic egg structure in L. squamata.},
}
@article {pmid38097150,
year = {2024},
author = {Hew, YX and Ya'cob, Z and Chen, CD and Lau, KW and Sofian-Azirun, M and Muhammad-Rasul, AH and Putt, QY and Tan, TK and Hadi, UK and Suana, IW and Takaoka, H and Low, VL},
title = {Co-occurrence of dual lineages within Simulium (Gomphostilbia) atratum De Meijere in the Indonesian Archipelago along Wallace's Line.},
journal = {Acta tropica},
volume = {250},
number = {},
pages = {107097},
doi = {10.1016/j.actatropica.2023.107097},
pmid = {38097150},
issn = {1873-6254},
mesh = {Animals ; Indonesia ; *Simuliidae/genetics ; Mitochondria ; Phylogeny ; Genetic Variation ; },
abstract = {Mitochondrial cytochrome c oxidase subunit I (COI) sequences were utilized to infer the population genetic structure of Simulium (Gomphostilbia) atratum De Meijere, an endemic simulid species to Indonesia. Both median-joining haplotype network and maximum-likelihood tree revealed two genetic lineages (A and B) within the species, with an overlap distribution in Lombok, which is situated along Wallace's line. Genetic differentiation and gene flow with varying frequencies (FST = 0.02-0.967; Nm = 0.01-10.58) were observed between populations of S. (G.) atratum, of which population pairs of different lineages showed high genetic differentiation. Notably, the high genetic distance of up to 5.92 % observed within S. (G.) atratum in Lombok was attributed to the existence of two genetically distinct lineages. The co-occurrence of distinct lineages in Lombok indicated that Wallace's line did not act as faunistic border for S. (G.) atratum in the present study. Moreover, both lineages also exhibited unimodal distributions and negative values of neutrality tests, suggesting a pattern of population expansion. The expansion and divergence time estimation suggested that the two lineages of S. (G.) atratum diverged and expanded during the Pleistocene era in Indonesia.},
}
@article {pmid38095728,
year = {2023},
author = {Chen, W and Zhang, H and Meng, R and Zhang, X and Duo, H and Guo, Z and Shen, X and Chen, C and Li, Z and Fu, Y},
title = {Genome-wide phylogenetic and genetic evolutionary analyses of mitochondria in Hypoderma bovis and H. sinense on the Qinghai-Tibetan Plateau.},
journal = {Parasitology research},
volume = {123},
number = {1},
pages = {43},
pmid = {38095728},
issn = {1432-1955},
mesh = {Animals ; Cattle ; Humans ; Phylogeny ; RNA, Ribosomal, 16S ; Tibet ; *Diptera ; Mitochondria/genetics ; Mammals ; },
abstract = {Hypoderma bovis (H. bovis) and Hypoderma sinense (H. sinense) are insects that cause hypodermosis in yaks and Bos taurus. Hypodermosis is a severe skin condition that not only impairs the development of local animal husbandry but also poses threats to human health as a zoonosis. The Qinghai-Tibetan Plateau (QTP) is known as the "Roof of the World." Its unique geographical environment and climate conditions have supported the growth of a wide range of mammals, providing favorable conditions for Hypoderma spp. to complete their life cycles. In this study, the whole mitochondrial genomes of H. bovis and H. sinense collected from the QTP were sequenced and phylogenetically analyzed. We found that the whole genomes of H. bovis and H. sinense are 16,283 bp and 16,300 bp in length, respectively. Both the H. bovis and H. sinense genomes have 37 mitochondrial genes, which include two rRNA genes (16S rRNA and 12S rRNA), 22 tRNA genes, the control region (D-loop region), the light chain replication initiation region, and 13 protein-coding genes (PCGs). The phylogenetic tree generated based on the 13 PCGs revealed close phylogenetic relationships between H. sinense, H. bovis, and Hypoderma lineatum. A similar result was also found in our phylogenetic analysis based on 18S rRNA and 28S rRNA. However, analysis of cytochrome oxidase subunit I (COI) showed cluster of H. bovis, H. sinense, and Cuterebra spp. on the same branch, all belonging to Oestridae. The differentiation time generated based on 13 PCGs indicates that H. bovis and H. sinense differentiated and formed ~4.69 million years ago (Mya) and ~4.06 Mya, respectively. This timing coincides with the differentiation and appearance of yak and Bos taurus in the Pliocene (~4.7 Mya), indicating that the parasites and mammals diverged in close temporal proximity. Of note, this period also witnessed a rapid uplift of the QTP, causing significant climate and environmental changes. Thus, we conjecture that the differentiation of Hypoderma spp. is potentially related to the differentiation of their host species, as well as climate changes caused by the uplift of the QTP. Overall, our study can provide valuable data to support further studies on the phylogeny and differentiation of Hypoderma spp. on the QTP.},
}
@article {pmid38093186,
year = {2023},
author = {Hamza, H and Villa, S and Torre, S and Marchesini, A and Benabderrahim, MA and Rejili, M and Sebastiani, F},
title = {Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {772},
pmid = {38093186},
issn = {1471-2164},
support = {GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; },
mesh = {*Phoeniceae/genetics ; *Genome, Chloroplast ; Phylogeny ; Plant Breeding ; Chloroplasts/genetics ; Mitochondria/genetics ; },
abstract = {BACKGROUND: Date palm (Phoenix dactylifera L.) is the most widespread crop in arid and semi-arid regions and has great traditional and socioeconomic importance, with its fruit well-known for its high nutritional and health value. However, the genetic variation of date palm cultivars is often neglected. The advent of high-throughput sequencing has made possible the resequencing of whole organelle (mitochondria and chloroplast) genomes to explore the genetic diversity and phylogenetic relationships of cultivated plants with unprecedented detail.<br><br>RESULTS: Whole organelle genomes of 171 Tunisian accessions (135 females and 36 males) were sequenced. Targeted bioinformatics pipelines were used to identify date palm haplotypes and genome variants, aiming to provide variant annotation and investigate patterns of evolutionary relationship. Our results revealed the existence of unique haplotypes, identified by 45 chloroplastic and 156 mitochondrial SNPs. Estimation of the effect of these SNPs on genes functions was predicted in silico.<br><br>CONCLUSIONS: The results of this study have important implications, in the light of ongoing environmental changes, for the conservation and sustainable use of the genetic resources of date palm cultivars in Tunisia, where monoculture threatens biodiversity leading to genetic erosion. These data will be useful for breeding and genetic improvement programs of the date palm through selective cross-breeding.},
}
@article {pmid38092275,
year = {2024},
author = {Gaudó, P and de Tomás-Mateo, E and Garrido-Pérez, N and Santana, A and Ruiz-Pesini, E and Montoya, J and Bayona-Bafaluy, P},
title = {"ATAD3C regulates ATAD3A assembly and function in the mitochondrial membrane".},
journal = {Free radical biology &amp; medicine},
volume = {211},
number = {},
pages = {114-126},
doi = {10.1016/j.freeradbiomed.2023.12.006},
pmid = {38092275},
issn = {1873-4596},
mesh = {Humans ; *Adenosine Triphosphatases/genetics/metabolism ; ATPases Associated with Diverse Cellular Activities/genetics/chemistry/metabolism ; Gene Duplication ; Membrane Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; *Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/metabolism ; },
abstract = {Mitochondrial ATAD3A is an ATPase Associated with diverse cellular Activities (AAA) domain containing enzyme, involved in the structural organization of the inner mitochondrial membrane and of increasing importance in childhood disease. In humans, two ATAD3A paralogs arose by gene duplication during evolution: ATAD3B and ATAD3C. Here we investigate the cellular activities of the ATAD3C paralog that has been considered a pseudogene. We detected unique ATAD3C peptides in HEK 293T cells, with expression similar to that in human tissues, and showed that it is an integral membrane protein that exposes its carboxy-terminus to the intermembrane space. Overexpression of ATAD3C, but not of ATAD3A, in fibroblasts caused a decrease in cell proliferation and oxygen consumption rate, and an increase of cellular ROS. This was due to the incorporation of ATAD3C monomers in ATAD3A complex in the mitochondrial membrane reducing its size. Consistent with a negative regulation of ATAD3A function in mitochondrial membrane organization, ATAD3C expression led to increased accumulation of respiratory chain dimeric CIII in the inner membrane, to the detriment to that assembled in respiratory supercomplexes. Our results demonstrate a negative dominant role of the ATAD3C paralog with implications for mitochondrial OXPHOS function and suggest that its expression regulates ATAD3A in the cell.},
}
@article {pmid38077409,
year = {2023},
author = {Santamaria, CA and Griffiths, CL},
title = {Cryptic diversity and phylogeographic patterns of Deto echinata (Isopoda: Detonidae) in southern Africa.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16529},
pmid = {38077409},
issn = {2167-8359},
mesh = {Humans ; Animals ; *Isopoda/genetics ; Phylogeny ; Phylogeography ; Africa, Southern ; Mitochondria ; },
abstract = {Recent phylogeographic studies of poorly-dispersing coastal invertebrates in highly biodiverse regions have led to the discovery of high levels of cryptic diversity and complex phylogeographic patterns that suggest isolation, geological, and ecological processes have shaped their biodiversity. Studies of southern African coastal invertebrates have uncovered cryptic diversity for various taxa and phylogeographic patterns that, although sharing some similarities across taxa, do differ. These findings underscore the need for additional studies to better understand the biodiversity levels, distributional patterns, and processes responsible for producing coastal biodiversity in that region. The coastal isopod Deto echinata is of particular interest, as its complex taxonomic history, poor dispersal capabilities, and broad geographic distribution suggest the potential for cryptic diversity. We use mitochondrial and nuclear sequences to characterize D. echinata individuals from localities ranging from northern Namibia to Glentana, about 2,500 km along the coastline on the south coast of South Africa. These are used to assess whether D. echinata harbors cryptic genetic diversity and whether phylogeographic distributional patterns correlate with those previously documented for other coastal isopods in the region. Analysis of mitochondrial and nuclear sequences revealed two deeply-divergent lineages that exhibit a distributional break in the Cape Peninsula region. These findings suggest D. echinata is a cryptic species complex in need of taxonomic revision and highlight the need for further taxonomic and phylogeographic studies of similarly poorly-dispersing coastal invertebrates in southern Africa.},
}
@article {pmid38075892,
year = {2023},
author = {Wolters, JF and LaBella, AL and Opulente, DA and Rokas, A and Hittinger, CT},
title = {Mitochondrial genome diversity across the subphylum Saccharomycotina.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1268944},
pmid = {38075892},
issn = {1664-302X},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
abstract = {INTRODUCTION: Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available.<br><br>METHODS: By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades.<br><br>RESULTS: Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements.<br><br>DISCUSSION: As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.},
}
@article {pmid38073308,
year = {2024},
author = {Lin, Y and Yang, H and Liu, H and Lu, X and Cao, H and Li, B and Chang, Y and Guo, Z and Ding, D and Hu, Y and Xue, Y and Liu, Z and Tang, J},
title = {A P-type pentatricopeptide repeat protein ZmRF5 promotes 5' region partial cleavages of atp6c transcripts to restore the fertility of CMS-C maize by recruiting a splicing factor.},
journal = {Plant biotechnology journal},
volume = {22},
number = {5},
pages = {1269-1281},
pmid = {38073308},
issn = {1467-7652},
support = {32272165//National Natural Science Foundation of China/ ; 31571745//National Natural Science Foundation of China/ ; },
mesh = {*Zea mays/genetics ; RNA Splicing Factors ; Cytoplasm/genetics ; *Fertility/genetics ; Mitochondria/genetics ; Plant Infertility/genetics ; },
abstract = {A fast evolution within mitochondria genome(s) often generates discords between nuclear and mitochondria, which is manifested as cytoplasmic male sterility (CMS) and fertility restoration (Rf) system. The maize CMS-C trait is regulated by the chimeric mitochondrial gene, atp6c, and can be recovered by the restorer gene ZmRf5. Through positional cloning in this study, we identified the nuclear restorer gene, ZmRf5, which encodes a P-type pentatricopeptide repeat (PPR) family protein. The over-expression of ZmRf5 brought back the fertility to CMS-C plants, whereas its genomic editing by CRISPR/Cas9 induced abortive pollens in the restorer line. ZmRF5 is sorted to mitochondria, and recruited RS31A, a splicing factor, through MORF8 to form a cleaving/restoring complex, which promoted the cleaving of the CMS-associated transcripts atp6c by shifting the major cleavage site from 480th nt to 344 th nt for fast degradation, and preserved just right amount of atp6c RNA for protein translation, providing adequate ATP6C to assembly complex V, thus restoring male fertility. Interestingly, ATP6C in the sterile line CMo17A, with similar cytology and physiology changes to YU87-1A, was accumulated much less than it in NMo17B, exhibiting a contrary trend in the YU87-1 nuclear genome previously reported, and was restored to normal level in the presence of ZmRF5. Collectively these findings unveil a new molecular mechanism underlying fertility restoration by which ZmRF5 cooperates with MORF8 and RS31A to restore CMS-C fertility in maize, complemented and perfected the sterility mechanism, and enrich the perspectives on communications between nucleus and mitochondria.},
}
@article {pmid38070787,
year = {2024},
author = {Das, PJ and Kumar, S and Choudhury, M and Banik, S and Pegu, SR and Kumar, S and Deb, R and Gupta, VK},
title = {Characterization of the complete mitochondrial genome and identification of signature sequence of Indian wild pig.},
journal = {Gene},
volume = {897},
number = {},
pages = {148070},
doi = {10.1016/j.gene.2023.148070},
pmid = {38070787},
issn = {1879-0038},
mesh = {Animals ; *Genome, Mitochondrial/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genomics ; Sequence Analysis, DNA ; },
abstract = {Mitochondrial DNA (mtDNA) serves as a valuable molecular marker for constructing matrilineal genealogies and tracing the evolutionary history of animals. This study aimed to characterize the complete mitochondrial genome of the Indian wild pig (IWB) (Sus scrofa cristatus) and identify IWB-specific DNA sequences that could be used as genomic signatures to differentiate IWB from domestic Indian pigs (IDP) in forensic cases. For the purpose, three wild IWB from a rescue centre were used for the characterization of the mitochondrial genome of the IWB. The mitochondrial genome was sequenced by the primer walking technique using 30 overlapping primers. The mitochondrial genome of the IWB was found to be 16,689 bp long containing 37 genes coding for 2 rRNAs, 22 tRNAs, 13 protein coding genes, and 1 D-loop region similar to the mitogenome of other pigs. Sequence analysis of the D-loop of IWB with other IDP indicated some signature sequence for IWB like duplication and transition event from 1090[th] to 1099[th] position, deletion of a 10 bp sequence at the 755[th] position, insertion of (CA) at the 137[th] position, and substitution of AT to GA at the 638[th] position. These variations specially the duplication along with transition event causes creation of unique signature sequence (-ACACAAACCT-) in the IWB that could serve as signature sequences for the IWB and be used as markers for differentiation of IWB from IDP breeds in academic as well as forensic or vetero-legal cases. Overall, a total of 36 polymorphic positions were identified in the IWB, with 29 sites being unique to the IWB only and seven being common to the Doom and HDK75 pig breeds. None of the common polymorphic sites were identified in prevailing domestic pig populations. Phylogenetic analysis of the mitochondrial genome revealed the distinct separation of the IWB from IDP. The results of genetic distance evaluation showed that the Doom pig breed was the closest to the IWB. This study provides valuable insights into the mitogenome characterisation, signature sequence and genetic distance analysis of the IWB and establishes a foundation for future studies on the conservation of this protected species.},
}
@article {pmid38062387,
year = {2023},
author = {Ouyang, L and Liu, Y and Yao, R and He, D and Yan, L and Chen, Y and Huai, D and Wang, Z and Yu, B and Kang, Y and Jiang, H and Lei, Y and Liao, B and Wang, X},
title = {Genome-wide analysis of UDP-glycosyltransferase gene family and identification of a flavonoid 7-O-UGT (AhUGT75A) enhancing abiotic stress in peanut (Arachis hypogaea L.).},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {626},
pmid = {38062387},
issn = {1471-2229},
support = {CARS-13//earmarked fund for China Agricultural Research System/ ; CARS-13//earmarked fund for China Agricultural Research System/ ; CARS-13//earmarked fund for China Agricultural Research System/ ; CAAS-ASTIP-2021-OCRI//Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences/ ; CAAS-ASTIP-2021-OCRI//Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences/ ; CAAS-ASTIP-2021-OCRI//Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences/ ; 32170278//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Arachis/genetics ; Glycosyltransferases/genetics ; Phylogeny ; Flavonoids ; Plant Breeding ; Stress, Physiological/genetics ; *Arabidopsis ; Uridine Diphosphate ; },
abstract = {BACKGROUND: Glycosylation, catalyzed by UDP-glycosyltransferase (UGT), was important for enhancing solubility, bioactivity, and diversity of flavonoids. Peanut (Arachis hypogaea L.) is an important oilseed and cash crop worldwide. In addition to provide high quality of edible oils and proteins, peanut seeds contain a rich source of flavonoid glycosides that benefit human health. However, information of UGT gene family was quite limited in peanut.<br><br>RESULTS: In present study, a total of 267 AhUGTs clustered into 15 phylogenetic groups were identified in peanut genome. Group I has greatly expanded to contain the largest number of AhUGT genes. Segmental duplication was the major driving force for AhUGT gene family expansion. Transcriptomic analysis of gene expression profiles in various tissues and under different abiotic stress treatments indicated AhUGTs were involved in peanut growth and abiotic stress response. AhUGT75A (UGT73CG33), located in mitochondria, was characterized as a flavonoid 7-O-UGT by in vitro enzyme assays. The transcript level of AhUGT75A was strongly induced by abiotic stress. Overexpression of AhUGT75A resulted in accumulating less amount of malondialdehyde (MDA) and superoxide, and enhancing tolerance against drought and/or salt stress in transgenic Arabidopsis. These results indicated AhUGT75A played important roles in conferring abiotic stress tolerance through reactive oxygen species scavenging.<br><br>CONCLUSIONS: Our research only not provides valuable information for functional characterization of UGTs in peanut, but also gives new insights into potential applications in breeding new cultivars with both desirable stress tolerance and health benefits.},
}
@article {pmid38060519,
year = {2023},
author = {Novák, LVF and Treitli, SC and Pyrih, J and Hałakuc, P and Pipaliya, SV and Vacek, V and Brzoň, O and Soukal, P and Eme, L and Dacks, JB and Karnkowska, A and Eliáš, M and Hampl, V},
title = {Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria.},
journal = {PLoS genetics},
volume = {19},
number = {12},
pages = {e1011050},
pmid = {38060519},
issn = {1553-7404},
support = {R21 ES021028/ES/NIEHS NIH HHS/United States ; },
mesh = {Phylogeny ; *Eukaryota/genetics ; *Oxymonadida/genetics/metabolism ; Mitochondria/genetics ; Genomics ; },
abstract = {The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the genera Trimastix and Paratrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-living Paratrimastix pyriformis and the oxymonad Blattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis, B. nauphoetae, and Streblomastix strix), suggesting the amitochondriate status is common to a large part if not the whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.},
}
@article {pmid38053364,
year = {2023},
author = {Camus, MF and Inwongwan, S},
title = {Mitonuclear interactions modulate nutritional preference.},
journal = {Biology letters},
volume = {19},
number = {12},
pages = {20230375},
pmid = {38053364},
issn = {1744-957X},
mesh = {Animals ; Genotype ; *Mitochondria/genetics ; Haplotypes ; Drosophila/genetics ; *Life History Traits ; DNA, Mitochondrial/genetics ; Cell Nucleus/genetics ; },
abstract = {In nature, organisms are faced with constant nutritional options which fuel key life-history traits. Studies have shown that species can actively make nutritional decisions based on internal and external cues. Metabolism itself is underpinned by complex genomic interactions involving components from both nuclear and mitochondrial genomes. Products from these two genomes must coordinate how nutrients are extracted, used and recycled. Given the complicated nature of metabolism, it is not well understood how nutritional choices are affected by mitonuclear interactions. This is under the rationale that changes in genomic interactions will affect metabolic flux and change physiological requirements. To this end we used a large Drosophila mitonuclear genetic panel, comprising nine isogenic nuclear genomes coupled to nine mitochondrial haplotypes, giving a total of 81 different mitonuclear genotypes. We use a capillary-based feeding assay to screen this panel for dietary preference between carbohydrate and protein. We find significant mitonuclear interactions modulating nutritional choices, with these epistatic interactions also being dependent on sex. Our findings support the notion that complex genomic interactions can place a constraint on metabolic flux. This work gives us deeper insights into how key metabolic interactions can have broad implications on behaviour.},
}
@article {pmid38052127,
year = {2024},
author = {Fernández Miyakawa, ME and Casanova, NA and Kogut, MH},
title = {How did antibiotic growth promoters increase growth and feed efficiency in poultry?.},
journal = {Poultry science},
volume = {103},
number = {2},
pages = {103278},
pmid = {38052127},
issn = {1525-3171},
mesh = {Animals ; *Poultry ; Anti-Bacterial Agents/pharmacology/metabolism ; Chickens ; Mitochondria/metabolism ; *Gastrointestinal Microbiome ; },
abstract = {It has been hypothesized that reducing the bioenergetic costs of gut inflammation as an explanation for the effect of antibiotic growth promoters (AGPs) on animal efficiency, framing some observations but not explaining the increase in growth rate or the prevention of infectious diseases. The host's ability to adapt to alterations in environmental conditions and to maintain health involves managing all physiological interactions that regulate homeostasis. Thus, metabolic pathways are vital in regulating physiological health as the energetic demands of the host guides most biological functions. Mitochondria are not only the metabolic heart of the cell because of their role in energy metabolism and oxidative phosphorylation, but also a central hub of signal transduction pathways that receive messages about the health and nutritional states of cells and tissues. In response, mitochondria direct cellular and tissue physiological alterations throughout the host. The endosymbiotic theory suggests that mitochondria evolved from prokaryotes, emphasizing the idea that these organelles can be affected by some antibiotics. Indeed, therapeutic levels of several antibiotics can be toxic to mitochondria, but subtherapeutic levels may improve mitochondrial function and defense mechanisms by inducing an adaptive response of the cell, resulting in mitokine production which coordinates an array of adaptive responses of the host to the stressor(s). This adaptive stress response is also observed in several bacteria species, suggesting that this protective mechanism has been preserved during evolution. Concordantly, gut microbiome modulation by subinhibitory concentration of AGPs could be the result of direct stimulation rather than inhibition of determined microbial species. In eukaryotes, these adaptive responses of the mitochondria to internal and external environmental conditions, can promote growth rate of the organism as an evolutionary strategy to overcome potential negative conditions. We hypothesize that direct and indirect subtherapeutic AGP regulation of mitochondria functional output can regulate homeostatic control mechanisms in a manner similar to those involved with disease tolerance.},
}
@article {pmid38047232,
year = {2023},
author = {Charrasse, S and Poquillon, T and Saint-Omer, C and Pastore, M and Bordignon, B and Frye, RE and Reynes, C and Racine, V and Aouacheria, A},
title = {Quantitative assessment of mitochondrial morphology relevant for studies on cellular health and environmental toxicity.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {5609-5619},
pmid = {38047232},
issn = {2001-0370},
abstract = {Mitochondria are essential organelles that play crucial roles in cellular energy metabolism, calcium signaling and apoptosis. Their importance in tissue homeostasis and stress responses, combined to their ability to transition between various structural and functional states, make them excellent organelles for monitoring cellular health. Quantitative assessment of mitochondrial morphology can therefore provide valuable insights into environmentally-induced cell damage. High-content screening (HCS) provides a powerful tool for analyzing organelles and cellular substructures. We developed a fully automated and miniaturized HCS wet-plus-dry pipeline (MITOMATICS) exploiting mitochondrial morphology as a marker for monitoring cellular health or damage. MITOMATICS uses an in-house, proprietary software (MitoRadar) to enable fast, exhaustive and cost-effective analysis of mitochondrial morphology and its inherent diversity in live cells. We applied our pipeline and big data analytics software to assess the mitotoxicity of selected chemicals, using the mitochondrial uncoupler CCCP as an internal control. Six different pesticides (inhibiting complexes I, II and III of the mitochondrial respiratory chain) were tested as individual compounds and five other pesticides present locally in Occitanie (Southern France) were assessed in combination to determine acute mitotoxicity. Our results show that the assayed pesticides exhibit specific signatures when used as single compounds or chemical mixtures and that they function synergistically to impact mitochondrial architecture. Study of environment-induced mitochondrial damage has the potential to open new fields in mechanistic toxicology, currently underexplored by regulatory toxicology and exposome research. Such exploration could inform health policy guidelines and foster pharmacological intervention, water, air and soil pollution control and food safety.},
}
@article {pmid38047014,
year = {2023},
author = {Kobayashi, G},
title = {Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA).},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16446},
pmid = {38047014},
issn = {2167-8359},
mesh = {Humans ; Animals ; Genes, Mitochondrial ; Phylogeny ; *Annelida ; DNA, Mitochondrial/genetics ; *Polychaeta/genetics ; },
abstract = {BACKGROUND: The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA.<br><br>METHODS: The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank.<br><br>RESULTS AND DISCUSSION: mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22-24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.},
}
@article {pmid38042216,
year = {2024},
author = {Kong, D and Gan, Z and Li, X},
title = {Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes.},
journal = {Gene},
volume = {896},
number = {},
pages = {148054},
doi = {10.1016/j.gene.2023.148054},
pmid = {38042216},
issn = {1879-0038},
mesh = {Humans ; Phylogeny ; *Genome, Mitochondrial/genetics ; RNA, Transfer/genetics ; RNA, Ribosomal/genetics ; },
abstract = {The deep-sea environment is characterized by extreme and inhospitable conditions, including oxygen depletion, low temperatures, high pressure, absence of light, and limited food availability. Mitochondria and mitogenomes play a crudial role in aerobic respiration to generate energy for eukaryotes. Here, using the Illumina Hiseq 4000 platform, we performed mitogenome sequencing for five deep-sea caridean species: Lebbeus shinkaiae, Lebbeus Formosus, Glyphocrangon regalis, Heterocarpus dorsalis, and Heterocarpus laevigatus, and five deep-sea caridean mitogenomes were assembled and identified. Each of the five mitogenomes contained 13 protein-coding genes, 2 rRNAs and 22 tRNAs. Specific elements, such as tandem repeats and AT-rich sequences, were observed in the control regions of Lebbeus formosus and Lebbeus shinkaiae, potentially take a role in regulating mitochondrial genome replication and transcription. The gene order of all obtained mitogenomes follows caridean ancestral type organization. Phylogenetic analysis shows a robustly supported phylogenetic tree for the infraorder Caridea. The monophyly of the families included in this study was strongly supported. This study supports the monophyly of Oplophoroidea, but rejects the monophyletic status of Nematocarcinoidea, Crangonoidea, and Alpheoidea. At the genus level, Plesionika is polyphyletic and Rimicaris is paraphyletic in our analysis. Furthermore, Paralebbeus may be considered invalid and synonymous with Lebbeus. Positive selection analysis reveals evidence for adaptive changes in the mitogenome of different deep-sea caridean lineages. Nine residues located in cox1, cox3, atp6, nad1, nad2, nad4, nad5, nad6 and cytb were determined to have undergone positive selection. Mitogenome of different deep-sea lineages experienced different positive selection, and the lineage represented by Alvinocarididae living in deep-sea hydrothermal vents experienced the strongest positive selection. This study provides valuable insights into the adaptive evolution of deep-sea shrimps at the mitochondrial, highlighting the mitogenomic strategy that contribute to their unique adaptations in the deep-sea environment.},
}
@article {pmid38036853,
year = {2024},
author = {Ando, R and Shimozono, S and Ago, H and Takagi, M and Sugiyama, M and Kurokawa, H and Hirano, M and Niino, Y and Ueno, G and Ishidate, F and Fujiwara, T and Okada, Y and Yamamoto, M and Miyawaki, A},
title = {StayGold variants for molecular fusion and membrane-targeting applications.},
journal = {Nature methods},
volume = {21},
number = {4},
pages = {648-656},
pmid = {38036853},
issn = {1548-7105},
support = {JP15dm0207001//Japan Agency for Medical Research and Development (AMED)/ ; JP21am0101070//Japan Agency for Medical Research and Development (AMED)/ ; 21H05041//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 19H05794, 19H05795//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; JPM JCR20E2//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; },
mesh = {*Mitochondria/chemistry ; *Golgi Apparatus/metabolism ; Microtubules/metabolism ; Microscopy, Confocal/methods ; },
abstract = {Although StayGold is a bright and highly photostable fluorescent protein, its propensity for obligate dimer formation may hinder applications in molecular fusion and membrane targeting. To attain monovalent as well as bright and photostable labeling, we engineered tandem dimers of StayGold to promote dispersibility. On the basis of the crystal structure of this fluorescent protein, we disrupted the dimerization to generate a monomeric variant that offers improved photostability and brightness compared to StayGold. We applied the new monovalent StayGold tools to live-cell imaging experiments using spinning-disk laser-scanning confocal microscopy or structured illumination microscopy. We achieved cell-wide, high-spatiotemporal resolution and sustained imaging of dynamic subcellular events, including the targeting of endogenous condensin I to mitotic chromosomes, the movement of the Golgi apparatus and its membranous derivatives along microtubule networks, the distribution of cortical filamentous actin and the remolding of cristae membranes within mobile mitochondria.},
}
@article {pmid38019044,
year = {2024},
author = {Osiewacz, HD},
title = {Impact of Mitochondrial Architecture, Function, Redox Homeostasis, and Quality Control on Organismic Aging: Lessons from a Fungal Model System.},
journal = {Antioxidants &amp; redox signaling},
volume = {40},
number = {16-18},
pages = {948-967},
doi = {10.1089/ars.2023.0487},
pmid = {38019044},
issn = {1557-7716},
mesh = {*Mitochondria/metabolism ; *Homeostasis ; *Oxidation-Reduction ; *Aging/metabolism ; *Podospora/metabolism/genetics ; Humans ; *Reactive Oxygen Species/metabolism ; Oxidative Stress ; Models, Biological ; },
abstract = {Significance: Mitochondria are eukaryotic organelles with various essential functions. They are both the source and the targets of reactive oxygen species (ROS). Different branches of a mitochondrial quality control system (mQCS), such as ROS balancing, degradation of damaged proteins, or whole mitochondria, can mitigate the adverse effects of ROS stress. However, the capacity of mQCS is limited. Overwhelming this capacity leads to dysfunctions and aging. Strategies to interfere into mitochondria-dependent human aging with the aim to increase the healthy period of life, the health span, rely on the precise knowledge of mitochondrial functions. Experimental models such as Podospora anserina, a filamentous fungus with a clear mitochondrial aging etiology, proved to be instrumental to reach this goal. Recent Advances: Investigations of the P. anserina mQCS revealed that it is constituted by a complex network of different branches. Moreover, mitochondrial architecture and lipid homeostasis emerged to affect aging. Critical Issues: The regulation of the mQCS is only incompletely understood. Details about the involved signaling molecules and interacting pathways remain to be elucidated. Moreover, most of the currently generated experimental data were generated in well-controlled experiments that do not reflect the constantly changing natural life conditions and bear the danger to miss relevant aspects leading to incorrect conclusions. Future Directions: In P. anserina, the precise impact of redox signaling as well as of molecular damaging for aging remains to be defined. Moreover, natural fluctuation of environmental conditions needs to be considered to generate a realistic picture of aging mechanisms as they developed during evolution.},
}
@article {pmid38007160,
year = {2024},
author = {Gao, X and Feng, B and Du, C and Hou, C and Jin, S and Tang, D and Zhu, J and Lv, Y},
title = {Expression dynamics indicate the involvement of SPG7 in the reproduction and spermiogenesis of Phascolosoma esculenta.},
journal = {Gene},
volume = {895},
number = {},
pages = {148028},
doi = {10.1016/j.gene.2023.148028},
pmid = {38007160},
issn = {1879-0038},
mesh = {Animals ; Male ; ATPases Associated with Diverse Cellular Activities/genetics/metabolism ; *Mitochondria/genetics/metabolism ; Spermatogenesis/genetics ; *Spastic Paraplegia, Hereditary/genetics ; Metalloendopeptidases/genetics ; },
abstract = {Spastic paraplegia 7 (SPG7) is an m-AAA protease subunit involved in mitochondrial morphology and physiology. However, its function in animal reproduction is yet to be evaluated. In this study, its molecular features, subcellular localization, and expression dynamics were investigated to analyze its potential function in the reproduction of male Phascolosoma esculenta, an economically important marine species in China. The full-length cDNA of P. esculenta spg7 (Pe-spg7) measures 3053 bp and encodes an 853-amino acid protein (Pe-SPG7). Pe-SPG7 includes two transmembrane domains, an AAA domain and a proteolytic domain. Amino acid sequence alignment revealed that SPG7 was conserved during evolution. The mRNA and protein expression of spg7 indicated its involvement in reproduction. Its expression was the highest in coelomic fluid, where spermatids develop, and it was significantly higher in the breeding stage than in the nonbreeding stage. SPG7 was mainly found in the mitochondria of spermatids in the coelomic fluid, indicating that it functions in this organelle in spermatids. Immunofluorescence experiments showed that SPG7 was expressed and colocalized in the mitochondria during spermiogenesis, suggesting its involvement in P. esculenta spermiogenesis. Therefore, SPG7 may participate in spermiogenesis by functioning in the mitochondria and regulate the reproduction of male P. esculenta. This study provided insights into the function of SPG7 in animal reproduction and P. esculenta gametogenesis.},
}
@article {pmid38006556,
year = {2024},
author = {Duplouy, A},
title = {Validating a Mitochondrial Sweep Accompanying the Rapid Spread of a Maternally Inherited Symbiont.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {239-247},
pmid = {38006556},
issn = {1940-6029},
mesh = {*Maternal Inheritance ; *Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Polymorphism, Genetic ; Biological Evolution ; Symbiosis/genetics ; Phylogeny ; },
abstract = {Maternally inherited symbiotic bacteria that interfere with the reproduction of their hosts can contribute to selective sweeps of mitochondrial haplotypes through hitch-hiking or coordinate inheritance of cytoplasmic bacteria and host mitochondria. The sweep will be manifested by genetic variations of mitochondrial genomic DNA of symbiont-infected hosts relative to their uninfected counterparts. In particular, at the population level, infected specimens will show a reduced mitochondrial DNA polymorphism compared to that in the nuclear DNA. This may challenge the use of mitochondrial DNA sequences as neutral genetic markers, as the mitochondrial patterns will reflect the evolutionary history of parasitism, rather than the sole evolutionary history of the host. Here, I describe a detailed step-by-step procedure to infer the occurrence and timing of symbiont-induced mitochondrial sweeps in host species.},
}
@article {pmid38002320,
year = {2023},
author = {Nusir, A and Sinclair, P and Kabbani, N},
title = {Mitochondrial Proteomes in Neural Cells: A Systematic Review.},
journal = {Biomolecules},
volume = {13},
number = {11},
pages = {},
pmid = {38002320},
issn = {2218-273X},
mesh = {Humans ; *Proteome/metabolism ; *Neurodegenerative Diseases/metabolism ; Proteomics ; Mitochondria/metabolism ; Neurons/metabolism ; Mitochondrial Proteins/metabolism ; },
abstract = {Mitochondria are ancient endosymbiotic double membrane organelles that support a wide range of eukaryotic cell functions through energy, metabolism, and cellular control. There are over 1000 known proteins that either reside within the mitochondria or are transiently associated with it. These mitochondrial proteins represent a functional subcellular protein network (mtProteome) that is encoded by mitochondrial and nuclear genomes and significantly varies between cell types and conditions. In neurons, the high metabolic demand and differential energy requirements at the synapses are met by specific modifications to the mtProteome, resulting in alterations in the expression and functional properties of the proteins involved in energy production and quality control, including fission and fusion. The composition of mtProteomes also impacts the localization of mitochondria in axons and dendrites with a growing number of neurodegenerative diseases associated with changes in mitochondrial proteins. This review summarizes the findings on the composition and properties of mtProteomes important for mitochondrial energy production, calcium and lipid signaling, and quality control in neural cells. We highlight strategies in mass spectrometry (MS) proteomic analysis of mtProteomes from cultured cells and tissue. The research into mtProteome composition and function provides opportunities in biomarker discovery and drug development for the treatment of metabolic and neurodegenerative disease.},
}
@article {pmid37999092,
year = {2023},
author = {Liu, SP and Yin, HD and Li, WJ and Qin, ZH and Yang, Y and Huang, ZZ and Zong, L and Liu, XK and Du, Z and Fan, WL and Zhang, YQ and Zhang, D and Zhang, YE and Liu, XY and Yang, D and Ge, SQ},
title = {The Morphological Transformation of the Thorax during the Eclosion of Drosophila melanogaster (Diptera: Drosophilidae).},
journal = {Insects},
volume = {14},
number = {11},
pages = {},
pmid = {37999092},
issn = {2075-4450},
support = {32270460//National Science Foundation of China/ ; 2021xjkk0605//Third Xinjiang Scientific Expedition Program/ ; },
abstract = {The model organism Drosophila melanogaster, as a species of Holometabola, undergoes a series of transformations during metamorphosis. To deeply understand its development, it is crucial to study its anatomy during the key developmental stages. We describe the anatomical systems of the thorax, including the endoskeleton, musculature, nervous ganglion, and digestive system, from the late pupal stage to the adult stage, based on micro-CT and 3D visualizations. The development of the endoskeleton causes original and insertional changes in muscles. Several muscles change their shape during development in a non-uniform manner with respect to both absolute and relative size; some become longer and broader, while others shorten and become narrower. Muscular shape may vary during development. The number of muscular bundles also increases or decreases. Growing muscles are probably anchored by the tissues in the stroma. Some muscles and tendons are absent in the adult stage, possibly due to the hardened sclerites. Nearly all flight muscles are present by the third day of the pupal stage, which may be due to the presence of more myofibers with enough mitochondria to support flight power. There are sexual differences in the same developmental period. In contrast to the endodermal digestive system, the functions of most thoracic muscles change in the development from the larva to the adult in order to support more complex locomotion under the control of a more structured ventral nerve cord based on the serial homology proposed herein.},
}
@article {pmid37996801,
year = {2023},
author = {Song, Y and Du, X and Li, A and Fan, A and He, L and Sun, Z and Niu, Y and Qiao, Y},
title = {Assembly and analysis of the complete mitochondrial genome of Forsythia suspensa (Thunb.) Vahl.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {708},
pmid = {37996801},
issn = {1471-2164},
support = {20210302123390//the Basic Research Program of Shanxi Province/ ; 2023//Shanxi Province Modern Agricultural Chinese Herbal Medicine Industry Technology System Project/ ; CXGC2023041//Shanxi Agricultural University Science and Technology Innovation Promotion Project/ ; },
mesh = {*Forsythia/genetics/chemistry ; *Genome, Mitochondrial/genetics ; Phylogeny ; *Plants, Medicinal/chemistry/genetics ; *Nucleic Acids ; *Genome, Chloroplast ; },
abstract = {BACKGROUND: Forsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear and chloroplast genomes of F. suspensa have been published, its complete mitochondrial genome sequence has yet to be reported. In this study, the genomic DNA of F. suspensa yellowish leaf material was extracted, sequenced by using a mixture of Illumina Novaseq6000 short reads and Oxford Nanopore PromethION long reads, and the sequencing data were assembled and annotated.<br><br>RESULT: The F. suspensa mitochondrial genome was obtained in the length of 535,692&#xa0;bp with a circular structure, and the GC content was 44.90%. The genome contains 60 genes, including 36 protein-coding genes, 21 tRNA genes, and three rRNA genes. We further analyzed RNA editing of the protein-coding genes, relative synonymous codon usage, and sequence repeats based on the genomic data. There were 25 homologous sequences between F. suspensa mitochondria and chloroplast genome, which involved the transfer of 8 mitochondrial genes, and 9473 homologous sequences between mitochondrial and nuclear genomes. Analysis of the nucleic acid substitution rate, nucleic acid diversity, and collinearity of protein-coding genes of the F. suspensa mitochondrial genome revealed that the majority of genes may have undergone purifying selection, exhibiting a slower rate of evolution and a relatively conserved structure. Analysis of the phylogenetic relationships among different species revealed that F. suspensa was most closely related to Olea europaea subsp. Europaea.<br><br>CONCLUSION: In this study, we sequenced, assembled, and annotated a high-quality F. suspensa mitochondrial genome. The results of this study will enrich the mitochondrial genome data of Forsythia, lay a foundation for the phylogenetic development of Forsythia, and promote the evolutionary analysis of Oleaceae species.},
}
@article {pmid37995039,
year = {2024},
author = {Lee, YJ and Uh, YR and Kim, YM and Kim, CM and Jang, CS},
title = {Characterization and comparative analysis of the complete organelle genomes of three red macroalgae species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis) and development of molecular makers for their identification.},
journal = {Genes &amp; genomics},
volume = {46},
number = {3},
pages = {355-365},
pmid = {37995039},
issn = {2092-9293},
support = {20210656//Korea Institute of Marine Science and Technology promotion/ ; },
mesh = {Humans ; *Seaweed/genetics ; Phylogeny ; *Rhodophyta/genetics ; Chloroplasts/genetics ; *Edible Seaweeds ; *Porphyra ; },
abstract = {BACKGROUND: Many species of red algae belonging to the phylum Rhodophyta are consumed by humans as raw materials for nutrition and medicine. As the seaweed market grows, the importance of the laver species has increased. The classification of red algal species has changed significantly, and the accuracy of this classification has improved significantly in recent years. Here, we report the complete circular genomes of the chloroplasts (cp) and mitochondria (mt) of three laver species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis).<br><br>OBJECTIVE: This study aims to assemble, annotate, and characterize the organization of the organelle genomes of three laver species, conduct comparative genomic studies, and develop molecular markers based on SNPs.<br><br>METHODS: We analyzed organelle genome structures, repeat sequences, sequence divergence, gene rearrangements, and phylogenetic relationships of three laver species.<br><br>RESULTS: The chloroplast genomes of the three species contained an average of 212 protein-coding genes (PCGs), while the mitochondrial genomes contained an average of 25 PCGs. We reconstructed the phylogenetic trees based on both chloroplast and mitochondrial genomes using 201 and 23 PCGs (in cp and mt genomes, respectively) shared in the class Bangiophyceae (and five species of Florideophyceae class used as an outgroup). In addition, 12 species-specific molecular markers were developed for qRT-PCR analysis.<br><br>CONCLUSIONS: This is the first report of Neoporphyra seriata complete organellar genomes. With the results, this study provides useful genetic information regarding taxonomic discrepancies, the reconstruction of phylogenetic trees, and the evolution of red algae. Moreover, the species-specific markers can be used as fast and easy methods to identify a target species.},
}
@article {pmid37994879,
year = {2023},
author = {Záhonová, K and Füssy, Z and Stairs, CW and Leger, MM and Tachezy, J and Čepička, I and Roger, AJ and Hampl, V},
title = {Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans.},
journal = {Microbial genomics},
volume = {9},
number = {11},
pages = {},
pmid = {37994879},
issn = {2057-5858},
mesh = {Anaerobiosis ; *Mitochondria/genetics ; *Eukaryota ; Iron ; Sulfates ; },
abstract = {Archamoebae comprises free-living or endobiotic amoebiform protists that inhabit anaerobic or microaerophilic environments and possess mitochondrion-related organelles (MROs) adapted to function anaerobically. We compared in silico reconstructed MRO proteomes of eight species (six genera) and found that the common ancestor of Archamoebae possessed very few typical components of the protein translocation machinery, electron transport chain and tricarboxylic acid cycle. On the other hand, it contained a sulphate activation pathway and bacterial iron-sulphur (Fe-S) assembly system of MIS-type. The metabolic capacity of the MROs, however, varies markedly within this clade. The glycine cleavage system is widely conserved among Archamoebae, except in Entamoeba, probably owing to its role in catabolic function or one-carbon metabolism. MRO-based pyruvate metabolism was dispensed within subgroups Entamoebidae and Rhizomastixidae, whereas sulphate activation could have been lost in isolated cases of Rhizomastix libera, Mastigamoeba abducta and Endolimax sp. The MIS (Fe-S) assembly system was duplicated in the common ancestor of Mastigamoebidae and Pelomyxidae, and one of the copies took over Fe-S assembly in their MRO. In Entamoebidae and Rhizomastixidae, we hypothesize that Fe-S cluster assembly in both compartments may be facilitated by dual localization of the single system. We could not find evidence for changes in metabolic functions of the MRO in response to changes in habitat; it appears that such environmental drivers do not strongly affect MRO reduction in this group of eukaryotes.},
}
@article {pmid37988339,
year = {2023},
author = {Kang, N and Hu, H},
title = {Adaptive evidence of mitochondrial genes in Pteromalidae and Eulophidae (Hymenoptera: Chalcidoidea).},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0294687},
pmid = {37988339},
issn = {1932-6203},
mesh = {Animals ; *Hymenoptera/genetics ; Genes, Mitochondrial ; Phylogeny ; Bayes Theorem ; Ecosystem ; Ultraviolet Rays ; Mitochondrial Proteins/genetics ; *Genome, Mitochondrial ; },
abstract = {Pteromalidae and Eulophidae are predominant and abundant taxa within Chalcidoidea (Hymenoptera: Apocrita). These taxa are found in diverse ecosystems, ranging from basin deserts (200 m) to alpine grasslands (4500 m). Mitochondria, cellular powerhouses responsible for energy production via oxidative phosphorylation, are sensitive to various environmental factors such as extreme cold, hypoxia, and intense ultraviolet radiation characteristic of alpine regions. Whether the molecular evolution of mitochondrial genes in these parasitoids corresponds to changes in the energy requirements and alpine environmental adaptations remains unknown. In this study, we performed a comparative analysis of mitochondrial protein-coding genes from 11 alpine species of Pteromalidae and Eulophidae, along with 18 lowland relatives, including 16 newly sequenced species. We further examined the codon usage preferences (RSCU, ENC-GC3s, neutrality, and PR2 bias plot) in these mitochondrial protein-coding sequences and conducted positive selection analysis based on their Bayesian phylogenetic relationships, and identified positive selection sites in the ATP6, ATP8, COX1, COX3, and CYTB genes, emphasizing the crucial role of mitochondrial gene adaptive evolution in the adaptation of Pteromalidae and Eulophidae to alpine environments. The phylogenetically independent contrast (PIC) analysis results verified the ω ratio of 13 PCGs from Pteromalidae and Eulophidae increased with elevation, and results from generalized linear model confirm that ATP6, ATP8, COX3, and ND1 are closely correlated with temperature-related environmental factors. This research not only enriched the molecular data of endemic alpine species but also underscores the significance of mitochondrial genes in facilitating the adaptation of these minor parasitoids to plateau habitats.},
}
@article {pmid37978174,
year = {2023},
author = {Mahendrarajah, TA and Moody, ERR and Schrempf, D and Szánthó, LL and Dombrowski, N and Davín, AA and Pisani, D and Donoghue, PCJ and Szöllősi, GJ and Williams, TA and Spang, A},
title = {ATP synthase evolution on a cross-braced dated tree of life.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7456},
pmid = {37978174},
issn = {2041-1723},
support = {BB/N000919/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Phylogeny ; *Bacteria/genetics ; *Archaea/genetics ; Mitochondria/genetics ; Adenosine Triphosphate ; Evolution, Molecular ; Eukaryota/genetics ; Biological Evolution ; },
abstract = {The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.},
}
@article {pmid37958068,
year = {2023},
author = {Hui, M and Zhang, Y and Wang, A and Sha, Z},
title = {The First Genome Survey of the Snail Provanna glabra Inhabiting Deep-Sea Hydrothermal Vents.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {21},
pages = {},
pmid = {37958068},
issn = {2076-2615},
support = {XDA22050302 and XDB42000000//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 42025603//National Science Foundation for Distinguished Young Scholars/ ; LSKJ202203104//the Science and Technology Innovation Project of Laoshan Laboratory/ ; },
abstract = {The snail P. glabra is an endemic species in deep-sea chemosynthetic ecosystems of the Northwest Pacific Ocean. To obtain more genetic information on this species and provide the basis for subsequent whole-genome map construction, a genome survey was performed on this snail from the hydrothermal vent of Okinawa Trough. The genomic size of P. glabra was estimated to be 1.44 Gb, with a heterozygosity of 1.91% and a repeated sequence content of 69.80%. Based on the sequencing data, a draft genome of 1.32 Gb was assembled. Transposal elements (TEs) accounted for 40.17% of the entire genome, with DNA transposons taking the highest proportion. It was found that most TEs were inserted in the genome recently. In the simple sequence repeats, the dinucleotide motif was the most enriched microsatellite type, accounting for 53% of microsatellites. A complete mitochondrial genome of P. glabra with a total length of 16,268 bp was assembled from the sequencing data. After comparison with the published mitochondrial genome of Provanna sp. from a methane seep, 331 potential single nucleotide polymorphism (SNP) sites were identified in protein-coding genes (PCGs). Except for the cox1 gene, nad2, nad4, nad5, and cob genes are expected to be candidate markers for population genetic and phylogenetic studies of P. glabra and other deep-sea snails. Compared with shallow-water species, three mitochondrial genes of deep-sea gastropods exhibited a higher evolutionary rate, indicating strong selection operating on mitochondria of deep-sea species. This study provides insights into the genome characteristics of P. glabra and supplies genomic resources for further studies on the adaptive evolution of the snail in extreme deep-sea chemosynthetic environments.},
}
@article {pmid37955101,
year = {2023},
author = {Da Costa, RT and Riggs, LM and Solesio, ME},
title = {Inorganic polyphosphate and the regulation of mitochondrial physiology.},
journal = {Biochemical Society transactions},
volume = {51},
number = {6},
pages = {2153-2161},
pmid = {37955101},
issn = {1470-8752},
support = {R00 AG055701/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; Energy Metabolism ; Mammals/metabolism ; *Mitochondria/metabolism ; Mitochondrial Permeability Transition Pore/metabolism ; Polymers ; *Polyphosphates/metabolism ; },
abstract = {Inorganic polyphosphate (polyP) is an ancient polymer that is well-conserved throughout evolution. It is formed by multiple subunits of orthophosphates linked together by phosphoanhydride bonds. The presence of these bonds, which are structurally similar to those found in ATP, and the high abundance of polyP in mammalian mitochondria, suggest that polyP could be involved in the regulation of the physiology of the organelle, especially in the energy metabolism. In fact, the scientific literature shows an unequivocal role for polyP not only in directly regulating oxidative a phosphorylation; but also in the regulation of reactive oxygen species metabolism, mitochondrial free calcium homeostasis, and the formation and opening of mitochondrial permeability transitions pore. All these processes are closely interconnected with the status of mitochondrial bioenergetics and therefore play a crucial role in maintaining mitochondrial and cell physiology. In this invited review, we discuss the main scientific literature regarding the regulatory role of polyP in mammalian mitochondrial physiology, placing a particular emphasis on its impact on energy metabolism. Although the effects of polyP on the physiology of the organelle are evident; numerous aspects, particularly within mammalian cells, remain unclear and require further investigation. These aspects encompass, for example, advancing the development of more precise analytical methods, unraveling the mechanism responsible for sensing polyP levels, and understanding the exact molecular mechanism that underlies the effects of polyP on mitochondrial physiology. By increasing our understanding of the biology of this ancient and understudied polymer, we could unravel new pharmacological targets in diseases where mitochondrial dysfunction, including energy metabolism dysregulation, has been broadly described.},
}
@article {pmid37944010,
year = {2024},
author = {Pegan, TM and Berv, JS and Gulson-Castillo, ER and Kimmitt, AA and Winger, BM},
title = {The pace of mitochondrial molecular evolution varies with seasonal migration distance.},
journal = {Evolution; international journal of organic evolution},
volume = {78},
number = {1},
pages = {160-173},
doi = {10.1093/evolut/qpad200},
pmid = {37944010},
issn = {1558-5646},
support = {2146950//National Science Foundation/ ; //Jean Wright Cohn Endowment Fund/ ; //Robert W. Storer Endowment Fund/ ; //Mary Rhoda Swales Museum of Zoology Research Fund/ ; //William G. Fargo Fund/ ; //University of Michigan Museum of Zoology/ ; //William A and Nancy R Klamm Endowment/ ; //Cleveland Museum of Natural History/ ; DGE 1256260//NSF Graduate Research Fellowship/ ; //University of Michigan Rackham Graduate Student Research/ ; },
mesh = {Animals ; Seasons ; *Animal Migration ; Birds/genetics ; Evolution, Molecular ; *Life History Traits ; },
abstract = {Animals that engage in long-distance seasonal migration experience strong selective pressures on their metabolic performance and life history, with potential consequences for molecular evolution. Species with slow life histories typically show lower rates of synonymous substitution (dS) than "fast" species. Previous research suggests long-distance seasonal migrants have a slower life history strategy than short-distance migrants, raising the possibility that rates of molecular evolution may covary with migration distance. Additionally, long-distance migrants may face strong selection on metabolically-important mitochondrial genes due to their long-distance flights. Using over 1,000 mitochondrial genomes, we assessed the relationship between migration distance and mitochondrial molecular evolution in 39 boreal-breeding migratory bird species. We show that migration distance correlates negatively with dS, suggesting that the slow life history associated with long-distance migration is reflected in rates of molecular evolution. Mitochondrial genes in every study species exhibited evidence of purifying selection, but the strength of selection was greater in short-distance migrants, contrary to our predictions. This result may indicate effects of selection for cold tolerance on mitochondrial evolution among species overwintering at high latitudes. Our study demonstrates that the pervasive correlation between life history and molecular evolutionary rates exists in the context of differential adaptations to seasonality.},
}
@article {pmid37940011,
year = {2023},
author = {Lopez-Jimenez, J and Herrera, J and Alzate, JF},
title = {Expanding the knowledge frontier of mitoviruses in Cannabis sativa.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {116},
number = {},
pages = {105523},
doi = {10.1016/j.meegid.2023.105523},
pmid = {37940011},
issn = {1567-7257},
mesh = {*Cannabis/genetics ; Phylogeny ; *RNA Viruses/genetics ; Mitochondria/genetics ; Fungi ; },
abstract = {Mitoviruses were initially known for their presence in the mitochondria of fungi and were considered exclusive to these organisms. However, recent studies have shown that they are also present in a large number of plant species. Despite the potential impact that mitoviruses might have on the mitochondria of plant cells, there is a lack of information about these ancient RNA viruses, especially within the Cannabaceae family. Cannabis sativa has been in the spotlight in recent years due to the growing industrial applications of plant derivatives, such as fiber and secondary metabolites. Given the importance of Cannabis in today's agriculture, our study aimed to expand the knowledge frontier of Mitoviruses in C. sativa by increasing the number of reference genomes of CasaMV1 available in public databases and representing a larger number of crops in countries where its industrial-scale growth is legalized. To achieve this goal, we used transcriptomics to sequence the first mitoviral genomes of Colombian crops and analyzed RNA-seq datasets available in the SRA databank. Additionally, the evolutionary analysis performed using the mitovirus genomes revealed two main lineages of CasaMV1, termed CasaMV1_L1 and CasaMV1_L2. These mitoviral lineages showed strong clustering based on the geographic location of the crops and differential expression intensities.},
}
@article {pmid37939146,
year = {2023},
author = {Garcia, PS and Barras, F and Gribaldo, S},
title = {Components of iron-Sulfur cluster assembly machineries are robust phylogenetic markers to trace the origin of mitochondria and plastids.},
journal = {PLoS biology},
volume = {21},
number = {11},
pages = {e3002374},
pmid = {37939146},
issn = {1545-7885},
mesh = {Phylogeny ; *Iron-Sulfur Proteins/genetics/metabolism ; Plastids/genetics/metabolism ; Mitochondria/genetics/metabolism ; Iron/metabolism ; Sulfur/metabolism ; },
abstract = {Establishing the origin of mitochondria and plastids is key to understand 2 founding events in the origin and early evolution of eukaryotes. Recent advances in the exploration of microbial diversity and in phylogenomics approaches have indicated a deep origin of mitochondria and plastids during the diversification of Alphaproteobacteria and Cyanobacteria, respectively. Here, we strongly support these placements by analyzing the machineries for assembly of iron-sulfur ([Fe-S]) clusters, an essential function in eukaryotic cells that is carried out in mitochondria by the ISC machinery and in plastids by the SUF machinery. We assessed the taxonomic distribution of ISC and SUF in representatives of major eukaryotic supergroups and analyzed the phylogenetic relationships with their prokaryotic homologues. Concatenation datasets of core ISC proteins show an early branching of mitochondria within Alphaproteobacteria, right after the emergence of Magnetococcales. Similar analyses with the SUF machinery place primary plastids as sister to Gloeomargarita within Cyanobacteria. Our results add to the growing evidence of an early emergence of primary organelles and show that the analysis of essential machineries of endosymbiotic origin provide a robust signal to resolve ancient and fundamental steps in eukaryotic evolution.},
}
@article {pmid37935058,
year = {2023},
author = {Smith, CH and Mejia-Trujillo, R and Breton, S and Pinto, BJ and Kirkpatrick, M and Havird, JC},
title = {Mitonuclear Sex Determination? Empirical Evidence from Bivalves.},
journal = {Molecular biology and evolution},
volume = {40},
number = {11},
pages = {},
pmid = {37935058},
issn = {1537-1719},
support = {R35 GM142836/GM/NIGMS NIH HHS/United States ; 1R35GM142836/NH/NIH HHS/United States ; },
mesh = {Female ; Animals ; *Bivalvia/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genes, Mitochondrial ; *RNA, Small Untranslated ; },
abstract = {Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In certain bivalve lineages that possess doubly uniparental inheritance (DUI), mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination. In these cases, females transmit a female mtDNA to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short noncoding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA sheds a sncRNA partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system.},
}
@article {pmid37933590,
year = {2024},
author = {Khan, M and Joshi, M and Espeland, M and Huemer, P and Lopez-Vaamonde, C and Mutanen, M},
title = {Patterns of speciation in a parapatric pair of Saturnia moths as revealed by target capture.},
journal = {Molecular ecology},
volume = {33},
number = {1},
pages = {e17194},
doi = {10.1111/mec.17194},
pmid = {37933590},
issn = {1365-294X},
support = {314702//Academy of Finland/ ; 101081280//COFUND/ ; 00230503//Suomen Kulttuurirahasto/ ; projectInfoBioS//European Regional Development Fund (ERDF)/ ; EX011185//European Regional Development Fund (ERDF)/ ; },
mesh = {Animals ; Phylogeny ; *Moths/genetics ; Biological Evolution ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {The focus of this study has been to understand the evolutionary relationships and taxonomy of a widely distributed parapatric species pair of wild silk moths in Europe: Saturnia pavonia and Saturnia pavoniella (Lepidoptera: Saturniidae). To address species delimitation in these parapatric taxa, target enrichment and mtDNA sequencing was employed alongside phylogenetic, admixture, introgression, and species delimitation analyses. The dataset included individuals from both species close to and farther away from the contact zone as well as two hybrids generated in the lab. Nuclear markers strongly supported both S. pavonia and S. pavoniella as two distinct species, with hybrids forming a sister group to S. pavoniella. However, the Maximum Likelihood (ML) tree generated from mtDNA sequencing data presented a different picture, showing both taxa to be phylogenetically intermixed. This inconsistency is likely attributable to mitonuclear discordance, which can arise from biological factors (e.g., introgressive hybridization and/or incomplete lineage sorting). Our analyses indicate that past introgressions have taken place, but that there is no evidence to suggest an ongoing admixture between the two species, demonstrating that the taxa have reached full postzygotic reproductive isolation and hence represent two distinct biological species. Finally, we discuss our results from an evolutionary point of view taking into consideration the past climatic oscillations that have likely shaped the present dynamics between the two species. Overall, our study demonstrates the effectiveness of the target enrichment approach in resolving shallow phylogenetic relationships under complex evolutionary circumstances and that this approach is useful in establishing robust and well-informed taxonomic delimitations involving parapatric taxa.},
}
@article {pmid37931036,
year = {2023},
author = {Gu, H and Wen, J and Zhao, X and Zhang, X and Ren, X and Cheng, H and Qu, L},
title = {Evolution, Inheritance, and Strata Formation of the W Chromosome in Duck (Anas platyrhynchos).},
journal = {Genome biology and evolution},
volume = {15},
number = {11},
pages = {},
pmid = {37931036},
issn = {1759-6653},
mesh = {Animals ; Female ; *Ducks/genetics ; *Evolution, Molecular ; Sex Chromosomes ; Birds/genetics ; Inheritance Patterns ; },
abstract = {The nonrecombining female-limited W chromosome is predicted to experience unique evolutionary processes. Difficulties in assembling W chromosome sequences have hindered the identification of duck W-linked sequences and their evolutionary footprint. To address this, we conducted three initial contig-level genome assemblies and developed a rigorous pipeline by which to successfully expand the W-linked data set, including 11 known genes and 24 newly identified genes. Our results indicate that the W chromosome expression may not be subject to female-specific selection; a significant convergent pattern of upregulation associated with increased female-specific selection was not detected. The genetic stability of the W chromosome is also reflected in the strong evolutionary correlation between it and the mitochondria; the complete consistency of the cladogram topology constructed from their gene sequences proves the shared maternal coevolution. By detecting the evolutionary trajectories of W-linked sequences, we have found that recombination suppression started in four distinct strata, of which three were conserved across Neognathae. Taken together, our results have revealed a unique evolutionary pattern and an independent stratum evolutionary pattern for sex chromosomes.},
}
@article {pmid37930986,
year = {2023},
author = {Diaz-Recio Lorenzo, C and Patel, T and Arsenault-Pernet, EJ and Poitrimol, C and Jollivet, D and Martinez Arbizu, P and Gollner, S},
title = {Highly structured populations of deep-sea copepods associated with hydrothermal vents across the Southwest Pacific, despite contrasting life history traits.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0292525},
pmid = {37930986},
issn = {1932-6203},
mesh = {Animals ; *Copepoda/genetics ; *Hydrothermal Vents ; *Life History Traits ; DNA, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Ecosystem ; },
abstract = {Hydrothermal vents are extreme environments, where abundant communities of copepods with contrasting life history traits co-exist along hydrothermal gradients. Here, we discuss how these traits may contribute to the observed differences in molecular diversity and population genetic structure. Samples were collected from vent locations across the globe including active ridges and back-arc basins and compared to existing deep-sea hydrothermal vent and shallow water data, covering a total of 22 vents and 3 non-vent sites. A total of 806 sequences of mtDNA from the Cox1 gene were used to reconstruct the phylogeny, haplotypic relationship and demography within vent endemic copepods (Dirivultidae, Stygiopontius spp.) and non-vent-endemic copepods (Ameiridae, Miraciidae and Laophontidae). A species complex within Stygiopontius lauensis was studied across five pacific back-arc basins at eight hydrothermal vent fields, with cryptic species being restricted to the basins they were sampled from. Copepod populations from the Lau, North Fiji and Woodlark basins are undergoing demographic expansion, possibly linked to an increase in hydrothermal activity in the last 10 kya. Highly structured populations of Amphiascus aff. varians 2 were also observed from the Lau to the Woodlark basins with populations also undergoing expansion. Less abundant harpacticoids exhibit little to no population structure and stable populations. This study suggests that similarities in genetic structure and demography may arise in vent-associated copepods despite having different life history traits. As structured meta-populations may be at risk of local extinction should major anthropogenic impacts, such as deep-sea mining, occur, we highlight the importance of incorporating a trait-based approach to investigate patterns of genetic connectivity and demography, particularly regarding area-based management tools and environmental management plans.},
}
@article {pmid37929337,
year = {2023},
author = {Ibrahim, MK and Haria, A and Mehta, NV and Degani, MS},
title = {Antimicrobial potential of quaternary phosphonium salt compounds: a review.},
journal = {Future medicinal chemistry},
volume = {15},
number = {22},
pages = {2113-2141},
doi = {10.4155/fmc-2023-0188},
pmid = {37929337},
issn = {1756-8927},
mesh = {Phylogeny ; Microbial Sensitivity Tests ; *Anti-Infective Agents/pharmacology/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Mitochondria ; Quaternary Ammonium Compounds/chemistry ; },
abstract = {Given that mitochondrial dysregulation is a biomarker of many cancers, cationic quaternary phosphonium salt (QPS) conjugation is a widely utilized strategy for anticancer drug design. QPS-conjugated compounds exhibit greater cell permeation and accumulation in negatively charged mitochondria, and thus, show enhanced activity. Phylogenetic similarities between mitochondria and bacteria have provided a rationale for exploring the antibacterial properties of mitochondria-targeted compounds. Additionally, due to the importance of mitochondria in the survival of pathogenic microbes, including fungi and parasites, this strategy can be extended to these organisms as well. This review examines recent literature on the antimicrobial activities of various QPS-conjugated compounds and provides future directions for exploring the medicinal chemistry of these compounds.},
}
@article {pmid37924024,
year = {2023},
author = {Lu, G and Wang, W and Mao, J and Li, Q and Que, Y},
title = {Complete mitogenome assembly of Selenicereus monacanthus revealed its molecular features, genome evolution, and phylogenetic implications.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {541},
pmid = {37924024},
issn = {1471-2229},
support = {XZ202301ZY0020N//the Science and Technology Program of Tibet Autonomous Region/ ; },
mesh = {Phylogeny ; *Genome, Mitochondrial ; Genomics ; Evolution, Molecular ; *Cactaceae/genetics ; },
abstract = {BACKGROUND: Mitochondria are the powerhouse of the cell and are critical for plant growth and development. Pitaya (Selenicereus or Hylocereus) is the most important economic crop in the family Cactaceae and is grown worldwide, however its mitogenome is unreported.<br><br>RESULTS: This study assembled the complete mitogenome of the red skin and flesh of pitaya (Selenicereus monacanthus). It is a full-length, 2,290,019&#xa0;bp circular molecule encoding 59 unique genes that only occupy 2.17% of the entire length. In addition, 4,459 pairs of dispersed repeats (&#x2265;&#x2009;50&#xa0;bp) were identified, accounting for 84.78% of the total length, and three repeats (394,588, 124,827, and 13,437&#xa0;bp) mediating genomic recombination were identified by long read mapping and Sanger sequencing. RNA editing events were identified in all 32 protein-coding genes (PCGs), among which four sites (nad1-2, nad4L-2, atp9-copy3-223, and ccmFC-1309) were associated with the initiation or termination of PCGs. Seventy-eight homologous fragments of the chloroplast genome were identified in the mitogenome, the longest having 4,523&#xa0;bp. In addition, evolutionary analyses suggest that S. monacanthus may have undergone multiple genomic reorganization events during evolution, with the loss of at least nine PCGs (rpl2, rpl10, rps2, rps3, rps10, rps11, rps14, rps19, and sdh3).<br><br>CONCLUSIONS: This study revealed the genetic basis of the S. monacanthus mitogenome, and provided a scientific basis for further research on phenotypic traits and germplasm resource development.},
}
@article {pmid37919084,
year = {2023},
author = {Zhang, X and Lu, YC and Wang, JL},
title = {Assembly and Characterization of the Mitochondrial Genome of Fallopia aubertii (L. Henry) Holub.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {28},
number = {10},
pages = {233},
doi = {10.31083/j.fbl2810233},
pmid = {37919084},
issn = {2768-6698},
mesh = {*Genome, Mitochondrial/genetics ; *Fallopia/genetics ; Phylogeny ; Genes, Mitochondrial ; },
abstract = {BACKGROUND: Fallopia aubertii (L. Henry) Holub is a perennial semi-shrub with both ornamental and medicinal value. The mitochondrial genomes of plants contain valuable genetic traits that can be utilized for the exploitation of genetic resources. The parsing of F. aubertii mitochondrial genome can provide insight into the role of mitochondria in plant growth and development, metabolism regulation, evolution, and response to environmental stress.<br><br>METHODS: In this study, we sequenced the mitochondrial genome of F. aubertii using the Illumina NovaSeq 6000 platform and Nanopore platform. We conducted a comprehensive analysis of the mitochondrial genome of F. aubertii, which involved examining various aspects such as gene composition, repetitive sequences, RNA editing sites, phylogeny, and organelle genome homology. To achieve this, we employed several bioinformatics methods including sequence alignment analysis, repetitive sequence analysis, phylogeny analysis, and more.<br><br>RESULTS: The mitochondrial genome of F. aubertii has 64 genes, including 34 protein-coding genes (PCGs), three rRNAs, and 27 tRNAs. There were 77 short tandem repeat sequences detected in the mitochondrial genome, five tandem repeat sequences identified by Tandem Repeats Finder (TRF), and 50 scattered repeat sequences observed, including 22 forward repeat sequences and 28 palindrome repeat sequences. A total of 367 RNA coding sites were predicted in PCGs, with the highest number (33) found within ccmB. Ka/Ks values estimated for mitochondrial genes of F. aubertii and three closely related species representing Caryophyllales were less than 1 for most of the genes. The maximum likelihood evolutionary tree showed that F. aubertii and Nepenthes &#xd7;ventrata are most closely related.<br><br>CONCLUSIONS: In this study, we obtained basic information on the mitochondrial genome of F. aubertii and this study investigated repeat sequences and homologous segments, predicted RNA editing sites, and utilized the Ka/Ks ratio to estimate the selection pressure on mitochondrial genes of F. aubertii. We also discussed the systematic evolutionary position of F. aubertii based on mitochondrial genome sequences. Our study revealed variations in the sequence and structure of mitochondrial genomes in Caryophyllales. These findings are of great significance for identifying and improving valuable plant traits and serve as a reference for future molecular studies of F. aubertii.},
}
@article {pmid37917792,
year = {2023},
author = {Namasivayam, S and Sun, C and Bah, AB and Oberstaller, J and Pierre-Louis, E and Etheridge, RD and Feschotte, C and Pritham, EJ and Kissinger, JC},
title = {Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {45},
pages = {e2308569120},
pmid = {37917792},
issn = {1091-6490},
support = {R01 AI068908/AI/NIAID NIH HHS/United States ; R35 GM122550/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Toxoplasma/genetics ; Genome ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Evolution, Molecular ; Cell Nucleus/genetics ; Sequence Analysis, DNA ; },
abstract = {Toxoplasma gondii is a zoonotic protist pathogen that infects up to one third of the human population. This apicomplexan parasite contains three genome sequences: nuclear (65 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear integrants of mitochondrial DNA) and NUPTs (nuclear integrants of plastid DNA) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant T. gondii ME49 nuclear genome-the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not ku80 mutant, Toxoplasma parasites. Comparisons with Neospora caninum, a species that diverged from Toxoplasma ~28 mya, revealed that the movement and fixation of five NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb), and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together, these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.},
}
@article {pmid37903625,
year = {2024},
author = {Hacker, C and Sendra, K and Keisham, P and Filipescu, T and Lucocq, J and Salimi, F and Ferguson, S and Bhella, D and MacNeill, SA and Embley, M and Lucocq, J},
title = {Biogenesis, inheritance, and 3D ultrastructure of the microsporidian mitosome.},
journal = {Life science alliance},
volume = {7},
number = {1},
pages = {},
pmid = {37903625},
issn = {2575-1077},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Fungal Proteins/metabolism ; Mitochondria/metabolism ; *Microsporidia/genetics/metabolism ; Saccharomyces cerevisiae/metabolism ; Dynamins ; Mammals/metabolism ; },
abstract = {During the reductive evolution of obligate intracellular parasites called microsporidia, a tiny remnant mitochondrion (mitosome) lost its typical cristae, organellar genome, and most canonical functions. Here, we combine electron tomography, stereology, immunofluorescence microscopy, and bioinformatics to characterise mechanisms of growth, division, and inheritance of this minimal mitochondrion in two microsporidia species (grown within a mammalian RK13 culture-cell host). Mitosomes of Encephalitozoon cuniculi (2-12/cell) and Trachipleistophora hominis (14-18/nucleus) displayed incremental/non-phasic growth and division and were closely associated with an organelle identified as equivalent to the fungal microtubule-organising centre (microsporidian spindle pole body; mSPB). The mitosome-mSPB association was resistant to treatment with microtubule-depolymerising drugs nocodazole and albendazole. Dynamin inhibitors (dynasore and Mdivi-1) arrested mitosome division but not growth, whereas bioinformatics revealed putative dynamins Drp-1 and Vps-1, of which, Vps-1 rescued mitochondrial constriction in dynamin-deficient yeast (Schizosaccharomyces pombe). Thus, microsporidian mitosomes undergo incremental growth and dynamin-mediated division and are maintained through ordered inheritance, likely mediated via binding to the microsporidian centrosome (mSPB).},
}
@article {pmid37901222,
year = {2023},
author = {Brun, C and Chalet, L and Moulin, F and Bochaton, T and Ducreux, S and Paillard, M and Crola Da Silva, C},
title = {A bibliometric analysis: Ca[2+] fluxes and inflammatory phenotyping by flow cytometry in peripheral blood mononuclear cells.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1272809},
pmid = {37901222},
issn = {1664-3224},
mesh = {Humans ; *Leukocytes, Mononuclear/metabolism ; Flow Cytometry/methods ; Cell Line ; *Signal Transduction ; Inflammation/metabolism ; },
abstract = {BACKGROUND: The immune system, composed of organs, tissues, cells, and proteins, is the key to protecting the body from external biological attacks and inflammation. The latter occurs in several pathologies, such as cancers, type 1 diabetes, and human immunodeficiency virus infection. Immunophenotyping by flow cytometry is the method of choice for diagnosing these pathologies. Under inflammatory conditions, the peripheral blood mononuclear cells (PBMCs) are partially activated and generate intracellular pathways involving Ca[2+]-dependent signaling cascades leading to transcription factor expression. Ca[2+] signaling is typically studied by microscopy in cell lines but can present some limitations to explore human PBMCs, where flow cytometry can be a good alternative.<br><br>OBJECTIVE: In this review, we dived into the research field of inflammation and Ca[2+] signaling in PBMCs. We aimed to investigate the structure and evolution of this field in a physio-pathological context, and then we focused our review on flow cytometry analysis of Ca[2+] fluxes in PBMCs.<br><br>METHODS: From 1984 to 2022, 3865 articles on inflammation and Ca[2+] signaling in PBMCs were published, according to The Clarivate Web of Science (WOS) database used in this review. A bibliometric study was designed for this collection and consisted of a co-citation and bibliographic coupling analysis.<br><br>RESULTS: The co-citation analysis was performed on 133 articles: 4 clusters highlighted the global context of Ca[2+] homeostasis, including chemical probe development, identification of the leading players in Ca[2+] signaling, and the link with chemokine production in immune cell function. Next, the bibliographic coupling analysis combined 998 articles in 8 clusters. This analysis outlined the mechanisms of PBMC activation, from signal integration to cellular response. Further explorations of the bibliographic coupling network, focusing on flow cytometry, revealed 21 articles measuring cytosolic Ca[2+] in PBMCs, with only 5 since 2016. This final query showed that Ca[2+] signaling analysis in human PBMCs using flow cytometry is still underdeveloped and investigates mainly the cytosolic Ca[2+] compartment.<br><br>CONCLUSION: Our review uncovers remaining knowledge gaps of intracellular players involved in Ca[2+] signaling in PBMCs, such as reticulum and mitochondria, and presents flow cytometry as a solid option to supplement gold-standard microscopy studies.},
}
@article {pmid37900311,
year = {2023},
author = {Gonzalez-Jimenez, I and Perlin, DS and Shor, E},
title = {Reactive oxidant species induced by antifungal drugs: identity, origins, functions, and connection to stress-induced cell death.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1276406},
pmid = {37900311},
issn = {2235-2988},
support = {R01 AI109025/AI/NIAID NIH HHS/United States ; R21 AI168729/AI/NIAID NIH HHS/United States ; },
mesh = {*Antifungal Agents/pharmacology/therapeutic use ; Reactive Oxygen Species/metabolism ; *Oxidants ; Echinocandins/pharmacology ; Apoptosis ; },
abstract = {Reactive oxidant species (ROS) are unstable, highly reactive molecules that are produced by cells either as byproducts of metabolism or synthesized by specialized enzymes. ROS can be detrimental, e.g., by damaging cellular macromolecules, or beneficial, e.g., by participating in signaling. An increasing body of evidence shows that various fungal species, including both yeasts and molds, increase ROS production upon exposure to the antifungal drugs currently used in the clinic: azoles, polyenes, and echinocandins. However, the implications of these findings are still largely unclear due to gaps in knowledge regarding the chemical nature, molecular origins, and functional consequences of these ROS. Because the detection of ROS in fungal cells has largely relied on fluorescent probes that lack specificity, the chemical nature of the ROS is not known, and it may vary depending on the specific fungus-drug combination. In several instances, the origin of antifungal drug-induced ROS has been identified as the mitochondria, but further experiments are necessary to strengthen this conclusion and to investigate other potential cellular ROS sources, such as the ER, peroxisomes, and ROS-producing enzymes. With respect to the function of the ROS, several studies have shown that they contribute to the drugs' fungicidal activities and may be part of drug-induced programmed cell death (PCD). However, whether these "pro-death" ROS are a primary consequence of the antifungal mechanism of action or a secondary consequence of drug-induced PCD remains unclear. Finally, several recent studies have raised the possibility that ROS induction can serve an adaptive role, promoting antifungal drug tolerance and the evolution of drug resistance. Filling these gaps in knowledge will reveal a new aspect of fungal biology and may identify new ways to potentiate antifungal drug activity or prevent the evolution of antifungal drug resistance.},
}
@article {pmid37895071,
year = {2023},
author = {Olla, S and Siguri, C and Fais, A and Era, B and Fantini, MC and Di Petrillo, A},
title = {Inhibitory Effect of Quercetin on Oxidative Endogen Enzymes: A Focus on Putative Binding Modes.},
journal = {International journal of molecular sciences},
volume = {24},
number = {20},
pages = {},
pmid = {37895071},
issn = {1422-0067},
mesh = {*Quercetin/pharmacology ; Reactive Oxygen Species/metabolism ; *Antioxidants/pharmacology/metabolism ; Molecular Docking Simulation ; Oxidative Stress ; Xanthine Oxidase/metabolism ; Monoamine Oxidase/metabolism ; },
abstract = {Oxidative stress is defined as an imbalance between the production of free radicals and reactive oxygen species (ROS) and the ability of the body to neutralize them by anti-oxidant defense systems. Cells can produce ROS during physiological processes, but excessive ROS can lead to non-specific and irreversible damage to biological molecules, such as DNA, lipids, and proteins. Mitochondria mainly produce endogenous ROS during both physiological and pathological conditions. Enzymes like nicotinamide adenine dinucleotide phosphate oxidase (NOX), xanthine oxidase (XO), lipoxygenase (LOX), myeloperoxidase (MPO), and monoamine oxidase (MAO) contribute to this process. The body has enzymatic and non-enzymatic defense systems to neutralize ROS. The intake of bioactive phenols, like quercetin (Que), can protect against pro-oxidative damage by quenching ROS through a non-enzymatic system. In this study, we evaluate the ability of Que to target endogenous oxidant enzymes involved in ROS production and explore the mechanisms of action underlying its anti-oxidant properties. Que can act as a free radical scavenger by donating electrons through the negative charges in its phenolic and ketone groups. Additionally, it can effectively inhibit the activity of several endogenous oxidative enzymes by binding them with high affinity and specificity. Que had the best molecular docking results with XO, followed by MAO-A, 5-LOX, NOX, and MPO. Que's binding to these enzymes was confirmed by subsequent molecular dynamics, revealing different stability phases depending on the enzyme bound. The 500 ns simulation showed a net evolution of binding for NOX and MPO. These findings suggest that Que has potential as a natural therapy for diseases related to oxidative stress.},
}
@article {pmid37885664,
year = {2023},
author = {Ni, Y and Zhang, X and Li, J and Lu, Q and Chen, H and Ma, B and Liu, C},
title = {Genetic diversity of Coffea arabica L. mitochondrial genomes caused by repeat- mediated recombination and RNA editing.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1261012},
pmid = {37885664},
issn = {1664-462X},
abstract = {BACKGROUND: Coffea arabica L. is one of the most important crops widely cultivated in 70 countries across Asia, Africa, and Latin America. Mitochondria are essential organelles that play critical roles in cellular respiration, metabolism, and differentiation. C. arabica's nuclear and chloroplast genomes have been reported. However, its mitochondrial genome remained unreported. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments.<br><br>RESULTS: We sequenced the total DNA of C. arabica using Illumina and Nanopore platforms. We then assembled the mitochondrial genome with a hybrid strategy using Unicycler software. We found that the mitochondrial genome comprised two circular chromosomes with lengths of 867,678 bp and 153,529 bp, encoding 40 protein-coding genes, 26 tRNA genes, and three rRNA genes. We also detected 270 Simple Sequence Repeats and 34 tandem repeats in the mitochondrial genome. We found 515 high-scoring sequence pairs (HSPs) for a self-to-self similarity comparison using BLASTn. Three HSPs were found to mediate recombination by the mapping of long reads. Furthermore, we predicted 472 using deep-mt with the convolutional neural network model. Then we randomly validated 90 RNA editing events by PCR amplification and Sanger sequencing, with the majority being non-synonymous substitutions and only three being synonymous substitutions. These findings provide valuable insights into the genetic characteristics of the C. arabica mitochondrial genome, which can be helpful for future study on coffee breeding and mitochondrial genome evolution.<br><br>CONCLUSION: Our study sheds new light on the evolution of C. arabica organelle genomes and their potential use in genetic breeding, providing valuable data for developing molecular markers that can improve crop productivity and quality. Furthermore, the discovery of RNA editing events in the mitochondrial genome of C. arabica offers insights into the regulation of gene expression in this species, contributing to a better understanding of coffee genetics and evolution.},
}
@article {pmid37877347,
year = {2024},
author = {Choi, SW and Yu, HJ and Kim, JK},
title = {Comparative ontogeny and phylogenetic relationships of eight lizardfish species (Synodontidae) from the Northwest Pacific, with a focus on Trachinocephalus monophyly.},
journal = {Journal of fish biology},
volume = {104},
number = {1},
pages = {284-303},
doi = {10.1111/jfb.15595},
pmid = {37877347},
issn = {1095-8649},
support = {R2023001//the National Institute of Fisheries Science/ ; 2023//the National Marine Biodiversity Institute of Korea/ ; },
mesh = {Animals ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Fishes/anatomy &amp; histology ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Larva ; },
abstract = {Lizardfish (Aulopiforms: Synodontidae), distributed broadly in temperate to tropical waters, are represented globally by 83 species across four genera, with 10 species in Korea. Despite these numbers, few studies have been conducted on the early life history of lizardfishes compared to their adult counterparts. Thus, we conducted molecular identification of 123 Synodontidae larvae collected from the Northwest Pacific (Korea Strait, Yellow Sea, East China Sea, and East Sea) between June 2017 and July 2021, using mitochondrial DNA COI and 16S rRNA sequences. Significant morphological differences were observed in the larvae and juvenile, including variation in melanophore, count, morphometric characteristics, and body shape. The morphological traits of eight species (Harpadon nehereus, Saurida macrolepis, Saurida wanieso, Saurida sp., Synodus hoshinonis, Synodus kaianus, Synodus macrops, and Trachinocephalus trachinus) served as vital data for interpreting the phylogenetic relationships within the Northwest Pacific Synodontidae. Ultimately, the identification key revealed by this study will enable accurate identification of Synodontid larvae and juveniles, and further facilitate our understanding of the phylogenetic relationships within this family.},
}
@article {pmid37871810,
year = {2024},
author = {Coto, ALS and Pereira, AA and Oliveira, SD and Moritz, MNO and Franco da Rocha, AM and Dores-Silva, PR and da Silva, NSM and de Araújo Nogueira, AR and Gava, LM and Seraphim, TV and Borges, JC},
title = {Structural characterization of the human DjC20/HscB cochaperone in solution.},
journal = {Biochimica et biophysica acta. Proteins and proteomics},
volume = {1872},
number = {1},
pages = {140970},
doi = {10.1016/j.bbapap.2023.140970},
pmid = {37871810},
issn = {1878-1454},
mesh = {Humans ; Adenosine Triphosphatases/metabolism ; Edetic Acid ; *Heat-Shock Proteins/chemistry ; *HSP70 Heat-Shock Proteins/chemistry ; Molecular Chaperones/chemistry ; },
abstract = {J-domain proteins (JDPs) form a very large molecular chaperone family involved in proteostasis processes, such as protein folding, trafficking through membranes and degradation/disaggregation. JDPs are Hsp70 co-chaperones capable of stimulating ATPase activity as well as selecting and presenting client proteins to Hsp70. In mitochondria, human DjC20/HscB (a type III JDP that possesses only the conserved J-domain in some region of the protein) is involved in [FeS] protein biogenesis and assists human mitochondrial Hsp70 (HSPA9). Human DjC20 possesses a zinc-finger domain in its N-terminus, which closely contacts the J-domain and appears to be essential for its function. Here, we investigated the hDjC20 structure in solution as well as the importance of Zn[+2] for its stability. The recombinant hDjC20 was pure, folded and capable of stimulating HSPA9 ATPase activity. It behaved as a slightly elongated monomer, as attested by small-angle X-ray scattering and SEC-MALS. The presence of Zn[2+] in the hDjC20 samples was verified, a stoichiometry of 1:1 was observed, and its removal by high concentrations of EDTA and DTPA was unfeasible. However, thermal and chemical denaturation in the presence of EDTA led to a reduction in protein stability, suggesting a synergistic action between the chelating agent and denaturators that facilitate protein unfolding depending on metal removal. These data suggest that the affinity of Zn[+2] for the protein is very high, evidencing its importance for the hDjC20 structure.},
}
@article {pmid37859594,
year = {2024},
author = {Waters, ER and Bezanilla, M and Vierling, E},
title = {ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages.},
journal = {Plant &amp; cell physiology},
volume = {65},
number = {4},
pages = {493-502},
doi = {10.1093/pcp/pcad122},
pmid = {37859594},
issn = {1471-9053},
support = {IOS 1354960 MCB 2215727//National Science Foundation/ ; },
mesh = {*Mitochondrial Proteins/metabolism/genetics ; *Arabidopsis Proteins/metabolism/genetics ; Arabidopsis/genetics/metabolism ; Mitochondria/metabolism ; ATPases Associated with Diverse Cellular Activities/metabolism/genetics ; Eukaryota/genetics/metabolism ; Adenosine Triphosphatases/metabolism/genetics ; Phylogeny ; Animals ; },
abstract = {ATPase family AAA domain-containing 3 (ATAD3) proteins are unique mitochondrial proteins that arose deep in the eukaryotic lineage but that are surprisingly absent in Fungi and Amoebozoa. These ∼600-amino acid proteins are anchored in the inner mitochondrial membrane and are essential in metazoans and Arabidopsis thaliana. ATAD3s comprise a C-terminal ATPases Associated with a variety of cellular Activities (AAA+) matrix domain and an ATAD3_N domain, which is located primarily in the inner membrane space but potentially extends to the cytosol to interact with the ER. Sequence and structural alignments indicate that ATAD3 proteins are most similar to classic chaperone unfoldases in the AAA+ family, suggesting that they operate in mitochondrial protein quality control. A. thaliana has four ATAD3 genes in two distinct clades that appear first in the seed plants, and both clades are essential for viability. The four genes are generally coordinately expressed, and transcripts are highest in growing apices and imbibed seeds. Plants with disrupted ATAD3 have reduced growth, aberrant mitochondrial morphology, diffuse nucleoids and reduced oxidative phosphorylation complex I. These and other pleiotropic phenotypes are also observed in ATAD3 mutants in metazoans. Here, we discuss the distribution of ATAD3 proteins as they have evolved in the plant kingdom, their unique structure, what we know about their function in plants and the challenges in determining their essential roles in mitochondria.},
}
@article {pmid37850870,
year = {2023},
author = {Nicolini, F and Ghiselli, F and Luchetti, A and Milani, L},
title = {Bivalves as Emerging Model Systems to Study the Mechanisms and Evolution of Sex Determination: A Genomic Point of View.},
journal = {Genome biology and evolution},
volume = {15},
number = {10},
pages = {},
pmid = {37850870},
issn = {1759-6653},
mesh = {Humans ; Animals ; Phylogeny ; *Bivalvia/genetics ; Genome ; Genomics ; Mitochondria/genetics ; Sex Determination Processes/genetics ; Biological Evolution ; },
abstract = {Bivalves are a diverse group of molluscs that have recently attained a central role in plenty of biological research fields, thanks to their peculiar life history traits. Here, we propose that bivalves should be considered as emerging model systems also in sex-determination (SD) studies, since they would allow to investigate: 1) the transition between environmental and genetic SD, with respect to different reproductive backgrounds and sexual systems (from species with strict gonochorism to species with various forms of hermaphroditism); 2) the genomic evolution of sex chromosomes (SCs), considering that no heteromorphic SCs are currently known and that homomorphic SCs have been identified only in a few species of scallops; 3) the putative role of mitochondria at some level of the SD signaling pathway, in a mechanism that may resemble the cytoplasmatic male sterility of plants; 4) the evolutionary history of SD-related gene (SRG) families with respect to other animal groups. In particular, we think that this last topic may lay the foundations for expanding our understanding of bivalve SD, as our current knowledge is quite fragmented and limited to a few species. As a matter of fact, tracing the phylogenetic history and diversity of SRG families (such as the Dmrt, Sox, and Fox genes) would allow not only to perform more targeted functional experiments and genomic analyses, but also to foster the possibility of establishing a solid comparative framework.},
}
@article {pmid37847106,
year = {2023},
author = {Sharma, A and Ahlawat, S and Sharma, R and Arora, R and Singh, KV and Malik, D and Banik, S and Singh, TR and Tantia, MS},
title = {Tracing the genetic footprints: India's role as a gateway for pig migration and domestication across continents.},
journal = {Animal biotechnology},
volume = {34},
number = {9},
pages = {5173-5179},
doi = {10.1080/10495398.2023.2268683},
pmid = {37847106},
issn = {1532-2378},
mesh = {Swine/genetics ; Animals ; *Domestication ; *Sus scrofa/genetics ; India ; Mitochondria/genetics ; Haplotypes/genetics ; Phylogeny ; Genetic Variation/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {This study explored the maternal genetic diversity in the pig genetic resources of India by analyzing a mitochondrial D-loop fragment and comparing it with the corresponding sequences of previously published studies involving domestic pigs and wild boars. Sequencing of 103 samples representing different domestic pig populations revealed existence of 32 maternal haplotypes. The indices of haplotype and nucleotide diversity in Indian domestic pigs were 0.9421 and 0.015, respectively. Median-Joining network revealed that Indian pigs belong to Clade A and show conformity to 6 haplogroups reported worldwide (D1a, D1a1, D1a2, D1e, D1h and D3a). Among these, D1e and D1a2 were shared with Asian wild boars too. Interestingly, haplotype sharing was evident between Indian pigs and samples from other countries representing Africa, Asia, Europe and Oceania. This study substantiates India's contribution as a possible pig domestication center and highlights the importance of the Indian subcontinent in dispersal of the species to other continents. Additionally, genetic evidence suggested the influence of trading routes and historical interactions in shaping pig genetic exchange. Overall, this investigation provides valuable insights into the genetic diversity, historical migration, and domestication of Indian domestic pigs, contributing to the broader understanding of global pig genetic resources and their evolutionary history.},
}
@article {pmid37844192,
year = {2023},
author = {Borghi, F and Saiardi, A},
title = {Evolutionary perspective on mammalian inorganic polyphosphate (polyP) biology.},
journal = {Biochemical Society transactions},
volume = {51},
number = {5},
pages = {1947-1956},
pmid = {37844192},
issn = {1470-8752},
support = {MR/T028904/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Polyphosphates ; *Mammals ; Eukaryotic Cells ; Mitochondria ; Biology ; },
abstract = {Inorganic polyphosphate (polyP), the polymeric form of phosphate, is attracting ever-growing attention due to the many functions it appears to perform within mammalian cells. This essay does not aim to systematically review the copious mammalian polyP literature. Instead, we examined polyP synthesis and functions in various microorganisms and used an evolutionary perspective to theorise key issues of this field and propose solutions. By highlighting the presence of VTC4 in distinct species of very divergent eucaryote clades (Opisthokonta, Viridiplantae, Discoba, and the SAR), we propose that whilst polyP synthesising machinery was present in the ancestral eukaryote, most lineages subsequently lost it during evolution. The analysis of the bacteria-acquired amoeba PPK1 and its unique polyP physiology suggests that eukaryote cells must have developed mechanisms to limit cytosolic polyP accumulation. We reviewed the literature on polyP in the mitochondria from the perspective of its endosymbiotic origin from bacteria, highlighting how mitochondria could possess a polyP physiology reminiscent of their 'bacterial' beginning that is not yet investigated. Finally, we emphasised the similarities that the anionic polyP shares with the better-understood negatively charged polymers DNA and RNA, postulating that the nucleus offers an ideal environment where polyP physiology might thrive.},
}
@article {pmid37843218,
year = {2024},
author = {Zhang, J and Zhu, Q and Wang, J and Peng, Z and Zhuang, Z and Hang, C and Li, W},
title = {Mitochondrial dysfunction and quality control lie at the heart of subarachnoid hemorrhage.},
journal = {Neural regeneration research},
volume = {19},
number = {4},
pages = {825-832},
pmid = {37843218},
issn = {1673-5374},
abstract = {The dramatic increase in intracranial pressure after subarachnoid hemorrhage leads to a decrease in cerebral perfusion pressure and a reduction in cerebral blood flow. Mitochondria are directly affected by direct factors such as ischemia, hypoxia, excitotoxicity, and toxicity of free hemoglobin and its degradation products, which trigger mitochondrial dysfunction. Dysfunctional mitochondria release large amounts of reactive oxygen species, inflammatory mediators, and apoptotic proteins that activate apoptotic pathways, further damaging cells. In response to this array of damage, cells have adopted multiple mitochondrial quality control mechanisms through evolution, including mitochondrial protein quality control, mitochondrial dynamics, mitophagy, mitochondrial biogenesis, and intercellular mitochondrial transfer, to maintain mitochondrial homeostasis under pathological conditions. Specific interventions targeting mitochondrial quality control mechanisms have emerged as promising therapeutic strategies for subarachnoid hemorrhage. This review provides an overview of recent research advances in mitochondrial pathophysiological processes after subarachnoid hemorrhage, particularly mitochondrial quality control mechanisms. It also presents potential therapeutic strategies to target mitochondrial quality control in subarachnoid hemorrhage.},
}
@article {pmid37818890,
year = {2023},
author = {Chen, H and Shi, BY and Du, LN and Sun, HY},
title = {Description of a New Species of Hua (Gastropoda: Semisulcospiridae) from Guizhou, China, Based on Morphology and Molecular Evidence.},
journal = {Zoological science},
volume = {40},
number = {5},
pages = {414-421},
doi = {10.2108/zs230025},
pmid = {37818890},
issn = {0289-0003},
mesh = {Female ; Animals ; *Gastropoda/anatomy &amp; histology ; Phylogeny ; China ; Mitochondria ; },
abstract = {A new species of Hua, Hua qiannanensis sp. nov., is described from Guizhou Province, China, based on morphological and molecular evidence. The new species can be distinguished from its congeners by the following combination of characters: the smooth shell, only three smaller cusps of lateral teeth on the inner side, outer marginal teeth with eight flattened and rounded denticles, an ovipositor pore in females, and BW/H ≥ 80%, B/H = 76.8-82.3%. Molecular analysis based on partial mitochondrial COI and 16S rDNA also supports the systematic position of the new taxon.},
}
@article {pmid37815994,
year = {2023},
author = {Chen, YH and Miller, WB and Hay, A},
title = {Postharvest bacterial succession on cut flowers and vase water.},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0292537},
pmid = {37815994},
issn = {1932-6203},
mesh = {*Water ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Ecosystem ; *Asteraceae ; Flowers ; Bacteria/genetics ; },
abstract = {In cut flowers, xylem occlusion or blockage by bacteria negatively affects water balance and postharvest quality. Many studies have used culture-based methods to examine bacterial populations in vase water and their effects on flower longevity. It is still unclear if and how bacterial communities at the 16S rRNA gene (16S) level change during the vase period and how such change might correlate with postharvest longevity. This study compared the sequences of 16S amplicons from 4 different types of flowers and their vase water over the course of 7 days (Rosa spp., Gerbera jamesonii, and two Lilium varieties). The relative abundance of plant chloroplast and mitochondria 16S decreased significantly over the course 7 days in all 4 flowers as bacterial diversity increased. Richness and evenness of the bacterial communities increased over time, as did the number of rare taxa and phylogenetic diversity. Bacterial communities varied with time, as well as by flower source, types, and sample location (water, stem surface, whole stem). Some taxa, such as Enterobacteriacea and Bradyhizobiaceae decreased significantly over time while others such as Pseudomonas spp. increased. For example, Pseudomonas veronii, implicated in soft rot of calla lily, increased in both whole stem samples and water samples from Gerbera jamesonii. Erwinia spp., which includes plant pathogenic species, also increased in water samples. This work highlights the dynamic and complex nature of bacterial succession in the flower vase ecosystem. More work is needed to understand if and how bacterial community structure can be managed to improve cut flower vase life.},
}
@article {pmid37810794,
year = {2023},
author = {Rodriguez, D and Harding, SF and Sirsi, S and McNichols-O'Rourke, K and Morris, T and Forstner, MRJ and Schwalb, AN},
title = {Mitochondrial sequence data reveal population structure within Pustulosa pustulosa.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15974},
pmid = {37810794},
issn = {2167-8359},
mesh = {Humans ; Animals ; Phylogeny ; Mitochondria ; *Bivalvia ; *Unionidae/genetics ; Texas ; Ontario ; },
abstract = {Unionid mussels are among the most imperiled group of organisms in North America, and Pustulosa pustulosa is a freshwater species with a relatively wide latitudinal distribution that extends from southern Ontario, Canada, to Texas, USA. Considerable morphological and geographic variation in the genus Pustulosa (formerly Cyclonaias) has led to uncertainty over species boundaries, and recent studies have suggested revisions to species-level classifications by synonymizing C. aurea, C. houstonensis, C. mortoni, and C. refulgens with C. pustulosa (currently P. pustulosa). Owing to its wide range and shallow phylogenetic differentiation, we analyzed individuals of P. pustulosa using mitochondrial DNA sequence data under a population genetics framework. We included 496 individuals, which were comprised of 166 samples collected during this study and 330 additional sequences retrieved from GenBank. Pairwise ΦST measures based on ND1 data suggested there may be up to five major geographic groups present within P. pustulosa. Genetic differentiation between regions within Texas was higher compared to populations from the Mississippi and Great Lakes populations, which may reflect differences in historical connectivity. Mitochondrial sequence data also revealed varying demographic histories for each major group suggesting each geographic region has also experienced differential population dynamics in the past. Future surveys should consider exploring variation within species after phylogeographic delimitation has been performed. In this study, we begin to address this need for freshwater mussels via the P. pustulosa system.},
}
@article {pmid37796022,
year = {2023},
author = {Usey, MM and Huet, D},
title = {ATP synthase-associated coiled-coil-helix-coiled-coil-helix (CHCH) domain-containing proteins are critical for mitochondrial function in Toxoplasma gondii.},
journal = {mBio},
volume = {14},
number = {5},
pages = {e0176923},
pmid = {37796022},
issn = {2150-7511},
support = {R00 AI137218/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Toxoplasma/genetics/metabolism ; Mitochondria/metabolism ; Proteins/metabolism ; *Parasites/metabolism ; Nitric Oxide Synthase/metabolism ; Adenosine Triphosphate/metabolism ; Protozoan Proteins/genetics/metabolism ; Mitochondrial Proteins/metabolism ; },
abstract = {Members of the coiled-coil-helix-coiled-coil-helix (CHCH) domain protein family are transported into the mitochondrial intermembrane space, where they play important roles in the biogenesis and function of the organelle. Unexpectedly, the ATP synthase of the apicomplexan Toxoplasma gondii harbors CHCH domain-containing subunits of unknown function. As no other ATP synthase studied to date contains this class of proteins, characterizing their function will be of broad interest to the fields of molecular parasitology and mitochondrial evolution. Here, we demonstrate that that two T. gondii ATP synthase subunits containing CHCH domains are required for parasite survival and for stability and function of the ATP synthase. We also show that knockdown disrupts multiple aspects of the mitochondrial morphology of T. gondii and that mutation of key residues in the CHCH domains caused mis-localization of the proteins. This work provides insight into the unique features of the apicomplexan ATP synthase, which could help to develop therapeutic interventions against this parasite and other apicomplexans, such as the malaria-causing parasite Plasmodium falciparum.},
}
@article {pmid37792908,
year = {2023},
author = {Motyčková, A and Voleman, L and Najdrová, V and Arbonová, L and Benda, M and Dohnálek, V and Janowicz, N and Malych, R and Šuťák, R and Ettema, TJG and Svärd, S and Stairs, CW and Doležal, P},
title = {Adaptation of the late ISC pathway in the anaerobic mitochondrial organelles of Giardia intestinalis.},
journal = {PLoS pathogens},
volume = {19},
number = {10},
pages = {e1010773},
pmid = {37792908},
issn = {1553-7374},
mesh = {Humans ; *Giardia lamblia/genetics/metabolism ; Anaerobiosis ; *Iron-Sulfur Proteins/genetics/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; },
abstract = {Mitochondrial metabolism is entirely dependent on the biosynthesis of the [4Fe-4S] clusters, which are part of the subunits of the respiratory chain. The mitochondrial late ISC pathway mediates the formation of these clusters from simpler [2Fe-2S] molecules and transfers them to client proteins. Here, we characterized the late ISC pathway in one of the simplest mitochondria, mitosomes, of the anaerobic protist Giardia intestinalis that lost the respiratory chain and other hallmarks of mitochondria. In addition to IscA2, Nfu1 and Grx5 we identified a novel BolA1 homologue in G. intestinalis mitosomes. It specifically interacts with Grx5 and according to the high-affinity pulldown also with other core mitosomal components. Using CRISPR/Cas9 we were able to establish full bolA1 knock out, the first cell line lacking a mitosomal protein. Despite the ISC pathway being the only metabolic role of the mitosome no significant changes in the mitosome biology could be observed as neither the number of the mitosomes or their capability to form [2Fe-2S] clusters in vitro was affected. We failed to identify natural client proteins that would require the [2Fe-2S] or [4Fe-4S] cluster within the mitosomes, with the exception of [2Fe-2S] ferredoxin, which is itself part of the ISC pathway. The overall uptake of iron into the cellular proteins remained unchanged as also observed for the grx5 knock out cell line. The pull-downs of all late ISC components were used to build the interactome of the pathway showing specific position of IscA2 due to its interaction with the outer mitosomal membrane proteins. Finally, the comparative analysis across Metamonada species suggested that the adaptation of the late ISC pathway identified in G. intestinalis occurred early in the evolution of this supergroup of eukaryotes.},
}
@article {pmid37783374,
year = {2023},
author = {Igamberdiev, AU and Gordon, R},
title = {Macroevolution, differentiation trees, and the growth of coding systems.},
journal = {Bio Systems},
volume = {234},
number = {},
pages = {105044},
doi = {10.1016/j.biosystems.2023.105044},
pmid = {37783374},
issn = {1872-8324},
mesh = {*Cell Differentiation/genetics ; Morphogenesis/genetics ; Phylogeny ; },
abstract = {An open process of evolution of multicellular organisms is based on the rearrangement and growth of the program of differentiation that underlies biological morphogenesis. The maintenance of the final (adult) stable non-equilibrium state (stasis) of a developmental system determines the direction of the evolutionary process. This state is achieved via the sequence of differentiation events representable as differentiation trees. A special type of morphogenetic code, acting as a metacode governing gene expression, may include electromechanical signals appearing as differentiation waves. The excessive energy due to the incorporation of mitochondria in eukaryotic cells resulted not only in more active metabolism but also in establishing the differentiation code for interconnecting cells and forming tissues, which fueled the evolutionary process. The "invention" of "continuing differentiation" distinguishes multicellular eukaryotes from other organisms. The Janus-faced control, involving both top-down control by differentiation waves and bottom-up control via the mechanical consequences of cell differentiations, underlies the process of morphogenesis and results in the achievement of functional stable final states. Duplications of branches of the differentiation tree may be the basis for continuing differentiation and macroevolution, analogous to gene duplication permitting divergence of genes. Metamorphoses, if they are proven to be fusions of disparate species, may be classified according to the topology of fusions of two differentiation trees. In the process of unfolding of morphogenetic structures, microevolution can be defined as changes of the differentiation tree that preserve topology of the tree, while macroevolution represents any change that alters the topology of the differentiation tree.},
}
@article {pmid37778286,
year = {2023},
author = {Duarte Hospital, C and Tête, A and Debizet, K and Imler, J and Tomkiewicz-Raulet, C and Blanc, EB and Barouki, R and Coumoul, X and Bortoli, S},
title = {SDHi fungicides: An example of mitotoxic pesticides targeting the succinate dehydrogenase complex.},
journal = {Environment international},
volume = {180},
number = {},
pages = {108219},
doi = {10.1016/j.envint.2023.108219},
pmid = {37778286},
issn = {1873-6750},
mesh = {Animals ; Humans ; *Fungicides, Industrial/toxicity ; *Pesticides ; Succinate Dehydrogenase/genetics/metabolism ; Fungi/metabolism ; Succinic Acid ; Succinates ; },
abstract = {Succinate dehydrogenase inhibitors (SDHi) are fungicides used to control the proliferation of pathogenic fungi in crops. Their mode of action is based on blocking the activity of succinate dehydrogenase (SDH), a universal enzyme expressed by all species harboring mitochondria. The SDH is involved in two interconnected metabolic processes for energy production: the transfer of electrons in the mitochondrial respiratory chain and the oxidation of succinate to fumarate in the Krebs cycle. In humans, inherited SDH deficiencies may cause major pathologies including encephalopathies and cancers. The cellular and molecular mechanisms related to such genetic inactivation have been well described in neuroendocrine tumors, in which it induces an oxidative stress, a pseudohypoxic phenotype, a metabolic, epigenetic and transcriptomic remodeling, and alterations in the migration and invasion capacities of cancer cells, in connection with the accumulation of succinate, an oncometabolite, substrate of the SDH. We will discuss recent studies reporting toxic effects of SDHi in non-target organisms and their implications for risk assessment of pesticides. Recent data show that the SDH structure is highly conserved during evolution and that SDHi can inhibit SDH activity in mitochondria of non-target species, including humans. These observations suggest that SDHi are not specific inhibitors of fungal SDH. We hypothesize that SDHi could have toxic effects in other species, including humans. Moreover, the analysis of regulatory assessment reports shows that most SDHi induce tumors in animals without evidence of genotoxicity. Thus, these substances could have a non-genotoxic mechanism of carcinogenicity that still needs to be fully characterized and that could be related to SDH inhibition. The use of pesticides targeting mitochondrial enzymes encoded by tumor suppressor genes raises questions on the risk assessment framework of mitotoxic pesticides. The issue of SDHi fungicides is therefore a textbook case that highlights the urgent need for changes in regulatory assessment.},
}
@article {pmid37766465,
year = {2023},
author = {Dial, DT and Weglarz, KM and Brunet, BMT and Havill, NP and von Dohlen, CD and Burke, GR},
title = {Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae).},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {1},
pages = {},
pmid = {37766465},
issn = {2160-1836},
support = {DEB-1655182//National Science Foundation/ ; //Utah Agricultural Experiment Station/ ; },
mesh = {Animals ; *Hemiptera/genetics ; Ecosystem ; *Aphids/genetics ; Ecology ; North America ; },
abstract = {The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha.},
}
@article {pmid37761909,
year = {2023},
author = {Mendivil, A and Ramírez, R and Morin, J and Ramirez, JL and Siccha-Ramirez, R and Britzke, R and Rivera, F and Ampuero, A and Oliveros, N and Congrains, C},
title = {Comparative Mitogenome Analysis of Two Native Apple Snail Species (Ampullariidae, Pomacea) from Peruvian Amazon.},
journal = {Genes},
volume = {14},
number = {9},
pages = {},
pmid = {37761909},
issn = {2073-4425},
mesh = {Animals ; Peru ; Phylogeny ; *Genome, Mitochondrial/genetics ; Snails/genetics ; Mitochondria/genetics ; },
abstract = {Apple snails of the genus Pomacea Perry, 1810 (Mollusca: Caenogastropoda: Ampullariidae) are native to the Neotropics and exhibit high species diversity, holding cultural and ecological significance as an important protein source in Peru. However, most genetic studies in Pomacea have focused mostly on invasive species, especially in Southeast Asia, where they are considered important pests. In this study, we assembled and annotated the mitochondrial genomes of two Pomacea species native to the Peruvian Amazon: Pomacea reevei Ampuero &amp; Ramírez, 2023 and Pomacea aulanieri (Deville &amp; Hupé, 1850). The mitogenomes of P. reevei and P. aulanieri comprise 15,660 and 16,096 bp, respectively, and contain the typical 37 genes of the animal mitochondria with a large control region of 292 bp in P. reevei and 524 bp in P. aulanieri-which fall within the range of what is currently known in Pomacea. Comparisons with previously published mitogenomes in Pomacea revealed differences in the overlapping of adjacent genes, the size of certain protein-coding genes (PCGs) and the secondary structure of some tRNAs that are consistent with the phylogenetic relationships between these species. These findings provide valuable insights into the systematics and genomics of the genus Pomacea.},
}
@article {pmid37761841,
year = {2023},
author = {Koshkina, O and Deniskova, T and Dotsev, A and Kunz, E and Selionova, M and Medugorac, I and Zinovieva, N},
title = {Phylogenetic Analysis of Russian Native Sheep Breeds Based on mtDNA Sequences.},
journal = {Genes},
volume = {14},
number = {9},
pages = {},
pmid = {37761841},
issn = {2073-4425},
mesh = {Sheep/genetics ; Animals ; *DNA, Mitochondrial/genetics ; Phylogeny ; *Mitochondria/genetics ; Animals, Domestic/genetics ; Russia ; },
abstract = {Eurasia is represented by all climatic zones and various environments. A unique breed variety of farm animals has been developed in Russia, whose territory covers a large area of the continent. A total of 69 local breeds and types of dairy, wool, and meat sheep (Ovis aries) are maintained here. However, the genetic diversity and maternal origin of these local breeds have not been comprehensively investigated. In this study, we describe the diversity and phylogeny of Russian sheep breeds inhabiting different geographical regions based on the analysis of complete sequences of mitochondrial genomes (mtDNA). Complete mtDNA sequences of the studied sheep were obtained using next-generation sequencing technology (NGS). All investigated geographical groups of sheep were characterized by high haplotype (Hd = 0.9992) and nucleotide diversity (π = 0.00378). Analysis of the AMOVA results showed that genetic diversity was majorly determined by within-population differences (77.87%). We identified 128 haplotypes in all studied sheep. Haplotypes belonged to the following haplogroups: B (64.8%), A (28.9%), C (5.5%), and D (0.8%). Haplogroup B was predominant in the western part of Russia. A high level of mtDNA polymorphism in the studied groups of local sheep indicates the presence of a significant reserve of unique genotypes in Russia, which is to be explored.},
}
@article {pmid37760086,
year = {2023},
author = {Subczynski, WK and Pasenkiewicz-Gierula, M and Widomska, J},
title = {Protecting the Eye Lens from Oxidative Stress through Oxygen Regulation.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {12},
number = {9},
pages = {},
pmid = {37760086},
issn = {2076-3921},
support = {R01 EY015526/EY/NEI NIH HHS/United States ; },
abstract = {Molecular oxygen is a primary oxidant that is involved in the formation of active oxygen species and in the oxidation of lipids and proteins. Thus, controlling oxygen partial pressure (concentration) in the human organism, tissues, and organs can be the first step in protecting them against oxidative stress. However, it is not an easy task because oxygen is necessary for ATP synthesis by mitochondria and in many biochemical reactions taking place in all cells in the human body. Moreover, the blood circulatory system delivers oxygen to all parts of the body. The eye lens seems to be the only organ that is protected from the oxidative stress through the regulation of oxygen partial pressure. The basic mechanism that developed during evolution to protect the eye lens against oxidative damage is based on the maintenance of a very low concentration of oxygen within the lens. This antioxidant mechanism is supported by the resistance of both the lipid components of the lens membrane and cytosolic proteins to oxidation. Any disturbance, continuous or acute, in the working of this mechanism increases the oxygen concentration, in effect causing cataract development. Here, we describe the biophysical basis of the mechanism and its correlation with lens transparency.},
}
@article {pmid37752851,
year = {2023},
author = {Togashi, T and Parker, GA and Horinouchi, Y},
title = {Mitochondrial uniparental inheritance achieved after fertilization challenges the nuclear-cytoplasmic conflict hypothesis for anisogamy evolution.},
journal = {Biology letters},
volume = {19},
number = {9},
pages = {20230352},
pmid = {37752851},
issn = {1744-957X},
mesh = {Male ; Humans ; *Mitochondria ; *DNA, Mitochondrial/genetics ; Inheritance Patterns ; Polymerase Chain Reaction ; Fertilization ; },
abstract = {In eukaryotes, a fundamental phenomenon underlying sexual selection is the evolution of gamete size dimorphism between the sexes (anisogamy) from an ancestral gametic system with gametes of the same size in both mating types (isogamy). The nuclear-cytoplasmic conflict hypothesis has been one of the major theoretical hypotheses for the evolution of anisogamy. It proposes that anisogamy evolved as an adaptation for preventing nuclear-cytoplasmic conflict by minimizing male gamete size to inherit organelles uniparentally. In ulvophycean green algae, biparental inheritance of organelles is observed in isogamous species, as the hypothesis assumes. So we tested the hypothesis by examining whether cytoplasmic inheritance is biparental in Monostroma angicava, a slightly anisogamous ulvophycean that produces large male gametes. We tracked the fates of mitochondria in intraspecific crosses with PCR-RFLP markers. We confirmed that mitochondria are maternally inherited. However, paternal mitochondria enter the zygote, where their DNA can be detected for over 14 days. This indicates that uniparental inheritance is enforced by eliminating paternal mitochondrial DNA in the zygote, rather than by decreasing male gamete size to the minimum. Thus, uniparental cytoplasmic inheritance is achieved by an entirely different mechanism, and is unlikely to drive the evolution of anisogamy in ulvophyceans.},
}
@article {pmid37748065,
year = {2023},
author = {Zhang, K and Zhao, X and Zhao, Y and Zhang, Z and Liu, Z and Liu, Z and Yu, Y and Li, J and Ma, Y and Dong, Y and Pang, X and Jin, X and Li, N and Liu, B and Wendel, JF and Zhai, J and Long, Y and Wang, T and Gong, L},
title = {Cell type-specific cytonuclear coevolution in three allopolyploid plant species.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {40},
pages = {e2310881120},
pmid = {37748065},
issn = {1091-6490},
mesh = {*Mitochondria/genetics ; *Plastids ; Cell Differentiation ; Solitary Nucleus ; },
abstract = {Cytonuclear disruption may accompany allopolyploid evolution as a consequence of the merger of different nuclear genomes in a cellular environment having only one set of progenitor organellar genomes. One path to reconcile potential cytonuclear mismatch is biased expression for maternal gene duplicates (homoeologs) encoding proteins that target to plastids and/or mitochondria. Assessment of this transcriptional form of cytonuclear coevolution at the level of individual cells or cell types remains unexplored. Using single-cell (sc-) and single-nucleus (sn-) RNAseq data from eight tissues in three allopolyploid species, we characterized cell type-specific variations of cytonuclear coevolutionary homoeologous expression and demonstrated the temporal dynamics of expression patterns across development stages during cotton fiber development. Our results provide unique insights into transcriptional cytonuclear coevolution in plant allopolyploids at the single-cell level.},
}
@article {pmid37744223,
year = {2023},
author = {Suárez Menéndez, M and Rivera-León, VE and Robbins, J and Berube, M and Palsbøll, PJ},
title = {PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16028},
pmid = {37744223},
issn = {2167-8359},
mesh = {Animals ; *Heteroplasmy ; Fluorescence ; *Humpback Whale ; Mitochondria ; Nucleotides ; },
abstract = {Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).},
}
@article {pmid37742881,
year = {2024},
author = {Zhang, T and Vďačný, P},
title = {Deciphering phylogenetic relationships of and delimiting species boundaries within the controversial ciliate genus Conchophthirus using an integrative morpho-evo approach.},
journal = {Molecular phylogenetics and evolution},
volume = {190},
number = {},
pages = {107931},
doi = {10.1016/j.ympev.2023.107931},
pmid = {37742881},
issn = {1095-9513},
mesh = {Phylogeny ; Sequence Analysis, DNA ; *Oligohymenophorea ; *Ciliophora/genetics ; Mitochondria ; },
abstract = {The phylum Ciliophora (ciliates) comprises about 2600 symbiotic and over 5500 free-living species. The inclusion of symbiotic ciliates in phylogenetic analyses often challenges traditional classification frameworks due to their morphological adaptions to the symbiotic lifestyle. Conchophthirus is such a controversial obligate endocommensal genus whose affinities to other symbiotic and free-living scuticociliates are still poorly understood. Using uni- and multivariate morphometrics as well as 2D-based molecular and phylogenetic analyses, we attempted to test for the monophyly of Conchophthirus, study the boundaries of Conchophthirus species isolated from various bivalves at mesoscale, and reveal the phylogenetic relationships of Conchophthirus to other scuticociliates. Multidimensional analyses of morphometric and cell geometric data generated the same homogenous clusters, as did phylogenetic analyses based on 144 new sequences of two mitochondrial and five nuclear molecular markers. Conchophthirus is not closely related to 'core' scuticociliates represented by the orders Pleuronematida and Philasterida, as assumed in the past using morphological data. Nuclear and mitochondrial markers consistently showed the free-living Dexiotricha and the mouthless endosymbiotic Haptophrya to be the nearest relatives of Conchophthirus. These three highly morphologically and ecologically dissimilar genera represent an orphan clade from the early radiation of scuticociliates in molecular phylogenies.},
}
@article {pmid37735485,
year = {2023},
author = {Sidorczuk, K and Mackiewicz, P and Pietluch, F and Gagat, P},
title = {Characterization of signal and transit peptides based on motif composition and taxon-specific patterns.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {15751},
pmid = {37735485},
issn = {2045-2322},
mesh = {Amino Acid Sequence ; *Amino Acids ; *Antimicrobial Peptides ; Chloroplasts ; Computational Biology ; },
abstract = {Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum, and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hypothesized to have evolved from antimicrobial peptides (AMPs), which are responsible for the host defence against microorganisms, including bacteria, fungi and viruses. In this study, we performed comprehensive bioinformatic analyses of amino acid motifs of targeting peptides and AMPs using a curated set of experimentally verified proteins. We identified motifs frequently occurring in each type of presequence showing specific patterns associated with their amino acid composition, and investigated their position within the presequence. We also compared motif patterns among different taxonomic groups and identified taxon-specific features, providing some evolutionary insights. Considering the functional relevance and many practical applications of targeting peptides and AMPs, we believe that our analyses will prove useful for their design, and better understanding of protein import mechanism and presequence evolution.},
}
@article {pmid37717227,
year = {2024},
author = {Chen, S and Tran, TTT and Yeh, AY and Yang, H and Chen, J and Yang, Y and Wang, X},
title = {The Globodera rostochiensis Gr29D09 Effector with a Role in Defense Suppression Targets the Potato Hexokinase 1 Protein.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {37},
number = {1},
pages = {25-35},
doi = {10.1094/MPMI-07-23-0095-R},
pmid = {37717227},
issn = {0894-0282},
mesh = {Animals ; *Solanum tuberosum ; Hexokinase/genetics ; Reactive Oxygen Species ; Phylogeny ; Proteins/genetics ; *Nematoda ; *Tylenchoidea/physiology ; },
abstract = {The potato cyst nematode (Globodera rostochiensis) is an obligate root pathogen of potatoes. G. rostochiensis encodes several highly expanded effector gene families, including the Gr4D06 family; however, little is known about the function of this effector family. We cloned four 29D09 genes from G. rostochiensis (named Gr29D09v1/v2/v3/v4) that share high sequence similarity and are homologous to the Hg29D09 and Hg4D06 effector genes from the soybean cyst nematode (Heterodera glycines). Phylogenetic analysis revealed that Gr29D09 genes belong to a subgroup of the Gr4D06 family. We showed that Gr29D09 genes are expressed exclusively within the nematode's dorsal gland cell and are dramatically upregulated in parasitic stages, indicating involvement of Gr29D09 effectors in nematode parasitism. Transgenic potato lines overexpressing Gr29D09 variants showed increased susceptibility to G. rostochiensis. Transient expression assays in Nicotiana benthamiana demonstrated that Gr29D09v3 could suppress reactive oxygen species (ROS) production and defense gene expression induced by flg22 and cell death mediated by immune receptors. These results suggest a critical role of Gr29D09 effectors in defense suppression. The use of affinity purification coupled with nanoliquid chromatography-tandem mass spectrometry identified potato hexokinase 1 (StHXK1) as a candidate target of Gr29D09. The Gr29D09-StHXK1 interaction was further confirmed using in planta protein-protein interaction assays. Plant HXKs have been implicated in defense regulation against pathogen infection. Interestingly, we found that StHXK1 could enhance flg22-induced ROS production, consistent with a positive role of plant HXKs in defense. Altogether, our results suggest that targeting StHXK1 by Gr29D09 effectors may impair the positive function of StHXK1 in plant immunity, thereby aiding nematode parasitism. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.},
}
@article {pmid37715276,
year = {2023},
author = {Leal-Dutra, CA and Yuen, LM and Guedes, BAM and Contreras-Serrano, M and Marques, PE and Shik, JZ},
title = {Evidence that the domesticated fungus Leucoagaricus gongylophorus recycles its cytoplasmic contents as nutritional rewards to feed its leafcutter ant farmers.},
journal = {IMA fungus},
volume = {14},
number = {1},
pages = {19},
pmid = {37715276},
issn = {2210-6340},
support = {ERC-2017-STG-757810/ERC_/European Research Council/International ; },
abstract = {Leafcutter ants farm a fungal cultivar (Leucoagaricus gongylophorus) that converts inedible vegetation into food that sustains colonies with up to millions of workers. Analogous to edible fruits of crops domesticated by humans, L. gongylophorus has evolved specialized nutritional rewards-swollen hyphal cells called gongylidia that package metabolites and are consumed by ant farmers. Yet, little is known about how gongylidia form, and thus how fungal physiology and ant provisioning collectively govern farming performance. We explored the process of gongylidium formation using advanced microscopy to image the cultivar at scales of nanometers, and both in vitro experiments and in silico analyses to examine the mechanisms of gongylidia formation when isolated from ant farmers. We first used transmission electron, fluorescence, and confocal microscopy imaging to see inside hyphal cells. This imaging showed that the cultivar uses a process called autophagy to recycle its own cellular material (e.g. cytosol, mitochondria) and then shuttles the resulting metabolites into a vacuole whose continual expansion displaces other organelles and causes the gongylidium cell's bulging bulb-like appearance. We next used scanning electron microscopy and light microscopy to link this intracellular rearrangement to the external branching patterns of gongylidium cells as they clump together into edible bundles called staphyla. We next confirmed that autophagy plays a critical role in gongylidium formation both: (1) in vitro as gongylidium suppression occurred when isolated fungal cultures were grown on media with autophagy inhibitors, and (2) in silico as differential transcript expression (RNA-seq) analyses showed upregulation of multiple autophagy gene isoforms in gongylidia relative to undifferentiated hyphae. While autophagy is a ubiquitous and often highly derived process across the tree of life, our study reveals a new role for autophagy as a mechanism of functional integration between ant farmers and their fungal crop, and potentially as a signifier of higher-level homeostasis between uniquely life-time committed ectosymbionts.},
}
@article {pmid37708410,
year = {2023},
author = {Khachaturyan, M and Reusch, TBH and Dagan, T},
title = {Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant.},
journal = {Genome biology and evolution},
volume = {15},
number = {9},
pages = {},
pmid = {37708410},
issn = {1759-6653},
mesh = {Humans ; Metagenomics ; *Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; *Magnoliopsida/genetics ; },
abstract = {Mitochondrial genomes (mitogenomes) of flowering plants are composed of multiple chromosomes. Recombination within and between the mitochondrial chromosomes may generate diverse DNA molecules termed isoforms. The isoform copy number and composition can be dynamic within and among individual plants due to uneven replication and homologous recombination. Nonetheless, despite their functional importance, the level of mitogenome conservation within species remains understudied. Whether the ontogenetic variation translates to evolution of mitogenome composition over generations is currently unknown. Here we show that the mitogenome composition of the seagrass Zostera marina is conserved among worldwide populations that diverged ca. 350,000 years ago. Using long-read sequencing, we characterized the Z. marina mitochondrial genome and inferred the repertoire of recombination-induced configurations. To characterize the mitochondrial genome architecture worldwide and study its evolution, we examined the mitogenome in Z. marina meristematic region sampled in 16 populations from the Pacific and Atlantic oceans. Our results reveal a striking similarity in the isoform relative copy number, indicating a high conservation of the mitogenome composition among distantly related populations and within the plant germline, despite a notable variability during individual ontogenesis. Our study supplies a link between observations of dynamic mitogenomes at the level of plant individuals and long-term mitochondrial evolution.},
}
@article {pmid37685874,
year = {2023},
author = {Maffeo, B and Panuzzo, C and Moraca, A and Cilloni, D},
title = {A Leukemic Target with a Thousand Faces: The Mitochondria.},
journal = {International journal of molecular sciences},
volume = {24},
number = {17},
pages = {},
pmid = {37685874},
issn = {1422-0067},
mesh = {Humans ; *Mitochondria ; Cell Division ; Clonal Evolution ; Clone Cells ; *Leukemia ; },
abstract = {In the era of personalized medicine greatly improved by molecular diagnosis and tailor-made therapies, the survival rate of acute myeloid leukemia (AML) at 5 years remains unfortunately low. Indeed, the high heterogeneity of AML clones with distinct metabolic and molecular profiles allows them to survive the chemotherapy-induced changes, thus leading to resistance, clonal evolution, and relapse. Moreover, leukemic stem cells (LSCs), the quiescent reservoir of residual disease, can persist for a long time and activate the recurrence of disease, supported by significant metabolic differences compared to AML blasts. All these points highlight the relevance to develop combination therapies, including metabolism inhibitors to improve treatment efficacy. In this review, we summarized the metabolic differences in AML blasts and LSCs, the molecular pathways related to mitochondria and metabolism are druggable and targeted in leukemia therapies, with a distinct interest for Venetoclax, which has revolutionized the therapeutic paradigms of several leukemia subtype, unfit for intensive treatment regimens.},
}
@article {pmid37667092,
year = {2023},
author = {Kar, C and Mariyambi, PC and Raghavan, R and Sureshkumar, S},
title = {Mitochondrial phylogeny of fusilier fishes (family Caesionidae) from the Laccadive archipelago reveals a new species and two new records from the Central Indian Ocean.},
journal = {Journal of fish biology},
volume = {103},
number = {6},
pages = {1445-1451},
doi = {10.1111/jfb.15553},
pmid = {37667092},
issn = {1095-8649},
support = {CRG/2020/004498//Department of Science and Technology, Government of India/ ; 200510341520//University Grants Commission/ ; },
mesh = {Animals ; Phylogeny ; Indian Ocean ; *Fishes/genetics ; *Mitochondria/genetics ; Genes, Mitochondrial ; Pacific Ocean ; },
abstract = {Fusiliers of the family Caesionidae comprise a group of Indo-Pacific reef fishes important in the live bait and artisanal fisheries in many parts of its range, particularly in the Indian Ocean region. Using newly generated mitochondrial COI sequences of 10 species of caesionid fishes from the Laccadive archipelago, we carried out a molecular phylogenetic analysis, which has helped improve our understanding of the diversity, distribution, and systematics of this poorly known group of fishes. The two speciose genera within Caesionidae, Caesio and Pterocaesio, were revealed to be paraphyletic, and as a result, four names earlier considered as subgenera within Caesionidae (Flavicaesio, Odontonectes, Pisinnicaesio, and Squamosicaesio) were elevated to the status of distinct genera. We also discovered the presence of a new lineage in the Central Indian Ocean, sister to Caesio caerulaurea and Caesio xanthalytos, but distinct from both in several morphological characters and a genetic distance of between 2% and 3% in the mitochondrial COI gene. We describe this lineage as Caesio idreesi, a new species, with a distribution spanning the Laccadive Sea and the Bay of Bengal. Our genetic data also helped confirm the first confirmed records of two species, Pisinnicaesio digramma and Squamosicaesio randalli, from the Central Indian Ocean, and a new distribution record for C. xanthalytos in the Laccadive Sea. Combined, these results have helped bridge key biodiversity knowledge gaps of the family Caesionidae and form an excellent baseline for further investigations on their taxonomy, systematics, and life history.},
}
@article {pmid37664184,
year = {2023},
author = {Mendoza-Hoffmann, F and Yang, L and Buratto, D and Brito-Sánchez, J and Garduño-Javier, G and Salinas-López, E and Uribe-Álvarez, C and Ortega, R and Sotelo-Serrano, O and Cevallos, M&#xc1; and Ramírez-Silva, L and Uribe-Carvajal, S and Pérez-Hernández, G and Celis-Sandoval, H and García-Trejo, JJ},
title = {Inhibitory to non-inhibitory evolution of the ζ subunit of the F1FO-ATPase of Paracoccus denitrificans and α-proteobacteria as related to mitochondrial endosymbiosis.},
journal = {Frontiers in molecular biosciences},
volume = {10},
number = {},
pages = {1184200},
pmid = {37664184},
issn = {2296-889X},
abstract = {Introduction: The ζ subunit is a potent inhibitor of the F1FO-ATPase of Paracoccus denitrificans (PdF1FO-ATPase) and related α-proteobacteria different from the other two canonical inhibitors of bacterial (ε) and mitochondrial (IF1) F1FO-ATPases. ζ mimics mitochondrial IF1 in its inhibitory N-terminus, blocking the PdF1FO-ATPase activity as a unidirectional pawl-ratchet and allowing the PdF1FO-ATP synthase turnover. ζ is essential for the respiratory growth of P. denitrificans, as we showed by a Δζ knockout. Given the vital role of ζ in the physiology of P. denitrificans, here, we assessed the evolution of ζ across the α-proteobacteria class. Methods: Through bioinformatic, biochemical, molecular biology, functional, and structural analyses of several ζ subunits, we confirmed the conservation of the inhibitory N-terminus of ζ and its divergence toward its C-terminus. We reconstituted homologously or heterologously the recombinant ζ subunits from several α-proteobacteria into the respective F-ATPases, including free-living photosynthetic, facultative symbiont, and intracellular facultative or obligate parasitic α-proteobacteria. Results and discussion: The results show that ζ evolved, preserving its inhibitory function in free-living α-proteobacteria exposed to broad environmental changes that could compromise the cellular ATP pools. However, the ζ inhibitory function was diminished or lost in some symbiotic α-proteobacteria where ζ is non-essential given the possible exchange of nutrients and ATP from hosts. Accordingly, the ζ gene is absent in some strictly parasitic pathogenic Rickettsiales, which may obtain ATP from the parasitized hosts. We also resolved the NMR structure of the ζ subunit of Sinorhizobium meliloti (Sm-ζ) and compared it with its structure modeled in AlphaFold. We found a transition from a compact ordered non-inhibitory conformation into an extended α-helical inhibitory N-terminus conformation, thus explaining why the Sm-ζ cannot exert homologous inhibition. However, it is still able to inhibit the PdF1FO-ATPase heterologously. Together with the loss of the inhibitory function of α-proteobacterial ε, the data confirm that the primary inhibitory function of the α-proteobacterial F1FO-ATPase was transferred from ε to ζ and that ζ, ε, and IF1 evolved by convergent evolution. Some key evolutionary implications on the endosymbiotic origin of mitochondria, as most likely derived from α-proteobacteria, are also discussed.},
}
@article {pmid37662149,
year = {2023},
author = {Liu, H and Hou, Z and Xu, L and Ma, Q and Wei, M and Tembrock, LR and Zhang, S and Wu, Z},
title = {Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1228551},
pmid = {37662149},
issn = {1664-462X},
abstract = {Chrysanthemum indicum, a species native to Eastern Asia is well known as one of the progenitor species of the cultivated Chrysanthemum which is grown for its ornamental and medicinal value. Previous genomic studies on Chrysanthemum have largely ignored the dynamics of plastid genome (plastome) and mitochondria genome (mitogenome) evolution when analyzing this plant lineage. In this study, we sequenced and assembled the plastomes and mitogenomes of diploid and tetraploid C. indicum as well as the morphologically divergent variety C. indicum var. aromaticum. We used published data from 27 species with both plastome and mitogenome complete sequences to explore differences in sequence evolution between the organellar genomes. The size and structure of organellar genome between diploid and tetraploid C. indicum were generally similar but the tetraploid C. indicum and C. indicum var. aromaticum were found to contain unique sequences in the mitogenomes which also contained previously undescribed open reading frames (ORFs). Across Chrysanthemum mitogenome structure varied greatly but sequences transferred from plastomes in to the mitogenomes were conserved. Finally, differences observed between mitogenome and plastome gene trees may be the result of the difference in the rate of sequence evolution between genes in these two genomes. In total the findings presented here greatly expand the resources for studying Chrysanthemum organellar genome evolution with possible applications to conservation, breeding, and gene banking in the future.},
}
@article {pmid37644003,
year = {2023},
author = {French, CM and Bertola, LD and Carnaval, AC and Economo, EP and Kass, JM and Lohman, DJ and Marske, KA and Meier, R and Overcast, I and Rominger, AJ and Staniczenko, PPA and Hickerson, MJ},
title = {Global determinants of insect mitochondrial genetic diversity.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5276},
pmid = {37644003},
issn = {2041-1723},
mesh = {Animals ; *Insecta/genetics ; *Mitochondria ; DNA, Mitochondrial/genetics ; Biodiversity ; Genetic Variation ; },
abstract = {Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.},
}
@article {pmid37638880,
year = {2023},
author = {Gupta, SV and Campos, L and Schmidt, KH},
title = {Mitochondrial superoxide dismutase Sod2 suppresses nuclear genome instability during oxidative stress.},
journal = {Genetics},
volume = {225},
number = {2},
pages = {},
pmid = {37638880},
issn = {1943-2631},
support = {R01 GM139296/GM/NIGMS NIH HHS/United States ; R01GM018245/NH/NIH HHS/United States ; },
mesh = {Antioxidants ; DNA ; Genomic Instability ; Oxidative Stress ; Reactive Oxygen Species ; RecQ Helicases/metabolism ; *Saccharomyces cerevisiae/metabolism ; *Saccharomyces cerevisiae Proteins/genetics/metabolism ; Superoxide Dismutase/genetics/metabolism ; },
abstract = {Oxidative stress can damage DNA and thereby contribute to genome instability. To avoid an imbalance or overaccumulation of reactive oxygen species (ROS), cells are equipped with antioxidant enzymes that scavenge excess ROS. Cells lacking the RecQ-family DNA helicase Sgs1, which contributes to homology-dependent DNA break repair and chromosome stability, are known to accumulate ROS, but the origin and consequences of this oxidative stress phenotype are not fully understood. Here, we show that the sgs1 mutant exhibits elevated mitochondrial superoxide, increased mitochondrial mass, and accumulation of recombinogenic DNA lesions that can be suppressed by antioxidants. Increased mitochondrial mass in the sgs1Δ mutant is accompanied by increased mitochondrial branching, which was also inducible in wildtype cells by replication stress. Superoxide dismutase Sod2 genetically interacts with Sgs1 in the suppression of nuclear chromosomal rearrangements under paraquat (PQ)-induced oxidative stress. PQ-induced chromosome rearrangements in the absence of Sod2 are promoted by Rad51 recombinase and the polymerase subunit Pol32. Finally, the dependence of chromosomal rearrangements on the Rev1/Pol ζ mutasome suggests that under oxidative stress successful DNA synthesis during DNA break repair depends on translesion DNA synthesis.},
}
@article {pmid37636868,
year = {2023},
author = {Le Cam, S and Brémaud, J and Malkócs, T and Kreckelbergh, E and Becquet, V and Dubillot, E and Garcia, P and Breton, S and Pante, E},
title = {LAMP-based molecular sexing in a gonochoric marine bivalve (Macoma balthica rubra) with divergent sex-specific mitochondrial genomes.},
journal = {Ecology and evolution},
volume = {13},
number = {8},
pages = {e10320},
pmid = {37636868},
issn = {2045-7758},
abstract = {Taking advantage of the unique system of doubly uniparental inheritance (DUI) of mitochondria, we developed a reliable molecular method to sex individuals of the marine bivalve Macoma balthica rubra. In species with DUI (~100 known bivalves), both sexes transmit their mitochondria: males bear both a male- and female-type mitogenome, while females bear only the female type. Male and female mitotypes are sufficiently divergent to reliably PCR-amplify them specifically. Loop-mediated isothermal amplification (LAMP) is a precise, economical and portable alternative to PCR for molecular sexing and we demonstrate its application in this context. We used 154 individuals sampled along the Atlantic coast of France and sexed microscopically by gonad examination to test for the congruence among gamete type, PCR sexing and LAMP sexing. We show an exact match among the sexing results from these three methods using the male and female mt-cox1 genes. DUI can be disrupted in inter-specific hybrids, causing unexpected distribution of mitogenomes, such as homoplasmic males or heteroplasmic females. To our knowledge, DUI disruption at the intra-specific scale has never been tested. We applied our sexing protocol to control for unexpected heteroplasmy caused by hybridization between divergent genetic lineages and found no evidence of disruption in the mode of mitochondrial inheritance in M. balthica rubra. We propose LAMP as a useful tool to accelerate eco-evolutionary studies of DUI. It offers the opportunity to investigate the potential role of, previously unaccounted-for, sex-specific patterns such as sexual selection or sex-specific dispersal bias in the evolution of free-spawning benthic species.},
}
@article {pmid37636259,
year = {2023},
author = {Fiedler, L and Middendorf, M and Bernt, M},
title = {Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1250907},
pmid = {37636259},
issn = {1664-8021},
abstract = {A wide range of scientific fields, such as forensics, anthropology, medicine, and molecular evolution, benefits from the analysis of mitogenomic data. With the development of new sequencing technologies, the amount of mitochondrial sequence data to be analyzed has increased exponentially over the last few years. The accurate annotation of mitochondrial DNA is a prerequisite for any mitogenomic comparative analysis. To sustain with the growth of the available mitochondrial sequence data, highly efficient automatic computational methods are, hence, needed. Automatic annotation methods are typically based on databases that contain information about already annotated (and often pre-curated) mitogenomes of different species. However, the existing approaches have several shortcomings: 1) they do not scale well with the size of the database; 2) they do not allow for a fast (and easy) update of the database; and 3) they can only be applied to a relatively small taxonomic subset of all species. Here, we present a novel approach that does not have any of these aforementioned shortcomings, (1), (2), and (3). The reference database of mitogenomes is represented as a richly annotated de Bruijn graph. To generate gene predictions for a new user-supplied mitogenome, the method utilizes a clustering routine that uses the mapping information of the provided sequence to this graph. The method is implemented in a software package called DeGeCI (De Bruijn graph Gene Cluster Identification). For a large set of mitogenomes, for which expert-curated annotations are available, DeGeCI generates gene predictions of high conformity. In a comparative evaluation with MITOS2, a state-of-the-art annotation tool for mitochondrial genomes, DeGeCI shows better database scalability while still matching MITOS2 in terms of result quality and providing a fully automated means to update the underlying database. Moreover, unlike MITOS2, DeGeCI can be run in parallel on several processors to make use of modern multi-processor systems.},
}
@article {pmid37634556,
year = {2023},
author = {Theriault, JE and Shaffer, C and Dienel, GA and Sander, CY and Hooker, JM and Dickerson, BC and Barrett, LF and Quigley, KS},
title = {A functional account of stimulation-based aerobic glycolysis and its role in interpreting BOLD signal intensity increases in neuroimaging experiments.},
journal = {Neuroscience and biobehavioral reviews},
volume = {153},
number = {},
pages = {105373},
pmid = {37634556},
issn = {1873-7528},
support = {R01 AG071173/AG/NIA NIH HHS/United States ; R01 MH109464/MH/NIMH NIH HHS/United States ; R21 MH129902/MH/NIMH NIH HHS/United States ; R01 MH113234/MH/NIMH NIH HHS/United States ; U01 CA193632/CA/NCI NIH HHS/United States ; R01 CA258269/CA/NCI NIH HHS/United States ; R00 DA043629/DA/NIDA NIH HHS/United States ; },
mesh = {Humans ; *Glycolysis/physiology ; *Adenosine Triphosphate ; Brain/diagnostic imaging/metabolism ; Glucose/metabolism ; Neuroimaging ; },
abstract = {In aerobic glycolysis, oxygen is abundant, and yet cells metabolize glucose without using it, decreasing their ATP per glucose yield by 15-fold. During task-based stimulation, aerobic glycolysis occurs in localized brain regions, presenting a puzzle: why produce ATP inefficiently when, all else being equal, evolution should favor the efficient use of metabolic resources? The answer is that all else is not equal. We propose that a tradeoff exists between efficient ATP production and the efficiency with which ATP is spent to transmit information. Aerobic glycolysis, despite yielding little ATP per glucose, may support neuronal signaling in thin (< 0.5 µm), information-efficient axons. We call this the efficiency tradeoff hypothesis. This tradeoff has potential implications for interpretations of task-related BOLD "activation" observed in fMRI. We hypothesize that BOLD "activation" may index local increases in aerobic glycolysis, which support signaling in thin axons carrying "bottom-up" information, or "prediction error"-i.e., the BIAPEM (BOLD increases approximate prediction error metabolism) hypothesis. Finally, we explore implications of our hypotheses for human brain evolution, social behavior, and mental disorders.},
}
@article {pmid37629135,
year = {2023},
author = {Cai, H and Ren, Y and Du, J and Liu, L and Long, L and Yang, M},
title = {Analysis of the RNA Editing Sites and Orthologous Gene Function of Transcriptome and Chloroplast Genomes in the Evolution of Five Deutzia Species.},
journal = {International journal of molecular sciences},
volume = {24},
number = {16},
pages = {},
pmid = {37629135},
issn = {1422-0067},
support = {No.21326301D//Province Key Research and Development Program of Hebei/ ; },
mesh = {*Transcriptome/genetics ; *Genome, Chloroplast ; Phylogeny ; RNA Editing/genetics ; Gene Expression Profiling ; },
abstract = {In this study, the chloroplast genomes and transcriptomes of five Deutzia genus species were sequenced, characterized, combined, and analyzed. A phylogenetic tree was constructed, including 32 other chloroplast genome sequences of Hydrangeoideae species. The results showed that the five Deutzia chloroplast genomes were typical circular genomes 156,860-157,025 bp in length, with 37.58-37.6% GC content. Repeat analysis showed that the Deutzia species had 41-45 scattered repeats and 199-201 simple sequence repeats. Comparative genomic and pi analyses indicated that the genomes are conservative and that the gene structures are stable. According to the phylogenetic tree, Deutzia species appear to be closely related to Kirengeshoma palmata and Philadelphus. By combining chloroplast genomic and transcriptomic analyses, 29-31 RNA editing events and 163-194 orthologous genes were identified. The ndh, rpo, rps, and atp genes had the most editing sites, and all RNA editing events were of the C-to-U type. Most of the orthologous genes were annotated to the chloroplast, mitochondria, and nucleus, with functions including energy production and conversion, translation, and protein transport. Genes related to the biosynthesis of monoterpenoids and flavonoids were also identified from the transcriptome of Deutzia spp. Our results will contribute to further studies of the genomic information and potential uses of the Deutzia spp.},
}
@article {pmid37629077,
year = {2023},
author = {Zalewska, A and Antonowicz, B and Szulimowska, J and Zieniewska-Siemieńczuk, I and Leśniewska, B and Borys, J and Zięba, S and Kostecka-Sochoń, P and Żendzian-Piotrowska, M and Lo Giudice, R and Lo Giudice, G and Żukowski, P and Maciejczyk, M},
title = {Mitochondrial Redox Balance of Fibroblasts Exposed to Ti-6Al-4V Microplates Subjected to Different Types of Anodizing.},
journal = {International journal of molecular sciences},
volume = {24},
number = {16},
pages = {},
pmid = {37629077},
issn = {1422-0067},
support = {B.SUB.23.309//Medical University in Bialystok/ ; },
mesh = {Humans ; *Titanium/pharmacology ; *Mitochondria ; Fibroblasts ; Oxidation-Reduction ; },
abstract = {Despite the high biocompatibility of titanium and its alloys, the need to remove titanium implants is increasingly being debated due to the potential for adverse effects associated with long-term retention. Therefore, new solutions are being sought to enhance the biocompatibility of titanium implants. One of them is to increase the thickness of the passive layer of the implant made of titanium dioxide. We were the first to evaluate the effect of hard-anodized (type II) Ti-6Al-4V alloy discs on the cytotoxicity, mitochondrial function, and redox balance of fibroblasts mitochondria compared to standard-anodized (type III) and non-anodized discs. The study used fibroblasts obtained from human gingival tissue. The test discs were applied to the bottom of 12-well plates. Cells were cultured for 24 h and 7, 14, and 21 days and mitochondria were isolated. We demonstrated the occurrence of oxidative stress in the mitochondria of fibroblasts of all tested groups, regardless of the presence and type of anodization. Type II anodization prevented changes in complex II activity (vs. control). The lowest degree of citrate synthase inhibition occurred in mitochondria exposed to titanium discs with type II anodization. In the last phase of culture, the presence of type II anodization reduced the degree of cytochrome c oxidase inhibition compared to the other tests groups and the control group, and prevented apoptosis. Throughout the experiment, the release of titanium, aluminium, and vanadium ions from titanium discs with a hard-anodized passive layer was higher than from the other titanium discs, but decreased with time. The obtained results proved the existence of dysfunction and redox imbalance in the mitochondria of fibroblasts exposed to hard-anodized titanium discs, suggesting the need to search for new materials perhaps biodegradable in tissues of the human body.},
}
@article {pmid37628665,
year = {2023},
author = {Havaš Auguštin, D and Šarac, J and Reidla, M and Tamm, E and Grahovac, B and Kapović, M and Novokmet, N and Rudan, P and Missoni, S and Marjanović, D and Korolija, M},
title = {Refining the Global Phylogeny of Mitochondrial N1a, X, and HV2 Haplogroups Based on Rare Mitogenomes from Croatian Isolates.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628665},
issn = {2073-4425},
mesh = {Humans ; Phylogeny ; Croatia ; *Genome, Mitochondrial/genetics ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Mitochondrial DNA (mtDNA) has been used for decades as a predominant tool in population genetics and as a valuable addition to forensic genetic research, owing to its unique maternal inheritance pattern that enables the tracing of individuals along the maternal lineage across numerous generations. The dynamic interplay between evolutionary forces, primarily genetic drift, bottlenecks, and the founder effect, can exert significant influence on genetic profiles. Consequently, the Adriatic islands have accumulated a subset of lineages that exhibits remarkable absence or rarity within other European populations. This distinctive genetic composition underscores the islands' potential as a significant resource in phylogenetic research, with implications reaching beyond regional boundaries to contribute to a global understanding. In the initial attempt to expand the mitochondrial forensic database of the Croatian population with haplotypes from small isolated communities, we sequenced mitogenomes of rare haplogroups from different Croatian island and mainland populations using next-generation sequencing (NGS). In the next step and based on the obtained results, we refined the global phylogeny of haplogroup N1a, HV2, and X by analyzing rare haplotypes, which are absent from the current phylogenetic tree. The trees were based on 16 novel and 52 previously published samples, revealing completely novel branches in the X and HV2 haplogroups and a new European cluster in the ancestral N1a variant, previously believed to be an exclusively African-Asian haplogroup. The research emphasizes the importance of investigating geographically isolated populations and their unique characteristics within a global context.},
}
@article {pmid37628588,
year = {2023},
author = {Baldo, MS and Nogueira, C and Pereira, C and Janeiro, P and Ferreira, S and Lourenço, CM and Bandeira, A and Martins, E and Magalhães, M and Rodrigues, E and Santos, H and Ferreira, AC and Vilarinho, L},
title = {Leigh Syndrome Spectrum: A Portuguese Population Cohort in an Evolutionary Genetic Era.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628588},
issn = {2073-4425},
mesh = {Child ; Infant ; Humans ; *Leigh Disease/genetics ; Portugal ; DNA, Mitochondrial/genetics ; Mitochondria ; Biological Evolution ; },
abstract = {Mitochondrial diseases are the most common inherited inborn error of metabolism resulting in deficient ATP generation, due to failure in homeostasis and proper bioenergetics. The most frequent mitochondrial disease manifestation in children is Leigh syndrome (LS), encompassing clinical, neuroradiological, biochemical, and molecular features. It typically affects infants but occurs anytime in life. Considering recent updates, LS clinical presentation has been stretched, and is now named LS spectrum (LSS), including classical LS and Leigh-like presentations. Apart from clinical diagnosis challenges, the molecular characterization also progressed from Sanger techniques to NGS (next-generation sequencing), encompassing analysis of nuclear (nDNA) and mitochondrial DNA (mtDNA). This upgrade resumed steps and favored diagnosis. Hereby, our paper presents molecular and clinical data on a Portuguese cohort of 40 positive cases of LSS. A total of 28 patients presented mutation in mtDNA and 12 in nDNA, with novel mutations identified in a heterogeneous group of genes. The present results contribute to the better knowledge of the molecular basis of LS and expand the clinical spectrum associated with this syndrome.},
}
@article {pmid37628587,
year = {2023},
author = {Hernández, CL},
title = {Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628587},
issn = {2073-4425},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Anthropology ; Biological Evolution ; Inheritance Patterns ; },
abstract = {Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.},
}
@article {pmid37604791,
year = {2023},
author = {Fernández-Álvarez, F&#xc1; and Sanchez, G and Deville, D and Taite, M and Villanueva, R and Allcock, AL},
title = {Atlantic Oceanic Squids in the "Grey Speciation Zone".},
journal = {Integrative and comparative biology},
volume = {63},
number = {6},
pages = {1214-1225},
pmid = {37604791},
issn = {1557-7023},
support = {IJC2020-043170-I//Generalitat de Catalunya/ ; GOIPD/2019/460//Irish Research Council/ ; 22K15085//Grant-in-Aid for Early-Career Scientists/ ; //Ministerio de Ciencia e Innovaci&#xf3;n/ ; //European Union/ ; CEX2019-000928-S//Spanish Government/ ; CTM2016-78853-R//FEDER/ ; },
mesh = {Animals ; Phylogeny ; *Decapodiformes ; Oceans and Seas ; *Biodiversity ; Mitochondria ; },
abstract = {Cryptic species complexes represent an important challenge for the adequate characterization of Earth's biodiversity. Oceanic organisms tend to have greater unrecognized cryptic biodiversity since the marine realm was often considered to lack hard barriers to genetic exchange. Here, we tested the effect of several Atlantic and Mediterranean oceanic barriers on 16 morphospecies of oceanic squids of the orders Oegopsida and Bathyteuthida using three mitochondrial and one nuclear molecular marker and five species delimitation methods. Number of species recognized within each morphospecies differed among different markers and analyses, but we found strong evidence of cryptic biodiversity in at least four of the studied species (Chtenopteryx sicula, Chtenopteryx canariensis, Ancistrocheirus lesueurii, and Galiteuthis armata). There were highly geographically structured units within Helicocranchia navossae that could either represent recently diverged species or population structure. Although the species studied here can be considered relatively passive with respect to oceanic currents, cryptic speciation patterns showed few signs of being related to oceanic currents. We hypothesize that the bathymetry of the egg masses and duration of the paralarval stage might influence the geographic distribution of oceanic squids. Because the results of different markers and different species delimitation methods are inconsistent and because molecular data encompassing broad geographic sampling areas for oceanic squids are scarce and finding morphological diagnostic characters for early life stages is difficult, it is challenging to assess the species boundaries for many of these species. Thus, we consider many to be in the "grey speciation zone." As many oceanic squids have cosmopolitan distributions, new studies combining genomic and morphological information from specimens collected worldwide are needed to correctly assess the actual oceanic squid biodiversity.},
}
@article {pmid37603398,
year = {2023},
author = {Ratliffe, J and Kataura, T and Otten, EG and Korolchuk, VI},
title = {The evolution of selective autophagy as a mechanism of oxidative stress response: The evolutionarily acquired ability of selective autophagy receptors to respond to oxidative stress is beneficial for human longevity.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {11},
pages = {e2300076},
doi = {10.1002/bies.202300076},
pmid = {37603398},
issn = {1521-1878},
support = {EP/W524700/1//EPSRC PhD studentship/ ; BB/M023389/1//BBSRC/ ; BB/R008167/2//BBSRC/ ; //The International Medical Research Foundation/ ; //Uehara Memorial Foundation/ ; },
abstract = {Ageing is associated with a decline in autophagy and elevated reactive oxygen species (ROS), which can breach the capacity of antioxidant systems. Resulting oxidative stress can cause further cellular damage, including DNA breaks and protein misfolding. This poses a challenge for longevous organisms, including humans. In this review, we hypothesise that in the course of human evolution selective autophagy receptors (SARs) acquired the ability to sense and respond to localised oxidative stress. We posit that in the vicinity of protein aggregates and dysfunctional mitochondria oxidation of key cysteine residues in SARs induces their oligomerisation which initiates autophagy. The degradation of damaged cellular components thus could reduce ROS production and restore redox homeostasis. This evolutionarily acquired function of SARs may represent one of the biological adaptations that contributed to longer lifespan. Inversely, loss of this mechanism can lead to age-related diseases associated with impaired autophagy and oxidative stress.},
}
@article {pmid37602330,
year = {2023},
author = {Das, P and Pal, S and Das, N and Chakraborty, K and Chatterjee, K and Mal, S and Choudhuri, T},
title = {Endogenous PTEN acts as the key determinant for mTOR inhibitor sensitivity by inducing the stress-sensitized PTEN-mediated death axis in KSHV-associated malignant cells.},
journal = {Frontiers in molecular biosciences},
volume = {10},
number = {},
pages = {1062462},
pmid = {37602330},
issn = {2296-889X},
abstract = {As a part of viral cancer evolution, KSHV-infected human endothelial cells exert a unique transcriptional program via upregulated mTORC1 signaling. This event makes them sensitive to mTOR inhibitors. Master transcriptional regulator PTEN acts as the prime regulator of mTOR and determining factor for mTOR inhibitory drug resistance and sensitivity. PTEN is post-translationally modified in KSHV-associated cell lines and infected tissues. Our current study is an attempt to understand the functional role of upstream modulator PTEN in determining the sensitivity of mTOR inhibitors against KSHV-infected cells in an in vitro stress-responsive model. Our analysis shows that, despite phosphorylation, endogenous levels of intact PTEN in different KSHV-infected cells compared to normal and non-infected cells are quite high. Genetic overexpression of intact PTEN showed functional integrity of this gene in the infected cells in terms of induction of a synchronized cell death process via cell cycle regulation and mitochondria-mediated apoptosis. PTEN overexpression enhanced the mTOR inhibitory drug activity, the silencing of which hampers the process against KSHV-infected cells. Additionally, we have shown that endogenous PTEN acts as a stress balancer molecule inside KSHV-infected cells and can induce stress-sensitized death program post mTOR inhibitor treatment, lined up in the ATM-chk2-p53 axis. Moreover, autophagic regulation was found as a major regulator in mTOR inhibitor-induced PTEN-mediated death axis from our study. The current work critically intersected the PTEN-mediated stress balancing mechanism where autophagy has been utilized as a part of the KSHV stress management system and is specifically fitted and switched toward autophagy-mediated apoptosis directing toward a therapeutic perspective.},
}
@article {pmid37599162,
year = {2024},
author = {Braun, HP and Klusch, N},
title = {Promotion of oxidative phosphorylation by complex I-anchored carbonic anhydrases?.},
journal = {Trends in plant science},
volume = {29},
number = {1},
pages = {64-71},
doi = {10.1016/j.tplants.2023.07.007},
pmid = {37599162},
issn = {1878-4372},
mesh = {*Carbonic Anhydrases/chemistry/metabolism ; Oxidative Phosphorylation ; Mitochondria/metabolism ; Plants/metabolism ; Hydrogen-Ion Concentration ; },
abstract = {The mitochondrial NADH-dehydrogenase complex of the respiratory chain, known as complex I, includes a carbonic anhydrase (CA) module attached to its membrane arm on the matrix side in protozoans, algae, and plants. Its physiological role is so far unclear. Recent electron cryo-microscopy (cryo-EM) structures show that the CA module may directly provide protons for translocation across the inner mitochondrial membrane at complex I. CAs can have a central role in adjusting the proton concentration in the mitochondrial matrix. We suggest that CA anchoring in complex I represents the original configuration to secure oxidative phosphorylation (OXPHOS) in the context of early endosymbiosis. After development of 'modern mitochondria' with pronounced cristae structures, this anchoring became dispensable, but has been retained in protozoans, algae, and plants.},
}
@article {pmid37596708,
year = {2024},
author = {Golik, P},
title = {RNA processing and degradation mechanisms shaping the mitochondrial transcriptome of budding yeasts.},
journal = {IUBMB life},
volume = {76},
number = {1},
pages = {38-52},
doi = {10.1002/iub.2779},
pmid = {37596708},
issn = {1521-6551},
mesh = {*Transcriptome ; Saccharomyces cerevisiae/genetics/metabolism ; *Saccharomycetales/genetics/metabolism ; Transcription, Genetic ; RNA Processing, Post-Transcriptional ; RNA ; RNA, Transfer/genetics/metabolism ; },
abstract = {Yeast mitochondrial genes are expressed as polycistronic transcription units that contain RNAs from different classes and show great evolutionary variability. The promoters are simple, and transcriptional control is rudimentary. Posttranscriptional mechanisms involving RNA maturation, stability, and degradation are thus the main force shaping the transcriptome and determining the expression levels of individual genes. Primary transcripts are fragmented by tRNA excision by RNase P and tRNase Z, additional processing events occur at the dodecamer site at the 3' end of protein-coding sequences. groups I and II introns are excised in a self-splicing reaction that is supported by protein splicing factors encoded by the nuclear genes, or by the introns themselves. The 3'-to-5' exoribonucleolytic complex called mtEXO is the main RNA degradation activity involved in RNA turnover and processing, supported by an auxiliary 5'-to-3' exoribonuclease Pet127p. tRNAs and, to a lesser extent, rRNAs undergo several different base modifications. This complex gene expression system relies on the coordinated action of mitochondrial and nuclear genes and undergoes rapid evolution, contributing to speciation events. Moving beyond the classical model yeast Saccharomyces cerevisiae to other budding yeasts should provide important insights into the coevolution of both genomes that constitute the eukaryotic genetic system.},
}
@article {pmid37587350,
year = {2023},
author = {Merchant, A and Ramirez, BI and Reyes, MN and Van, D and Martinez-Colin, M and Ojo, DO and Mazuca, EL and De La O, HJ and Glenn, AM and Lira, CG and Ehsan, H and Yu, E and Kaneko, G},
title = {Genomic loss of the HSP70cA gene in the vertebrate lineage.},
journal = {Cell stress &amp; chaperones},
volume = {28},
number = {6},
pages = {1053-1067},
pmid = {37587350},
issn = {1466-1268},
mesh = {Animals ; Phylogeny ; *Evolution, Molecular ; *Vertebrates/genetics ; Genome/genetics ; Genomics ; },
abstract = {Metazoan 70 kDa heat shock protein (HSP70) genes have been classified into four lineages: cytosolic A (HSP70cA), cytosolic B (HSP70cB), endoplasmic reticulum (HSP70er), and mitochondria (HSP70m). Because previous studies have identified no HSP70cA genes in vertebrates, we hypothesized that this gene was lost on the evolutionary path to vertebrates. To test this hypothesis, the present study conducted a comprehensive database search followed by phylogenetic and synteny analyses. HSP70cA genes were found in invertebrates and in two of the three subphyla of Chordata, Cephalochordata (lancelets) and Tunicata (tunicates). However, no HSP70cA gene was found in the genomes of Craniata (another subphylum of Chordata; lamprey, hagfish, elephant shark, and coelacanth), suggesting the loss of the HSP70cA gene in the early period of vertebrate evolution. Synteny analysis using available genomic resources indicated that the synteny around the HSP70 genes was generally conserved between tunicates but was largely different between tunicates and lamprey. These results suggest the presence of dynamic chromosomal rearrangement in early vertebrates that possibly caused the loss of the HSP70cA gene in the vertebrate lineage.},
}
@article {pmid37584544,
year = {2023},
author = {Yang, C and Li, X and Zhou, J and Gao, C},
title = {Autophagy contributes to positive feedback regulation of SnRK1 signaling in plants.},
journal = {Autophagy},
volume = {19},
number = {12},
pages = {3248-3250},
pmid = {37584544},
issn = {1554-8635},
mesh = {*Arabidopsis Proteins/metabolism ; AMP-Activated Protein Kinases/metabolism ; Feedback ; Autophagy ; *Arabidopsis/metabolism ; Plants/metabolism ; Transcription Factors/metabolism ; Adenosine Monophosphate ; Gene Expression Regulation, Plant ; Protein Serine-Threonine Kinases/metabolism ; Vesicular Transport Proteins/metabolism ; },
abstract = {SnRK1 (SNF1-related protein kinase 1) is a plant ortholog of yeast Snf1 and mammalian adenosine monophosphate-activated protein kinase (AMPK) that acts as a positive regulator of macroautophagy/autophagy. However, whether and how the autophagy pathway modulates SnRK1 activity remains elusive. Recently, we identified a clade of plant-specific FLZ (FCS-like zinc finger) proteins as novel ATG8 (autophagy-related 8)-interacting partners in Arabidopsis thaliana. These AtFLZs, which mainly localize on the surface of mitochondria, can inhibit SnRK1 signaling by repressing the T-loop phosphorylation of its catalytic α subunits, thereby negatively regulating carbon starvation-induced autophagy and plant tolerance to energy deprivation. Upon energy starvation, autophagy is activated to mediate the degradation of these AtFLZs, thus relieving their repression of SnRK1. More importantly, the ATG8-FLZ-SnRK1 regulatory axis appears to be functionally conserved during seed plant evolution. These findings highlight the positive role of autophagy in SnRK1 signaling activation under energy-limiting conditions in plants.Abbreviations: ADS, AIMs docking site; AIM, ATG8-interacting motif; AMPK, adenosine monophosphate-activated protein kinase; ATG, autophagy-related; ESCRT, endosomal sorting complexes required for transport; FLZ, FCS-like zinc finger protein; FREE1, FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1; RAPTOR, REGULATORY-ASSOCIATED PROTEIN OF TOR; Snf1, SUCROSE NON-FERMENTING 1; SnRK1, SNF1-related kinase 1; TOR, TARGET OF RAPAMYCIN.},
}
@article {pmid37582787,
year = {2023},
author = {Meadows, JRS and Kidd, JM and Wang, GD and Parker, HG and Schall, PZ and Bianchi, M and Christmas, MJ and Bougiouri, K and Buckley, RM and Hitte, C and Nguyen, AK and Wang, C and Jagannathan, V and Niskanen, JE and Frantz, LAF and Arumilli, M and Hundi, S and Lindblad-Toh, K and Ginja, C and Agustina, KK and André, C and Boyko, AR and Davis, BW and Drögemüller, M and Feng, XY and Gkagkavouzis, K and Iliopoulos, G and Harris, AC and Hytönen, MK and Kalthoff, DC and Liu, YH and Lymberakis, P and Poulakakis, N and Pires, AE and Racimo, F and Ramos-Almodovar, F and Savolainen, P and Venetsani, S and Tammen, I and Triantafyllidis, A and vonHoldt, B and Wayne, RK and Larson, G and Nicholas, FW and Lohi, H and Leeb, T and Zhang, YP and Ostrander, EA},
title = {Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {187},
pmid = {37582787},
issn = {1474-760X},
support = {R01 GM140135/GM/NIGMS NIH HHS/United States ; R24 GM082910/GM/NIGMS NIH HHS/United States ; },
mesh = {Dogs ; Animals ; *Wolves/genetics ; Chromosome Mapping ; Alleles ; Polymorphism, Single Nucleotide ; Nucleotides ; Demography ; },
abstract = {BACKGROUND: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.<br><br>RESULTS: We report the analysis of&#x2009;>&#x2009;48&#xa0;M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50&#xa0;bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.<br><br>CONCLUSIONS: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.},
}
@article {pmid37577532,
year = {2023},
author = {Wolters, JF and LaBella, AL and Opulente, DA and Rokas, A and Hittinger, CT},
title = {Mitochondrial Genome Diversity across the Subphylum Saccharomycotina.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37577532},
issn = {2692-8205},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
abstract = {Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.},
}
@article {pmid37565789,
year = {2023},
author = {Yang, Y and Oldenkott, B and Ramanathan, S and Lesch, E and Takenaka, M and Schallenberg-Rüdinger, M and Knoop, V},
title = {DYW cytidine deaminase domains have a long-range impact on RNA recognition by the PPR array of chimeric plant C-to-U RNA editing factors and strongly affect target selection.},
journal = {The Plant journal : for cell and molecular biology},
volume = {116},
number = {3},
pages = {840-854},
doi = {10.1111/tpj.16412},
pmid = {37565789},
issn = {1365-313X},
mesh = {RNA, Plant/metabolism ; *Plant Proteins/metabolism ; *RNA Editing/genetics ; Cytidine Deaminase/chemistry/genetics/metabolism ; Chloroplasts/metabolism ; },
abstract = {The protein factors for the specific C-to-U RNA editing events in plant mitochondria and chloroplasts possess unique arrays of RNA-binding pentatricopeptide repeats (PPRs) linked to carboxy-terminal cytidine deaminase DYW domains via the extension motifs E1 and E2. The E1 and E2 motifs have distant similarities to tetratricopeptide repeats known to mediate protein-protein interactions but their precise function is unclear. Here, we investigate the tolerance of PPR56 and PPR65, two functionally characterized RNA editing factors of the moss Physcomitrium patens, for the creation of chimeras by variably replacing their C-terminal protein regions. Making use of a heterologous RNA editing assay system in Escherichia coli we find that heterologous DYW domains can strongly restrict or widen the spectrum of off-targets in the bacterial transcriptome for PPR56. Surprisingly, our data suggest that these changes are not only caused by the preference of a given heterologous DYW domain for the immediate sequence environment of the cytidine to be edited but also by a long-range impact on the nucleotide selectivity of the upstream PPRs.},
}
@article {pmid37558671,
year = {2023},
author = {Kuhle, B and Hirschi, M and Doerfel, LK and Lander, GC and Schimmel, P},
title = {Structural basis for a degenerate tRNA identity code and the evolution of bimodal specificity in human mitochondrial tRNA recognition.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4794},
pmid = {37558671},
issn = {2041-1723},
support = {R01 NS095892/NS/NINDS NIH HHS/United States ; R01 NS092829/NS/NINDS NIH HHS/United States ; S10 OD021634/OD/NIH HHS/United States ; R01 GM125908/GM/NIGMS NIH HHS/United States ; R21 GM142196/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; RNA, Mitochondrial ; *RNA, Transfer/genetics/metabolism ; *Amino Acyl-tRNA Synthetases/genetics/metabolism ; Mitochondria/genetics/metabolism ; },
abstract = {Animal mitochondrial gene expression relies on specific interactions between nuclear-encoded aminoacyl-tRNA synthetases and mitochondria-encoded tRNAs. Their evolution involves an antagonistic interplay between strong mutation pressure on mtRNAs and selection pressure to maintain their essential function. To understand the molecular consequences of this interplay, we analyze the human mitochondrial serylation system, in which one synthetase charges two highly divergent mtRNA[Ser] isoacceptors. We present the cryo-EM structure of human mSerRS in complex with mtRNA[Ser(UGA)], and perform a structural and functional comparison with the mSerRS-mtRNA[Ser(GCU)] complex. We find that despite their common function, mtRNA[Ser(UGA)] and mtRNA[Ser(GCU)] show no constrain to converge on shared structural or sequence identity motifs for recognition by mSerRS. Instead, mSerRS evolved a bimodal readout mechanism, whereby a single protein surface recognizes degenerate identity features specific to each mtRNA[Ser]. Our results show how the mutational erosion of mtRNAs drove a remarkable innovation of intermolecular specificity rules, with multiple evolutionary pathways leading to functionally equivalent outcomes.},
}
@article {pmid37557975,
year = {2023},
author = {Weaver, RJ and McDonald, AE},
title = {Mitochondrial alternative oxidase across the tree of life: Presence, absence, and putative cases of lateral gene transfer.},
journal = {Biochimica et biophysica acta. Bioenergetics},
volume = {1864},
number = {4},
pages = {149003},
doi = {10.1016/j.bbabio.2023.149003},
pmid = {37557975},
issn = {1879-2650},
mesh = {Animals ; *Gene Transfer, Horizontal ; *Plant Proteins/genetics ; Oxidoreductases/genetics ; Mitochondria/genetics ; Plants ; Eukaryota/genetics ; },
abstract = {The alternative oxidase (AOX) is a terminal oxidase in the electron transport system that plays a role in mitochondrial bioenergetics. The past 20 years of research shows AOX has a wide yet patchy distribution across the tree of life. AOX has been suggested to have a role in stress tolerance, growth, and development in plants, but less is known about its function in other groups, including animals. In this study, we analyzed the taxonomic distribution of AOX across >2800 species representatives from prokaryotes and eukaryotes and developed a standardized workflow for finding and verifying the authenticity of AOX sequences. We found that AOX is limited to proteobacteria among prokaryotes, but is widely distributed in eukaryotes, with the highest prevalence in plants, fungi, and protists. AOX is present in many invertebrates, but is absent in others including most arthropods, and is absent from vertebrates. We found aberrant AOX sequences associated with some animal groups. Some of these aberrant AOXs were contaminants, but we also found putative cases of lateral gene transfer of AOX from fungi and protists to nematodes, springtails, fungus gnats, and rotifers. Our findings provide a robust and detailed analysis of the distribution of AOX and a method for identifying and verifying putative AOX sequences, which will be useful as more sequence data becomes available on public repositories.},
}
@article {pmid37556561,
year = {2023},
author = {Raval, PK and Martin, WF and Gould, SB},
title = {Mitochondrial evolution: Gene shuffling, endosymbiosis, and signaling.},
journal = {Science advances},
volume = {9},
number = {32},
pages = {eadj4493},
pmid = {37556561},
issn = {2375-2548},
mesh = {*Symbiosis/genetics ; *Mitochondria/genetics ; Eukaryotic Cells/metabolism ; Genes, Mitochondrial ; Phylogeny ; Biological Evolution ; Evolution, Molecular ; },
abstract = {Genes for cardiolipin and ceramide synthesis occur in some alphaproteobacterial genomes. They shed light on mitochondrial origin and signaling in the first eukaryotic cells.},
}
@article {pmid37551058,
year = {2023},
author = {Huynh, SD and Melonek, J and Colas des Francs-Small, C and Bond, CS and Small, I},
title = {A unique C-terminal domain contributes to the molecular function of Restorer-of-fertility proteins in plant mitochondria.},
journal = {The New phytologist},
volume = {240},
number = {2},
pages = {830-845},
doi = {10.1111/nph.19166},
pmid = {37551058},
issn = {1469-8137},
mesh = {*Genes, Plant ; Mitochondria/metabolism ; Cytoplasm/metabolism ; Plant Proteins/metabolism ; *Arabidopsis/genetics/metabolism ; Fertility/genetics ; Plant Infertility/genetics ; },
abstract = {Restorer-of-fertility (Rf) genes encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a distinct domain, which we called RfCTD (Restorer-of-fertility C-terminal domain), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target. A screen of 219 angiosperm genomes from 123 genera using a sequence profile that can quickly and accurately identify RfCTD sequences revealed considerable variation in RFL/RfCTD gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility. We show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2-nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria. We provide a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins and the evolution of fertility restoration in flowering plants.},
}
@article {pmid37548336,
year = {2023},
author = {Ryan, K and Greenway, R and Landers, J and Arias-Rodriguez, L and Tobler, M and Kelley, JL},
title = {Selection on standing genetic variation mediates convergent evolution in extremophile fish.},
journal = {Molecular ecology},
volume = {32},
number = {18},
pages = {5042-5054},
doi = {10.1111/mec.17081},
pmid = {37548336},
issn = {1365-294X},
mesh = {Animals ; *Hydrogen Sulfide/toxicity ; *Extremophiles ; Ecosystem ; Sulfides ; *Poecilia/genetics ; Genetic Variation/genetics ; Selection, Genetic ; },
abstract = {Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including energy production in the mitochondria, yet fish in the Poecilia mexicana species complex have independently evolved sulfide tolerance several times. Despite clear evidence for convergence at the phenotypic level in these fishes, it is unclear if the repeated evolution of hydrogen sulfide tolerance is the result of similar genomic changes. To address this gap, we used a targeted capture approach to sequence genes associated with sulfide processes and toxicity from five sulfidic and five nonsulfidic populations in the species complex. By comparing sequence variation in candidate genes to a reference set, we identified similar population structure and differentiation, suggesting that patterns of variation in most genes associated with sulfide processes and toxicity are due to demographic history and not selection. But the presence of tree discordance for a subset of genes suggests that several loci are evolving divergently between ecotypes. We identified two differentiation outlier genes that are associated with sulfide detoxification in the mitochondria that have signatures of selection in all five sulfidic populations. Further investigation into these regions identified long, shared haplotypes among sulfidic populations. Together, these results reveal that selection on standing genetic variation in putatively adaptive genes may be driving phenotypic convergence in this species complex.},
}
@article {pmid37538245,
year = {2023},
author = {Zhang, H and Li, X and Fan, W and Pandovski, S and Tian, Y and Dillin, A},
title = {Inter-tissue communication of mitochondrial stress and metabolic health.},
journal = {Life metabolism},
volume = {2},
number = {1},
pages = {},
pmid = {37538245},
issn = {2755-0230},
support = {R01 AG059566/AG/NIA NIH HHS/United States ; R01 ES021667/ES/NIEHS NIH HHS/United States ; },
abstract = {Mitochondria function as a hub of the cellular metabolic network. Mitochondrial stress is closely associated with aging and a variety of diseases, including neurodegeneration and cancer. Cells autonomously elicit specific stress responses to cope with mitochondrial stress to maintain mitochondrial homeostasis. Interestingly, mitochondrial stress responses may also be induced in a non-autonomous manner in cells or tissues that are not directly experiencing such stress. Such non-autonomous mitochondrial stress responses are mediated by secreted molecules called mitokines. Due to their significant translational potential in improving human metabolic health, there has been a surge in mitokine-focused research. In this review, we summarize the findings regarding inter-tissue communication of mitochondrial stress in animal models. In addition, we discuss the possibility of mitokine-mediated intercellular mitochondrial communication originating from bacterial quorum sensing.},
}
@article {pmid37522604,
year = {2023},
author = {Chukaew, T and Isomura, N and Mezaki, T and Matsumoto, H and Kitano, YF and Nozawa, Y and Tachikawa, H and Fukami, H},
title = {Molecular Phylogeny and Taxonomy of the Coral Genus Cyphastrea (Cnidaria, Scleractinia, Merulinidae) in Japan, With the First Records of Two Species.},
journal = {Zoological science},
volume = {40},
number = {4},
pages = {326-340},
doi = {10.2108/zs230009},
pmid = {37522604},
issn = {0289-0003},
mesh = {Animals ; Phylogeny ; *Anthozoa/genetics ; Japan ; DNA, Ribosomal/genetics ; Mitochondria/genetics ; Sequence Analysis, DNA ; },
abstract = {The scleractinian coral genus Cyphastrea is widely distributed in the Indo-Pacific region and is common from the subtropical to the warm-temperate regions in Japan. Three new species in this genus have recently been reported from south-eastern Australia or the Red Sea. However, taxonomic and species diversity have been little studied so far in Japan. In this study, we analyzed 112 specimens of Cyphastrea collected from the subtropical to the warm-temperate regions in Japan to clarify the species diversity in the country. This analysis was based on skeletal morphological and molecular analyses using three genetic markers of the nuclear 28S rDNA, histone H3 gene, and the mitochondrial noncoding intergenic region between COI and tRNAmet. The molecular phylogenetic trees showed that our specimens are separated mainly into four clades. Considering the morphological data with the molecular phylogenetic relationships, we confirmed a total of nine species, including two species, C. magna and C. salae, recorded for the first time in Japan. Although eight out of nine species were genetically included within Cyphastrea, one species, C. agassizi, was genetically distant from all other species and was closely related to the genus Leptastrea, suggesting the return of this species to the genus to which it was originally ascribed. Two newly recorded species were reciprocally monophyletic, while the other six species (excluding C. agassizi) clustered in two clades without forming species-specific lineages, including three polyphyletic species. Thus, the species boundary between species in Cyphastrea remains unclear in most species using these three sequenced loci.},
}
@article {pmid37518710,
year = {2023},
author = {Russell, PJC and Pateman, JE and Gagarina, AV and Lukhtanov, VA},
title = {Investigations into the Melitaea ornata species complex in the Levant: M. telona and the newly erected species Melitaea klili Benyamini, 2021 (Lepidoptera: Nymphalidae).},
journal = {Zootaxa},
volume = {5285},
number = {1},
pages = {187-195},
doi = {10.11646/zootaxa.5285.1.9},
pmid = {37518710},
issn = {1175-5334},
mesh = {Male ; Animals ; *Butterflies/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genes, Mitochondrial ; DNA Barcoding, Taxonomic ; },
abstract = {Melitaea klili Benyamini, 2021 was recently described from Israel as a species closely related to M. telona Fruhstorfer, 1908, but different in phenology, ecological preferences and with an allopatric distribution. Here, based on comparative examinations of mitochondrial DNA-barcodes, male genitalia and larval behaviour under laboratory conditions, we synonymize M. klili with M. telona. The COI barcodes of M. klili were found to be identical to those of M. telona. Analysis of 658 bp fragment of the mitochondrial gene COI demonstrated that the minimum uncorrected p-distance between M. ornata and M. telona was 1.98%. This value is remarkably less than the 3% threshold traditionally accepted as a species boundary in DNA barcoding studies. The morphological differences between these taxa are minimal. In fact, M. ornata and M. telona represent two phylogenetic lineages, the taxonomic status of which (separate species or subspecies of the same species) is intermediate and debatable.},
}
@article {pmid37518527,
year = {2023},
author = {Kuhara, N and Nozaki, T and Zhang, AO and Zhou, X},
title = {DNA barcoding facilitates discovery and description of two new species of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) in Japan.},
journal = {Zootaxa},
volume = {5306},
number = {2},
pages = {215-231},
doi = {10.11646/zootaxa.5306.2.3},
pmid = {37518527},
issn = {1175-5334},
mesh = {Female ; Animals ; Male ; Japan ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Holometabola ; Mitochondria ; },
abstract = {We examined adult specimens of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) collected in Japan and confirm three species including M. azureus Linnaeus 1761 and two new species, M. rivularis and M. moritai. Males and females of the new species are described. Mystacides azureus in Japan is shown to have a considerable variation in morphology of the male tergum X. We analyzed mitochondrial COI barcodes of the genus Mystacides including these three species to confirm their species status. A maximum likelihood phylogeny based on COI barcodes shows monophyly of the new species. It also supports the hypothesis that morphological variation of the male tergum X in Japanese populations is intraspecific in only M. azureus.},
}
@article {pmid37518493,
year = {2023},
author = {Tomimori, Y and Matsui, M and Okawa, H and Nishikawa, K and Tanabe, S and Kamasaka, R},
title = {Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae).},
journal = {Zootaxa},
volume = {5293},
number = {1},
pages = {145-160},
doi = {10.11646/zootaxa.5293.1.6},
pmid = {37518493},
issn = {1175-5334},
mesh = {Animals ; *Urodela/genetics ; Phylogeny ; Japan ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {Hynobius akiensis sensu lato has recently been split into three species based on short sequence analyses of cyt-b gene of mtDNA and without data of nuclear DNA, and strange sympatric distribution in some areas has been indicated in two species. We analyzed nuclear DNA marker (SNPs) and complete sequence of cyt-b in H. akiensis sensu lato to reassess species delimitation and genetic introgression among species. As a result, we found two lineages with discordant mitochondrial and nuclear DNA in some areas. Of H. akiensis sensu lato, each of the two contains the type locality of two species recently reported (H. sumidai and H. geiyoensis), and the use of these names has been previously advocated. However, their sympatric distribution was rejected based on nuclear DNA data, which we consider is more reliable than mtDNA. We thus clarify geographic boundary of these two species and revise the species delimitations.},
}
@article {pmid37518286,
year = {2023},
author = {Zhang, G and Gao, JJ and Takano, KT and Yafuso, M and Suwito, A and Meleng, PA and Toda, MJ},
title = {Phylogenetic classification and palm-inflorescence anthophily of the Colocasiomyia zeylanica species group (Diptera: Drosophilidae), with descriptions of five new species.},
journal = {Zootaxa},
volume = {5278},
number = {2},
pages = {201-238},
doi = {10.11646/zootaxa.5278.2.1},
pmid = {37518286},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; *Drosophilidae/genetics ; Phylogeny ; Inflorescence ; Mitochondria ; },
abstract = {The zeylanica group is one of the six species groups of the anthophilic genus Colocasiomyia de Meijere in the family Drosophilidae. In addition to two known species, five morphospecies have been recognized as members of this species group but left undescribed formally. In this study, species delimitation of these putatively new species was determined by barcoding of the mitochondrial COI (cytochrome c oxydase subunit I) gene and morphological comparison. Phylogenetic relationships within the genus Colocasiomyia were inferred by a cladistic analysis of 89 morphological characters. Based on the results of these analyses, we redefined the zeylanica species group and established two subgroups within it: the zeylanica subgroup comprised of C. zeylanica, C. nepalensis, C. pinangae sp. nov., C. besaris sp. nov. and C. luciphila sp. nov., and the oligochaeta subgroup of C. oligochaeta sp. nov. and C. grimaldii sp. nov. In addition, we briefly address the anthophilic habits of drosophilid flies using palm (Arecaceae) inflorescences, especially of the zeylanica group, compiling scattered collection records from the Oriental and Papuan regions.},
}
@article {pmid37515372,
year = {2024},
author = {Fernández-Moncada, I and Rodrigues, RS and Fundazuri, UB and Bellocchio, L and Marsicano, G},
title = {Type-1 cannabinoid receptors and their ever-expanding roles in brain energy processes.},
journal = {Journal of neurochemistry},
volume = {168},
number = {5},
pages = {693-703},
doi = {10.1111/jnc.15922},
pmid = {37515372},
issn = {1471-4159},
support = {//INSERM/ ; Micabra, ERC-2017-AdG-786467//the European Research Council/ ; DRM20101220445//Fondation pour la Recherche Medicale/ ; ALTF87-2018//EMBO/ ; //the Human Frontiers Science Program/ ; 17219710//Region Aquitaine/ ; CanBrain, AAP2022A-2021-16763610//Region Aquitaine/ ; ANR-19-CE14-0039//French State/Agence Nationale de la Recherche/ ; ERA-Net Neuron CanShank, ANR-21-NEU2-0001-04//French State/Agence Nationale de la Recherche/ ; MitObesity, ANR 18-CE14-0029-01//French State/Agence Nationale de la Recherche/ ; CaCoVi, ANR 18-CE16-0001-02//French State/Agence Nationale de la Recherche/ ; GPR BRAIN_2030//University of Bordeaux's IdEx "Investments for the Future" program/ ; },
mesh = {*Receptor, Cannabinoid, CB1/metabolism ; Humans ; Animals ; *Brain/metabolism ; *Energy Metabolism/physiology ; Mitochondria/metabolism ; Neurons/metabolism ; },
abstract = {The brain requires large quantities of energy to sustain its functions. At the same time, the brain is isolated from the rest of the body, forcing this organ to develop strategies to control and fulfill its own energy needs. Likely based on these constraints, several brain-specific mechanisms emerged during evolution. For example, metabolically specialized cells are present in the brain, where intercellular metabolic cycles are organized to separate workload and optimize the use of energy. To orchestrate these strategies across time and space, several signaling pathways control the metabolism of brain cells. One of such controlling systems is the endocannabinoid system, whose main signaling hub in the brain is the type-1 cannabinoid (CB1) receptor. CB1 receptors govern a plethora of different processes in the brain, including cognitive function, emotional responses, or feeding behaviors. Classically, the mechanisms of action of CB1 receptors on brain function had been explained by its direct targeting of neuronal synaptic function. However, new discoveries have challenged this view. In this review, we will present and discuss recent data about how a small fraction of CB1 receptors associated to mitochondrial membranes (mtCB1), are able to exert a powerful control on brain functions and behavior. mtCB1 receptors impair mitochondrial functions both in neurons and astrocytes. In the latter cells, this effect is linked to an impairment of astrocyte glycolytic function, resulting in specific behavioral outputs. Finally, we will discuss the potential implications of (mt)CB1 expression on oligodendrocytes and microglia metabolic functions, with the aim to encourage interdisciplinary approaches to better understand the role of (mt)CB1 receptors in brain function and behavior.},
}
@article {pmid37512520,
year = {2023},
author = {Hu, M and Jiang, Y and Xu, JJ},
title = {Characterization of Arabidopsis thaliana Coq9 in the CoQ Biosynthetic Pathway.},
journal = {Metabolites},
volume = {13},
number = {7},
pages = {},
pmid = {37512520},
issn = {2218-1989},
support = {no//Yunnan Revitalization Talent Support Program "Top Team" Project/ ; PFGR202201//Open Fund of Shanghai Key Laboratory of Plant Functional Genomics and Resources under Grant/ ; 222414//Special Fund for Shanghai Landscaping Administration Bureau Program/ ; YDZX20223100001003//Ministry of Science and Technology of the People's Republic of China/ ; },
abstract = {Coenzyme Q, also known as ubiquinone, is a fat-soluble isoprene quinone that serves as a cofactor for numerous enzymes across all domains of life. However, the biosynthetic pathway for this important molecule in plants has been examined in only a limited number of studies. In yeast and mammals, Coq9, an isoprenoid-lipid-binding protein, is essential for CoQ biosynthesis. Previous studies showed that Arabidopsis thaliana Coq9 failed to complement the fission yeast Schizosaccharomyces pombe coq9 null mutant, and its function in plants remains unknown. In this study, we demonstrated that expression of Arabidopsis Coq9 rescued the growth of a yeast temperature-sensitive coq9 mutant and increased CoQ content. Phylogenetic analysis revealed that Coq9 is widely present in green plants. Green fluorescent protein (GFP) fusion experiments showed that Arabidopsis Coq9 is targeted to mitochondria. Disruption of the Coq9 gene in Arabidopsis results in lower amounts of CoQ. Our work suggests that plant Coq9 is required for efficient CoQ biosynthesis. These findings provide new insights into the evolution of CoQ biosynthesis in plants. The identification of Coq9 as a key player in CoQ biosynthesis in plants opens up new avenues for understanding the regulation of this important metabolic pathway.},
}
@article {pmid37511042,
year = {2023},
author = {Luo, L and Xu, Y and Wang, S and Zhang, R and Guo, K and Xu, W and Zhao, Z},
title = {Complete Mitochondrial Genome Sequence and Phylogenetic Analysis of Procambarus clarkii and Cambaroides dauricus from China.},
journal = {International journal of molecular sciences},
volume = {24},
number = {14},
pages = {},
pmid = {37511042},
issn = {1422-0067},
support = {2020YFD0900402//the National Key Research and Development Project/ ; 2020TD56//the Central Public-interest Scienti&#xfb01;c Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; },
mesh = {Animals ; *Genome, Mitochondrial/genetics ; Astacoidea/genetics ; Phylogeny ; NAD/genetics ; Sequence Analysis, DNA ; },
abstract = {To enhance the management and protection of crayfish genetic diversity and germplasm resources in Cambaroides dauricus (C. dauricus), a common species of Procambarus clarkii (P. clarkii) was used as a control group to compare the whole mitochondrial genome sequence using Illumina sequencing technology. This study found that the mitochondrial genome of C. dauricus is 15580 bp in length, with a base composition of A (31.84%), G (17.66%), C (9.42%), and T (41.08%) and a C + G content of 27.08%. The C + G in the D-loop is rich in 17.06%, indicating a significant preference. The mitochondrial genome of C. dauricus contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, with most of the genes labeled in the negative direction, except for a few genes that are labeled in the positive direction. The start codons of the ten coding sequences are ATG, and the quintessential TAA and TAG are the stop codons. This study also found that the Ka/Ks ratios of most protein-coding genes in the mitochondria of both shrimps are lower than 1, indicating weak natural selection, except for nad 2, nad 5, and cox 1. The Ka/Ks ratio of cox 3 is the lowest (less than 0.1), indicating that this protein-coding gene bears strong natural selection pressure and functional constraint in the process of mitochondrial genetic evolution of both shrimps. Furthermore, we constructed phylogenetic analyses based on the entire sequence, which effectively distinguishes the high body from other shrimp species of the genus based on the mitochondrial genome. This study provides molecular genetic data for the diversity investigation and protection of fishery resources with Chinese characteristics and a scientific reference for the evolutionary study of Procambarus.},
}
@article {pmid37508434,
year = {2023},
author = {Preziuso, A and Piccirillo, S and Cerqueni, G and Serfilippi, T and Terenzi, V and Vinciguerra, A and Orciani, M and Amoroso, S and Magi, S and Lariccia, V},
title = {Exploring the Role of NCX1 and NCX3 in an In Vitro Model of Metabolism Impairment: Potential Neuroprotective Targets for Alzheimer's Disease.},
journal = {Biology},
volume = {12},
number = {7},
pages = {},
pmid = {37508434},
issn = {2079-7737},
support = {2017YH3SXK//Ministry of Education, Universities and Research/ ; },
abstract = {Alzheimer's disease (AD) is a widespread neurodegenerative disorder, affecting a large number of elderly individuals worldwide. Mitochondrial dysfunction, metabolic alterations, and oxidative stress are regarded as cooperating drivers of the progression of AD. In particular, metabolic impairment amplifies the production of reactive oxygen species (ROS), resulting in detrimental alterations to intracellular Ca[2+] regulatory processes. The Na[+]/Ca[2+] exchanger (NCX) proteins are key pathophysiological determinants of Ca[2+] and Na[+] homeostasis, operating at both the plasma membrane and mitochondria levels. Our study aimed to explore the role of NCX1 and NCX3 in retinoic acid (RA) differentiated SH-SY5Y cells treated with glyceraldehyde (GA), to induce impairment of the default glucose metabolism that typically precedes Aβ deposition or Tau protein phosphorylation in AD. By using an RNA interference-mediated approach to silence either NCX1 or NCX3 expression, we found that, in GA-treated cells, the knocking-down of NCX3 ameliorated cell viability, increased the intracellular ATP production, and reduced the oxidative damage. Remarkably, NCX3 silencing also prevented the enhancement of Aβ and pTau levels and normalized the GA-induced decrease in NCX reverse-mode activity. By contrast, the knocking-down of NCX1 was totally ineffective in preventing GA-induced cytotoxicity except for the increase in ATP synthesis. These findings indicate that NCX3 and NCX1 may differently influence the evolution of AD pathology fostered by glucose metabolic dysfunction, thus providing a potential target for preventing AD.},
}
@article {pmid37507225,
year = {2023},
author = {Esposti, MD},
title = {Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis.},
journal = {FEBS letters},
volume = {597},
number = {19},
pages = {2484-2496},
doi = {10.1002/1873-3468.14708},
pmid = {37507225},
issn = {1873-3468},
abstract = {The merger of two very different microbes, an anaerobic archaeon and an aerobic bacterium, led to the birth of eukaryotic cells. Current models hypothesize that an archaeon engulfed bacteria through external protrusions that then fused together forming the membrane organelles of eukaryotic cells, including mitochondria. Images of cultivated Lokiarchaea sustain this concept, first proposed in the inside-out model which assumes that the membrane traffic system of archaea drove the merging with bacterial cells through membrane expansions containing inositol lipids, considered to have evolved first in archaea. This assumption has been evaluated here in detail. The data indicate that inositol lipids first emerged in bacteria, not in archaea. The implications of this finding for the models of eukaryogenesis are discussed.},
}
@article {pmid37503831,
year = {2023},
author = {Sanchez-Puerta, MV and Ceriotti, LF and Gatica-Soria, LM and Roulet, ME and Garcia, LE and Sato, HA},
title = {Invited Review Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites.},
journal = {Annals of botany},
volume = {132},
number = {5},
pages = {909-928},
pmid = {37503831},
issn = {1095-8290},
support = {PICT2020-01018//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 06/A092-T1//Universidad Nacional de Cuyo/ ; },
mesh = {*Magnoliopsida/genetics ; Plants/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; Plastids ; Phylogeny ; },
abstract = {BACKGROUND: The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and is found in ~10 % of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments.<br><br>SCOPE: This review summarizes current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles.<br><br>CONCLUSIONS: Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.},
}
@article {pmid37502859,
year = {2023},
author = {Cal, K and Leyva, A and Rodríguez-Duarte, J and Ruiz, S and Santos, L and Colella, L and Ingold, M and Vilaseca, C and Galliussi, G and Ziegler, L and Peclat, TR and Bresque, M and Handy, RM and King, R and Dos Reis, LM and Espasandin, C and Breining, P and Dapueto, R and Lopez, A and Thompson, KL and Agorrody, G and DeVallance, E and Meadows, E and Lewis, SE and Barbosa, GCS and de Souza, LOL and Chichierchio, MS and Valez, V and Aicardo, A and Contreras, P and Vendelbo, MH and Jakobsen, S and Kamaid, A and Porcal, W and Calliari, A and Verdes, JM and Du, J and Wang, Y and Hollander, JM and White, TA and Radi, R and Moyna, G and Quijano, C and O'Doherty, R and Moraes-Vieira, P and Holloway, GP and Leonardi, R and Mori, MA and Camacho-Pereira, J and Kelley, EE and Duran, R and Lopez, GV and Batthyány, C and Chini, EN and Escande, C},
title = {A nitroalkene derivative of salicylate alleviates diet-induced obesity by activating creatine metabolism and non-shivering thermogenesis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37502859},
issn = {2693-5015},
support = {R01 HL128485/HL/NHLBI NIH HHS/United States ; R01 HL153532/HL/NHLBI NIH HHS/United States ; R35 GM119528/GM/NIGMS NIH HHS/United States ; R01 HL168290/HL/NHLBI NIH HHS/United States ; R01 DK124510/DK/NIDDK NIH HHS/United States ; },
abstract = {Obesity-related type II diabetes (diabesity) has increased global morbidity and mortality dramatically. Previously, the ancient drug salicylate demonstrated promise for the treatment of type II diabetes, but its clinical use was precluded due to high dose requirements. In this study, we present a nitroalkene derivative of salicylate, 5-(2-nitroethenyl)salicylic acid (SANA), a molecule with unprecedented beneficial effects in diet-induced obesity (DIO). SANA reduces DIO, liver steatosis and insulin resistance at doses up to 40 times lower than salicylate. Mechanistically, SANA stimulated mitochondrial respiration and increased creatine-dependent energy expenditure in adipose tissue. Indeed, depletion of creatine resulted in the loss of SANA action. Moreover, we found that SANA binds to creatine kinases CKMT1/2, and downregulation CKMT1 interferes with the effect of SANA in vivo. Together, these data demonstrate that SANA is a first-in-class activator of creatine-dependent energy expenditure and thermogenesis in adipose tissue and emerges as a candidate for the treatment of diabesity.},
}
@article {pmid37498958,
year = {2024},
author = {Schmid, LM and Manavski, N and Chi, W and Meurer, J},
title = {Chloroplast Ribosome Biogenesis Factors.},
journal = {Plant &amp; cell physiology},
volume = {65},
number = {4},
pages = {516-536},
doi = {10.1093/pcp/pcad082},
pmid = {37498958},
issn = {1471-9053},
support = {ME 1794/10 TRR 175 A03//Deutsche Forschungsgemeinschaft/ ; 2022YFF1001700//National Key Research and Development Program of China/ ; },
mesh = {*Ribosomes/metabolism ; *Chloroplasts/metabolism ; RNA, Ribosomal/genetics/metabolism ; Plants/metabolism/genetics ; },
abstract = {The formation of chloroplasts can be traced back to an ancient event in which a eukaryotic host cell containing mitochondria ingested a cyanobacterium. Since then, chloroplasts have retained many characteristics of their bacterial ancestor, including their transcription and translation machinery. In this review, recent research on the maturation of rRNA and ribosome assembly in chloroplasts is explored, along with their crucial role in plant survival and their implications for plant acclimation to changing environments. A comparison is made between the ribosome composition and auxiliary factors of ancient and modern chloroplasts, providing insights into the evolution of ribosome assembly factors. Although the chloroplast contains ancient proteins with conserved functions in ribosome assembly, newly evolved factors have also emerged to help plants acclimate to changes in their environment and internal signals. Overall, this review offers a comprehensive analysis of the molecular mechanisms underlying chloroplast ribosome assembly and highlights the importance of this process in plant survival, acclimation and adaptation.},
}
@article {pmid37497665,
year = {2023},
author = {Millet, AMC and Coustham, C and Champigny, C and Botella, M and Demeilliers, C and Devin, A and Galinier, A and Belenguer, P and Bordeneuve-Guibé, J and Davezac, N and Merabet, N},
title = {OPA1 deficiency impairs oxidative metabolism in cycling cells, underlining a translational approach for degenerative diseases.},
journal = {Disease models &amp; mechanisms},
volume = {16},
number = {9},
pages = {},
pmid = {37497665},
issn = {1754-8411},
mesh = {Humans ; *Optic Atrophy, Autosomal Dominant/genetics/metabolism ; Reactive Oxygen Species/metabolism ; Mitochondria/metabolism ; Cell Respiration ; Oxidative Stress ; GTP Phosphohydrolases/genetics/metabolism ; },
abstract = {Dominant optic atrophy is an optic neuropathy with varying clinical symptoms and progression. A severe disorder is associated with certain OPA1 mutations and includes additional symptoms for >20% of patients. This underscores the consequences of OPA1 mutations in different cellular populations, not only retinal ganglionic cells. We assessed the effects of OPA1 loss of function on oxidative metabolism and antioxidant defences using an RNA-silencing strategy in a human epithelial cell line. We observed a decrease in the mitochondrial respiratory chain complexes, associated with a reduction in aconitase activity related to an increase in reactive oxygen species (ROS) production. In response, the NRF2 (also known as NFE2L2) transcription factor was translocated into the nucleus and upregulated SOD1 and GSTP1. This study highlights the effects of OPA1 deficiency on oxidative metabolism in replicative cells, as already shown in neurons. It underlines a translational process to use cycling cells to circumvent and describe oxidative metabolism. Moreover, it paves the way to predict the evolution of dominant optic atrophy using mathematical models that consider mitochondrial ROS production and their detoxifying pathways.},
}
@article {pmid37493549,
year = {2023},
author = {Jagielska, M and Hałakuc, P and Płecha, M and Milanowski, R},
title = {[Mitochondrial genomes – unity and diversity].},
journal = {Postepy biochemii},
volume = {69},
number = {2},
pages = {113-121},
doi = {10.18388/pb.2021_486},
pmid = {37493549},
issn = {0032-5422},
mesh = {*Genome, Mitochondrial ; Evolution, Molecular ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Cell Nucleus ; Phylogeny ; },
abstract = {The emergence of mitochondria was one of the most important events in the history of life on Earth. The engulfed bacterial cell, transformed into a mitochondrion, retained its genome, which then underwent numerous modifications. Through massive loss and numerous gene transfers into the nuclear genome, the autonomous bacterium eventually evolved into the organelle we know today. As a result of changes taking place independently in different evolutionary lineages, we observe a great diversity of mitochondrial genomes with respect to structure and gene content. In most cases, mitochondrial DNA has a circular shape, but linear molecules of mitochondrial DNA are also observed in some eukaryotes. In extreme cases, such as in reduced mitochondrial-derived organelles, the genome has been completely lost. In this article, we discuss the diversity of mitochondrial genome structures within the largest groups of Eukarya.},
}
@article {pmid37491455,
year = {2023},
author = {von der Dunk, SHA and Hogeweg, P and Snel, B},
title = {Obligate endosymbiosis enables genome expansion during eukaryogenesis.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {777},
pmid = {37491455},
issn = {2399-3642},
mesh = {Phylogeny ; *Eukaryotic Cells/metabolism ; *Symbiosis/genetics ; Biological Evolution ; Mitochondria/genetics ; },
abstract = {The endosymbiosis of an alpha-proteobacterium that gave rise to mitochondria was one of the key events in eukaryogenesis. One striking outcome of eukaryogenesis was a much more complex cell with a large genome. Despite the existence of many alternative hypotheses for this and other patterns potentially related to endosymbiosis, a constructive evolutionary model in which these hypotheses can be studied is still lacking. Here, we present a theoretical approach in which we focus on the consequences rather than the causes of mitochondrial endosymbiosis. Using a constructive evolutionary model of cell-cycle regulation, we find that genome expansion and genome size asymmetry arise from emergent host-symbiont cell-cycle coordination. We also find that holobionts with large host and small symbiont genomes perform best on long timescales and mimic the outcome of eukaryogenesis. By designing and studying a constructive evolutionary model of obligate endosymbiosis, we uncovered some of the forces that may drive the patterns observed in nature. Our results provide a theoretical foundation for patterns related to mitochondrial endosymbiosis, such as genome size asymmetry, and reveal evolutionary outcomes that have not been considered so far, such as cell-cycle coordination without direct communication.},
}
@article {pmid37491310,
year = {2023},
author = {Costa, RD and Thomaz Neto, FJ and Moustafa, MT and Atilano, SR and Chwa, M and Cáceres-Del-Carpi, J and Mohamed, MH and Kenney, MC and Kuppermann, BD},
title = {The role of mitochondrial genes on nuclear gene expression in neovascular age related macular degeneration: analysis of nuclear VEGF gene expression after ranibizumab treatment in cytoplasmic hybrid retinal pigment epithelial cell lines correlated with clinical evolution.},
journal = {International journal of retina and vitreous},
volume = {9},
number = {1},
pages = {44},
pmid = {37491310},
issn = {2056-9920},
support = {P30 EY034070/EY/NEI NIH HHS/United States ; },
abstract = {PURPOSE: The present study tests the hypothesis that mitochondrial genes have retrograde signaling capacity that influences the expression of nuclear genes related to angiogenesis pathways. Cytoplasmic hybrid (cybrid) in vitro cell lines with patient specific mitochondria inserted into an immortalized retinal pigment epithelial cell line (ARPE-19) were used to test this hypothesis. This type of analysis can provide important information to identify the optimal regimen of anti-VEGF treatment, personalizing age-related macular degeneration (AMD) therapies.<br><br>METHODS: Mitochondria deficient ARPE-19 cells (Rho0) were fused with AMD donor's platelets to create individual cybrid cell lines containing mitochondria from patients with phenotypic AMD disease and nuclear DNA from the immortalized RPE cell line. The cybrids were treated with Ranibizumab (Lucentis, Genentech, San Francisco, CA), at 4 different concentrations for 24&#xa0;h, and subsequently the levels of reactive oxygen species (ROS), gene expression for VEGF-A, hypoxia-inducible factor 1-alpha (HIF1-a) and manganese superoxide dismutase (SOD2) were measured. The clinical evolution of the two AMD-donors were correlated with the molecular findings found in their 'personalized' cybrids.<br><br>RESULTS: Cybrids from Patient-01 showed down-regulation of gene expression of VEGF-A and HIF-1a at both 1X and 4X Ranibizumab concentrations. Patient-01 AMD cybrid cultures had an increase in the ROS levels at 1X (P&#x2009;=&#x2009;0.0317), no changes at 2X (P&#x2009;=&#x2009;0.8350) and a decrease at 4X (P&#x2009;=&#x2009;0.0015) and 10X (P&#x2009;=&#x2009;0.0011) of Ranibizumab. Clinically, Patient-01 responded to anti-VEGF therapy but eventually developed geographic atrophy. Patient-02 cybrids demonstrated up-regulation of gene expression of VEGF-A and HIF-1a at Ranibizumab 1X and 4X concentrations. There was decreased ROS levels with Ranibizumab 1X (P&#x2009;=&#x2009;0.1606), 2X (P&#x2009;=&#x2009;0.0388), 4X (P&#x2009;=&#x2009;0.0010) and 10X (P&#x2009;=&#x2009;&#x2009;<&#x2009;0.0001). Clinically, Patient-02 presented with a neovascular lesion associated with a prominent production of intraretinal fluid in clinical follow-up requiring regular and repeated intravitreal injections of Ranibizumab with recurrent subretinal fluid.<br><br>CONCLUSIONS: Our cybrid model has the potential to help personalize the treatment regimen with anti-VEGF drugs in patients with neovascular AMD. Further investigation is needed to better understand the role that the mitochondria play in the cellular response to anti-VEGF drugs. Future studies that focus on this model have the potential to help personalize anti-VEGF treatment.},
}
@article {pmid37489100,
year = {2023},
author = {Yordanov, G and Palova, N and Mehandjyiski, I and Hristov, P},
title = {Mitochondrial DNA sequencing illuminates genetic diversity and origin of Hunagrian Nonius horse breed and his relatives - Danubian horse and Serbian Nonius.},
journal = {Animal biotechnology},
volume = {34},
number = {8},
pages = {3897-3907},
doi = {10.1080/10495398.2023.2237533},
pmid = {37489100},
issn = {1532-2378},
mesh = {Animals ; Horses/genetics ; Female ; *DNA, Mitochondrial/genetics ; Serbia ; *Genetic Variation/genetics ; Mitochondria/genetics ; Sequence Analysis, DNA ; Haplotypes/genetics ; Phylogeny ; },
abstract = {From a historical perspective, horse breeding in Bulgaria has been very well developed since the time of the Thracians (early Bronze Age c. 3000 BCE). Archaeological discoveries from this era present us with an extremely rich type diversity, including wild and local primitive horses, the prototype of heavy draft horses, and fine riding horses.The objective of this study was to investigate the genetic structure of unexamined populations of three closely related horse breeds - the Danubian Nonius Hungarian Nonius and Serbian Nonius horses. A 608 bp long fragment of the mtDNA D-loop region was amplified and sequenced. The obtained results showed completely different genetic profiles between the investigated breeds. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fell into M, L, G, and O'P lineages, which reflects the genetic profiles of the ancestral mares that were probably used at the initial stages of formation of the breeds. The population of the Danubian horse was characterized by a high prevalence of Central Asian specific haplogroup G (45%), followed by Western Eurasian specific haplogroups L and M (both about 21%). In contrast to the Danubian horse, in the Nonius breed the highest frequency of Western Eurasian haplogroup M (43.5%) was found, followed by Middle Eastern haplogroups O'P (26.1%) Central Asian specific E (13.0%) and G (13.1%). The Serbian Nonius horse showed a completely different genetic profile with a prevalence of the rare for Europe haplogroup D (66.7%), followed by Central Asian specific G (16.7%). The high mitochondrial haplotype diversity (Hd = 0.886) found in the investigated samples is evidence for multiple maternal origins in all populations.In conclusion, the obtained results demonstrated a high percentage of haplogroup sharing especially in the Danubian and Hungarian Nonius horse breeds, which reflects the possible common origins of the two breeds. In contrast to these breeds, the Serbian Nonius, despite the small number of investigated animals, showed a specific genetic profile, which could be explained by different and independent origins.},
}
@article {pmid37481257,
year = {2023},
author = {Collington, E and Lobb, B and Mazen, NA and Doxey, AC and Glerum, DM},
title = {Phylogenomic Analysis of 155 Helminth Species Reveals Widespread Absence of Oxygen Metabolic Capacity.},
journal = {Genome biology and evolution},
volume = {15},
number = {8},
pages = {},
pmid = {37481257},
issn = {1759-6653},
mesh = {Animals ; Phylogeny ; Reactive Oxygen Species/metabolism ; *Parasites ; Electron Transport Complex IV/genetics ; Caenorhabditis elegans/genetics/metabolism ; Oxygen/metabolism ; },
abstract = {The terminal electron acceptor of most aerobic respiratory chains, cytochrome c oxidase (COX), has been highly conserved throughout evolution, from aerobic prokaryotes to complex eukaryotes. Oxygen metabolism in parasitic helminths differs significantly from that of most aerobic eukaryotes, as these organisms can switch between aerobic and anaerobic metabolisms throughout their life cycles. Early studies suggested a lack of COX activity in certain parasitic helminths, and the role of COX in helminth mitochondria remains unclear. To determine whether a functional COX is widely present in helminths, we analyzed the phylogenetic distribution of oxygen metabolism systems across 155 helminth genomes, investigating three distinct sets of protein-coding genes involved in different aspects of oxygen metabolism: COX and its assembly factors, peroxisomes, and the most abundant reactive oxygen species (ROS)-metabolizing proteins. While glycolytic and citric acid cycle enzymes are highly conserved in helminthic species, we observed an apparent widespread absence of essential COX genes across 52% of helminth species investigated. While the most common proteins involved in the defense against ROS are highly maintained across virtually all lineages, we also observed an apparent absence of essential peroxisomal protein-coding genes in 42% of species investigated. Our results suggest that a subset of parasitic helminths utilize oxygen differently from related, nonparasitic species such as Caenorhabditis elegans, with significant differences in their mitochondrial electron transport chains and peroxisomes. The identification of substantive differences between parasite and host metabolism offers a new avenue for the development of anthelmintic agents that could target these divergent pathways.},
}
@article {pmid37481145,
year = {2023},
author = {DeCicco, LH and DeRaad, DA and Ostrow, EN and Moyle, RG},
title = {A complete species-level phylogeny of the Erythrura parrotfinches (Aves: Estrildidae).},
journal = {Molecular phylogenetics and evolution},
volume = {187},
number = {},
pages = {107883},
doi = {10.1016/j.ympev.2023.107883},
pmid = {37481145},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Passeriformes/genetics ; DNA ; Genes, Mitochondrial ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Sequence Analysis, DNA ; },
abstract = {Identifying species boundaries and phylogenetic relationships among groups of closely related species provides a necessary framework for understanding how biodiversity evolves in natural systems. Here we present a complete phylogeny of the avian genus Erythrura (family Estrildidae) commonly known as parrotfinches, which includes species threatened by habitat loss and the pet trade. Using both mitogenome and reduced-representation genome-wide nuclear DNA sequence data, we reconstructed the evolutionary history of the group by sampling all 12 recognized species, four of which had not previously been studied in a phylogenetic context. We included intra-species geographic sampling that allowed us to comment on species limits in some taxa. We recovered the Gouldian Finch (Chloebia gouldiae) of Australia which has often been placed in the monotypic genus Chloebia, as being sister to a clade comprising all Erythrura species. In addition, we recovered a well-supported clade comprising eight species distributed throughout the Pacific Island eco-region, whereas those species occurring in continental southeast Asia, the Greater Sundas, and the Philippines, were recovered as earlier branching lineages. Of note was the early branching of the Fiji-endemic E. kleinschmidti which corroborates its unique phenotype. We also found a deep phylogenetic split (8.59% corrected, 7.89% uncorrected divergence in the mitochondrial gene ND2) between the Java and Philippine populations of E. hyperythra, indicating unrecognized species-level diversity within this taxon. In contrast, genome-wide nuclear data suggested that the New Guinea endemic species E. papuana is embedded within the widespread species E. trichroa in all phylogenetic reconstructions, corroborating previously published mitochondrial data that suggested a similar pattern. By generating a phylogenetic hypothesis for the relationships among all species of Erythrura parrotfinches, we provide a framework for better understanding the extant diversity and evolutionary history of this group.},
}
@article {pmid37479726,
year = {2023},
author = {Falchi, FA and Forti, F and Carnelli, C and Genco, A and Pizzoccheri, R and Manzari, C and Pavesi, G and Briani, F},
title = {Human PNPase causes RNA stabilization and accumulation of R-loops in the Escherichia coli model system.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {11771},
pmid = {37479726},
issn = {2045-2322},
mesh = {Humans ; *Escherichia coli/genetics ; *R-Loop Structures ; Causality ; Gene Expression Regulation ; RNA/genetics ; },
abstract = {Polyribonucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. In Escherichia coli, PNPase controls complex phenotypic traits like biofilm formation and growth at low temperature. In human cells, PNPase is located in mitochondria, where it is implicated in the RNA import from the cytoplasm, the mitochondrial RNA degradation and the processing of R-loops, namely stable RNA-DNA hybrids displacing a DNA strand. In this work, we show that the human PNPase (hPNPase) expressed in E. coli causes oxidative stress, SOS response activation and R-loops accumulation. Hundreds of E. coli RNAs are stabilized in presence of hPNPase, whereas only few transcripts are destabilized. Moreover, phenotypic traits typical of E. coli strains lacking PNPase are strengthened in presence of the human enzyme. We discuss the hypothesis that hPNPase expressed in E. coli may bind, but not degrade, the RNA, in agreement with previous in vitro data showing that phosphate concentrations in the range of those found in the bacterial cytoplasm and, more relevant, in the mitochondria, inhibit its activity.},
}
@article {pmid37479023,
year = {2023},
author = {Boël, M and Voituron, Y and Roussel, D},
title = {Body mass dependence of oxidative phosphorylation efficiency in liver mitochondria from mammals.},
journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology},
volume = {284},
number = {},
pages = {111490},
doi = {10.1016/j.cbpa.2023.111490},
pmid = {37479023},
issn = {1531-4332},
mesh = {Animals ; *Oxidative Phosphorylation ; *Mitochondria, Liver/metabolism ; Adenosine Triphosphate/metabolism ; Mitochondria/metabolism ; Mammals/metabolism ; Oxygen Consumption/physiology ; },
abstract = {In eukaryotes, the performances of an organism are dependent on body mass and chemically supported by the mitochondrial production of ATP. Although the relationship between body mass and mitochondrial oxygen consumption is well described, the allometry of the transduction efficiency from oxygen to ATP production (ATP/O) is still poorly understood. Using a comparative approach, we investigated the oxygen consumption and ATP production of liver mitochondria from twelve species of mammals ranging from 5 g to 600 kg. We found that both oxygen consumption and ATP production are mass dependent but not the ATP/O at the maximal phosphorylating state. The results also showed that for sub-maximal phosphorylating states the ATP/O value positively correlated with body mass, irrespective of the metabolic intensity. This result contrasts with previous data obtained in mammalian muscles, suggesting a tissue-dependence of the body mass effect on mitochondrial efficiency.},
}
@article {pmid37464732,
year = {2023},
author = {Wang, F and Zhang, N and Zhao, C and Song, Z and Caiyan, X},
title = {Codon usage bias analysis of mitochondrial protein-coding genes in 12 species of Candida.},
journal = {Journal of genetics},
volume = {102},
number = {},
pages = {},
pmid = {37464732},
issn = {0973-7731},
mesh = {Humans ; *Codon Usage ; *Candida/genetics ; Codon/genetics ; Mitochondrial Proteins/genetics ; Mitochondria/genetics ; Nucleotides/genetics ; },
abstract = {The incidence of diseases that are caused by fungal infection is gradually increasing, together with antibiotic abuse and the number of patients with hypoimmunity. The many challenges in clinical anti-fungi treatment include serious adverse effects and drug resistance. The mitochondria of fungi have been found to be closely associated with pathopoiesia and drug resistance. Hence, we investigated patterns in Candida mitochondrial genes codon usage bias to provide new information to guide anti-fungal research. According to the nucleotide composition results, most mitochondrial genes of the analysed Candida tended to use A/T bases rather than G/C bases. The relative synonymous codon usage values demonstrated that UUA, AGU, CCU, GCU, UGA, AGA and GGU were the common preferential codons of mitochondrial genes in 12 Candida species. Codon adaptation index (CAI) analysis indicated that the ATP9 of Candida parapsilosis had the highest value, and the ND6 of C. auris had the lowest value. The CAI clearly correlated with the codon bias index, except in C. maltose and C. viswanathii, and was significantly positively correlated with the average GC content. Together, our results suggested that the codon usage pattern is affected by multiple factors, among which GC content is critical. Nucleotide composition, selection pressure and mutation pressure influence codon bias in Candida mitochondrial genes, with dominant status to mutation pressure. Codon usage bias analyses of Candida mitochondrial genes may provide new insight into its evolution.},
}
@article {pmid37463427,
year = {2023},
author = {Warren, JM and Broz, AK and Martinez-Hottovy, A and Elowsky, C and Christensen, AC and Sloan, DB},
title = {Rewiring of Aminoacyl-tRNA Synthetase Localization and Interactions in Plants With Extensive Mitochondrial tRNA Gene Loss.},
journal = {Molecular biology and evolution},
volume = {40},
number = {7},
pages = {},
pmid = {37463427},
issn = {1537-1719},
mesh = {*Amino Acyl-tRNA Synthetases/genetics ; RNA, Transfer/genetics ; Cell Nucleus/genetics ; Mitochondria/genetics ; Genome, Plant ; },
abstract = {The number of tRNAs encoded in plant mitochondrial genomes varies considerably. Ongoing loss of bacterial-like mitochondrial tRNA genes in many lineages necessitates the import of nuclear-encoded counterparts that share little sequence similarity. Because tRNAs are involved in highly specific molecular interactions, this replacement process raises questions about the identity and trafficking of enzymes necessary for the maturation and function of newly imported tRNAs. In particular, the aminoacyl-tRNA synthetases (aaRSs) that charge tRNAs are usually divided into distinct classes that specialize on either organellar (mitochondrial and plastid) or nuclear-encoded (cytosolic) tRNAs. Here, we investigate the evolution of aaRS subcellular localization in a plant lineage (Sileneae) that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts (PacBio Iso-Seq), we found predicted retargeting of many ancestrally cytosolic aaRSs to the mitochondrion and confirmed these results with colocalization microscopy assays. However, we also found cases where aaRS localization does not appear to change despite functional tRNA replacement, suggesting evolution of novel interactions and charging relationships. Therefore, the history of repeated tRNA replacement in Sileneae mitochondria reveals that differing constraints on tRNA/aaRS interactions may determine which of these alternative coevolutionary paths is used to maintain organellar translation in plant cells.},
}
@article {pmid37453725,
year = {2023},
author = {Shively, CA and Frye, BM and Negrey, JD and Johnson, CSC and Sutphen, CL and Molina, AJA and Yadav, H and Snyder-Mackler, N and Register, TC},
title = {The interactive effects of psychosocial stress and diet composition on health in primates.},
journal = {Neuroscience and biobehavioral reviews},
volume = {152},
number = {},
pages = {105320},
pmid = {37453725},
issn = {1873-7528},
support = {R01 HL122393/HL/NHLBI NIH HHS/United States ; T32 AG033534/AG/NIA NIH HHS/United States ; RF1 AG058829/AG/NIA NIH HHS/United States ; T32 AG052354/AG/NIA NIH HHS/United States ; R01 HL087103/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Primates ; Stress, Psychological ; Anxiety ; *Diet, Mediterranean ; Social Isolation ; },
abstract = {Social disadvantage and diet composition independently impact myriad dimensions of health. They are closely entwined, as social disadvantage often yields poor diet quality, and may interact to fuel differential health outcomes. This paper reviews effects of psychosocial stress and diet composition on health in nonhuman primates and their implications for aging and human health. We examined the effects of social subordination stress and Mediterranean versus Western diet on multiple systems. We report that psychosocial stress and Western diet have independent and additive adverse effects on hypothalamic-pituitary-adrenal and autonomic nervous system reactivity to psychological stressors, brain structure, and ovarian function. Compared to the Mediterranean diet, the Western diet resulted in accelerated aging, nonalcoholic fatty liver disease, insulin resistance, gut microbial changes associated with increased disease risk, neuroinflammation, neuroanatomical perturbations, anxiety, and social isolation. This comprehensive, multisystem investigation lays the foundation for future investigations of the mechanistic underpinnings of psychosocial stress and diet effects on health, and advances the promise of the Mediterranean diet as a therapeutic intervention on psychosocial stress.},
}
@article {pmid37453661,
year = {2023},
author = {Dreishpoon, MB and Bick, NR and Petrova, B and Warui, DM and Cameron, A and Booker, SJ and Kanarek, N and Golub, TR and Tsvetkov, P},
title = {FDX1 regulates cellular protein lipoylation through direct binding to LIAS.},
journal = {The Journal of biological chemistry},
volume = {299},
number = {9},
pages = {105046},
pmid = {37453661},
issn = {1083-351X},
support = {R01 CA279550/CA/NCI NIH HHS/United States ; R35 CA242457/CA/NCI NIH HHS/United States ; R35 GM122595/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Humans ; *Ferredoxins/genetics/metabolism ; *Lipoylation/genetics ; Protein Binding ; Cell Respiration/genetics ; Cell Proliferation/genetics ; Metabolome ; *Sulfurtransferases/metabolism ; },
abstract = {Ferredoxins are a family of iron-sulfur (Fe-S) cluster proteins that serve as essential electron donors in numerous cellular processes that are conserved through evolution. The promiscuous nature of ferredoxins as electron donors enables them to participate in many metabolic processes including steroid, heme, vitamin D, and Fe-S cluster biosynthesis in different organisms. However, the unique natural function(s) of each of the two human ferredoxins (FDX1 and FDX2) are still poorly characterized. We recently reported that FDX1 is both a crucial regulator of copper ionophore-induced cell death and serves as an upstream regulator of cellular protein lipoylation, a mitochondrial lipid-based post-translational modification naturally occurring on four mitochondrial enzymes that are crucial for TCA cycle function. Here we show that FDX1 directly regulates protein lipoylation by binding the lipoyl synthase (LIAS) enzyme promoting its functional binding to the lipoyl carrier protein GCSH and not through indirect regulation of cellular Fe-S cluster biosynthesis. Metabolite profiling revealed that the predominant cellular metabolic outcome of FDX1 loss of function is manifested through the regulation of the four lipoylation-dependent enzymes ultimately resulting in loss of cellular respiration and sensitivity to mild glucose starvation. Transcriptional profiling established that FDX1 loss-of-function results in the induction of both compensatory metabolism-related genes and the integrated stress response, consistent with our findings that FDX1 loss-of-function is conditionally lethal. Together, our findings establish that FDX1 directly engages with LIAS, promoting its role in cellular protein lipoylation, a process essential in maintaining cell viability under low glucose conditions.},
}
@article {pmid37451476,
year = {2023},
author = {Záhonová, K and Valach, M and Tripathi, P and Benz, C and Opperdoes, FR and Barath, P and Lukáčová, V and Danchenko, M and Faktorová, D and Horváth, A and Burger, G and Lukeš, J and Škodová-Sveráková, I},
title = {Subunit composition of mitochondrial dehydrogenase complexes in diplonemid flagellates.},
journal = {Biochimica et biophysica acta. General subjects},
volume = {1867},
number = {9},
pages = {130419},
doi = {10.1016/j.bbagen.2023.130419},
pmid = {37451476},
issn = {1872-8006},
mesh = {*Mitochondria/metabolism ; *Pyruvate Dehydrogenase Complex/metabolism ; Multienzyme Complexes/metabolism ; Ketoglutarate Dehydrogenase Complex/metabolism ; Pyruvates/metabolism ; },
abstract = {In eukaryotes, pyruvate, a key metabolite produced by glycolysis, is converted by a tripartite mitochondrial pyruvate dehydrogenase (PDH) complex to acetyl-coenzyme A, which is fed into the tricarboxylic acid cycle. Two additional enzyme complexes with analogous composition catalyze similar oxidative decarboxylation reactions albeit using different substrates, the branched-chain ketoacid dehydrogenase (BCKDH) complex and the 2-oxoglutarate dehydrogenase (OGDH) complex. Comparative transcriptome analyses of diplonemids, one of the most abundant and diverse groups of oceanic protists, indicate that the conventional E1, E2, and E3 subunits of the PDH complex are lacking. E1 was apparently replaced in the euglenozoan ancestor of diplonemids by an AceE protein of archaeal type, a substitution that we also document in dinoflagellates. Here, we demonstrate that the mitochondrion of the model diplonemid Paradiplonema papillatum displays pyruvate and 2-oxoglutarate dehydrogenase activities. Protein mass spectrometry of mitochondria reveal that the AceE protein is as abundant as the E1 subunit of BCKDH. This corroborates the view that the AceE subunit is a functional component of the PDH complex. We hypothesize that by acquiring AceE, the diplonemid ancestor not only lost the eukaryotic-type E1, but also the E2 and E3 subunits of the PDH complex, which are present in other euglenozoans. We posit that the PDH activity in diplonemids seems to be carried out by a complex, in which the AceE protein partners with the E2 and E3 subunits from BCKDH and/or OGDH.},
}
@article {pmid37437976,
year = {2023},
author = {Atayik, MC and Çakatay, U},
title = {Mitochondria-associated cellular senescence mechanisms: Biochemical and pharmacological perspectives.},
journal = {Advances in protein chemistry and structural biology},
volume = {136},
number = {},
pages = {117-155},
doi = {10.1016/bs.apcsb.2023.03.003},
pmid = {37437976},
issn = {1876-1631},
mesh = {*Mitochondria ; *Cellular Senescence ; Signal Transduction ; },
abstract = {Initially, endosymbiotic relation of mitochondria and other cellular compartments had been continued mutually. However, that evolutionary adaptation impaired because of the deterioration of endosymbiotic crosstalk due to aging and several pathological consequences in cellular redox status are seen, such as deterioration in redox integrity of mitochondria, interfered inter-organelle redox signaling and inefficient antioxidant response element mediated gene expression. Although the dysfunction of mitochondria is known to be a classical pattern of senescence, it is unresolved that why dysfunctional mitochondria is the core of senescence-associated secretory phenotype (SASP). Redox impairment and SASP-related disease development are generally together with weaken immunity. Impaired mitochondrial redox integrity and its ineffectiveness in immunity control render elders to be more prone to age-related diseases. As senotherapeutic agents, senolytics remove senescent cells whilst senomorphics/senostatics inhibits the secretion of SASP. Senotherapeutics and the novel approaches for ameliorating SASP-related unfavorable effects are recently thought to be promising ways as mitochondria-targeted gerotherapeutic options.},
}
@article {pmid37429369,
year = {2023},
author = {Ahlawat, S and Sharma, U and Arora, R and Sharma, R and Chhabra, P and Veer Singh, K and Vijh, RK},
title = {Mitogenomic phylogeny reveals the predominance of the Nubian lineage of African wild ass in Indian donkeys.},
journal = {Gene},
volume = {880},
number = {},
pages = {147627},
doi = {10.1016/j.gene.2023.147627},
pmid = {37429369},
issn = {1879-0038},
mesh = {Animals ; Humans ; *Equidae/genetics ; Phylogeny ; *DNA, Mitochondrial/genetics ; Africa ; Domestication ; Haplotypes ; Genetic Variation ; },
abstract = {To contribute to the knowledge of maternal genetic diversity in domestic donkeys, this study investigated the mitochondrial DNA variations and analyzed the genetic structure in Indian donkeys based on 31 mitogenome sequences representing four breeds/populations (Agra, Halari, Kachchhi and Spiti). A total of 27 haplotypes with a haplotype diversity value of 0.989 were evident in the donkey genetic resources of India. The genetic differentiation between the investigated populations was evaluated using population pairwise FST values, which showed maximum differentiation between Kachchhi and Halari donkeys. The Neighbor-Joining (NJ) tree based on the whole mitogenome sequence and the Median-Joining (MJ) network for partial D-loop fragment showed clear demarcation of Indian donkeys into Nubian and Somali clades, substantiating African maternal origin of Indian domestic donkeys. The topology of the MJ network excluded the Asian wild asses as the possible progenitors of Indian donkeys. Halari and Agra donkeys showed conformity exclusively to the Nubian lineage of the African wild asses. However, representation of both the Nubian and Somali lineages was observed in Kachchhi and Spiti donkeys. Comprehensive analysis carried out by retrieving D-loop sequences from different countries representing Asia, Africa, Europe and South America revealed existence of shared haplotypes across geographically isolated regions of the globe. This observation is indicative of utility of donkeys as pack animals across inter-continental trading routes during development of human civilizations. Our results represent a valuable contribution to maternal genetic diversity of Indian donkeys and provide insights into the worldwide spread of the species following initial domestication in Africa.},
}
@article {pmid37429000,
year = {2023},
author = {Wan, H and Zhang, Y and Wu, L and Zhou, G and Pan, L and Fernie, AR and Ruan, YL},
title = {Evolution of cytosolic and organellar invertases empowered the colonization and thriving of land plants.},
journal = {Plant physiology},
volume = {193},
number = {2},
pages = {1227-1243},
pmid = {37429000},
issn = {1532-2548},
mesh = {Humans ; Cytosol/metabolism ; *beta-Fructofuranosidase/metabolism ; Plants/genetics/metabolism ; *Embryophyta/metabolism ; Carbon/metabolism ; Evolution, Molecular ; },
abstract = {The molecular innovation underpinning efficient carbon and energy metabolism during evolution of land plants remains largely unknown. Invertase-mediated sucrose cleavage into hexoses is central to fuel growth. Why some cytoplasmic invertases (CINs) function in the cytosol, whereas others operate in chloroplasts and mitochondria, is puzzling. We attempted to shed light on this question from an evolutionary perspective. Our analyses indicated that plant CINs originated from a putatively orthologous ancestral gene in cyanobacteria and formed the plastidic CIN (α1 clade) through endosymbiotic gene transfer, while its duplication in algae with a loss of its signal peptide produced the β clade CINs in the cytosol. The mitochondrial CINs (α2) were derived from duplication of the plastidic CINs and coevolved with vascular plants. Importantly, the copy number of mitochondrial and plastidic CINs increased upon the emergence of seed plants, corresponding with the rise of respiratory, photosynthetic, and growth rates. The cytosolic CIN (β subfamily) kept expanding from algae to gymnosperm, indicating its role in supporting the increase in carbon use efficiency during evolution. Affinity purification mass spectrometry identified a cohort of proteins interacting with α1 and 2 CINs, which points to their roles in plastid and mitochondrial glycolysis, oxidative stress tolerance, and the maintenance of subcellular sugar homeostasis. Collectively, the findings indicate evolutionary roles of α1 and α2 CINs in chloroplasts and mitochondria for achieving high photosynthetic and respiratory rates, respectively, which, together with the expanding of cytosolic CINs, likely underpin the colonization of land plants through fueling rapid growth and biomass production.},
}
@article {pmid37424790,
year = {2023},
author = {Margenat, M and Betancour, G and Irving, V and Costábile, A and García-Cedrés, T and Portela, MM and Carrión, F and Herrera, FE and Villarino, A},
title = {Characteristics of Mycobacterium tuberculosis PtpA interaction and activity on the alpha subunit of human mitochondrial trifunctional protein, a key enzyme of lipid metabolism.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1095060},
pmid = {37424790},
issn = {2235-2988},
mesh = {Humans ; Lipid Metabolism ; *Mycobacterium tuberculosis ; Phylogeny ; Ubiquitins ; *Mitochondrial Trifunctional Protein/metabolism ; *Bacterial Proteins/metabolism ; },
abstract = {During Mycobacterium tuberculosis (Mtb) infection, the virulence factor PtpA belonging to the protein tyrosine phosphatase family is delivered into the cytosol of the macrophage. PtpA interacts with numerous eukaryotic proteins modulating phagosome maturation, innate immune response, apoptosis, and potentially host-lipid metabolism, as previously reported by our group. In vitro, the human trifunctional protein enzyme (hTFP) is a bona fide PtpA substrate, a key enzyme of mitochondrial β-oxidation of long-chain fatty acids, containing two alpha and two beta subunits arranged in a tetramer structure. Interestingly, it has been described that the alpha subunit of hTFP (ECHA, hTFPα) is no longer detected in mitochondria during macrophage infection with the virulent Mtb H37Rv. To better understand if PtpA could be the bacterial factor responsible for this effect, in the present work, we studied in-depth the PtpA activity and interaction with hTFPα. With this aim, we performed docking and in vitro dephosphorylation assays defining the P-Tyr-271 as the potential target of mycobacterial PtpA, a residue located in the helix-10 of hTFPα, previously described as relevant for its mitochondrial membrane localization and activity. Phylogenetic analysis showed that Tyr-271 is absent in TFPα of bacteria and is present in more complex eukaryotic organisms. These results suggest that this residue is a specific PtpA target, and its phosphorylation state is a way of regulating its subcellular localization. We also showed that phosphorylation of Tyr-271 can be catalyzed by Jak kinase. In addition, we found by molecular dynamics that PtpA and hTFPα form a stable protein complex through the PtpA active site, and we determined the dissociation equilibrium constant. Finally, a detailed study of PtpA interaction with ubiquitin, a reported PtpA activator, showed that additional factors are required to explain a ubiquitin-mediated activation of PtpA. Altogether, our results provide further evidence supporting that PtpA could be the bacterial factor that dephosphorylates hTFPα during infection, potentially affecting its mitochondrial localization or β-oxidation activity.},
}
@article {pmid37424728,
year = {2023},
author = {Gospodaryov, DV and Ballard, JWO and Camus, MF and DeSalle, R and Garvin, MR and Richter, U},
title = {Editorial: Energy-producing organelles and the nucleus: a phenomenal genomic friendship.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1230032},
pmid = {37424728},
issn = {1664-8021},
}
@article {pmid37419430,
year = {2023},
author = {Françoso, E and Zuntini, AR and Ricardo, PC and Araujo, NS and Silva, JPN and Brown, MJF and Arias, MC},
title = {The complete mitochondrial genome of Trigonisca nataliae (Hymenoptera, Apidae) assemblage reveals heteroplasmy in the control region.},
journal = {Gene},
volume = {881},
number = {},
pages = {147621},
doi = {10.1016/j.gene.2023.147621},
pmid = {37419430},
issn = {1879-0038},
mesh = {Bees/genetics ; Animals ; *Hymenoptera/genetics ; *Genome, Mitochondrial ; Heteroplasmy ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {The evolution of mitochondrial genomes in the stingless bees is surprisingly dynamic, making them a model system to understand mitogenome structure, function, and evolution. Out of the seven mitogenomes available in this group, five exhibit atypical characteristics, including extreme rearrangements, rapid evolution and complete mitogenome duplication. To further explore the mitogenome diversity in these bees, we utilized isolated mtDNA and Illumina sequencing to assemble the complete mitogenome of Trigonisca nataliae, a species found in Northern Brazil. The mitogenome of T. nataliae was highly conserved in gene content and structure when compared to Melipona species but diverged in the control region (CR). Using PCR amplification, cloning and Sanger sequencing, six different CR haplotypes, varying in size and content, were recovery. These findings indicate that heteroplasmy, where different mitochondrial haplotypes coexist within individuals, occurs in T. nataliae. Consequently, we argue that heteroplasmy might indeed be a common phenomenon in bees that could be associated with variations in mitogenome size and challenges encountered during the assembly process.},
}
@article {pmid37408307,
year = {2023},
author = {Yang, C and Li, X and Yang, L and Chen, S and Liao, J and Li, K and Zhou, J and Shen, W and Zhuang, X and Bai, M and Bassham, DC and Gao, C},
title = {A positive feedback regulation of SnRK1 signaling by autophagy in plants.},
journal = {Molecular plant},
volume = {16},
number = {7},
pages = {1192-1211},
doi = {10.1016/j.molp.2023.07.001},
pmid = {37408307},
issn = {1752-9867},
mesh = {Protein Serine-Threonine Kinases/genetics/metabolism ; *Arabidopsis Proteins/genetics/metabolism ; *Arabidopsis/metabolism ; Feedback ; Autophagy/genetics ; Gene Expression Regulation, Plant ; },
abstract = {SnRK1, an evolutionarily conserved heterotrimeric kinase complex that acts as a key metabolic sensor in maintaining energy homeostasis in plants, is an important upstream activator of autophagy that serves as a cellular degradation mechanism for the healthy growth of plants. However, whether and how the autophagy pathway is involved in regulating SnRK1 activity remains unknown. In this study, we identified a clade of plant-specific and mitochondria-localized FCS-like zinc finger (FLZ) proteins as currently unknown ATG8-interacting partners that actively inhibit SnRK1 signaling by repressing the T-loop phosphorylation of the catalytic α subunits of SnRK1, thereby negatively modulating autophagy and plant tolerance to energy deprivation caused by long-term carbon starvation. Interestingly, these AtFLZs are transcriptionally repressed by low-energy stress, and AtFLZ proteins undergo a selective autophagy-dependent pathway to be delivered to the vacuole for degradation, thereby constituting a positive feedback regulation to relieve their repression of SnRK1 signaling. Bioinformatic analyses show that the ATG8-FLZ-SnRK1 regulatory axis first appears in gymnosperms and seems to be highly conserved during the evolution of seed plants. Consistent with this, depletion of ATG8-interacting ZmFLZ14 confers enhanced tolerance, whereas overexpression of ZmFLZ14 leads to reduced tolerance to energy deprivation in maize. Collectively, our study reveals a previously unknown mechanism by which autophagy contributes to the positive feedback regulation of SnRK1 signaling, thereby enabling plants to better adapt to stressful environments.},
}
@article {pmid37408243,
year = {2023},
author = {Frigo, E and Tommasin, L and Lippe, G and Carraro, M and Bernardi, P},
title = {The Haves and Have-Nots: The Mitochondrial Permeability Transition Pore across Species.},
journal = {Cells},
volume = {12},
number = {10},
pages = {},
pmid = {37408243},
issn = {2073-4409},
mesh = {Animals ; *Mitochondrial Permeability Transition Pore/metabolism ; *Mitochondrial Membrane Transport Proteins/metabolism ; Drosophila melanogaster/metabolism ; Mitochondria/metabolism ; Saccharomyces cerevisiae/metabolism ; Adenosine Triphosphate/metabolism ; Mammals/metabolism ; },
abstract = {The demonstration that F1FO (F)-ATP synthase and adenine nucleotide translocase (ANT) can form Ca[2+]-activated, high-conductance channels in the inner membrane of mitochondria from a variety of eukaryotes led to renewed interest in the permeability transition (PT), a permeability increase mediated by the PT pore (PTP). The PT is a Ca[2+]-dependent permeability increase in the inner mitochondrial membrane whose function and underlying molecular mechanisms have challenged scientists for the last 70 years. Although most of our knowledge about the PTP comes from studies in mammals, recent data obtained in other species highlighted substantial differences that could be perhaps attributed to specific features of F-ATP synthase and/or ANT. Strikingly, the anoxia and salt-tolerant brine shrimp Artemia franciscana does not undergo a PT in spite of its ability to take up and store Ca[2+] in mitochondria, and the anoxia-resistant Drosophila melanogaster displays a low-conductance, selective Ca[2+]-induced Ca[2+] release channel rather than a PTP. In mammals, the PT provides a mechanism for the release of cytochrome c and other proapoptotic proteins and mediates various forms of cell death. In this review, we cover the features of the PT (or lack thereof) in mammals, yeast, Drosophila melanogaster, Artemia franciscana and Caenorhabditis elegans, and we discuss the presence of the intrinsic pathway of apoptosis and of other forms of cell death. We hope that this exercise may help elucidate the function(s) of the PT and its possible role in evolution and inspire further tests to define its molecular nature.},
}
@article {pmid37407024,
year = {2023},
author = {Healy, TM and Burton, RS},
title = {Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence.},
journal = {Evolution; international journal of organic evolution},
volume = {77},
number = {9},
pages = {2100-2108},
doi = {10.1093/evolut/qpad122},
pmid = {37407024},
issn = {1558-5646},
mesh = {Animals ; *Copepoda/genetics ; Mitochondria/genetics/metabolism ; Chromosomes ; Genome ; Genotype ; DNA, Mitochondrial/genetics ; },
abstract = {All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins, which are critical for mitochondrial performance and eukaryotic fitness. Coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within a taxon, but hybridization can disrupt coevolved interactions, resulting in hybrid breakdown. Thus, mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Here we utilize Pool-seq to assess the effects of mitochondrial genotype on nuclear allele frequencies in fast- and slow-developing reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. We show that mitonuclear interactions lead to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on two chromosomes in crosses between populations with 1.5% or 9.6% fixed differences in mitochondrial DNA nucleotide sequence. However, we also find evidence of excess mismatched (i.e., noncoevolved) alleles on three or four chromosomes per cross, respectively, and of allele frequency differences consistent with effects involving only nuclear loci (i.e., unaffected by mitochondrial genotype). Thus, our results for low-divergence crosses suggest an underlying role for mitonuclear interactions in variation in hybrid developmental rate, but despite substantial effects of mitonuclear coevolution on individual chromosomes, no clear bias favoring coevolved interactions overall.},
}
@article {pmid37406344,
year = {2023},
author = {Lamb, IM and Okoye, IC and Mather, MW and Vaidya, AB},
title = {Unique Properties of Apicomplexan Mitochondria.},
journal = {Annual review of microbiology},
volume = {77},
number = {},
pages = {541-560},
pmid = {37406344},
issn = {1545-3251},
support = {R01 AI028398/AI/NIAID NIH HHS/United States ; R01 AI100569/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Mitochondria/genetics/metabolism ; *Toxoplasma/metabolism ; Biological Evolution ; *Malaria ; },
abstract = {Apicomplexan parasites constitute more than 6,000 species infecting a wide range of hosts. These include important pathogens such as those causing malaria and toxoplasmosis. Their evolutionary emergence coincided with the dawn of animals. Mitochondrial genomes of apicomplexan parasites have undergone dramatic reduction in their coding capacity, with genes for only three proteins and ribosomal RNA genes present in scrambled fragments originating from both strands. Different branches of the apicomplexans have undergone rearrangements of these genes, with Toxoplasma having massive variations in gene arrangements spread over multiple copies. The vast evolutionary distance between the parasite and the host mitochondria has been exploited for the development of antiparasitic drugs, especially those used to treat malaria, wherein inhibition of the parasite mitochondrial respiratory chain is selectively targeted with little toxicity to the host mitochondria. We describe additional unique characteristics of the parasite mitochondria that are being investigated and provide greater insights into these deep-branching eukaryotic pathogens.},
}
@article {pmid37389212,
year = {2023},
author = {Stefano, GB and Büttiker, P and Weissenberger, S and Esch, T and Anders, M and Raboch, J and Kream, RM and Ptacek, R},
title = {Independent and sensory human mitochondrial functions reflecting symbiotic evolution.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1130197},
pmid = {37389212},
issn = {2235-2988},
mesh = {Humans ; *Mitochondria ; *Genes, Bacterial ; Quorum Sensing ; Virion ; },
abstract = {The bacterial origin of mitochondria has been a widely accepted as an event that occurred about 1.45 billion years ago and endowed cells with internal energy producing organelle. Thus, mitochondria have traditionally been viewed as subcellular organelle as any other - fully functionally dependent on the cell it is a part of. However, recent studies have given us evidence that mitochondria are more functionally independent than other organelles, as they can function outside the cells, engage in complex "social" interactions, and communicate with each other as well as other cellular components, bacteria and viruses. Furthermore, mitochondria move, assemble and organize upon sensing different environmental cues, using a process akin to bacterial quorum sensing. Therefore, taking all these lines of evidence into account we hypothesize that mitochondria need to be viewed and studied from a perspective of a more functionally independent entity. This view of mitochondria may lead to new insights into their biological function, and inform new strategies for treatment of disease associated with mitochondrial dysfunction.},
}
@article {pmid37386734,
year = {2023},
author = {Arnqvist, G and Rowe, L},
title = {Ecology, the pace-of-life, epistatic selection and the maintenance of genetic variation in life-history genes.},
journal = {Molecular ecology},
volume = {32},
number = {17},
pages = {4713-4724},
doi = {10.1111/mec.17062},
pmid = {37386734},
issn = {1365-294X},
mesh = {*Polymorphism, Genetic ; Selection, Genetic ; Biological Evolution ; Alleles ; *Life History Traits ; Models, Genetic ; Genetic Variation ; Epistasis, Genetic ; },
abstract = {Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that natural selection is ultimately a manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous ecological effect that may have fundamental effects on the maintenance of genetic variation. Negative frequency dependency is a well-established emergent property of density dependence in ecology, because the relative profitability of different modes of exploiting or utilizing limiting resources tends to be inversely proportional to their frequency in a population. We suggest that this may often generate negative frequency-dependent selection (NFDS) on major effect loci that affect rate-dependent physiological processes, such as metabolic rate, that are phenotypically manifested as polymorphism in pace-of-life syndromes. When such a locus under NFDS shows stable intermediate frequency polymorphism, this should generate epistatic selection potentially involving large numbers of loci with more minor effects on life-history (LH) traits. When alternative alleles at such loci show sign epistasis with a major effect locus, this associative NFDS will promote the maintenance of polygenic variation in LH genes. We provide examples of the kind of major effect loci that could be involved and suggest empirical avenues that may better inform us on the importance and reach of this process.},
}
@article {pmid37381996,
year = {2023},
author = {Zhao, JH and Chen, YC and Hua, ZY and Liu, TR and Zhao, YY and Huang, LQ and Yuan, Y},
title = {[Cloning and gene function of dicarboxylate-tricarboxylate carrier protein in Gastrodia elata].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {48},
number = {12},
pages = {3140-3148},
doi = {10.19540/j.cnki.cjcmm.20230310.102},
pmid = {37381996},
issn = {1001-5302},
mesh = {*Gastrodia/genetics ; Phylogeny ; Amino Acids ; Cloning, Molecular ; },
abstract = {The gene GeDTC encoding the dicarboxylate-tricarboxylate carrier protein in Gastrodia elata was cloned by specific primers which were designed based on the transcriptome data of G. elata. Bioinformatics analysis on GeDTC gene was carried out by using ExPASY, ClustalW, MEGA, etc. Positive transgenic plants and potato minituber were obtained by virtue of the potato genetic transformation system. Agronomic characters, such as size, weight, organic acid content, and starch content, of potato minituber were tested and analyzed and GeDTC gene function was preliminarily investigated. The results showed that the open reading frame of GeDTC gene was 981 bp in length and 326 amino acid residues were encoded, with a relative molecular weight of 35.01 kDa. It was predicted that the theoretical isoelectric point of GeDTC protein was 9.83, the instability coefficient was 27.88, and the average index of hydrophilicity was 0.104, which was indicative of a stable hydrophilic protein. GeDTC protein had a transmembrane structure and no signal peptide and was located in the inner membrane of mitochondria. The phylogenetic tree showed that GeDTC was highly homologous with DTC proteins of other plant species, among which GeDTC had the highest homology with DcDTC(XP＿020675804.1) in Dendrobium candidum, reaching 85.89%. GeDTC overexpression vector pCambia1300-35Spro-GeDTC was constructed by double digests, and transgenic potato plants were obtained by Agrobacterium-mediated gene transformation. Compared with the wild-type plants, transgenic potato minituber harvested by transplanting had smaller size, lighter weight, lower organic acid content, and no significant difference in starch content. It is preliminarily induced that GeDTC is the efflux channel of tricarboxylate and related to the tuber development, which lays a foundation for further elucidating the molecular mechanism of G. elata tuber development.},
}
@article {pmid37371486,
year = {2023},
author = {Ding, Y and Zhang, S and Guo, Q and Leng, J},
title = {Mitochondrial Diabetes Is Associated with the ND4 G11696A Mutation.},
journal = {Biomolecules},
volume = {13},
number = {6},
pages = {},
pmid = {37371486},
issn = {2218-273X},
mesh = {Adult ; Aged ; Humans ; Middle Aged ; *Diabetes Mellitus, Type 2/genetics ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Mutation ; *NADH Dehydrogenase/genetics ; Phylogeny ; },
abstract = {Type 2 diabetes mellitus (T2DM) is a common endocrine disorder which remains a large challenge for clinicians. Previous studies have suggested that mitochondrial dysfunction plays an active role in T2DM progression, but a detailed mechanism is still elusive. In the current study, two Han Chinese families with maternally inherited T2DM were evaluated using clinical, genetic, molecular, and biochemical analyses. The mitochondrial genomes were PCR amplified and sequenced. Phylogenetic and bioinformatic analyses were used to assess the potential pathogenicity of mitochondrial DNA (mtDNA) mutations. Interestingly, the matrilineal relatives of these pedigrees exhibited variable severity of T2DM, in particular, the age at onset of T2DM varied from 26 to 65 years, with an average of 49 years. Sequence analysis revealed the presence of ND4 G11696A mutation, which resulted in the substitution of an isoleucine for valine at amino acid (AA) position 312. Indeed, this mutation was present in homoplasmy only in the maternal lineage, not in other members of these families, as well as 200 controls. Furthermore, the m.C5601T in the tRNA[Ala] and novel m.T5813C in the tRNA[Cys], showing high evolutional conservation, may contribute to the phenotypic expression of ND4 G11696A mutation. In addition, biochemical analysis revealed that cells with ND4 G11696A mutation exhibited higher levels of reactive oxygen species (ROS) productions than the controls. In contrast, the levels of mitochondrial membrane potential (MMP), ATP, mtDNA copy number (mtDNA-CN), Complex I activity, and NAD[+]/NADH ratio significantly decreased in cell lines carrying the m.G11696A and tRNA mutations, suggesting that these mutations affected the respiratory chain function and led to mitochondrial dysfunction that was involved in T2DM. Thus, our study broadened the clinical phenotypes of m.G11696A mutation.},
}
@article {pmid37368881,
year = {2023},
author = {Tanabe, TS and Grosser, M and Hahn, L and Kümpel, C and Hartenfels, H and Vtulkin, E and Flegler, W and Dahl, C},
title = {Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes.},
journal = {PLoS biology},
volume = {21},
number = {6},
pages = {e3002177},
pmid = {37368881},
issn = {1545-7885},
mesh = {*Thioctic Acid/genetics/metabolism ; Peptide Synthases/genetics/metabolism ; Phylogeny ; Bacterial Proteins/metabolism ; Sulfur ; },
abstract = {Lipoic acid is an essential biomolecule found in all domains of life and is involved in central carbon metabolism and dissimilatory sulfur oxidation. The machineries for lipoate assembly in mitochondria and chloroplasts of higher eukaryotes, as well as in the apicoplasts of some protozoa, are all of prokaryotic origin. Here, we provide experimental evidence for a novel lipoate assembly pathway in bacteria based on a sLpl(AB) lipoate:protein ligase, which attaches octanoate or lipoate to apo-proteins, and 2 radical SAM proteins, LipS1 and LipS2, which work together as lipoyl synthase and insert 2 sulfur atoms. Extensive homology searches combined with genomic context analyses allowed us to precisely distinguish between the new and established pathways and map them on the tree of life. This not only revealed a much wider distribution of lipoate biogenesis systems than expected, in particular, the novel sLpl(AB)-LipS1/S2 pathway, and indicated a highly modular nature of the enzymes involved, with unforeseen combinations, but also provided a new framework for the evolution of lipoate assembly. Our results show that dedicated machineries for both de novo lipoate biogenesis and scavenging from the environment were implemented early in evolution and that their distribution in the 2 prokaryotic domains was shaped by a complex network of horizontal gene transfers, acquisition of additional genes, fusions, and losses. Our large-scale phylogenetic analyses identify the bipartite archaeal LplAB ligase as the ancestor of the bacterial sLpl(AB) proteins, which were obtained by horizontal gene transfer. LipS1/S2 have a more complex evolutionary history with multiple of such events but probably also originated in the domain archaea.},
}
@article {pmid37367622,
year = {2023},
author = {van der Walt, D and Steenkamp, ET and Wingfield, BD and Wilken, PM},
title = {Evidence of Biparental Mitochondrial Inheritance from Self-Fertile Crosses between Closely Related Species of Ceratocystis.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {6},
pages = {},
pmid = {37367622},
issn = {2309-608X},
abstract = {Hybridization is recognized as a notable driver of evolution and adaptation, which closely related species may exploit in the form of incomplete reproductive barriers. Three closely related species of Ceratocystis (i.e., C. fimbriata, C. manginecans and C. eucalypticola) have previously been shown to hybridize. In such studies, naturally occurring self-sterile strains were mated with an unusual laboratory-generated sterile isolate type, which could have impacted conclusions regarding the prevalence of hybridization and inheritance of mitochondria. In the current study, we investigated whether interspecific crosses between fertile isolates of these three species are possible and, if so, how mitochondria are inherited by the progeny. For this purpose, a PCR-RFLP method and a mitochondrial DNA-specific PCR technique were custom-made. These were applied in a novel approach of typing complete ascospore drops collected from the fruiting bodies in each cross to distinguish between self-fertilizations and potential hybridization. These markers showed hybridization between C. fimbriata and C. eucalypticola and between C. fimbriata and C. manginecans, while no hybridization was detected in the crosses involving C. manginecans and C. eucalypticola. In both sets of hybrid progeny, we detected biparental inheritance of mitochondria. This study was the first to successfully produce hybrids from a cross involving self-fertile isolates of Ceratocystis and also provided the first direct evidence of biparental mitochondrial inheritance in the Ceratocystidaceae. This work lays the foundation for further research focused on investigating the role of hybridization in the speciation of Ceratocystis species and if mitochondrial conflict could have influenced the process.},
}
@article {pmid37364695,
year = {2023},
author = {Barrera, CA and Ortega, J and Gutierrez-Guerrero, YT and Baeza, JA},
title = {Comparative mitochondrial genomics of American nectar-feeding long-nosed bats Leptonycteris spp. with insights into the phylogeny of the family Phyllostomidae.},
journal = {Gene},
volume = {879},
number = {},
pages = {147588},
doi = {10.1016/j.gene.2023.147588},
pmid = {37364695},
issn = {1879-0038},
mesh = {Animals ; Phylogeny ; *Chiroptera/genetics ; Plant Nectar ; Genomics ; Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; RNA, Transfer/genetics ; },
abstract = {Among leaf-nosed bats (family Phyllostomidae), the genus Leptonycteris (subfamily Glossophaginae), contains three migratory and obligate nectar-dwelling species of great ecological and economic importance; the greater long-nosed bat L. nivalis, the lesser long-nosed bat L. yerbabuenae, and the southern long-nosed bat L. curasoae. According to the IUCN, the three species are categorized as 'vulnerable', 'endangered', and 'near threatened', respectively. In this study, we assembled and characterized in detail the mitochondrial genome of Leptonycteris spp. and examined the phylogenetic position of this genus in the family Phyllostomidae based on protein coding genes (PCGs). The mitogenomes of L. nivalis, L. curasoae, and L. yerbabuenae are 16,708, 16,758, and 16,729 bp in length and each encode 13 PCGs, 22 transfer RNA genes, 2 rRNA genes, and a putative control region (CR). Mitochondrial gene order is identical to that reported before for the family Phyllostomidae. All tRNAs exhibit a 'cloverleaf' secondary structure, except tRNA-Serine-1 that is missing the DHU arm in the three species. All PCGs are exposed to purifying selection with atp8 experiencing the most relaxed purifying selection as the ω ratio was higher for this gene compared to the other PCGs in each species. The CR of each species contains three functional domains: extended termination associated sequence (ETAS), Central, and conserved sequence block domain (CSB). A phylomitogenomic analysis revealed that Leptonycteris is monophyletic and most closely related to the genus Glossophaga. The analysis also supported the monophyly of the family Glossophaginae in the speciose family Phyllostomidae. The mitochondria characterization of these species provides relevant information to develop molecular markers for conservation purposes.},
}
@article {pmid37364099,
year = {2023},
author = {Lynch, M},
title = {Mutation pressure, drift, and the pace of molecular coevolution.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {27},
pages = {e2306741120},
pmid = {37364099},
issn = {1091-6490},
support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; R35-GM122566-01/NH/NIH HHS/United States ; },
mesh = {*Evolution, Molecular ; Mutation ; *Mutation Rate ; Genome ; Genetic Drift ; },
abstract = {Most aspects of the molecular biology of cells involve tightly coordinated intermolecular interactions requiring specific recognition at the nucleotide and/or amino acid levels. This has led to long-standing interest in the degree to which constraints on interacting molecules result in conserved vs. accelerated rates of sequence evolution, with arguments commonly being made that molecular coevolution can proceed at rates exceeding the neutral expectation. Here, a fairly general model is introduced to evaluate the degree to which the rate of evolution at functionally interacting sites is influenced by effective population sizes (Ne), mutation rates, strength of selection, and the magnitude of recombination between sites. This theory is of particular relevance to matters associated with interactions between organelle- and nuclear-encoded proteins, as the two genomic environments often exhibit dramatic differences in the power of mutation and drift. Although genes within low Ne environments can drive the rate of evolution of partner genes experiencing higher Ne, rates exceeding the neutral expectation require that the former also have an elevated mutation rate. Testable predictions, some counterintuitive, are presented on how patterns of coevolutionary rates should depend on the relative intensities of drift, selection, and mutation.},
}
@article {pmid37338543,
year = {2023},
author = {Wong, JE and Zíková, A and Gahura, O},
title = {The Ancestral Shape of the Access Proton Path of Mitochondrial ATP Synthases Revealed by a Split Subunit-a.},
journal = {Molecular biology and evolution},
volume = {40},
number = {6},
pages = {},
pmid = {37338543},
issn = {1537-1719},
mesh = {*Mitochondrial Proton-Translocating ATPases/genetics/chemistry/metabolism ; *Proton-Translocating ATPases/metabolism ; Protons ; Eukaryota/metabolism ; Escherichia coli/genetics/metabolism ; Adenosine Triphosphate/metabolism ; },
abstract = {The passage of protons across membranes through F1Fo-ATP synthases spins their rotors and drives the synthesis of ATP. While the principle of torque generation by proton transfer is known, the mechanisms and routes of proton access and release and their evolution are not fully understood. Here, we show that the entry site and path of protons in the lumenal half channel of mitochondrial ATP synthases are largely defined by a short N-terminal α-helix of subunit-a. In Trypanosoma brucei and other Euglenozoa, the α-helix is part of another polypeptide chain that is a product of subunit-a gene fragmentation. This α-helix and other elements forming the proton pathway are widely conserved across eukaryotes and in Alphaproteobacteria, the closest extant relatives of mitochondria, but not in other bacteria. The α-helix blocks one of two proton routes found in Escherichia coli, resulting in a single proton entry site in mitochondrial and alphaproteobacterial ATP synthases. Thus, the shape of the access half channel predates eukaryotes and originated in the lineage from which mitochondria evolved by endosymbiosis.},
}
@article {pmid37336341,
year = {2023},
author = {Liu, S and Xu, S and Liu, S and Chen, H},
title = {Importance of DJ-1 in autophagy regulation and disease.},
journal = {Archives of biochemistry and biophysics},
volume = {743},
number = {},
pages = {109672},
doi = {10.1016/j.abb.2023.109672},
pmid = {37336341},
issn = {1096-0384},
mesh = {Humans ; Reactive Oxygen Species/metabolism ; *Oxidative Stress/physiology ; Hypoxia/metabolism ; *Neoplasms ; Autophagy/physiology ; Protein Deglycase DJ-1/metabolism ; },
abstract = {Autophagy is a highly conserved biological process that has evolved across evolution. It can be activated by various external stimuli including oxidative stress, amino acid starvation, infection, and hypoxia. Autophagy is the primary mechanism for preserving cellular homeostasis and is implicated in the regulation of metabolism, cell differentiation, tolerance to starvation conditions, and resistance to aging. As a multifunctional protein, DJ-1 is commonly expressed in vivo and is associated with a variety of biological processes. Its most widely studied role is its function as an oxidative stress sensor that inhibits the production of excessive reactive oxygen species (ROS) in the mitochondria and subsequently the cellular damage caused by oxidative stress. In recent years, many studies have identified DJ-1 as another important factor regulating autophagy; it regulates autophagy in various ways, most commonly by regulating the oxidative stress response. In particular, DJ-1-regulated autophagy is involved in cancer progression and plays a key role in alleviating neurodegenerative diseases(NDS) and defective reperfusion diseases. It could serve as a potential target for the regulation of autophagy and participate in disease treatment as a meaningful modality. Therefore, exploring DJ-1-regulated autophagy could provide new avenues for future disease treatment.},
}
@article {pmid37333265,
year = {2023},
author = {Hanson, SE and Doyle, MT and Bernstein, HD},
title = {The patatin-like protein PlpD forms novel structurally dynamic homodimers in the Pseudomonas aeruginosa outer membrane.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37333265},
issn = {2692-8205},
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 found 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.},
}
@article {pmid37330026,
year = {2023},
author = {Nguyen, TP and Nguyen, BT and Dao, TNL and Ho, TH and Lee, PT},
title = {Investigation of the functional role of UNC93B1 in Nile tilapia (Oreochromis niloticus): mRNA expression, subcellular localization, and physical interaction with fish-specific TLRs.},
journal = {Fish &amp; shellfish immunology},
volume = {139},
number = {},
pages = {108902},
doi = {10.1016/j.fsi.2023.108902},
pmid = {37330026},
issn = {1095-9947},
mesh = {Humans ; Animals ; Mice ; *Cichlids ; Phylogeny ; Fish Proteins/chemistry ; Toll-Like Receptors/genetics/metabolism ; Phagocytosis ; Streptococcus agalactiae/physiology ; *Fish Diseases ; *Streptococcal Infections/veterinary ; Gene Expression Regulation ; Immunity, Innate/genetics ; Membrane Transport Proteins/genetics ; },
abstract = {Nile tilapia (Oreochromis niloticus) is one of the major food fish worldwide. The farming business, on the other hand, has faced considerable obstacles, such as disease infestations. Toll-like receptors (TLRs) play an important function in the activation of the innate immune system in response to infections. Unc-93 homolog B1 (UNC93B1) is a key regulator of nucleic acid (NA)-sensing TLRs. Here the UNC93B1 gene, which was cloned from Nile tilapia tissue for this investigation, had the same genetic structure as a homologous gene in humans and mice. Phylogenetic analysis revealed that Nile tilapia UNC93B1 clustered with UNC93B1 from other species and separately from the UNC93A clade. The gene structure of the Nile tilapia UNC93B1 was found to be identical to that of human UNC93B1. Our gene expression studies revealed that Nile tilapia UNC93B1 was highly expressed in the spleen, followed by other immune-related tissues such as the head kidney, gills, and intestine. Moreover, Nile tilapia UNC93B1 mRNA transcripts were up-regulated in vivo in the head kidney and spleen tissues from poly I:C and Streptococcus agalactiae injected Nile tilapia, as well as in vitro in LPS stimulated Tilapia head kidney (THK) cells. The Nile tilapia UNC93B1-GFP protein signal was detected in the cytosol of THK cells and was co-localized with endoplasmic reticulum and lysosome but not with mitochondria. Moreover, the results of a co-immunoprecipitation and immunostaining analysis showed that Nile tilapia UNC93B1 can be pulled down with fish-specific TLRs such as TLR18 and TLR25 from Nile tilapia, and was found to be co-localized with these fish-specific TLRs in the THK cells. Overall, our findings highlight the potential role of UNC93B1 as an accessory protein in fish-specific TLR signaling.},
}
@article {pmid37327832,
year = {2023},
author = {Thacker, CE and Tyler McCraney, W and Harrington, RC and Near, TJ and Shelley, JJ and Adams, M and Hammer, MP and Unmack, PJ},
title = {Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families.},
journal = {Molecular phylogenetics and evolution},
volume = {186},
number = {},
pages = {107841},
doi = {10.1016/j.ympev.2023.107841},
pmid = {37327832},
issn = {1095-9513},
mesh = {Humans ; Animals ; Phylogeny ; *Fishes/genetics ; *Perciformes/genetics ; Mitochondria ; Fossils ; },
abstract = {Eleotridae (sleepers) and five smaller families are the earliest diverging lineages within Gobioidei. Most inhabit freshwaters in and around the Indo-Pacific, but Eleotridae also includes species that have invaded the Neotropics as well as several inland radiations in the freshwaters of Australia, New Zealand, and New Guinea. Previous efforts to infer phylogeny of these families have been based on sets of mitochondrial or nuclear loci and have yielded uncertain resolution of clades within Eleotridae. We expand the taxon sampling of previous studies and use genomic data from nuclear ultraconserved elements (UCEs) to infer phylogeny, then calibrate the hypothesis with recently discovered fossils. Our hypothesis clarifies ambiguously resolved relationships, provides a timescale for divergences, and indicates the core crown Eleotridae diverged over a short period 24.3-26.3 Ma in the late Oligocene. Within Eleotridae, we evaluate diversification dynamics with BAMM and find evidence for an overall slowdown in diversification over the past 35 Ma, but with a sharp increase 3.5 Ma in the genus Mogurnda, a clade of brightly colored species found in the freshwaters of Australia and New Guinea.},
}
@article {pmid37325898,
year = {2023},
author = {Sabbah, HN and Taylor, C and Vernon, HJ},
title = {Temporal evolution of the heart failure phenotype in Barth syndrome and treatment with elamipretide.},
journal = {Future cardiology},
volume = {19},
number = {4},
pages = {211-225},
doi = {10.2217/fca-2023-0008},
pmid = {37325898},
issn = {1744-8298},
mesh = {Humans ; *Barth Syndrome/genetics/pathology ; *Heart Failure/drug therapy ; Stroke Volume ; Phenotype ; Cardiolipins ; },
abstract = {Barth syndrome (BTHS) is a rare genetic disorder caused by pathogenic variants in TAFAZZIN leading to reduced remodeled cardiolipin (CL), a phospholipid essential to mitochondrial function and structure. Cardiomyopathy presents in most patients with BTHS, typically appearing as dilated cardiomyopathy (DCM) in infancy and evolving to hypertrophic cardiomyopathy (HCM) resembling heart failure (HF) with preserved ejection fraction (HFpEF) in some patients ≥12 years. Elamipretide localizes to the inner mitochondrial membrane where it associates with CL, improving mitochondrial function, structure and bioenergetics, including ATP synthesis. Numerous preclinical and clinical studies in BTHS and other forms of HF have demonstrated that elamipretide improves left ventricular relaxation by ameliorating mitochondrial dysfunction, making it well suited for therapeutic use in adolescent and adult patients with BTHS.},
}
@article {pmid37311262,
year = {2023},
author = {Annes, K and Ferreira, CR and Valente, RS and Marsico, TV and Tannura, JH and da Silveira, JC and Silva, FH and Landim-Alvarenga, FDC and Mesquista, FS and Sudano, MJ},
title = {Contribution of lipids to the organelle differential profile of in vitro-produced bovine embryos.},
journal = {Theriogenology},
volume = {208},
number = {},
pages = {109-118},
doi = {10.1016/j.theriogenology.2023.06.005},
pmid = {37311262},
issn = {1879-3231},
mesh = {Female ; Pregnancy ; Cattle ; Animals ; *Endoplasmic Reticulum ; *Mitochondria ; Lipid Droplets ; Blastocyst ; Ceramides ; },
abstract = {Each living organism is unique because of the lipid identity of its organelles. The diverse distribution of these molecules also contributes to the role of each organelle in cellular activity. The lipid profiles of whole embryos are well documented in the literature. However, this approach can often lead to the loss of relevant information at the subcellular and consequently, metabolic levels, hindering a deeper understanding of key physiological processes during preimplantation development. Therefore, we aimed to characterize four organelles in vitro-produced bovine embryos: lipid droplets (LD), endoplasmic reticulum (ER), mitochondria (MIT), and nuclear membrane (NUC), and evaluate the contribution of the lipid species to each organelle evaluated. Expanded blastocysts were subjected to cell organelle isolation. Thereafter, lipid extraction from cell organelles and lipid analysis using the Multiple Reaction Monitoring (MRM) profiling method were performed. The LD and ER displayed a greater number of lipids (Phosphatidylcholine - PC, Ceramide - Cer, and Sphingomielin - SM) with high signal-to-noise intensities. This result is due to the high rate of biosynthesis, lipid distribution, and ability to store and recycle lipid species of these organelles. The NUC had a more distinct lipid profile than the other three organelles, with high relative intensities of PC, SM, and triacylglycerols (TG), which is consistent with its high nuclear activity. MIT had an intermediate profile that was close to that of LD and ER, which aligns with its autonomous metabolism for some classes of phospholipids (PL). Our study revealed the lipid composition of each organelle studied, and the roles of these lipids could be associated with the characteristic organellar activity. Our findings highlight the lipid species and classes that are relevant for the homeostasis and function of each associated organelle and provide tentative biomarkers for the determination of in vitro embryonic development and quality.},
}
@article {pmid37305924,
year = {2023},
author = {Floriano, AM and Batisti Biffignandi, G and Castelli, M and Olivieri, E and Clementi, E and Comandatore, F and Rinaldi, L and Opara, M and Plantard, O and Palomar, AM and Noël, V and Vijay, A and Lo, N and Makepeace, BL and Duron, O and Jex, A and Guy, L and Sassera, D},
title = {The evolution of intramitochondriality in Midichloria bacteria.},
journal = {Environmental microbiology},
volume = {25},
number = {11},
pages = {2102-2117},
doi = {10.1111/1462-2920.16446},
pmid = {37305924},
issn = {1462-2920},
mesh = {Animals ; *Ixodes/microbiology ; Bacteria/genetics ; Mitochondria/genetics ; Phylogeny ; Symbiosis ; },
abstract = {Midichloria spp. are intracellular bacterial symbionts of ticks. Representatives of this genus colonise mitochondria in the cells of their hosts. To shed light on this unique interaction we evaluated the presence of an intramitochondrial localization for three Midichloria in the respective tick host species and generated eight high-quality draft genomes and one closed genome, showing that this trait is non-monophyletic, either due to losses or multiple acquisitions. Comparative genomics supports the first hypothesis, as the genomes of non-mitochondrial symbionts are reduced subsets of those capable of colonising the organelles. We detect genomic signatures of mitochondrial tropism, including the differential presence of type IV secretion system and flagellum, which could allow the secretion of unique effectors and/or direct interaction with mitochondria. Other genes, including adhesion molecules, proteins involved in actin polymerisation, cell wall and outer membrane proteins, are only present in mitochondrial symbionts. The bacteria could use these to manipulate host structures, including mitochondrial membranes, to fuse with the organelles or manipulate the mitochondrial network.},
}
@article {pmid37303610,
year = {2023},
author = {Liang, Y and Fang, X and Zheng, L and Wu, H and He, Z and Xiong, Z and Hong, J and Ai, X and Liang, G},
title = {The complete mitochondrial genome of Choristoneura metasequoiacola Liu,1983 (Lepidoptera: Tortricidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {8},
number = {6},
pages = {653-657},
pmid = {37303610},
issn = {2380-2359},
abstract = {Choristoneura metasequoiacola Liu, 1983 is an important caterpillar species that specifically infests the leaves and branches of Metasequoia glyptostroboides Hu &amp; W. C. Cheng 1948 with short larval infestations, long-term dormancy, and has a limited distribution in Lichuan, Hubei, China. The complete mitochondria genome of C. metasequoiacola was determined by using Illumina NovaSeq, and analyzed based on previously annotated sibling species. In total, we obtained mitochondria genome with 15,128 bp in length, circular in shape with a double-stranded closed ring structure, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and an AT-rich region. Of which the nucleotide composition was highly A + T biased, accounting for 81.98% of the whole mitogenome. Thirteen protein-coding genes (PCGs) were 11,142 bp; Twenty-two tRNA genes and AT-rich region were 1,472 and 199 bp, respectively. Phylogenetically, the relationship between Choristoneura spp. (containing C. metasequoiacola) and Adoxophyes spp. was closer than any other two genera from Tortricidae, and the relationship between C. metasequoiacola and C.murinana was the closest among nine sibling species from that genus, which helps to explain species evolution within the family Tortricidae.},
}
@article {pmid37299482,
year = {2023},
author = {Manilla, V and Santopaolo, F and Gasbarrini, A and Ponziani, FR},
title = {Type 2 Diabetes Mellitus and Liver Disease: Across the Gut-Liver Axis from Fibrosis to Cancer.},
journal = {Nutrients},
volume = {15},
number = {11},
pages = {},
pmid = {37299482},
issn = {2072-6643},
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Diabetes Mellitus, Type 2/complications/pathology ; *Carcinoma, Hepatocellular/metabolism ; Dysbiosis/complications/pathology ; *Liver Neoplasms/metabolism ; Liver/metabolism ; Liver Cirrhosis ; Fibrosis ; },
abstract = {Type 2 diabetes mellitus is a widespread disease worldwide, and is one of the cornerstones of metabolic syndrome. The existence of a strong relationship between diabetes and the progression of liver fibrosis has been demonstrated by several studies, using invasive and noninvasive techniques. Patients with type 2 diabetes mellitus (T2DM) and nonalcoholic fatty liver disease (NAFLD) show faster progression of fibrosis than patients without diabetes. Many confounding factors make it difficult to determine the exact mechanisms involved. What we know so far is that both liver fibrosis and T2DM are expressions of metabolic dysfunction, and we recognize similar risk factors. Interestingly, both are promoted by metabolic endotoxemia, a low-grade inflammatory condition caused by increased endotoxin levels and linked to intestinal dysbiosis and increased intestinal permeability. There is broad evidence on the role of the gut microbiota in the progression of liver disease, through both metabolic and inflammatory mechanisms. Therefore, dysbiosis that is associated with diabetes can act as a modifier of the natural evolution of NAFLD. In addition to diet, hypoglycemic drugs play an important role in this scenario, and their benefit is also the result of effects exerted in the gut. Here, we provide an overview of the mechanisms that explain why diabetic patients show a more rapid progression of liver disease up to hepatocellular carcinoma (HCC), focusing especially on those involving the gut-liver axis.},
}
@article {pmid37295735,
year = {2023},
author = {Gul, I and Abbas, MN and Kausar, S and Luo, J and Gao, X and Mu, Y and Fan, W and Cui, H},
title = {Insight into crustacean cathepsins: Structure-evolutionary relationships and functional roles in physiological processes.},
journal = {Fish &amp; shellfish immunology},
volume = {139},
number = {},
pages = {108852},
doi = {10.1016/j.fsi.2023.108852},
pmid = {37295735},
issn = {1095-9947},
mesh = {Animals ; *Cathepsins/genetics/chemistry ; Proteins ; Biological Evolution ; *Physiological Phenomena ; },
abstract = {Cathepsins belong to a group of proteins that are present in both prokaryotic and eukaryotic organisms and have an extremely high degree of evolutionary conservation. These proteins are functionally active in extracellular environments as soluble enzymatic proteins or attached to plasma membrane receptors. In addition, they occur in cellular secretory vesicles, mitochondria, the cytosol, and within the nuclei of eukaryotic cells. Cathepsins are classified into various groups based on their sequence variations, leading to their structural and functional diversification. The molecular understanding of the physiology of crustaceans has shown that proteases, including cathepsins, are expressed ubiquitously. They also contain one of the central regulatory systems for crustacean reproduction, growth, and immune responses. This review focuses on various aspects of the crustaceans cathepsins and emphasizes their biological roles in different physiological processes such as reproduction, growth, development, and immune responses. We also describe the bioactivity of crustaceans cathepsins. Because of the vital biological roles that cathepsins play as cellular proteases in physiological processes, they have been proposed as potential novel targets for the development of management strategies for the aquaculture industries.},
}
@article {pmid37291154,
year = {2023},
author = {Lee, Y and Cho, CH and Noh, C and Yang, JH and Park, SI and Lee, YM and West, JA and Bhattacharya, D and Jo, K and Yoon, HS},
title = {Origin of minicircular mitochondrial genomes in red algae.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3363},
pmid = {37291154},
issn = {2041-1723},
mesh = {Phylogeny ; *Genome, Mitochondrial/genetics ; Eukaryotic Cells ; Mitochondria/genetics ; *Rhodophyta/genetics ; Evolution, Molecular ; },
abstract = {Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.},
}
@article {pmid37289794,
year = {2023},
author = {Hebert, PDN and Bock, DG and Prosser, SWJ},
title = {Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness.},
journal = {PloS one},
volume = {18},
number = {6},
pages = {e0286620},
pmid = {37289794},
issn = {1932-6203},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Genome, Insect ; Mitochondria/genetics ; Insecta/genetics ; Risk Assessment ; Cell Nucleus/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.},
}
@article {pmid37286063,
year = {2023},
author = {Abalde, S and Crocetta, F and Tenorio, MJ and D'Aniello, S and Fassio, G and Rodríguez-Flores, PC and Uribe, JE and Afonso, CML and Oliverio, M and Zardoya, R},
title = {Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus.},
journal = {Molecular phylogenetics and evolution},
volume = {186},
number = {},
pages = {107838},
doi = {10.1016/j.ympev.2023.107838},
pmid = {37286063},
issn = {1095-9513},
mesh = {Humans ; Animals ; Phylogeny ; *Mitochondria/genetics ; Genetic Speciation ; *Genome, Mitochondrial ; Snails/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red + blue + orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.},
}
@article {pmid37279941,
year = {2023},
author = {Sheikh, S and Pánek, T and Gahura, O and Týč, J and Záhonová, K and Lukeš, J and Eliáš, M and Hashimi, H},
title = {A Novel Group of Dynamin-Related Proteins Shared by Eukaryotes and Giant Viruses Is Able to Remodel Mitochondria From Within the Matrix.},
journal = {Molecular biology and evolution},
volume = {40},
number = {6},
pages = {},
pmid = {37279941},
issn = {1537-1719},
mesh = {*Giant Viruses/genetics/metabolism ; Phylogeny ; Mitochondrial Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; Dynamins/genetics/metabolism ; Saccharomyces cerevisiae/genetics ; },
abstract = {The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, which remodel the mitochondrial inner membrane in fungi and metazoans, respectively. Via an exhaustive search of genomic and metagenomic databases, we found previously unknown DRP types occurring in diverse eukaryotes and giant viruses (phylum Nucleocytoviricota). One novel DRP clade, termed MidX, combined hitherto uncharacterized proteins from giant viruses and six distantly related eukaryote taxa (Stramenopiles, Telonemia, Picozoa, Amoebozoa, Apusomonadida, and Choanoflagellata). MidX stood out because it was not only predicted to be mitochondria-targeted but also to assume a tertiary structure not observed in other DRPs before. To understand how MidX affects mitochondria, we exogenously expressed MidX from Hyperionvirus in the kinetoplastid Trypanosoma brucei, which lacks Mgm1 or Opa1 orthologs. MidX massively affected mitochondrial morphology from inside the matrix, where it closely associates with the inner membrane. This unprecedented mode of action contrasts to those of Mgm1 and Opa1, which mediate inner membrane remodeling in the intermembrane space. We speculate that MidX was acquired in Nucleocytoviricota evolution by horizontal gene transfer from eukaryotes and is used by giant viruses to remodel host mitochondria during infection. MidX's unique structure may be an adaptation for reshaping mitochondria from the inside. Finally, Mgm1 forms a sister group to MidX and not Opa1 in our phylogenetic analysis, throwing into question the long-presumed homology of these DRPs with similar roles in sister lineages.},
}
@article {pmid37278219,
year = {2023},
author = {Markaki, M and Tsagkari, D and Tavernarakis, N},
title = {Mitophagy and long-term neuronal homeostasis.},
journal = {Journal of cell science},
volume = {136},
number = {11},
pages = {},
doi = {10.1242/jcs.260638},
pmid = {37278219},
issn = {1477-9137},
support = {ERC-GA695190-MANNA/ERC_/European Research Council/International ; },
mesh = {Humans ; *Mitophagy/physiology ; Autophagy/physiology ; Neurons/metabolism ; *Neurodegenerative Diseases/metabolism ; Homeostasis ; },
abstract = {Neurons are highly polarized, post-mitotic cells that are characterized by unique morphological diversity and complexity. As highly differentiated cells that need to survive throughout organismal lifespan, neurons face exceptional energy challenges in time and space. Therefore, neurons are heavily dependent on a healthy mitochondrial network for their proper function and maintenance under both physiological and stress conditions. Multiple quality control systems have evolved to fine-tune mitochondrial number and quality, thus preserving neuronal energy homeostasis. Here, we review the contribution of mitophagy, a selective form of autophagy that targets dysfunctional or superfluous mitochondria for degradation, in maintaining nervous system homeostasis. In addition, we discuss recent evidence implicating defective or dysregulated mitophagy in the pathogenesis of neurodegenerative diseases.},
}
@article {pmid37277654,
year = {2023},
author = {Devant, P and Kagan, JC},
title = {Molecular mechanisms of gasdermin D pore-forming activity.},
journal = {Nature immunology},
volume = {24},
number = {7},
pages = {1064-1075},
pmid = {37277654},
issn = {1529-2916},
mesh = {*Intracellular Signaling Peptides and Proteins/genetics/metabolism ; *Gasdermins ; Pyroptosis ; Interleukin-1/metabolism ; Cell Membrane/metabolism ; Inflammasomes/metabolism ; },
abstract = {The regulated disruption of the plasma membrane, which can promote cell death, cytokine secretion or both is central to organismal health. The protein gasdermin D (GSDMD) is a key player in this process. GSDMD forms membrane pores that can promote cytolysis and the release of interleukin-1 family cytokines into the extracellular space. Recent discoveries have revealed biochemical and cell biological mechanisms that control GSDMD pore-forming activity and its diverse downstream immunological effects. Here, we review these multifaceted regulatory activities, including mechanisms of GSDMD activation by proteolytic cleavage, dynamics of pore assembly, regulation of GSDMD activities by posttranslational modifications, membrane repair and the interplay of GSDMD and mitochondria. We also address recent insights into the evolution of the gasdermin family and their activities in species across the kingdoms of life. In doing so, we hope to condense recent progress and inform future studies in this rapidly moving field in immunology.},
}
@article {pmid37276405,
year = {2023},
author = {Kumar, P and Babu, KSD and Singh, AK and Singh, DK and Nalli, A and Mukul, SJ and Roy, A and Mazeed, M and Raman, B and Kruparani, SP and Siddiqi, I and Sankaranarayanan, R},
title = {Distinct localization of chiral proofreaders resolves organellar translation conflict in plants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {24},
pages = {e2219292120},
pmid = {37276405},
issn = {1091-6490},
mesh = {*Organelles/metabolism ; Mitochondria/metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Chloroplasts/metabolism ; RNA, Transfer/metabolism ; *Arabidopsis/genetics ; },
abstract = {Plants have two endosymbiotic organelles originated from two bacterial ancestors. The transition from an independent bacterium to a successful organelle would have required extensive rewiring of biochemical networks for its integration with archaeal host. Here, using Arabidopsis as a model system, we show that plant D-aminoacyl-tRNA deacylase 1 (DTD1), of bacterial origin, is detrimental to organellar protein synthesis owing to its changed tRNA recognition code. Plants survive this conflict by spatially restricting the conflicted DTD1 to the cytosol. In addition, plants have targeted archaeal DTD2 to both the organelles as it is compatible with their translation machinery due to its strict D-chiral specificity and lack of tRNA determinants. Intriguingly, plants have confined bacterial-derived DTD1 to work in archaeal-derived cytosolic compartment whereas archaeal DTD2 is targeted to bacterial-derived organelles. Overall, the study provides a remarkable example of the criticality of optimization of biochemical networks for survival and evolution of plant mitochondria and chloroplast.},
}
@article {pmid37275157,
year = {2023},
author = {Himmelstrand, K and Brandström Durling, M and Karlsson, M and Stenlid, J and Olson, &#xc5;},
title = {Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1159811},
pmid = {37275157},
issn = {1664-302X},
abstract = {INTRODUCTION: Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species.<br><br>METHODS: In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers.<br><br>RESULTS AND DISCUSSION: Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.},
}
@article {pmid37269314,
year = {2023},
author = {Patriarcheas, D and Momtareen, T and Gallagher, JEG},
title = {Yeast of Eden: microbial resistance to glyphosate from a yeast perspective.},
journal = {Current genetics},
volume = {69},
number = {4-6},
pages = {203-212},
pmid = {37269314},
issn = {1432-0983},
support = {R03 ES034881/ES/NIEHS NIH HHS/United States ; NIH NIEHS R03 ES034881/NH/NIH HHS/United States ; NIH NIEHS R03 ES034881/NH/NIH HHS/United States ; },
mesh = {Saccharomyces cerevisiae/genetics/metabolism ; *Herbicides/pharmacology ; Glycine/pharmacology/metabolism ; Plants ; Amino Acids, Aromatic ; },
abstract = {First marketed as RoundUp, glyphosate is history's most popular herbicide because of its low acute toxicity to metazoans and broad-spectrum effectiveness across plant species. The development of glyphosate-resistant crops has led to increased glyphosate use and consequences from the use of glyphosate-based herbicides (GBH). Glyphosate has entered the food supply, spurred glyphosate-resistant weeds, and exposed non-target organisms to glyphosate. Glyphosate targets EPSPS/AroA/Aro1 (orthologs across plants, bacteria, and fungi), the rate-limiting step in the production of aromatic amino acids from the shikimate pathway. Metazoans lacking this pathway are spared from acute toxicity and acquire their aromatic amino acids from their diet. However, glyphosate resistance is increasing in non-target organisms. Mutations and natural genetic variation discovered in Saccharomyces cerevisiae illustrate similar types of glyphosate resistance mechanisms in fungi, plants, and bacteria, in addition to known resistance mechanisms such as mutations in Aro1 that block glyphosate binding (target-site resistance (TSR)) and mutations in efflux drug transporters non-target-site resistance (NTSR). Recently, genetic variation and mutations in an amino transporter affecting glyphosate resistance have uncovered potential off-target effects of glyphosate in fungi and bacteria. While glyphosate is a glycine analog, it is transported into cells using an aspartic/glutamic acid (D/E) transporter. The size, shape, and charge distribution of glyphosate closely resembles D/E, and, therefore, glyphosate is a D/E amino acid mimic. The mitochondria use D/E in several pathways and mRNA-encoding mitochondrial proteins are differentially expressed during glyphosate exposure. Mutants downstream of Aro1 are not only sensitive to glyphosate but also a broad range of other chemicals that cannot be rescued by exogenous supplementation of aromatic amino acids. Glyphosate also decreases the pH when unbuffered and many studies do not consider the differences in pH that affect toxicity and resistance mechanisms.},
}
@article {pmid37268349,
year = {2023},
author = {Pellielo, G and Agyapong, ED and Pinton, P and Rimessi, A},
title = {Control of mitochondrial functions by Pseudomonas aeruginosa in cystic fibrosis.},
journal = {International review of cell and molecular biology},
volume = {377},
number = {},
pages = {19-43},
doi = {10.1016/bs.ircmb.2023.03.008},
pmid = {37268349},
issn = {1937-6448},
mesh = {Humans ; *Cystic Fibrosis ; Pseudomonas aeruginosa/physiology ; Persistent Infection ; Inflammation/genetics ; Mitochondria ; },
abstract = {Cystic fibrosis (CF) is a genetic disease characterized by mutations of cystic fibrosis transmembrane conductance regulator (CFTR) gene, which lead to a dysfunctional chloride and bicarbonate channel. Abnormal mucus viscosity, persistent infections and hyperinflammation that preferentially affect the airways, referred to the pathogenesis of CF lung disease. It has largely demonstrated that Pseudomonas aeruginosa (P. aeruginosa) represents the most important pathogen that affect CF patients, leading to worsen inflammation by stimulating pro-inflammatory mediators release and tissue destruction. The conversion to mucoid phenotype and formation of biofilms, together with the increased frequency of mutations, are only few changes that characterize the P. aeruginosa's evolution during CF lung chronic infection. Recently, mitochondria received increasing attention due to their involvement in inflammatory-related diseases, including in CF. Alteration of mitochondrial homeostasis is sufficient to stimulate immune response. Exogenous or endogenous stimuli that perturb mitochondrial activity are used by cells, which, through the mitochondrial stress, potentiate immunity programs. Studies show the relationship between mitochondria and CF, supporting the idea that mitochondrial dysfunction endorses the exacerbation of inflammatory responses in CF lung. In particular, evidences suggest that mitochondria in CF airway cells are more susceptible to P. aeruginosa infection, with consequent detrimental effects that lead to amplify the inflammatory signals. This review discusses the evolution of P. aeruginosa in relationship with the pathogenesis of CF, a fundamental step to establish chronic infection in CF lung disease. Specifically, we focus on the role of P. aeruginosa in the exacerbation of inflammatory response, by triggering mitochondria in CF.},
}
@article {pmid37267944,
year = {2023},
author = {Záhonová, K and Low, RS and Warren, CJ and Cantoni, D and Herman, EK and Yiangou, L and Ribeiro, CA and Phanprasert, Y and Brown, IR and Rueckert, S and Baker, NL and Tachezy, J and Betts, EL and Gentekaki, E and van der Giezen, M and Clark, CG and Jackson, AP and Dacks, JB and Tsaousis, AD},
title = {Evolutionary analysis of cellular reduction and anaerobicity in the hyper-prevalent gut microbe Blastocystis.},
journal = {Current biology : CB},
volume = {33},
number = {12},
pages = {2449-2464.e8},
doi = {10.1016/j.cub.2023.05.025},
pmid = {37267944},
issn = {1879-0445},
mesh = {Animals ; Humans ; *Blastocystis/genetics ; *Gastrointestinal Microbiome/genetics ; Mitochondria/genetics/metabolism ; Organelles/metabolism ; Eukaryota ; },
abstract = {Blastocystis is the most prevalent microbial eukaryote in the human and animal gut, yet its role as commensal or parasite is still under debate. Blastocystis has clearly undergone evolutionary adaptation to the gut environment and possesses minimal cellular compartmentalization, reduced anaerobic mitochondria, no flagella, and no reported peroxisomes. To address this poorly understood evolutionary transition, we have taken a multi-disciplinary approach to characterize Proteromonas lacertae, the closest canonical stramenopile relative of Blastocystis. Genomic data reveal an abundance of unique genes in P. lacertae but also reductive evolution of the genomic complement in Blastocystis. Comparative genomic analysis sheds light on flagellar evolution, including 37 new candidate components implicated with mastigonemes, the stramenopile morphological hallmark. The P. lacertae membrane-trafficking system (MTS) complement is only slightly more canonical than that of Blastocystis, but notably, we identified that both organisms encode the complete enigmatic endocytic TSET complex, a first for the entire stramenopile lineage. Investigation also details the modulation of mitochondrial composition and metabolism in both P. lacertae and Blastocystis. Unexpectedly, we identify in P. lacertae the most reduced peroxisome-derived organelle reported to date, which leads us to speculate on a mechanism of constraint guiding the dynamics of peroxisome-mitochondrion reductive evolution on the path to anaerobiosis. Overall, these analyses provide a launching point to investigate organellar evolution and reveal in detail the evolutionary path that Blastocystis has taken from a canonical flagellated protist to the hyper-divergent and hyper-prevalent animal and human gut microbe.},
}
@article {pmid37262983,
year = {2023},
author = {Camus, MF and Dhawanjewar, AS},
title = {Multilevel selection on mitochondrial genomes.},
journal = {Current opinion in genetics &amp; development},
volume = {80},
number = {},
pages = {102050},
doi = {10.1016/j.gde.2023.102050},
pmid = {37262983},
issn = {1879-0380},
mesh = {*Genome, Mitochondrial/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Biological Evolution ; Eukaryota/genetics ; Evolution, Molecular ; },
abstract = {Mitochondria are vital organelles for life in eukaryotes, taking centre stage in the process of cellular respiration. This process is regulated via a series of finely coordinated obligate interactions of molecules encoded by two genomes: nuclear DNA and mitochondrial DNA. Both genomes are required to work harmoniously to provide cellular energy, with detrimental consequences occurring when there is miscommunication between them. Whilst the need for cooperation is strong, vast differences between genomes (ploidy, size, and inheritance) create an arena for conflict. Here, we examine the varying levels of selection operating on the mitochondrial genome and the consequences they have on all these levels. We conclude by highlighting the potential for conflict when selection at different levels is driven by different evolutionary forces.},
}
@article {pmid37254790,
year = {2023},
author = {López-García, P and Moreira, D},
title = {The symbiotic origin of the eukaryotic cell.},
journal = {Comptes rendus biologies},
volume = {346},
number = {},
pages = {55-73},
doi = {10.5802/crbiol.118},
pmid = {37254790},
issn = {1768-3238},
mesh = {*Eukaryotic Cells ; *Symbiosis ; Phylogeny ; Archaea/genetics ; Eukaryota/genetics ; Biological Evolution ; },
abstract = {Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.},
}
@article {pmid37249052,
year = {2023},
author = {Chen, Y and Guo, Y and Xie, X and Wang, Z and Miao, L and Yang, Z and Jiao, Y and Xie, C and Liu, J and Hu, Z and Xin, M and Yao, Y and Ni, Z and Sun, Q and Peng, H and Guo, W},
title = {Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae.},
journal = {Plant physiology},
volume = {193},
number = {1},
pages = {578-594},
pmid = {37249052},
issn = {1532-2548},
mesh = {*Poaceae/genetics ; Triticum/genetics ; Genome, Plant/genetics ; *Oryza/genetics ; Zea mays/genetics ; Evolution, Molecular ; },
abstract = {Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.},
}
@article {pmid37239904,
year = {2023},
author = {Rossi, F and Picone, G and Cappadone, C and Sorrentino, A and Columbaro, M and Farruggia, G and Catelli, E and Sciutto, G and Prati, S and Oliete, R and Pasini, A and Pereiro, E and Iotti, S and Malucelli, E},
title = {Shedding Light on Osteosarcoma Cell Differentiation: Impact on Biomineralization and Mitochondria Morphology.},
journal = {International journal of molecular sciences},
volume = {24},
number = {10},
pages = {},
pmid = {37239904},
issn = {1422-0067},
mesh = {Humans ; Osteogenesis ; Biomineralization ; Cell Line, Tumor ; *Osteosarcoma/metabolism ; Cell Differentiation/physiology ; Mitochondria/metabolism ; *Bone Neoplasms/metabolism ; Cell Proliferation/physiology ; },
abstract = {Osteosarcoma (OS) is the most common primary malignant bone tumor and its etiology has recently been associated with osteogenic differentiation dysfunctions. OS cells keep a capacity for uncontrolled proliferation showing a phenotype similar to undifferentiated osteoprogenitors with abnormal biomineralization. Within this context, both conventional and X-ray synchrotron-based techniques have been exploited to deeply characterize the genesis and evolution of mineral depositions in a human OS cell line (SaOS-2) exposed to an osteogenic cocktail for 4 and 10 days. A partial restoration of the physiological biomineralization, culminating with the formation of hydroxyapatite, was observed at 10 days after treatment together with a mitochondria-driven mechanism for calcium transportation within the cell. Interestingly, during differentiation, mitochondria showed a change in morphology from elongated to rounded, indicating a metabolic reprogramming of OS cells possibly linked to an increase in glycolysis contribution to energy metabolism. These findings add a dowel to the genesis of OS giving new insights on the development of therapeutic strategies able to restore the physiological mineralization in OS cells.},
}
@article {pmid37239358,
year = {2023},
author = {Ran, B and Zhu, W and Zhao, X and Li, L and Yi, Z and Li, M and Wang, T and Li, D},
title = {Studying Genetic Diversity and Relationships between Mountainous Meihua Chickens Using Mitochondrial DNA Control Region.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239358},
issn = {2073-4425},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Chickens/genetics ; Genetic Variation/genetics ; Phylogeny ; Mitochondria/genetics ; },
abstract = {The Mountainous Meihua chicken is a unique regional germplasm resource from Tongjiang County, Bazhong City, China, but its genetic structure and evolutionary relationships with other native chicken breeds in the Sichuan region remain unclear. Here, we analyzed a total of 469 sequences, including 199 Mountainous Meihua chicken sequences generated in this study, together with 30 sequences representing 13 clades and 240 sequences from seven different Sichuan local chicken breeds downloaded from NCBI. These sequences were further used to analyze genetic diversity, patterns of population differentiation, and phylogenetic relationships between groups. We show that Mountainous Meihua chicken mtDNA sequences have high haplotypic and nucleotide diversity (0.876 and 0.012, respectively) and with a T bias that is suggestive of good breeding potential. Phylogenetic analysis showed that Mountainous Meihua chickens belong to clades A, B, E, and G and have a low affinity to other chicken breeds, with a moderate degree of differentiation. A non-significant Tajima's D indicates that no demographic expansions occurred in the past. Finally, the four maternal lineages identified in Mountainous Meihua chicken showed unique genetic characteristics.},
}
@article {pmid37239339,
year = {2023},
author = {Wu, Z and Yang, T and Qin, R and Liu, H},
title = {Complete Mitogenome and Phylogenetic Analysis of the Carthamus tinctorius L.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239339},
issn = {2073-4425},
mesh = {Phylogeny ; *Carthamus tinctorius/genetics ; *Genome, Mitochondrial/genetics ; Repetitive Sequences, Nucleic Acid ; },
abstract = {Carthamus tinctorius L. 1753 (Asteraceae), also called safflower, is a cash crop with both edible and medical properties. We analyzed and reported the safflower mitogenome based on combined short and long reads obtained from Illumina and Pacbio platforms, respectively. This safflower mitogenome mainly contained two circular chromosomes, with a total length of 321,872 bp, and encoded 55 unique genes, including 34 protein-coding genes (PCGs), 3 rRNA genes, and 18 tRNA genes. The total length of repeat sequences greater than 30 bp was 24,953 bp, accounting for 7.75% of the whole mitogenome. Furthermore, we characterized the RNA editing sites of protein-coding genes located in the safflower mitogenome, and the total number of RNA editing sites was 504. Then, we revealed partial sequence transfer events between plastid and mitochondria, in which one plastid-derived gene (psaB) remained intact in the mitogenome. Despite extensive arrangement events among the three mitogenomes of C. tinctorius, Arctium lappa, and Saussurea costus, the constructed phylogenetic tree based on mitogenome PCGs showed that C. tinctorius has a closer relationship with three Cardueae species, A. lappa, A. tomentosum, and S. costus, which is similar to the phylogeny constructed from the PCGs of plastid genomes. This mitogenome not only enriches the genetic information of safflower but also will be useful in the phylogeny and evolution study of the Asteraceae.},
}
@article {pmid37231782,
year = {2023},
author = {Shi, J and Yan, S and Li, W and Yang, X and Cui, Z and Li, J and Li, G and Li, Y and Hu, Y and Gao, S},
title = {PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes.},
journal = {RNA biology},
volume = {20},
number = {1},
pages = {248-256},
pmid = {37231782},
issn = {1555-8584},
mesh = {Animals ; *Genome, Chloroplast ; Gene Expression Profiling ; Molecular Sequence Annotation ; Transcriptome ; DNA, Mitochondrial/genetics ; Chloroplasts/genetics ; *Arabidopsis/genetics ; },
abstract = {Chloroplast and mitochondrial DNA (cpDNA and mtDNA) are apart from nuclear DNA (nuDNA) in a eukaryotic cell. The transcription system of chloroplasts differs from those of mitochondria and eukaryotes. In contrast to nuDNA and animal mtDNA, the transcription of cpDNA is still not well understood, primarily due to the unresolved identification of transcription initiation sites (TISs) and transcription termination sites (TTSs) on the genome scale. In the present study, we characterized the transcription of chloroplast (cp) genes with greater accuracy and comprehensive information using PacBio full-length transcriptome data from Arabidopsis thaliana. The major findings included the discovery of four types of artifacts, the validation and correction of cp gene annotations, the exact identification of TISs that start with G, and the discovery of polyA-like sites as TTSs. Notably, we proposed a new model to explain cp transcription initiation and termination at the whole-genome level. Four types of artifacts, degraded RNAs and splicing intermediates deserve the attention from researchers working with PacBio full-length transcriptome data, as these contaminant sequences can lead to incorrect downstream analysis. Cp transcription initiates at multiple promoters and terminates at polyA-like sites. Our study provides new insights into cp transcription and new clues to study the evolution of promoters, TISs, TTSs and polyA tails of eukaryotic genes.},
}
@article {pmid37221926,
year = {2023},
author = {Dong, X and Zhang, H and Zhu, X and Wang, K and Xue, H and Ye, Z and Zheng, C and Bu, W},
title = {Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae).},
journal = {Molecular phylogenetics and evolution},
volume = {184},
number = {},
pages = {107802},
doi = {10.1016/j.ympev.2023.107802},
pmid = {37221926},
issn = {1095-9513},
mesh = {Animals ; *Heteroptera ; Phylogeny ; China ; *Genome, Mitochondrial ; Mitochondria ; Mitomycin ; },
abstract = {Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.},
}
@article {pmid37221210,
year = {2023},
author = {Paukszto, &#x141; and Górski, P and Krawczyk, K and Maździarz, M and Szczecińska, M and Ślipiko, M and Sawicki, J},
title = {The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8303},
pmid = {37221210},
issn = {2045-2322},
mesh = {*Hepatophyta ; *Genome, Mitochondrial ; Phylogeny ; Mitochondria ; *Genome, Plastid ; *Anemone ; },
abstract = {Organellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less known. Hybrid assembly, using both short- and long-read technologies enabled the assembly of repeat-rich mitogenomes of Pellia and Apopellia revealing extraordinary reduction of length in the latter which impacts only intergenic spacers. The mitogenomes of Apopellia were revealed to be the smallest among all known liverworts-109 k bp, despite retaining all introns. The study also showed the loss of one tRNA gene in Apopellia mitogenome, although it had no impact on the codon usage pattern of mitochondrial protein coding genes. Moreover, it was revealed that Apopellia and Pellia differ in codon usage by plastome CDSs, despite identical tRNA gene content. Molecular identification of species is especially important where traditional taxonomic methods fail, especially within Pellidae where cryptic speciation is well recognized. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. Application of super-barcodes, based on complete mitochondrial or plastid genomes sequences enable identification of all cryptic lineages within Apopellia and Pellia genera, however in some particular cases, mitogenomes were more efficient in species delimitation than plastomes.},
}
@article {pmid37214873,
year = {2023},
author = {Cronin, SJF and Yu, W and Hale, A and Licht-Mayer, S and Crabtree, MJ and Korecka, JA and Tretiakov, EO and Sealey-Cardona, M and Somlyay, M and Onji, M and An, M and Fox, JD and Turnes, BL and Gomez-Diaz, C and da Luz Scheffer, D and Cikes, D and Nagy, V and Weidinger, A and Wolf, A and Reither, H and Chabloz, A and Kavirayani, A and Rao, S and Andrews, N and Latremoliere, A and Costigan, M and Douglas, G and Freitas, FC and Pifl, C and Walz, R and Konrat, R and Mahad, DJ and Koslov, AV and Latini, A and Isacson, O and Harkany, T and Hallett, PJ and Bagby, S and Woolf, CJ and Channon, KM and Je, HS and Penninger, JM},
title = {Crucial neuroprotective roles of the metabolite BH4 in dopaminergic neurons.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37214873},
issn = {2692-8205},
support = {DOC 33/FWF_/Austrian Science Fund FWF/Austria ; R01 NS112266/NS/NINDS NIH HHS/United States ; R35 NS105076/NS/NINDS NIH HHS/United States ; },
abstract = {Dopa-responsive dystonia (DRD) and Parkinson's disease (PD) are movement disorders caused by the dysfunction of nigrostriatal dopaminergic neurons. Identifying druggable pathways and biomarkers for guiding therapies is crucial due to the debilitating nature of these disorders. Recent genetic studies have identified variants of GTP cyclohydrolase-1 (GCH1), the rate-limiting enzyme in tetrahydrobiopterin (BH4) synthesis, as causative for these movement disorders. Here, we show that genetic and pharmacological inhibition of BH4 synthesis in mice and human midbrain-like organoids accurately recapitulates motor, behavioral and biochemical characteristics of these human diseases, with severity of the phenotype correlating with extent of BH4 deficiency. We also show that BH4 deficiency increases sensitivities to several PD-related stressors in mice and PD human cells, resulting in worse behavioral and physiological outcomes. Conversely, genetic and pharmacological augmentation of BH4 protects mice from genetically- and chemically induced PD-related stressors. Importantly, increasing BH4 levels also protects primary cells from PD-affected individuals and human midbrain-like organoids (hMLOs) from these stressors. Mechanistically, BH4 not only serves as an essential cofactor for dopamine synthesis, but also independently regulates tyrosine hydroxylase levels, protects against ferroptosis, scavenges mitochondrial ROS, maintains neuronal excitability and promotes mitochondrial ATP production, thereby enhancing mitochondrial fitness and cellular respiration in multiple preclinical PD animal models, human dopaminergic midbrain-like organoids and primary cells from PD-affected individuals. Our findings pinpoint the BH4 pathway as a key metabolic program at the intersection of multiple protective mechanisms for the health and function of midbrain dopaminergic neurons, identifying it as a potential therapeutic target for PD.},
}
@article {pmid37212044,
year = {2023},
author = {Postel, Z and Sloan, DB and Gallina, S and Godé, C and Schmitt, E and Mangenot, S and Drouard, L and Varré, JS and Touzet, P},
title = {The decoupled evolution of the organellar genomes of Silene nutans leads to distinct roles in the speciation process.},
journal = {The New phytologist},
volume = {239},
number = {2},
pages = {766-777},
doi = {10.1111/nph.18966},
pmid = {37212044},
issn = {1469-8137},
mesh = {*Silene/genetics ; Plant Breeding ; Cell Nucleus/genetics ; Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; Phylogeny ; },
abstract = {There is growing evidence that cytonuclear incompatibilities (i.e. disruption of cytonuclear coadaptation) might contribute to the speciation process. In a former study, we described the possible involvement of plastid-nuclear incompatibilities in the reproductive isolation between four lineages of Silene nutans (Caryophyllaceae). Because organellar genomes are usually cotransmitted, we assessed whether the mitochondrial genome could also be involved in the speciation process, knowing that the gynodioecious breeding system of S. nutans is expected to impact the evolutionary dynamics of this genome. Using hybrid capture and high-throughput DNA sequencing, we analyzed diversity patterns in the genic content of the organellar genomes in the four S. nutans lineages. Contrary to the plastid genome, which exhibited a large number of fixed substitutions between lineages, extensive sharing of polymorphisms between lineages was found in the mitochondrial genome. In addition, numerous recombination-like events were detected in the mitochondrial genome, loosening the linkage disequilibrium between the organellar genomes and leading to decoupled evolution. These results suggest that gynodioecy shaped mitochondrial diversity through balancing selection, maintaining ancestral polymorphism and, thus, limiting the involvement of the mitochondrial genome in evolution of hybrid inviability between S. nutans lineages.},
}
@article {pmid37208299,
year = {2023},
author = {Dapper, AL and Diegel, AE and Wade, MJ},
title = {Relative rates of evolution of male-beneficial nuclear compensatory mutations and male-harming Mother's Curse mitochondrial alleles.},
journal = {Evolution; international journal of organic evolution},
volume = {77},
number = {9},
pages = {1945-1955},
doi = {10.1093/evolut/qpad087},
pmid = {37208299},
issn = {1558-5646},
mesh = {Female ; Animals ; Male ; Humans ; *Mothers ; Alleles ; *Mitochondria/genetics ; Cell Nucleus/genetics ; Mutation ; },
abstract = {Mother's Curse alleles represent a significant source of potential male fitness defects. The maternal inheritance of mutations with the pattern of sex-specific fitness effects, s♀>0>s♂, allows Mother's Curse alleles to spread through a population even though they reduce male fitness. Although the mitochondrial genomes of animals contain only a handful of protein-coding genes, mutations in many of these genes have been shown to have a direct effect on male fertility. The evolutionary process of nuclear compensation is hypothesized to counteract the male-limited mitochondrial defects that spread via Mother's Curse. Here we use population genetic models to investigate the evolution of compensatory autosomal nuclear mutations that act to restore the loss of fitness caused by mitochondrial mutation pressures. We derive the rate of male fitness deterioration by Mother's Curse and the rate of restoration by nuclear compensatory evolution. We find that the rate of nuclear gene compensation is many times slower than that of its deterioration by cytoplasmic mutation pressure, resulting in a significant lag in the recovery of male fitness. Thus, the numbers of nuclear genes capable of restoring male mitochondrial fitness defects must be large in order to sustain male fitness in the face of mutation pressures.},
}
@article {pmid37199915,
year = {2023},
author = {Begeman, A and Babaian, A and Lewis, SC},
title = {Metatranscriptomic analysis uncovers prevalent viral ORFs compatible with mitochondrial translation.},
journal = {mSystems},
volume = {8},
number = {3},
pages = {e0100222},
pmid = {37199915},
issn = {2379-5077},
support = {R00 GM129456/GM/NIGMS NIH HHS/United States ; R35 GM147218/GM/NIGMS NIH HHS/United States ; T32 GM007232/GM/NIGMS NIH HHS/United States ; R00GM129456/NH/NIH HHS/United States ; },
mesh = {Open Reading Frames ; *RNA Viruses/genetics ; *Viruses/genetics ; Codon ; RNA-Dependent RNA Polymerase/genetics ; },
abstract = {RNA viruses are ubiquitous components of the global virosphere, yet relatively little is known about their genetic diversity or the cellular mechanisms by which they exploit the biology of their diverse eukaryotic hosts. A hallmark of (+)ssRNA (positive single-stranded RNA) viruses is the ability to remodel host endomembranes for their own replication. However, the subcellular interplay between RNA viruses and host organelles that harbor gene expression systems, such as mitochondria, is complex and poorly understood. Here we report the discovery of 763 new virus sequences belonging to the family Mitoviridae by metatranscriptomic analysis, the identification of previously uncharacterized mitovirus clades, and a putative new viral class. With this expanded understanding of the diversity of mitovirus and encoded RNA-dependent RNA polymerases (RdRps), we annotate mitovirus-specific protein motifs and identify hallmarks of mitochondrial translation, including mitochondrion-specific codons. This study expands the known diversity of mitochondrial viruses and provides additional evidence that they co-opt mitochondrial biology for their survival. IMPORTANCE Metatranscriptomic studies have rapidly expanded the cadre of known RNA viruses, yet our understanding of how these viruses navigate the cytoplasmic milieu of their hosts to survive remains poorly characterized. In this study, we identify and assemble 763 new viral sequences belonging to the Mitoviridae, a family of (+)ssRNA viruses thought to interact with and remodel host mitochondria. We exploit this genetic diversity to identify new clades of Mitoviridae, annotate clade-specific sequence motifs that distinguish the mitoviral RdRp, and reveal patterns of RdRp codon usage consistent with translation on host cell mitoribosomes. These results serve as a foundation for understanding how mitoviruses co-opt mitochondrial biology for their proliferation.},
}
@article {pmid37198654,
year = {2023},
author = {Kienzle, L and Bettinazzi, S and Choquette, T and Brunet, M and Khorami, HH and Jacques, JF and Moreau, M and Roucou, X and Landry, CR and Angers, A and Breton, S},
title = {A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {111},
pmid = {37198654},
issn = {1741-7007},
mesh = {Humans ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; HeLa Cells ; Mitochondria/genetics ; Open Reading Frames ; Peptides ; *NADH Dehydrogenase/genetics ; },
abstract = {BACKGROUND: Mitochondria have a central role in cellular functions, aging, and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternatives open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed.<br><br>RESULTS: We found a downstream alternative ATG initiation codon in the&#x2009;+&#x2009;3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino-acid-long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology.<br><br>CONCLUSIONS: Many human mitochondrial translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.},
}
@article {pmid37188954,
year = {2023},
author = {Lee, SY and Cheah, JS and Zhao, B and Xu, C and Roh, H and Kim, CK and Cho, KF and Udeshi, ND and Carr, SA and Ting, AY},
title = {Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells.},
journal = {Nature methods},
volume = {20},
number = {6},
pages = {908-917},
pmid = {37188954},
issn = {1548-7105},
support = {R01 DK121409/DK/NIDDK NIH HHS/United States ; RC2 DK129964/DK/NIDDK NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; },
mesh = {*Proteomics ; *Mitochondria ; Endoplasmic Reticulum ; Biotin ; },
abstract = {The incorporation of light-responsive domains into engineered proteins has enabled control of protein localization, interactions and function with light. We integrated optogenetic control into proximity labeling, a cornerstone technique for high-resolution proteomic mapping of organelles and interactomes in living cells. Through structure-guided screening and directed evolution, we installed the light-sensitive LOV domain into the proximity labeling enzyme TurboID to rapidly and reversibly control its labeling activity with low-power blue light. 'LOV-Turbo' works in multiple contexts and dramatically reduces background in biotin-rich environments such as neurons. We used LOV-Turbo for pulse-chase labeling to discover proteins that traffic between endoplasmic reticulum, nuclear and mitochondrial compartments under cellular stress. We also showed that instead of external light, LOV-Turbo can be activated by bioluminescence resonance energy transfer from luciferase, enabling interaction-dependent proximity labeling. Overall, LOV-Turbo increases the spatial and temporal precision of proximity labeling, expanding the scope of experimental questions that can be addressed with proximity labeling.},
}
@article {pmid37179826,
year = {2023},
author = {Casanova, A and Wevers, A and Navarro-Ledesma, S and Pruimboom, L},
title = {Mitochondria: It is all about energy.},
journal = {Frontiers in physiology},
volume = {14},
number = {},
pages = {1114231},
pmid = {37179826},
issn = {1664-042X},
abstract = {Mitochondria play a key role in both health and disease. Their function is not limited to energy production but serves multiple mechanisms varying from iron and calcium homeostasis to the production of hormones and neurotransmitters, such as melatonin. They enable and influence communication at all physical levels through interaction with other organelles, the nucleus, and the outside environment. The literature suggests crosstalk mechanisms between mitochondria and circadian clocks, the gut microbiota, and the immune system. They might even be the hub supporting and integrating activity across all these domains. Hence, they might be the (missing) link in both health and disease. Mitochondrial dysfunction is related to metabolic syndrome, neuronal diseases, cancer, cardiovascular and infectious diseases, and inflammatory disorders. In this regard, diseases such as cancer, Alzheimer's, Parkinson's, amyotrophic lateral sclerosis (ALS), chronic fatigue syndrome (CFS), and chronic pain are discussed. This review focuses on understanding the mitochondrial mechanisms of action that allow for the maintenance of mitochondrial health and the pathways toward dysregulated mechanisms. Although mitochondria have allowed us to adapt to changes over the course of evolution, in turn, evolution has shaped mitochondria. Each evolution-based intervention influences mitochondria in its own way. The use of physiological stress triggers tolerance to the stressor, achieving adaptability and resistance. This review describes strategies that could recover mitochondrial functioning in multiple diseases, providing a comprehensive, root-cause-focused, integrative approach to recovering health and treating people suffering from chronic diseases.},
}
@article {pmid37175542,
year = {2023},
author = {Ke, SJ and Liu, DK and Tu, XD and He, X and Zhang, MM and Zhu, MJ and Zhang, DY and Zhang, CL and Lan, SR and Liu, ZJ},
title = {Apostasia Mitochondrial Genome Analysis and Monocot Mitochondria Phylogenomics.},
journal = {International journal of molecular sciences},
volume = {24},
number = {9},
pages = {},
pmid = {37175542},
issn = {1422-0067},
support = {72202200205//Fujian Agriculture and Forestry University/ ; },
mesh = {Phylogeny ; *Genome, Mitochondrial ; Mitochondria/genetics ; RNA, Ribosomal/genetics ; *Orchidaceae/genetics ; },
abstract = {Apostasia shenzhenica belongs to the subfamily Apostasioideae and is a primitive group located at the base of the Orchidaceae phylogenetic tree. However, the A. shenzhenica mitochondrial genome (mitogenome) is still unexplored, and the phylogenetic relationships between monocots mitogenomes remain unexplored. In this study, we discussed the genetic diversity of A. shenzhenica and the phylogenetic relationships within its monocotyledon mitogenome. We sequenced and assembled the complete mitogenome of A. shenzhenica, resulting in a circular mitochondrial draft of 672,872 bp, with an average read coverage of 122× and a GC content of 44.4%. A. shenzhenica mitogenome contained 36 protein-coding genes, 16 tRNAs, two rRNAs, and two copies of nad4L. Repeat sequence analysis revealed a large number of medium and small repeats, accounting for 1.28% of the mitogenome sequence. Selection pressure analysis indicated high mitogenome conservation in related species. RNA editing identified 416 sites in the protein-coding region. Furthermore, we found 44 chloroplast genomic DNA fragments that were transferred from the chloroplast to the mitogenome of A. shenzhenica, with five plastid-derived genes remaining intact in the mitogenome. Finally, the phylogenetic analysis of the mitogenomes from A. shenzhenica and 28 other monocots showed that the evolution and classification of most monocots were well determined. These findings enrich the genetic resources of orchids and provide valuable information on the taxonomic classification and molecular evolution of monocots.},
}
@article {pmid37171259,
year = {2023},
author = {Dowling, DK and Wolff, JN},
title = {Evolutionary genetics of the mitochondrial genome: insights from Drosophila.},
journal = {Genetics},
volume = {224},
number = {3},
pages = {},
pmid = {37171259},
issn = {1943-2631},
mesh = {Animals ; *Drosophila/genetics ; *Genome, Mitochondrial ; Eukaryota/genetics ; Mitochondria/genetics ; Oxidative Phosphorylation ; DNA, Mitochondrial ; },
abstract = {Mitochondria are key to energy conversion in virtually all eukaryotes. Intriguingly, despite billions of years of evolution inside the eukaryote, mitochondria have retained their own small set of genes involved in the regulation of oxidative phosphorylation (OXPHOS) and protein translation. Although there was a long-standing assumption that the genetic variation found within the mitochondria would be selectively neutral, research over the past 3 decades has challenged this assumption. This research has provided novel insight into the genetic and evolutionary forces that shape mitochondrial evolution and broader implications for evolutionary ecological processes. Many of the seminal studies in this field, from the inception of the research field to current studies, have been conducted using Drosophila flies, thus establishing the species as a model system for studies in mitochondrial evolutionary biology. In this review, we comprehensively review these studies, from those focusing on genetic processes shaping evolution within the mitochondrial genome, to those examining the evolutionary implications of interactions between genes spanning mitochondrial and nuclear genomes, and to those investigating the dynamics of mitochondrial heteroplasmy. We synthesize the contribution of these studies to shaping our understanding of the evolutionary and ecological implications of mitochondrial genetic variation.},
}
@article {pmid37166639,
year = {2023},
author = {Maiti, P and Fontanesi, F},
title = {Metabolic Labeling of Mitochondrial Translation Products in Whole Cells and Isolated Organelles.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2661},
number = {},
pages = {193-215},
pmid = {37166639},
issn = {1940-6029},
mesh = {Animals ; *Protein Biosynthesis ; *Mitochondria/metabolism ; Methionine/metabolism ; Amino Acids/metabolism ; Mitochondrial Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Mammals/genetics ; },
abstract = {Mitochondria retain their own genome and translational apparatus that is highly specialized in the synthesis of a handful of proteins, essential components of the oxidative phosphorylation system. During evolution, the players and mechanisms involved in mitochondrial translation have acquired some unique features, which we have only partially disclosed. The study of the mitochondrial translation process has been historically hampered by the lack of an in vitro translational system and has largely relied on the analysis of the incorporation rate of radiolabeled amino acids into mitochondrial proteins in cellulo or in organello. In this chapter, we describe methods to monitor mitochondrial translation by labeling newly synthesized mitochondrial polypeptides with [S[35]]-methionine in either yeast or mammalian whole cells or isolated mitochondria.},
}
@article {pmid37166631,
year = {2023},
author = {Chrzanowska-Lightowlers, ZM and Lightowlers, RN},
title = {Translation in Mitochondrial Ribosomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2661},
number = {},
pages = {53-72},
pmid = {37166631},
issn = {1940-6029},
support = {203105/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Mitochondrial Ribosomes/metabolism ; Cryoelectron Microscopy ; *Mitochondria/genetics/metabolism ; Protein Biosynthesis ; Oxidative Phosphorylation ; Mitochondrial Proteins/genetics/metabolism ; },
abstract = {Mitochondrial protein synthesis is essential for the life of aerobic eukaryotes. Without it, oxidative phosphorylation cannot be coupled. Evolution has shaped a battery of factors and machinery that are key to production of just a handful of critical proteins. In this general concept chapter, we attempt to briefly summarize our current knowledge of the overall process in mitochondria from a variety of species, breaking this down to the four parts of translation: initiation, elongation, termination, and recycling. Where appropriate, we highlight differences between species and emphasize gaps in our understanding. Excitingly, with the current revolution in cryoelectron microscopy and mitochondrial genome editing, it is highly likely that many of these gaps will be resolved in the near future. However, the absence of a faithful in vitro reconstituted system to study mitochondrial translation is still problematic.},
}
@article {pmid37166629,
year = {2023},
author = {Agrawal, RK and Majumdar, S},
title = {Evolution: Mitochondrial Ribosomes Across Species.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2661},
number = {},
pages = {7-21},
pmid = {37166629},
issn = {1940-6029},
support = {R01 GM061576/GM/NIGMS NIH HHS/United States ; R01 GM139277/GM/NIGMS NIH HHS/United States ; R01 AI132422/AI/NIAID NIH HHS/United States ; R01 AI155473/AI/NIAID NIH HHS/United States ; },
mesh = {*Mitochondrial Ribosomes/metabolism ; *Mitochondria/genetics/metabolism ; Ribosomes/metabolism ; Eukaryota/genetics/metabolism ; Eukaryotic Cells/metabolism ; Mitochondrial Proteins/metabolism ; Cryoelectron Microscopy ; Ribosomal Proteins/metabolism ; },
abstract = {The ribosome is among the most complex and ancient cellular macromolecular assemblies that plays a central role in protein biosynthesis in all living cells. Its function of translation of genetic information encoded in messenger RNA into protein molecules also extends to subcellular compartments in eukaryotic cells such as apicoplasts, chloroplasts, and mitochondria. The origin of mitochondria is primarily attributed to an early endosymbiotic event between an alpha-proteobacterium and a primitive (archaeal) eukaryotic cell. The timeline of mitochondrial acquisition, the nature of the host, and their diversification have been studied in great detail and are continually being revised as more genomic and structural data emerge. Recent advancements in high-resolution cryo-EM structure determination have provided architectural details of mitochondrial ribosomes (mitoribosomes) from various species, revealing unprecedented diversifications among them. These structures provide novel insights into the evolution of mitoribosomal structure and function. Here, we present a brief overview of the existing mitoribosomal structures in the context of the eukaryotic evolution tree showing their diversification from their last common ancestor.},
}
@article {pmid37162347,
year = {2023},
author = {Ezawa, T and Silvestri, A and Maruyama, H and Tawaraya, K and Suzuki, M and Duan, Y and Turina, M and Lanfranco, L},
title = {Structurally distinct mitoviruses: are they an ancestral lineage of the Mitoviridae exclusive to arbuscular mycorrhizal fungi (Glomeromycotina)?.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0024023},
pmid = {37162347},
issn = {2150-7511},
mesh = {*Mycorrhizae/genetics ; Symbiosis ; Phylogeny ; Ecosystem ; *Glomeromycota/genetics ; Plants/microbiology ; *RNA Viruses/genetics ; RNA-Dependent RNA Polymerase/genetics ; },
abstract = {Mitoviruses in the family Mitoviridae are the mitochondria-replicating "naked RNA viruses" with genomes encoding only the replicase RNA-dependent RNA polymerase (RdRp) and prevalent across fungi, plants, and invertebrates. Arbuscular mycorrhizal fungi in the subphylum Glomeromycotina are obligate plant symbionts that deliver water and nutrients to the host. We discovered distinct mitoviruses in glomeromycotinian fungi, namely "large duamitovirus," encoding unusually large RdRp with a unique N-terminal motif that is endogenized in some host genomes. More than 400 viral sequences similar to the large duamitoviruses are present in metatranscriptome databases. They are globally distributed in soil ecosystems, consistent with the cosmopolitan distribution of glomeromycotinian fungi, and formed the most basal clade of the Mitoviridae in phylogenetic analysis. Given that glomeromycotinian fungi are the only confirmed hosts of these viruses, we propose the hypothesis that large duamitoviruses are the most ancestral lineage of the Mitoviridae that have been maintained exclusively in glomeromycotinian fungi.},
}
@article {pmid37158879,
year = {2023},
author = {Shamanskiy, V and Mikhailova, AA and Tretiakov, EO and Ushakova, K and Mikhailova, AG and Oreshkov, S and Knorre, DA and Ree, N and Overdevest, JB and Lukowski, SW and Gostimskaya, I and Yurov, V and Liou, CW and Lin, TK and Kunz, WS and Reymond, A and Mazunin, I and Bazykin, GA and Fellay, J and Tanaka, M and Khrapko, K and Gunbin, K and Popadin, K},
title = {Secondary structure of the human mitochondrial genome affects formation of deletions.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {103},
pmid = {37158879},
issn = {1741-7007},
support = {DOC 33/FWF_/Austrian Science Fund FWF/Austria ; UL1 TR001873/TR/NCATS NIH HHS/United States ; K23 DC019678/DC/NIDCD NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Genome, Mitochondrial ; Mitochondria ; DNA, Mitochondrial/genetics ; Genome, Human ; Protein Structure, Secondary ; DNA, Single-Stranded ; Mammals ; },
abstract = {BACKGROUND: Aging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain their distribution. Here, we hypothesized that the close proximity of direct repeats on single-stranded mitochondrial DNA (mtDNA) might play a role in the formation of deletions.<br><br>RESULTS: By analyzing human mtDNA deletions in the major arc of mtDNA, which is single-stranded during replication and is characterized by a high number of deletions, we found a non-uniform distribution with a "hot spot" where one deletion breakpoint occurred within the region of 6-9&#xa0;kb and another within 13-16&#xa0;kb of the mtDNA. This distribution was not explained by the presence of direct repeats, suggesting that other factors, such as the spatial proximity of these two regions, can be the cause. In silico analyses revealed that the single-stranded major arc may be organized as a large-scale hairpin-like loop with a center close to 11&#xa0;kb and contacting regions between 6-9&#xa0;kb and 13-16&#xa0;kb, which would explain the high deletion activity in this contact zone. The direct repeats located within the contact zone, such as the well-known common repeat with a first arm at 8470-8482&#xa0;bp (base pair) and a second arm at 13,447-13,459&#xa0;bp, are three times more likely to cause deletions compared to direct repeats located outside of the contact zone. A comparison of age- and disease-associated deletions demonstrated that the contact zone plays a crucial role in explaining the age-associated deletions, emphasizing its importance in the rate of healthy aging.<br><br>CONCLUSIONS: Overall, we provide topological insights into the mechanism of age-associated deletion formation in human mtDNA, which could be used to predict somatic deletion burden and maximum lifespan in different human haplogroups and mammalian species.},
}
@article {pmid37156858,
year = {2023},
author = {Smirnova, J and Loerke, J and Kleinau, G and Schmidt, A and Bürger, J and Meyer, EH and Mielke, T and Scheerer, P and Bock, R and Spahn, CMT and Zoschke, R},
title = {Structure of the actively translating plant 80S ribosome at 2.2 Å resolution.},
journal = {Nature plants},
volume = {9},
number = {6},
pages = {987-1000},
pmid = {37156858},
issn = {2055-0278},
support = {416210002//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 221545957//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 394046635//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 421152132//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ZO 302/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB-TRR 175 (A4)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 956314//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Cytosol ; *RNA, Ribosomal/chemistry ; Cryoelectron Microscopy ; Phylogeny ; Models, Molecular ; *Ribosomes/chemistry ; Plants/genetics ; Nicotiana/genetics ; },
abstract = {In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing.},
}
@article {pmid37153218,
year = {2023},
author = {Xu, J and Li, B and Jiang, Z and Wang, W and Yang, Y and Yang, M and Ye, X},
title = {Genomic analyses provide insights into the genome evolution and environmental adaptation of the tobacco moth Ephestia elutella.},
journal = {Frontiers in physiology},
volume = {14},
number = {},
pages = {1187522},
pmid = {37153218},
issn = {1664-042X},
abstract = {Ephestia elutella is a major pest responsible for significant damage to stored tobacco over many years. Here, we conduct a comparative genomic analysis on this pest, aiming to explore the genetic bases of environmental adaptation of this species. We find gene families associated with nutrient metabolism, detoxification, antioxidant defense and gustatory receptors are expanded in the E. elutella genome. Detailed phylogenetic analysis of P450 genes further reveals obvious duplications in the CYP3 clan in E. elutella compared to the closely related species, the Indianmeal moth Plodia interpunctella. We also identify 229 rapidly evolving genes and 207 positively selected genes in E. elutella, respectively, and highlight two positively selected heat shock protein 40 (Hsp40) genes. In addition, we find a number of species-specific genes related to diverse biological processes, such as mitochondria biology and development. These findings advance our understanding of the mechanisms underlying processes of environmental adaptation on E. elutella and will enable the development of novel pest management strategies.},
}
@article {pmid37152468,
year = {2023},
author = {Kannan, B and Arumugam, P},
title = {The implication of mitochondrial DNA mutation and dysfunction in periodontal diseases.},
journal = {Journal of Indian Society of Periodontology},
volume = {27},
number = {2},
pages = {126-130},
pmid = {37152468},
issn = {0972-124X},
abstract = {Periodontitis is a chronic oral inflammatory disease that is caused by dental plaque pathogens. Periodontal disease development and evolution are based on the host immune system, humoral and cellular immunity, the integrity of the tissues, and certain endocrine and nutritional factors. Mitochondria are significantly involved in periodontal infections and inflammation, which play a role in the inflammatory response in a variety of ways. In general, oxidative stress causes a stressful environment that subsequently leads to tissue damage and chronic inflammation. Several mutations and alterations in mitochondrial DNA lead the disease to an aggressive condition, by causing dysregulated mitochondrial function. Such mutations are significantly associated with various diseases. Numerous studies indicate chronic periodontitis patients have a decreased level of mitochondrial membrane potential, as well as adenosine triphosphate, and an increased level of reactive oxygen species production, which causes cell death in the periodontium and affects tissue growth. Further studies into the association between mitochondria and periodontitis might be helpful for the treatment and prevention of the diseases.},
}
@article {pmid37141262,
year = {2023},
author = {Squires, TE and Rödin-Mörch, P and Formenti, G and Tracey, A and Abueg, L and Brajuka, N and Jarvis, E and Halapi, EC and Melsted, P and Höglund, J and Magnússon, KP},
title = {A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta).},
journal = {G3 (Bethesda, Md.)},
volume = {13},
number = {7},
pages = {},
pmid = {37141262},
issn = {2160-1836},
mesh = {Animals ; Female ; *Quail ; *Galliformes/genetics ; Repetitive Sequences, Nucleic Acid ; Chromosomes/genetics ; Genome ; Phylogeny ; },
abstract = {The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a high-quality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were 33605, 394, and 4265 bp, respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan's unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe while serving as a benchmark for species in the family Phasianidae (order Galliformes).},
}
@article {pmid37127113,
year = {2023},
author = {Hausdorf, B and Xu, J},
title = {Speciation of rock-dwelling snail species: Disjunct ranges and mosaic patterns reveal the importance of long-distance dispersal in Chilostoma (Cingulifera) in the European Southern Alps.},
journal = {Molecular phylogenetics and evolution},
volume = {184},
number = {},
pages = {107788},
doi = {10.1016/j.ympev.2023.107788},
pmid = {37127113},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Snails/genetics ; Europe ; *Mitochondria ; Genetic Variation ; },
abstract = {To better understand the origin of the high diversity and endemism in the Southern Alps of Europe, we investigated the phylogeny and population structure of the rock-dwelling snail group Chilostoma (Cingulifera) in the Southern Alps. We generated genomic ddRAD data and mitochondrial sequences of 104 Cingulifera specimens from 28 populations and 14 other Ariantinae. Until recently, about 30 Cingulifera taxa were classified as subspecies of a single polytypic species. The phylogenetic and population genetic analyses of the ddRAD data and mitochondrial sequences revealed that Cingulifera in the Southern Alps is differentiated into three species. Each of the three Chilostoma (Cingulifera) species occupies disjunct sub-areas, which are separated by areas occupied by other Chilostoma taxa. Neighbouring populations of different species show little or no admixture. Tests indicating that the genetic differentiation of the three Cingulifera taxa cannot be explained by isolation by distance confirmed their species status. The disjunct range patterns demonstrate the importance of stochastic events such as passive long-distance dispersal for the evolution of population structure and speciation in these snails, and of priority effects and ecological competition as important factors influencing species distributions.},
}
@article {pmid37126705,
year = {2023},
author = {Espino-Sanchez, TJ and Wienkers, H and Marvin, RG and Nalder, SA and García-Guerrero, AE and VanNatta, PE and Jami-Alahmadi, Y and Mixon Blackwell, A and Whitby, FG and Wohlschlegel, JA and Kieber-Emmons, MT and Hill, CP and Sigala, PA},
title = {Direct tests of cytochrome c and c1 functions in the electron transport chain of malaria parasites.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {19},
pages = {e2301047120},
pmid = {37126705},
issn = {1091-6490},
support = {P30 GM133894/GM/NIGMS NIH HHS/United States ; T32 DK007115/DK/NIDDK NIH HHS/United States ; R25 HL108828/HL/NHLBI NIH HHS/United States ; R01 GM089778/GM/NIGMS NIH HHS/United States ; U54 DK110858/DK/NIDDK NIH HHS/United States ; R35 GM133764/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Cytochromes c ; Electron Transport ; *Parasites ; *Antimalarials ; *Malaria, Falciparum ; Eukaryota ; Cytochromes c1 ; },
abstract = {The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome (cyt) functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs (c and c-2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c-2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c1 for inducible knockdown. Translational repression of cyt c and cyt c1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c-2 knockdown or knockout had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c-2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c-2 has an unusually open active site in which heme is stably coordinated by only a single axial amino acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution.},
}
@article {pmid37116483,
year = {2023},
author = {George, EE and Barcytė, D and Lax, G and Livingston, S and Tashyreva, D and Husnik, F and Lukeš, J and Eliáš, M and Keeling, PJ},
title = {A single cryptomonad cell harbors a complex community of organelles, bacteria, a phage, and selfish elements.},
journal = {Current biology : CB},
volume = {33},
number = {10},
pages = {1982-1996.e4},
doi = {10.1016/j.cub.2023.04.010},
pmid = {37116483},
issn = {1879-0445},
mesh = {*Cryptophyta ; *Genome ; Eukaryota/genetics ; Cell Nucleus/genetics ; Plastids/genetics ; Bacteria/genetics ; Symbiosis/genetics ; Phylogeny ; },
abstract = {Symbiosis between prokaryotes and microbial eukaryotes (protists) has broadly impacted both evolution and ecology. Endosymbiosis led to mitochondria and plastids, the latter spreading across the tree of eukaryotes by subsequent rounds of endosymbiosis. Present-day endosymbionts in protists remain both common and diverse, although what function they serve is often unknown. Here, we describe a highly complex community of endosymbionts and a bacteriophage (phage) within a single cryptomonad cell. Cryptomonads are a model for organelle evolution because their secondary plastid retains a relict endosymbiont nucleus, but only one previously unidentified Cryptomonas strain (SAG 25.80) is known to harbor bacterial endosymbionts. We carried out electron microscopy and FISH imaging as well as genomic sequencing on Cryptomonas SAG 25.80, which revealed a stable, complex community even after over 50 years in continuous cultivation. We identified the host strain as Cryptomonas gyropyrenoidosa, and sequenced genomes from its mitochondria, plastid, and nucleomorph (and partially its nucleus), as well as two symbionts, Megaira polyxenophila and Grellia numerosa, and one phage (MAnkyphage) infecting M. polyxenophila. Comparing closely related endosymbionts from other hosts revealed similar metabolic and genomic features, with the exception of abundant transposons and genome plasticity in M. polyxenophila from Cryptomonas. We found an abundance of eukaryote-interacting genes as well as many toxin-antitoxin systems, including in the MAnkyphage genome that also encodes several eukaryotic-like proteins. Overall, the Cryptomonas cell is an endosymbiotic conglomeration with seven distinct evolving genomes that all show evidence of inter-lineage conflict but nevertheless remain stable, even after more than 4,000 generations in culture.},
}
@article {pmid37115919,
year = {2023},
author = {Al Jewari, C and Baldauf, SL},
title = {An excavate root for the eukaryote tree of life.},
journal = {Science advances},
volume = {9},
number = {17},
pages = {eade4973},
pmid = {37115919},
issn = {2375-2548},
mesh = {*Eukaryota/genetics ; *Eukaryotic Cells ; Biological Evolution ; Phylogeny ; Evolution, Molecular ; },
abstract = {Much of the higher-order phylogeny of eukaryotes is well resolved, but the root remains elusive. We assembled a dataset of 183 eukaryotic proteins of archaeal ancestry to test this root. The resulting phylogeny identifies four lineages of eukaryotes currently classified as "Excavata" branching separately at the base of the tree. Thus, Parabasalia appear as the first major branch of eukaryotes followed sequentially by Fornicata, Preaxostyla, and Discoba. All four excavate branch points receive full statistical support from analyses with commonly used evolutionary models, a protein structure partition model that we introduce here, and various controls for deep phylogeny artifacts. The absence of aerobic mitochondria in Parabasalia, Fornicata, and Preaxostyla suggests that modern eukaryotes arose under anoxic conditions, probably much earlier than expected, and without the benefit of mitochondrial respiration.},
}
@article {pmid37113597,
year = {2023},
author = {Mahati, K and Padmasree, K},
title = {Brassinolide promotes interaction between chloroplasts and mitochondria during the optimization of photosynthesis by the mitochondrial electron transport chain in mesophyll cell protoplasts of Arabidopsis thaliana.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1099474},
pmid = {37113597},
issn = {1664-462X},
abstract = {The current experimental data unveils the role of brassinolide (BL), a phytohormone of class brassinosteroids (BRs), in augmenting the cross-talk between the mitochondrial electron transport chain (mETC) and chloroplasts to strengthen the efficiency of the Calvin-Benson cycle (CBC) for higher assimilation of carbon dioxide in the mesophyll cell protoplasts (MCP) of Arabidopsis thaliana. The outcome of total respiration (TR) and photosynthetic carbon assimilation (PCA) was monitored as O2 uptake under dark and NaHCO3-dependent O2 evolution under light, respectively, after pre-incubation of MCP at a broad spectrum of BL concentration from 0.05 pM to 5 pM at 25 °C and optimum light intensity of 1000 μmol m[-2] s[-1]. The addition of optimal concentration (0.5 pM) of BL to MCP stimulated the (i) TR, (ii) PCA, and (iii) para-benzoquinone-dependent O2 evolution (PSII activity). Further, in response to BL, the enzyme activity or transcript levels of redox-regulated CBC enzymes and glucose-6-phosphate raised considerably. Also, the addition of BL to MCP remarkably accelerated the capacity of the cytochrome oxidase (COX) and alternative oxidase (AOX) pathways concurrently with an increase in total cellular pyruvate and reactive oxygen species (ROS) levels. Besides, malate valve components (Malate, Chl-MDH, M-MDH) increased in response to BL. At the same time, the cellular redox ratios of pyridine nucleotides (NADPH and NADH) were kept low in the presence of BL. However, BL could not keep up the CBC activity of photosynthesis along with its associated light-activated enzymes/transcripts when mETC through COX or AOX pathway is restricted by antimycin A (AA) or salicylhydroxamic acid (SHAM), respectively. In contrast, adding BL to MCP under restricted mETC showed aggravation in total cellular ROS, pyruvate, malate, and redox ratio of pyridine nucleotides with a concomitant increase in transcripts associated with malate valve and antioxidant systems. These results suggest that BL enhances the PCA by coordinating in cross-talk of chloroplasts and mitochondria to regulate the cellular redox ratio or ROS through the involvement of COX and AOX pathways along with the malate valve and antioxidant systems.},
}
@article {pmid37107622,
year = {2023},
author = {Li, X and Zhe, M and Huang, Y and Fan, W and Yang, J and Zhu, A},
title = {The Evolution of Mitochondrial Genomes between Two Cymbidium Sister Species: Dozens of Circular Chromosomes and the Maintenance and Deterioration of Genome Synteny.},
journal = {Genes},
volume = {14},
number = {4},
pages = {},
pmid = {37107622},
issn = {2073-4425},
mesh = {*Genome, Mitochondrial/genetics ; Synteny ; Introns ; Chromosomes ; *Orchidaceae ; },
abstract = {Plant mitochondrial genomes (mitogenomes) exhibit fluid genome architectures, which could lead to the rapid erosion of genome synteny over a short evolutionary time scale. Among the species-rich orchid family, the leafy Cymbidium lancifolium and leafless Cymbidium macrorhizon are sister species with remarkable differences in morphology and nutritional physiology. Although our understanding of the evolution of mitochondria is incomplete, these sister taxa are ideal for examining this subject. In this study, the complete mitogenomes of C. lancifolium and C. macrorhizon, totaling 704,244 bp and 650,751 bp, respectively, were assembled. In the 2 mitogenomes, 38 protein-coding genes, 18 cis- and 6 trans-spliced introns, and approximately 611 Kb of homologous sequences are identical; overall, they have 99.4% genome-wide similarity. Slight variations in the mitogenomes of C. lancifolium and C. macrorhizon in repeat content (21.0 Kb and 21.6 Kb, respectively) and mitochondrial DNA of plastid origin (MIPT; 38.2 Kb and 37.5 Kb, respectively) were observed. The mitogenome architectures of C. lancifolium and C. macrorhizon are complex and comprise 23 and 22 mini-circular chromosomes, respectively. Pairwise comparisons indicate that the two mitogenomes are largely syntenic, and the disparity in chromosome numbers is likely due to repeat-mediated rearrangements among different chromosomes. Notably, approximately 93.2 Kb C. lancifolium mitochondrial sequences lack any homology in the C. macrorhizon mitogenome, indicating frequent DNA gains and losses, which accounts mainly for the size variation. Our findings provide unique insights into mitogenome evolution in leafy and leafless plants of sister species and shed light on mitogenome dynamics during the transition from mixotrophy to mycoheterotrophy.},
}
@article {pmid37107542,
year = {2023},
author = {De, AK and Sawhney, S and Sunder, J and Muthiyan, R and Ponraj, P and Sujatha, T and Malakar, D and Mondal, S and Bera, AK and Kumar, A and Chakurkar, EB and Bhattacharya, D},
title = {Peeping into Mitochondrial Diversity of Andaman Goats: Unveils Possibility of Maritime Transport with Diversified Geographic Signaling.},
journal = {Genes},
volume = {14},
number = {4},
pages = {},
pmid = {37107542},
issn = {2073-4425},
mesh = {Animals ; Cattle ; Swine ; *Goats/genetics ; Phylogeny ; *DNA, Mitochondrial/genetics ; Sequence Analysis, DNA ; Mitochondria/genetics ; },
abstract = {Andaman and Nicobar Islands, a part of South-East Asia, is enriched with the presence of native breeds of livestock (cattle, pig, goat) and poultry. There are two native goat breeds, viz., Andaman local goat and Teressa goat in Andaman and Nicobar Islands. However, to date, the origin and genetic makeup of these two breeds have not been detailed. Therefore, the present study describes the genetic makeup of Andaman goats through analysis of mitochondrial D-loop sequence for sequence polymorphism, phylogeographical signaling and population expansion events. The genetic diversity of the Teressa goat was less compared to the Andaman local goat due to its sole presence on Teressa Island. Out of 38 well-defined haplotypes of Andaman goats, the majority of haplotypes belonged to haplogroup A followed by haplogroup B and haplogroup D. The result of mismatch distribution and neutrality tests indicated no population expansion event of haplogroup A and B. Finally, based on poor geographical signaling, we hypothesize that Andaman goats have been imported to these Islands either through multidirectional diffusion or unidirectional diffusion. We justify our hypothesis of multidirectional diffusion on the basis of observation of the haplotype and nucleotide diversity of Andaman goats. Simultaneously, the probability of unidirectional diffusion of goats in these islands from the Indian subcontinent in different spells of domestication events through maritime routes cannot be ignored.},
}
@article {pmid37100315,
year = {2023},
author = {Françoso, E and Zuntini, AR and Ricardo, PC and Santos, PKF and de Souza Araujo, N and Silva, JPN and Gonçalves, LT and Brito, R and Gloag, R and Taylor, BA and Harpur, BA and Oldroyd, BP and Brown, MJF and Arias, MC},
title = {Rapid evolution, rearrangements and whole mitogenome duplication in the Australian stingless bees Tetragonula (Hymenoptera: Apidae): A steppingstone towards understanding mitochondrial function and evolution.},
journal = {International journal of biological macromolecules},
volume = {242},
number = {Pt 1},
pages = {124568},
doi = {10.1016/j.ijbiomac.2023.124568},
pmid = {37100315},
issn = {1879-0003},
mesh = {Animals ; Australia ; *Bees/genetics ; *Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {The extreme conservation of mitochondrial genomes in metazoans poses a significant challenge to understanding mitogenome evolution. However, the presence of variation in gene order or genome structure, found in a small number of taxa, can provide unique insights into this evolution. Previous work on two stingless bees in the genus Tetragonula (T. carbonaria and T. hockingsi) revealed highly divergent CO1 regions between them and when compared to the bees from the same tribe (Meliponini), indicating rapid evolution. Using mtDNA isolation and Illumina sequencing, we elucidated the mitogenomes of both species. In both species, there has been a duplication of the whole mitogenome to give a total genome size of 30,666 bp in T. carbonaria; and 30,662 bp in T. hockingsi. These duplicated genomes present a circular structure with two identical and mirrored copies of all 13 protein coding genes and 22 tRNAs, with the exception of a few tRNAs that are present as single copies. In addition, the mitogenomes are characterized by rearrangements of two block of genes. We believe that rapid evolution is present in the whole Indo-Malay/Australasian group of Meliponini but is extraordinarily elevated in T. carbonaria and T. hockingsi, probably due to founder effect, low effective population size and the mitogenome duplication. All these features - rapid evolution, rearrangements, and duplication - deviate significantly from the vast majority of the mitogenomes described so far, making the mitogenomes of Tetragonula unique opportunities to address fundamental questions of mitogenome function and evolution.},
}
@article {pmid37087094,
year = {2023},
author = {Carella, F and De Vico, G},
title = {Pathology, epidemiology, and phylogeny of mussel egg disease due to the microsporidian Steinhausia mytilovum (Field, 1924) in the Mediterranean mussel (Mytilus galloprovincialis).},
journal = {Journal of invertebrate pathology},
volume = {198},
number = {},
pages = {107927},
doi = {10.1016/j.jip.2023.107927},
pmid = {37087094},
issn = {1096-0805},
mesh = {Female ; Animals ; *Mytilus/microbiology ; *Microsporidia/genetics ; Phylogeny ; Italy ; Seafood ; },
abstract = {Microsporidia are well known fungal pathogens of aquatic animals. However, the taxonomy of microsporidia is generally poorly resolved, which has consequently constrained our understanding of their pathology and epidemiology in marine animals. To date, microsporidia have been reported in both bivalves and gastropods, and microsporidia from mollusks have been classified in different genera. Despite ongoing work to better describe these genera, including detailed microscopic and ultrastructural images, so far we lack information on microsporidian phylogeny and pathogenicity of species within these genera. Here we investigate the microsporidian parasite Steinhausia mytilovum associated with the mussel, Mytilus galloprovincialis, in natural beds and farms along coast of southern Italy. A survey of M. galloprovincialis was conducted in 13 mussel farms and one natural bed between 2009 and 2020. We found the presence of S. mytilovum in 10 of the investigated farms, with a prevalence ranging between 14 and 100% of female mussels, depending on the population and season in which they were sampled. The parasite developed in the oocytes within a sporophorous vesicle (SV) where it produced 1-3 spores per cell, both in the cytoplasm and in the nucleus. Stenhausia mytilovum elicited an infiltrative (24.8%) or a strong capsular inflammatory response (43.4%) at gonadal follicles and surrounding vesicular connective tissue, in some cases accompanied by gonadal atresia (24.8%), leading to loss of gonadal architecture. In 7% of cases no reaction was observed. Ultrastructural observations revealed a mitochondrial re-organization to interact with all the phases of parasite development; the mitochondria were arranged outside the parasitophorous vesicle (PV) or directly interacting with the spore inside vesicle. There are five taxonomic clades of microsporidians as identified by SSU ribosomal gene sequence data. Maximum likelihood analysis assigned S. mytilovum within the Clade IV, defined as the Class Terresporidia, with closest genetic relationship (83.6% identity) to an undetermined invertebrate ovarian microsporidian. The constant presence, prevalence, and severity of S. mytilovum in coastline populations of M. galloprovincialis populations in southern Italy may indirectly reflect immunocompetence at both individual and population levels.},
}
@article {pmid37082671,
year = {2023},
author = {Ibodeng, GO and Uche, IN and Mokua, R and Galo, M and Odigwe, B and Galeas, JN and Dasgupta, S},
title = {A snapshot of lung cancer: where are we now?-a narrative review.},
journal = {Annals of translational medicine},
volume = {11},
number = {6},
pages = {261},
pmid = {37082671},
issn = {2305-5839},
abstract = {BACKGROUND AND OBJECTIVE: The global impact of cancer and cancer-related deaths has been a huge challenge and continues to be a setback in the health sector and beyond even in recent times. Cancer is the second leading cause of death globally with lung cancer (LC) being the second most prevalent malignancy and the leading cause of mortality amongst cancers in men and women worldwide. LC still constitutes a major burden despite recent advances in diagnostic and treatment tools. In this article, we review the trends in LC with an emphasis on non-small cell LC. We aimed to identify nuclear and mitochondrial genetic alterations, microbiome dysbiosis, and their significance in non-small cell LC tumorigenesis as well as its relevance in the future management of LCs.<br><br>METHODS: We identified studies for this review by searching the PubMed, Cochrane, Education Resources Information Center (ERIC), and Surveillance, Epidemiology, and End Results (SEER) databases for English-Language articles published from January 1, 2000 through to July 30, 2022, using keywords: lung cancer, non-small cell lung cancer, early detection, treatment, mitochondria, microbiome and epigenetics.<br><br>KEY CONTENT AND FINDINGS: This review will highlight the genomic environment, mitochondrial and nuclear alterations that play a role in the etiopathogenesis of LC and its application in the progression as well as management of the disease. We also elaborate on current molecular tumor biomarkers and their therapeutic targets.<br><br>CONCLUSIONS: LC remains the leading cause of cancer-related deaths globally with poor prognosis despite available treatment options and even recent advances in both diagnostic tools and management guidelines. Human nuclear and mitochondrial alterations clearly play a role in tumorigenesis and progressive genomic evolution is crucial in the early carcinogenesis of LC which is strongly influenced by host immune surveillance. It is imperative that more research and clinical trials be undertaken to appreciate an in-depth understanding of LC from the molecular level to facilitate the discovery of more targeted therapy and overall better management of LC.},
}
@article {pmid37077029,
year = {2023},
author = {Park, D and Yu, Y and Kim, JH and Lee, J and Park, J and Hong, K and Seo, JK and Lim, C and Min, KT},
title = {Suboptimal Mitochondrial Activity Facilitates Nuclear Heat Shock Responses for Proteostasis and Genome Stability.},
journal = {Molecules and cells},
volume = {46},
number = {6},
pages = {374-386},
pmid = {37077029},
issn = {0219-1032},
mesh = {Humans ; *Proteostasis ; Reactive Oxygen Species/metabolism ; *Heat-Shock Response/genetics ; HSP70 Heat-Shock Proteins/metabolism ; Mitochondria/metabolism ; Nuclear Proteins/metabolism ; Genomic Instability ; },
abstract = {Thermal stress induces dynamic changes in nuclear proteins and relevant physiology as a part of the heat shock response (HSR). However, how the nuclear HSR is fine-tuned for cellular homeostasis remains elusive. Here, we show that mitochondrial activity plays an important role in nuclear proteostasis and genome stability through two distinct HSR pathways. Mitochondrial ribosomal protein (MRP) depletion enhanced the nucleolar granule formation of HSP70 and ubiquitin during HSR while facilitating the recovery of damaged nuclear proteins and impaired nucleocytoplasmic transport. Treatment of the mitochondrial proton gradient uncoupler masked MRP-depletion effects, implicating oxidative phosphorylation in these nuclear HSRs. On the other hand, MRP depletion and a reactive oxygen species (ROS) scavenger non-additively decreased mitochondrial ROS generation during HSR, thereby protecting the nuclear genome from DNA damage. These results suggest that suboptimal mitochondrial activity sustains nuclear homeostasis under cellular stress, providing plausible evidence for optimal endosymbiotic evolution via mitochondria-to-nuclear communication.},
}
@article {pmid37074804,
year = {2023},
author = {Mcguire, JA and Huang, X and Reilly, SB and Iskandar, DT and Wang-Claypool, CY and Werning, S and Chong, RA and Lawalata, SZS and Stubbs, AL and Frederick, JH and Brown, RM and Evans, BJ and Arifin, U and Riyanto, A and Hamidy, A and Arida, E and Koo, MS and Supriatna, J and Andayani, N and Hall, R},
title = {Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation.},
journal = {Systematic biology},
volume = {72},
number = {4},
pages = {885-911},
pmid = {37074804},
issn = {1076-836X},
support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; Phylogeny ; Indonesia ; *Lizards/genetics ; Phylogeography ; Genetics, Population ; Genetic Speciation ; },
abstract = {The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].},
}
@article {pmid37072481,
year = {2023},
author = {Christinaki, AC and Theelen, B and Zania, A and Coutinho, SDA and Cabañes, JF and Boekhout, T and Kouvelis, VN},
title = {Co-evolution of large inverted repeats and G-quadruplex DNA in fungal mitochondria may facilitate mitogenome stability: the case of Malassezia.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {6308},
pmid = {37072481},
issn = {2045-2322},
mesh = {Humans ; *Malassezia/genetics ; Phylogeny ; *Genome, Mitochondrial/genetics ; *G-Quadruplexes ; Mitochondria/genetics ; DNA ; },
abstract = {Mitogenomes are essential due to their contribution to cell respiration. Recently they have also been implicated in fungal pathogenicity mechanisms. Members of the basidiomycetous yeast genus Malassezia are an important fungal component of the human skin microbiome, linked to various skin diseases, bloodstream infections, and they are increasingly implicated in gut diseases and certain cancers. In this study, the comparative analysis of Malassezia mitogenomes contributed to phylogenetic tree construction for all species. The mitogenomes presented significant size and gene order diversity which correlates to their phylogeny. Most importantly, they showed the inclusion of large inverted repeats (LIRs) and G-quadruplex (G4) DNA elements, rendering Malassezia mitogenomes a valuable test case for elucidating the evolutionary mechanisms responsible for this genome diversity. Both LIRs and G4s coexist and convergently evolved to provide genome stability through recombination. This mechanism is common in chloroplasts but, hitherto, rarely found in mitogenomes.},
}
@article {pmid37071674,
year = {2023},
author = {Libby, E and Kempes, CP and Okie, JG},
title = {Metabolic compatibility and the rarity of prokaryote endosymbioses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {17},
pages = {e2206527120},
pmid = {37071674},
issn = {1091-6490},
mesh = {Phylogeny ; *Symbiosis/genetics ; *Prokaryotic Cells/metabolism ; Eukaryota/genetics ; Eukaryotic Cells/metabolism ; Biological Evolution ; },
abstract = {The evolution of the mitochondria was a significant event that gave rise to the eukaryotic lineage and most large complex life. Central to the origins of the mitochondria was an endosymbiosis between prokaryotes. Yet, despite the potential benefits that can stem from a prokaryotic endosymbiosis, their modern occurrence is exceptionally rare. While many factors may contribute to their rarity, we lack methods for estimating the extent to which they constrain the appearance of a prokaryotic endosymbiosis. Here, we address this knowledge gap by examining the role of metabolic compatibility between a prokaryotic host and endosymbiont. We use genome-scale metabolic flux models from three different collections (AGORA, KBase, and CarveMe) to assess the viability, fitness, and evolvability of potential prokaryotic endosymbioses. We find that while more than half of host-endosymbiont pairings are metabolically viable, the resulting endosymbioses have reduced growth rates compared to their ancestral metabolisms and are unlikely to gain mutations to overcome these fitness differences. In spite of these challenges, we do find that they may be more robust in the face of environmental perturbations at least in comparison with the ancestral host metabolism lineages. Our results provide a critical set of null models and expectations for understanding the forces that shape the structure of prokaryotic life.},
}
@article {pmid37070190,
year = {2023},
author = {Schönherr, S and Weissensteiner, H and Kronenberg, F and Forer, L},
title = {Haplogrep 3 - an interactive haplogroup classification and analysis platform.},
journal = {Nucleic acids research},
volume = {51},
number = {W1},
pages = {W263-W268},
pmid = {37070190},
issn = {1362-4962},
mesh = {Humans ; Phylogeny ; *Software ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Biological Evolution ; },
abstract = {Over the last decade, Haplogrep has become a standard tool for haplogroup classification in the field of human mitochondrial DNA and is widely used by medical, forensic, and evolutionary researchers. Haplogrep scales well for thousands of samples, supports many file formats and provides an intuitive graphical web interface. Nevertheless, the currently available version has limitations when applying it to large biobank-scale data. In this paper, we present a major upgrade to the software by adding (a) haplogroup summary statistics and variant annotations from various publicly available genome databases, (b) an interface to connect new phylogenetic trees, (c) a new state-of-the-art web framework managing large scale data, (d) algorithmic adaptions to improve FASTA classification using BWA-specific alignment rules and (e) a pre-classification quality control step for VCF samples. These improvements will give researchers the opportunity to classify thousands of samples as usual but providing additional ways to investigate the dataset directly in the browser. The web service and its documentation can be accessed freely without any registration at https://haplogrep.i-med.ac.at.},
}
@article {pmid37063179,
year = {2023},
author = {Tyszka, AS and Bretz, EC and Robertson, HM and Woodcock-Girard, MD and Ramanauskas, K and Larson, DA and Stull, GW and Walker, JF},
title = {Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1125107},
pmid = {37063179},
issn = {1664-462X},
abstract = {Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles' evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles' evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.},
}
@article {pmid37045318,
year = {2022},
author = {Hasan, ME and Hasan, A and Béarez, P and Shen, KN and Chang, CW and Tran, TTV and Golani, D and Al-Saboonchi, A and Siddiqui, PJA and Durand, JD},
title = {Planiliza lauvergnii (Eydoux &amp; Souleyet, 1850), a senior synonym of Planiliza affinis (Günther, 1861) with a re-evaluation of keeled back mullets&amp;nbsp;(Mugiliformes: Mugilidae).},
journal = {Zootaxa},
volume = {5194},
number = {4},
pages = {497-518},
doi = {10.11646/zootaxa.5194.4.2},
pmid = {37045318},
issn = {1175-5334},
mesh = {Animals ; *Smegmamorpha ; Phylogeny ; Fishes/genetics ; Biological Evolution ; Mitochondria ; },
abstract = {The taxonomic status of the keeled back mullets (Teleostei: Mugilidae) has been reinvestigated. Two nominal mugilid species having keeled backs from East Asia: Mugil lauvergnii Eydoux &amp; Souleyet, 1850 and Mugil affinis Günther, 1861 have been re-evaluated through examination of the holotypes and fresh specimens. Comparison of morpho-meristic characters of the holotypes shows that both species are identical. Phylogenetic analysis based on mitochondrial cytochrome c oxidase 1 (CO1) confirmed morphological data by highlighting presence of a single clade from East Asia. Mugil lauvergnii (=Planiliza lauvergnii) is thus the sole keeled back mullet from East Asia and a senior synonym of Mugil affinis (=Planiliza affinis). The taxonomic status of two other keeled back mullets, Planiliza carinata and P. klunzingeri, is also contentious due to their similar morphology. Meristic and morphometric variation as well as sequence divergence between the two species are limited but phylogenetic analyses delineate well-supported clades consistent with biogeography and currently accepted taxonomy. Planiliza carinata and P. klunzingeri share a recent common ancestor in a Maximum Likelihood tree, with separate distribution ranges while P. lauvergnii formed a paraphyletic lineage. Based on present findings, we suggest maintenance of the taxonomic distinction of P. klunzingeri and P. carinata and discuss its evolutionary significance.},
}
@article {pmid37045317,
year = {2022},
author = {Opler, PA and Stout, TL and Back, W and Zhang, J and Cong, Q and Shen, J and Grishin, NV},
title = {DNA barcodes reveal different speciation scenarios in the four North American Anthocharis Boisduval, Rambur, [Duménil] &amp; Graslin, [1833] (Lepidoptera: Pieridae: Pierinae: Anthocharidini) species groups.},
journal = {Zootaxa},
volume = {5194},
number = {4},
pages = {519-539},
doi = {10.11646/zootaxa.5194.4.3},
pmid = {37045317},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Butterflies/genetics ; DNA, Mitochondrial/genetics ; Mitochondria ; Phylogeny ; },
abstract = {The mitochondrial DNA COI barcode segment sequenced from American Anthocharis specimens across their distribution ranges partitions them into four well-separated species groups and reveals different levels of differentiation within these groups. The lanceolata group experienced the deepest divergence. About 2.7% barcode difference separates the two species: A. lanceolata Lucas, 1852 including A. lanceolata australis (F. Grinnell, 1908), from A. desertolimbus J. Emmel, T. Emmel &amp; Mattoon, 1998. The sara group consists of three species distinctly defined by more than 2% sequence divergence: A. sara Lucas, 1852, A. julia W. H. Edwards, 1872, and A. thoosa (Scudder, 1878). Our treatment is fully consistent with morphological evidence largely based on the characters of fifth instar larvae and pupal cone curvature (Stout, 2005, 2018). In barcodes, it is not possible to see evidence of introgression or hybridization between the three species, and identification by morphology of immature stages always agrees with DNA barcode identification. Interestingly, A. thoosa exhibited the largest intraspecific divergence in DNA barcodes, and several of its metapopulations are identifiable by haplotypes. The cethura group is characterized by the smallest divergence and is best considered as a single species variable in expression of yellow coloration: A cethura C. Felder &amp; R. Felder, 1865. Notably, the most sexually dimorphic subspecies A. cethura morrisoni W. H. Edwards, 1881 is the most distinct by the barcodes. Finally, the midea group barcodes do not always separate A. midea (Hübner, [1809]) and A. limonea (A. Butler, 1871) and we observe gradual accumulation of differences from north (northeastern USA) to south (Hidalgo, Mexico). This barcode gradient suggests a recent origin of the two midea group species and provides another example of vicariant sister species well defined by morphology, ecology and geography, but not necessarily by DNA barcodes.},
}
@article {pmid37044183,
year = {2023},
author = {Chen, H and Huang, L and Yu, J and Miao, Y and Liu, C},
title = {Mitochondrial genome of Artemisia argyi L. suggested conserved mitochondrial protein-coding genes among genera Artemisia, Tanacetum and Chrysanthemum.},
journal = {Gene},
volume = {871},
number = {},
pages = {147427},
doi = {10.1016/j.gene.2023.147427},
pmid = {37044183},
issn = {1879-0038},
mesh = {Humans ; *Genome, Mitochondrial ; *Artemisia/genetics ; *Tanacetum/genetics ; *Chrysanthemum/genetics ; Phylogeny ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; },
abstract = {BACKGROUND: Artemisia argyi L., also known as mugwort, is a perennial herb whose leaves are commonly used as a source of traditional medicines. However, the evolution and structure of the mitochondrial genome (mitogenome) in A. argyi remain unclear. In this study, the mitogenome of A. argyi was assembled and characterized for the first time.<br><br>RESULTS: The mitogenome of A. argyi was a circular molecule of 229,354&#xa0;bp. It encodes 56 genes, including 33 protein-coding genes (PCGs), 20 tRNA genes, and three rRNA genes, and three pseudogenes. Five trans-spliced introns were observed in three PCGs namely, nad1, nad2 and nad5. Repeat analysis identified 65 SSRs, 14 tandem repeats, and 167 dispersed repeats. The A. argyi mitogenome contains 12 plastid transfer sequences from 79&#xa0;bp to 2552&#xa0;bp. Five conserved MTPTs were identified in all 18 Asteraceae species. Comparison of mitogenome between A. argyi and one Artemisia specie and two Chrysanthemum species showed 14 conserved gene clusters. Phylogenetic analysis with organelle genomes of A. argyi and 18 other Anthemideae plants showed inconsistent phylogenetic trees, which implied that the evolutionary rates of PCGs and rrna genes derived from mitochondrion and plastid were incongruent. The Ka/Ks ratio of the 27 shared protein-coding genes in the 18 Anthemideae species are all less than 1 indicating that these genes were under the effect of purifying selection. Lastly, a total of 568 RNA editing sites in PCGs were further identified. The average editing frequency of non-synonymous changes was significantly higher than that of synonymous changes (one-sample Student's t-test, p-values&#xa0;&#x2264;&#xa0;0.05) in three tissues (root, leaf and stem).<br><br>CONCLUSIONS: In this study, the gene content, genome size, genome comparison, mitochondrial plastid sequences, dN/dS analysis of mitochondrial protein-coding genes, and RNA-editing events in A. argyi mitogenome were determined, providing insights into the phylogenetic relationships of Asteraceae plant.},
}
@article {pmid37042115,
year = {2023},
author = {Metcalfe, NB and Bellman, J and Bize, P and Blier, PU and Crespel, A and Dawson, NJ and Dunn, RE and Halsey, LG and Hood, WR and Hopkins, M and Killen, SS and McLennan, D and Nadler, LE and Nati, JJH and Noakes, MJ and Norin, T and Ozanne, SE and Peaker, M and Pettersen, AK and Przybylska-Piech, A and Rathery, A and Récapet, C and Rodríguez, E and Salin, K and Stier, A and Thoral, E and Westerterp, KR and Westerterp-Plantenga, MS and Wojciechowski, MS and Monaghan, P},
title = {Solving the conundrum of intra-specific variation in metabolic rate: A multidisciplinary conceptual and methodological toolkit: New technical developments are opening the door to an understanding of why metabolic rate varies among individual animals of a species: New technical developments are opening the door to an understanding of why metabolic rate varies among individual animals of a species.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {6},
pages = {e2300026},
doi = {10.1002/bies.202300026},
pmid = {37042115},
issn = {1521-1878},
support = {MC_UU_00014/4/MRC_/Medical Research Council/United Kingdom ; RG/17/12/33167/BHF_/British Heart Foundation/United Kingdom ; },
mesh = {Animals ; Humans ; *Basal Metabolism ; Phenotype ; },
abstract = {Researchers from diverse disciplines, including organismal and cellular physiology, sports science, human nutrition, evolution and ecology, have sought to understand the causes and consequences of the surprising variation in metabolic rate found among and within individual animals of the same species. Research in this area has been hampered by differences in approach, terminology and methodology, and the context in which measurements are made. Recent advances provide important opportunities to identify and address the key questions in the field. By bringing together researchers from different areas of biology and biomedicine, we describe and evaluate these developments and the insights they could yield, highlighting the need for more standardisation across disciplines. We conclude with a list of important questions that can now be addressed by developing a common conceptual and methodological toolkit for studies on metabolic variation in animals.},
}
@article {pmid37039888,
year = {2023},
author = {Zuccoli, GS and Nascimento, JM and Moraes-Vieira, PM and Rehen, SK and Martins-de-Souza, D},
title = {Mitochondrial, cell cycle control and neuritogenesis alterations in an iPSC-based neurodevelopmental model for schizophrenia.},
journal = {European archives of psychiatry and clinical neuroscience},
volume = {273},
number = {8},
pages = {1649-1664},
pmid = {37039888},
issn = {1433-8491},
support = {2016/04912-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/14666-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2014/21035-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2015/15626-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/25588-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/00098-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/01410-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Adult ; Humans ; *Schizophrenia/metabolism ; *Induced Pluripotent Stem Cells/metabolism ; Cell Differentiation/genetics ; Reactive Oxygen Species/metabolism ; Proteomics ; Cell Cycle Checkpoints ; Mitochondria/metabolism ; },
abstract = {Schizophrenia is a severe psychiatric disorder of neurodevelopmental origin that affects around 1% of the world's population. Proteomic studies and other approaches have provided evidence of compromised cellular processes in the disorder, including mitochondrial function. Most of the studies so far have been conducted on postmortem brain tissue from patients, and therefore, do not allow the evaluation of the neurodevelopmental aspect of the disorder. To circumvent that, we studied the mitochondrial and nuclear proteomes of neural stem cells (NSCs) and neurons derived from induced pluripotent stem cells (iPSCs) from schizophrenia patients versus healthy controls to assess possible alterations related to energy metabolism and mitochondrial function during neurodevelopment in the disorder. Our results revealed differentially expressed proteins in pathways related to mitochondrial function, cell cycle control, DNA repair and neuritogenesis and their possible implication in key process of neurodevelopment, such as neuronal differentiation and axonal guidance signaling. Moreover, functional analysis of NSCs revealed alterations in mitochondrial oxygen consumption in schizophrenia-derived cells and a tendency of higher levels of intracellular reactive oxygen species (ROS). Hence, this study shows evidence that alterations in important cellular processes are present during neurodevelopment and could be involved with the establishment of schizophrenia, as well as the phenotypic traits observed in adult patients. Neural stem cells (NSCs) and neurons were derived from induced pluripotent stem cells (iPSCs) from schizophrenia patients and controls. Proteomic analyses were performed on the enriched mitochondrial and nuclear fractions of NSCs and neurons. Whole-cell proteomic analysis was also performed in neurons. Our results revealed alteration in proteins related to mitochondrial function, cell cycle control, among others. We also performed energy pathway analysis and reactive oxygen species (ROS) analysis of NSCs, which revealed alterations in mitochondrial oxygen consumption and a tendency of higher levels of intracellular ROS in schizophrenia-derived cells.},
}
@article {pmid37029959,
year = {2023},
author = {Galindo, LJ and Prokina, K and Torruella, G and López-García, P and Moreira, D},
title = {Maturases and Group II Introns in the Mitochondrial Genomes of the Deepest Jakobid Branch.},
journal = {Genome biology and evolution},
volume = {15},
number = {4},
pages = {},
pmid = {37029959},
issn = {1759-6653},
mesh = {Humans ; Introns ; Phylogeny ; *Genome, Mitochondrial ; Eukaryota/genetics ; Eukaryotic Cells ; },
abstract = {Ophirinina is a recently described suborder of jakobid protists (Excavata) with only one described species to date, Ophirina amphinema. Despite the acquisition and analysis of massive transcriptomic and mitogenomic sequence data from O. amphinema, its phylogenetic position among excavates remained inconclusive, branching as sister group either to all Jakobida or to all Discoba. From a morphological perspective, it has not only several typical jakobid features but also unusual traits for this group, including the morphology of mitochondrial cristae (sac-shaped to flattened-curved cristae) and the presence of two flagellar vanes. In this study, we have isolated, morphologically characterized, and sequenced genome and transcriptome data of two new Ophirinina species: Ophirina chinija sp. nov. and Agogonia voluta gen. et sp. nov. Ophirina chinija differs from O. amphinema in having rounded cell ends, subapically emerging flagella and a posterior cell protrusion. The much more distantly related A. voluta has several unique ultrastructural characteristics, including sac-shaped mitochondrial cristae and a complex "B" fiber. Phylogenomic analyses with a large conserved-marker dataset supported the monophyly of Ophirina and Agogonia within the Ophirinina and, more importantly, resolved the conflicting position of ophirinids as the sister clade to all other jakobids. The characterization of the mitochondrial genomes showed that Agogonia differs from all known gene-rich jakobid mitogenomes by the presence of two group II introns and their corresponding maturase protein genes. A phylogenetic analysis of the diversity of known maturases confirmed that the Agogonia proteins are highly divergent from each other and define distant families among the prokaryotic and eukaryotic maturases. This opens the intriguing possibility that, compared to other jakobids, Ophirinina may have retained additional mitochondrial elements that may help to understand the early diversification of eukaryotes and the evolution of mitochondria.},
}
@article {pmid37023388,
year = {2023},
author = {Danial, JSH and Jenner, A and Garcia-Saez, AJ and Cosentino, K},
title = {Real-Time Growth Kinetics Analysis of Macromolecular Assemblies in Cells with Single Molecule Resolution.},
journal = {The journal of physical chemistry. A},
volume = {127},
number = {15},
pages = {3490-3496},
doi = {10.1021/acs.jpca.3c00368},
pmid = {37023388},
issn = {1520-5215},
mesh = {Kinetics ; *Software ; },
abstract = {Single molecule fluorescence microscopy has the unique advantage to provide real-time information on the spatiotemporal assembly of individual protein complexes in cellular membranes. This includes the assembly of proteins into oligomer species of numerous copy numbers. However, there is a need for improved tracing analysis of the real-time growth kinetics of these assemblies in cells with single molecule resolution. Here, we present an automated analysis software to accurately measure the real-time kinetics of assembly of individual high-order oligomer complexes. Our software comes with a simple Graphical User Interface (GUI), is available as a source code and an executable, and can analyze a full data set of several hundred to thousand molecules in less than 2 minutes. Importantly, this software is suitable for the analysis of intracellular protein oligomers, whose stoichiometry is usually more difficult to quantify due to variability in signal detection in the different areas of the cell. We validated our method with simulated ground-truth data and time-lapse images of diffraction-limited oligomeric assemblies of BAX and BAK proteins on mitochondria of cells undergoing apoptosis. Our approach provides the broad community of biologists with a fast, user-friendly tool to trace the compositional evolution of macromolecular assemblies, and potentially model their growth for a deeper understanding of the structural and biophysical mechanisms underlying their functions.},
}
@article {pmid37021319,
year = {2023},
author = {Grosser, MR and Sites, SK and Murata, MM and Lopez, Y and Chamusco, KC and Love Harriage, K and Grosser, JW and Graham, JH and Gmitter, FG and Chase, CD},
title = {Plant mitochondrial introns as genetic markers - conservation and variation.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1116851},
pmid = {37021319},
issn = {1664-462X},
abstract = {Plant genomes are comprised of nuclear, plastid and mitochondrial components characterized by different patterns of inheritance and evolution. Genetic markers from the three genomes provide complementary tools for investigations of inheritance, genetic relationships and phenotypic contributions. Plant mitochondrial genomes are challenging for universal marker development because they are highly variable in terms of size, gene order and intergenic sequences and highly conserved with respect to protein-coding sequences. PCR amplification of introns with primers that anneal to conserved, flanking exons is effective for the development of polymorphic nuclear genome markers. The potential for plant mitochondrial intron polymorphisms to distinguish between congeneric species or intraspecific varieties has not been systematically investigated and is possibly constrained by requirements for intron secondary structure and interactions with co-evolved organelle intron splicing factors. To explore the potential for broadly applicable plant mitochondrial intron markers, PCR primer sets based upon conserved sequences flanking 11 introns common to seven angiosperm species were tested across a range of plant orders. PCR-amplified introns were screened for indel polymorphisms among a group of cross-compatible Citrus species and relatives; two Raphanus sativus mitotypes; representatives of the two Phaseolus vulgaris gene pools; and congeneric pairs of Cynodon, Cenchrus, Solanum, and Vaccinium species. All introns were successfully amplified from each plant entry. Length polymorphisms distinguishable by gel electrophoresis were common among genera but infrequent within genera. Sequencing of three introns amplified from 16 entries identified additional short indel polymorphisms and nucleotide substitutions that separated Citrus, Cynodon, Cenchrus and Vaccinium congeners, but failed to distinguish Solanum congeners or representatives of the Phaseolus vulgaris major gene pools. The ability of primer sets to amplify a wider range of plant species' introns and the presence of intron polymorphisms that distinguish congeners was confirmed by in silico analysis. While mitochondrial intron variation is limited in comparison to nuclear introns, these exon-based primer sets provide robust tools for the amplification of mitochondrial introns across a wide range of plant species wherein useful polymorphisms can be identified.},
}
@article {pmid37017198,
year = {2023},
author = {Parida, M and Gouda, G and Chidambaranathan, P and Umakanta, N and Katara, JL and Sai, CB and Samantaray, S and Patra, BC and Mohapatra, T},
title = {Mitochondrial markers differentiate two distinct phylogenetic groups in indigenous rice landraces of northeast India: an evolutionary insight.},
journal = {Journal of genetics},
volume = {102},
number = {},
pages = {},
pmid = {37017198},
issn = {0973-7731},
mesh = {Phylogeny ; *Oryza/genetics ; India ; },
abstract = {The inheritance of the mitochondria genome and its diversity is unique for genetic and evolutionary studies relative to nuclear genomes. Northeast India and Himalayan regions are considered as one of the centres of indica rice origin. Also, rice diversity in northeast India is very distinct and highly suited for evolutionary studies. Although reports are available on the genetic diversity of indigenous northeast rice landraces, its relationship with the wild relatives is not yet properly explored and understood. In an attempt, mitochondrial markers were used to study the evolutionary relationship between the 68 landraces of northeast India and wild relatives (O. rufipogon and O. nivara) along with IR64 (indica) and Nipponbare (japonica) were taken as reference cultivars. Phylogenetically, the findings include two distinct clusters in the indigenous northeast India landraces representing indica and japonica groups. Further, the wild relatives and ~60% of northeast India landraces were identified to be closely related to the Nipponbare cluster. Besides, landraces of northeast India grouping with the indica group (IR64) are characterized by the absence of wild relatives. This indicates that there are two distinct evolutionary paths in the origin of northeast Indian rice landraces based on mitochondrial markers diversity and it is proposed that the inheritance of mitochondria, mitonuclear genome interactions, and bottleneck events could have genetically separated these two phylogenetically unique groups of northeast rice landraces.},
}
@article {pmid37009644,
year = {2023},
author = {Cheng, B and Zhou, M and Tang, T and Hassan, MJ and Zhou, J and Tan, M and Li, Z and Peng, Y},
title = {A Trifolium repens flavodoxin-like quinone reductase 1 (TrFQR1) improves plant adaptability to high temperature associated with oxidative homeostasis and lipids remodeling.},
journal = {The Plant journal : for cell and molecular biology},
volume = {115},
number = {2},
pages = {369-385},
doi = {10.1111/tpj.16230},
pmid = {37009644},
issn = {1365-313X},
support = {sccxtd-2020-16//Sichuan Forage Innovation Team Program/ ; 2022YFH0059//Sichuan Science and Technology Program/ ; },
mesh = {*Trifolium/genetics/metabolism ; Flavodoxin/genetics/metabolism ; Diglycerides/metabolism ; Phylogeny ; Temperature ; Plant Proteins/genetics/metabolism ; Oxidative Stress ; *Arabidopsis/genetics/metabolism ; Homeostasis ; Gene Expression Regulation, Plant ; Plants, Genetically Modified/metabolism ; },
abstract = {Maintenance of stable mitochondrial respiratory chains could enhance adaptability to high temperature, but the potential mechanism was not elucidated clearly in plants. In this study, we identified and isolated a TrFQR1 gene encoding the flavodoxin-like quinone reductase 1 (TrFQR1) located in mitochondria of leguminous white clover (Trifolium repens). Phylogenetic analysis indicated that amino acid sequences of FQR1 in various plant species showed a high degree of similarities. Ectopic expression of TrFQR1 protected yeast (Saccharomyces cerevisiae) from heat damage and toxic levels of benzoquinone, phenanthraquinone and hydroquinone. Transgenic Arabidopsis thaliana and white clover overexpressing TrFQR1 exhibited significantly lower oxidative damage and better photosynthetic capacity and growth than wild-type in response to high-temperature stress, whereas AtFQR1-RNAi A. thaliana showed more severe oxidative damage and growth retardation under heat stress. TrFQR1-transgenic white clover also maintained better respiratory electron transport chain than wild-type plants, as manifested by significantly higher mitochondrial complex II and III activities, alternative oxidase activity, NAD(P)H content, and coenzyme Q10 content in response to heat stress. In addition, overexpression of TrFQR1 enhanced the accumulation of lipids including phosphatidylglycerol, monogalactosyl diacylglycerol, sulfoquinovosyl diacylglycerol and cardiolipin as important compositions of bilayers involved in dynamic membrane assembly in mitochondria or chloroplasts positively associated with heat tolerance. TrFQR1-transgenic white clover also exhibited higher lipids saturation level and phosphatidylcholine:phosphatidylethanolamine ratio, which could be beneficial to membrane stability and integrity during a prolonged period of heat stress. The current study proves that TrFQR1 is essential for heat tolerance associated with mitochondrial respiratory chain, cellular reactive oxygen species homeostasis, and lipids remodeling in plants. TrFQR1 could be selected as a key candidate marker gene to screen heat-tolerant genotypes or develop heat-tolerant crops via molecular-based breeding.},
}
@article {pmid36994538,
year = {2023},
author = {Qiu, L and Dong, J and Li, X and Parey, SH and Tan, K and Orr, M and Majeed, A and Zhang, X and Luo, S and Zhou, X and Zhu, C and Ji, T and Niu, Q and Liu, S and Zhou, X},
title = {Defining honeybee subspecies in an evolutionary context warrants strategized conservation.},
journal = {Zoological research},
volume = {44},
number = {3},
pages = {483-493},
pmid = {36994538},
issn = {2095-8137},
mesh = {Bees/genetics ; Animals ; Phylogeny ; Phenotype ; *Mitochondria ; },
abstract = {Despite the urgent need for conservation consideration, strategic action plans for the preservation of the Asian honeybee, Apis cerana Fabricius, 1793, remain lacking. Both the convergent and divergent adaptations of this widespread insect have led to confusing phenotypical traits and inconsistent infraspecific taxonomy. Unclear subspecies boundaries pose a significant challenge to honeybee conservation efforts, as it is difficult to effectively prioritize conservation targets without a clear understanding of subspecies identities. Here, we investigated genome variations in 362 worker bees representing almost all populations of mainland A. cerana to understand how evolution has shaped its population structure. Whole-genome single nucleotide polymorphisms (SNPs) based on nuclear sequences revealed eight putative subspecies, with all seven peripheral subspecies exhibiting mutually exclusive monophyly and distinct genetic divergence from the widespread central subspecies. Our results demonstrated that most classic morphological traits, including body size, were related to the climatic variables of the local habitats and did not reflect the true evolutionary history of the organism. Thus, such morphological traits were not suitable for subspecific delineation. Conversely, wing vein characters showed relative independence to the environment and supported the subspecies boundaries inferred from nuclear genomes. Mitochondrial phylogeny further indicated that the present subspecies structure was a result of multiple waves of population divergence from a common ancestor. Based on our findings, we propose that criteria for subspecies delineation should be based on evolutionary independence, trait distinction, and geographic isolation. We formally defined and described eight subspecies of mainland A. cerana. Elucidation of the evolutionary history and subspecies boundaries enables a customized conservation strategy for both widespread and endemic honeybee conservation units, guiding colony introduction and breeding.},
}
@article {pmid36993903,
year = {2023},
author = {Dalle Carbonare, L and Jiménez, JC and Lichtenauer, S and van Veen, H},
title = {Plant responses to limited aeration: Advances and future challenges.},
journal = {Plant direct},
volume = {7},
number = {3},
pages = {e488},
pmid = {36993903},
issn = {2475-4455},
abstract = {Limited aeration that is caused by tissue geometry, diffusion barriers, high elevation, or a flooding event poses major challenges to plants and is often, but not exclusively, associated with low oxygen. These processes span a broad interest in the research community ranging from whole plant and crop responses, post-harvest physiology, plant morphology and anatomy, fermentative metabolism, plant developmental processes, oxygen sensing by ERF-VIIs, gene expression profiles, the gaseous hormone ethylene, and O2 dynamics at cellular resolution. The International Society for Plant Anaerobiosis (ISPA) gathers researchers from all over the world contributing to understand the causes, responses, and consequences of limited aeration in plants. During the 14th ISPA meeting, major research progress was related to the evolution of O2 sensing mechanisms and the intricate network that balances low O2 signaling. Here, the work moved beyond flooding stress and emphasized novel underexplored roles of low O2 and limited aeration in altitude adaptation, fruit development and storage, and the vegetative development of growth apices. Regarding tolerance towards flooding, the meeting stressed the relevance and regulation of developmental plasticity, aerenchyma, and barrier formation to improve internal aeration. Additional newly explored flood tolerance traits concerned resource balance, senescence, and the exploration of natural genetic variation for novel tolerance loci. In this report, we summarize and synthesize the major progress and future challenges for low O2 and aeration research presented at the conference.},
}
@article {pmid36981035,
year = {2023},
author = {Kundu, S and Kamalakannan, M and Mukherjee, T and Banerjee, D and Kim, HW},
title = {Genetic Characterization and Insular Habitat Enveloping of Endangered Leaf-Nosed Bat, Hipposideros nicobarulae (Mammalia: Chiroptera) in India: Phylogenetic Inference and Conservation Implication.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
pmid = {36981035},
issn = {2073-4425},
mesh = {Animals ; *Chiroptera/genetics ; Phylogeny ; Bayes Theorem ; Mammals ; Mitochondria ; },
abstract = {The Nicobar leaf-nosed Bat (Hipposideros nicobarulae) was described in the early 20th century; however, its systematic classification has been debated for over 100 years. This endangered and endemic species has achieved species status through morphological data in the last 10 years. However, the genetic information and phylogenetic relationships of H. nicobarulae remain neglected. The generated mitochondrial cytochrome b gene (mtCytb) sequences (438 bp) of H. nicobarulae contains 53.42-53.65% AT composition and 1.82% variable sites. The studied species, H. nicobarulae maintains an 8.1% to 22.6% genetic distance from other Hipposideros species. The genetic divergence estimated in this study is congruent with the concept of gene speciation in bats. The Bayesian and Maximum-Likelihood phylogenies clearly discriminated all Hipposideros species and showed a sister relationship between H. nicobarulae and H. cf. antricola. Current mtCytb-based investigations of H. nicobarulae have confirmed the species status at the molecular level. Further, the MaxEnt-based species distribution modelling illustrates the most suitable habitat of H. nicobarulae (294 km[2]), of which the majority (171 km[2]) is located on Great Nicobar Island. The present study suggests rigorous sampling across the range, taxonomic coverage, the generation of multiple molecular markers (mitochondrial and nuclear), as well as more ecological information, which will help in understanding population genetic structure, habitat suitability, and the implementation of appropriate conservation action plans for H. nicobarulae and other Hipposideros species.},
}
@article {pmid36980901,
year = {2023},
author = {Hammar, F and Miller, DL},
title = {Genetic Diversity in the mtDNA of Physarum polycephalum.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
pmid = {36980901},
issn = {2073-4425},
mesh = {*Physarum polycephalum/genetics ; DNA, Mitochondrial/genetics ; Base Sequence ; Mitochondria/genetics ; Genetic Variation/genetics ; },
abstract = {The mtDNA of the myxomycete Physarum polycephalum can contain as many as 81 genes. These genes can be grouped in three different categories. The first category includes 46 genes that are classically found on the mtDNA of many organisms. However, 43 of these genes are cryptogenes that require a unique type of RNA editing (MICOTREM). A second category of gene is putative protein-coding genes represented by 26 significant open reading frames. However, these genes do not appear to be transcribed during the growth of the plasmodium and are currently unassigned since they do not have any apparent similarity to other classical mitochondrial protein-coding genes. The third category of gene is found in the mtDNA of some strains of P. polycephalum. These genes derive from a linear mitochondrial plasmid with nine significant, but unassigned, open reading frames which can integrate into the mitochondrial DNA by recombination. Here, we review the mechanism and evolution of the RNA editing necessary for cryptogene expression, discuss possible origins for the 26 unassigned open reading frames based on tentative identification of their protein product, and discuss the implications to mtDNA structure and replication of the integration of the linear mitochondrial plasmid.},
}
@article {pmid36977381,
year = {2023},
author = {Michels, PAM and Ginger, ML},
title = {Evolution: 'Millefoglie' origin of mitochondrial cristae.},
journal = {Current biology : CB},
volume = {33},
number = {6},
pages = {R219-R221},
doi = {10.1016/j.cub.2023.02.037},
pmid = {36977381},
issn = {1879-0445},
mesh = {*Mitochondria/genetics/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; Mitochondrial Membranes/metabolism ; },
abstract = {Striated intracytoplasmic membranes in alphaproteobacteria are often reminiscent of millefoglie pastries. A new study reveals a protein complex homologous to that responsible for mitochondrial cristae formation drives intracytoplasmic membrane formation, thereby establishing bacterial ancestry for the biogenesis of mitochondrial cristae.},
}
@article {pmid36972795,
year = {2023},
author = {Benites, P and Zaldívar-Riverón, A and Meza-Lázaro, RN and Samacá-Sáenz, E and Gutiérrez-Rodríguez, J and Hernández-López, A},
title = {Multiple introgression events during the diversification history of the edible Mexican grasshopper genus Sphenarium (Orthoptera: Pyrgomorphidae).},
journal = {Molecular phylogenetics and evolution},
volume = {183},
number = {},
pages = {107774},
doi = {10.1016/j.ympev.2023.107774},
pmid = {36972795},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Grasshoppers/genetics ; Mexico ; DNA, Mitochondrial/genetics/chemistry ; Mitochondria/genetics ; },
abstract = {Speciation with gene flow often leads to ambiguous phylogenetic reconstructions, reticulate patterns of relatedness and conflicting nuclear versus mitochondrial (mt) lineages. Here we employed a fragment of the COI mtDNA gene and nuclear genome-wide data (3RAD) to assess the diversification history of Sphenarium, an orthopteran genus of great economic importance in Mexico that is presumed to have experienced hybridisation events in some of its species. We carried out separate phylogenetic analyses to evaluate the existence of mito-nuclear discordance in the species relationships, and also assessed the genomic diversity and population genomic structure and investigated the existence of interspecific introgression and species limits of the taxa involved based on the nuclear dataset. The species delineation analyses discriminated all the currently recognised species, but also supported the existence of four undescribed species. The mt and nuclear topologies had four discordant species relationships that can be explained by mt introgression, where the mt haplotypes of S. purpurascens appear to have replaced those of S. purpurascens A and B, S. variabile and S. zapotecum. Moreover, our analyses supported the existence of nuclear introgression events between four species pairs that are distributed in the Sierra Madre del Sur province in southeast Mexico, with three of them occurring in the Tehuantepec Isthmus region. Our study highlights the relevance of genomic data to address the relative importance of allopatric isolation versus gene flow in speciation.},
}
@article {pmid36971557,
year = {2023},
author = {Shaliutina-Loginova, A and Francetic, O and Doležal, P},
title = {Bacterial Type II Secretion System and Its Mitochondrial Counterpart.},
journal = {mBio},
volume = {14},
number = {2},
pages = {e0314522},
pmid = {36971557},
issn = {2150-7511},
mesh = {*Type II Secretion Systems/metabolism ; Bacterial Proteins/genetics/metabolism ; Gram-Negative Bacteria/metabolism ; Periplasm/metabolism ; Bacterial Secretion Systems/metabolism ; },
abstract = {Over the billions of years that bacteria have been around, they have evolved several sophisticated protein secretion nanomachines to deliver toxins, hydrolytic enzymes, and effector proteins into their environments. Of these, the type II secretion system (T2SS) is used by Gram-negative bacteria to export a wide range of folded proteins from the periplasm across the outer membrane. Recent findings have demonstrated that components of the T2SS are localized in mitochondria of some eukaryotic lineages, and their behavior is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). This review focuses on recent advances in the field and discusses open questions concerning the function and evolution of miT2SSs.},
}
@article {pmid36966978,
year = {2023},
author = {Edera, AA and Howell, KA and Nevill, PG and Small, I and Sanchez-Puerta, MV},
title = {Evolution of cox2 introns in angiosperm mitochondria and efficient splicing of an elongated cox2i691 intron.},
journal = {Gene},
volume = {869},
number = {},
pages = {147393},
doi = {10.1016/j.gene.2023.147393},
pmid = {36966978},
issn = {1879-0038},
mesh = {Introns/genetics ; *Magnoliopsida/genetics ; Mitochondria/genetics ; RNA Splicing ; Base Sequence ; },
abstract = {In angiosperms, the mitochondrial cox2 gene harbors up to two introns, commonly referred to as cox2i373 and cox2i691. We studied the cox2 from 222 fully-sequenced mitogenomes from 30 angiosperm orders and analyzed the evolution of their introns. Unlike cox2i373, cox2i691 shows a distribution among plants that is shaped by frequent intron loss events driven by localized retroprocessing. In addition, cox2i691 exhibits sporadic elongations, frequently in domain IV of introns. Such elongations are poorly related to repeat content and two of them showed the presence of LINE transposons, suggesting that increasing intron size is very likely due to nuclear intracelular DNA transfer followed by incorporation into the mitochondrial DNA. Surprisingly, we found that cox2i691 is erroneously annotated as absent in 30 mitogenomes deposited in public databases. Although each of the cox2 introns is ∼1.5 kb in length, a cox2i691 of 4.2 kb has been reported in Acacia ligulata (Fabaceae). It is still unclear whether its unusual length is due to a trans-splicing arrangement or the loss of functionality of the interrupted cox2. Through analyzing short-read RNA sequencing of Acacia with a multi-step computational strategy, we found that the Acacia cox2 is functional and its long intron is spliced in cis in a very efficient manner despite its length.},
}
@article {pmid36965057,
year = {2023},
author = {Speijer, D},
title = {How mitochondria showcase evolutionary mechanisms and the importance of oxygen.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {6},
pages = {e2300013},
doi = {10.1002/bies.202300013},
pmid = {36965057},
issn = {1521-1878},
mesh = {*Biological Evolution ; *Oxygen/metabolism ; Eukaryota/metabolism ; Bacteria/genetics/metabolism ; Mitochondria/metabolism ; },
abstract = {Darwinian evolution can be simply stated: natural selection of inherited variations increasing differential reproduction. However, formulated thus, links with biochemistry, cell biology, ecology, and population dynamics remain unclear. To understand interactive contributions of chance and selection, higher levels of biological organization (e.g., endosymbiosis), complexities of competing selection forces, and emerging biological novelties (such as eukaryotes or meiotic sex), we must analyze actual examples. Focusing on mitochondria, I will illuminate how biology makes sense of life's evolution, and the concepts involved. First, looking at the bacterium - mitochondrion transition: merging with an archaeon, it lost its independence, but played a decisive role in eukaryogenesis, as an extremely efficient aerobic ATP generator and internal ROS source. Second, surveying later mitochondrion adaptations and diversifications illustrates concepts such as constructive neutral evolution, dynamic interactions between endosymbionts and hosts, the contingency of life histories, and metabolic reprogramming. Without oxygen, mitochondria disappear; with (intermittent) oxygen diversification occurs in highly complex ways, especially upon (temporary) phototrophic substrate supply. These expositions show the Darwinian model to be a highly fruitful paradigm.},
}
@article {pmid36964263,
year = {2023},
author = {Jablonski, D and Ribeiro-Júnior, MA and Simonov, E and Šoltys, K and Meiri, S},
title = {A new, rare, small-ranged, and endangered mountain snake of the genus Elaphe from the Southern Levant.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {4839},
pmid = {36964263},
issn = {2045-2322},
mesh = {Animals ; Phylogeny ; *Colubridae ; Mitochondria/genetics ; Lebanon ; Syria ; DNA, Mitochondrial/genetics ; },
abstract = {The genus Elaphe Fitzinger, 1833 includes 17 species of charismatic, large-sized, non-venomous, Eurasian snakes. In the Western Palearctic, the genus is represented by three species from the Elaphe quatuorlineata group ranging from the Apennine peninsula to Central Asia. The southernmost population of this group is distributed in the mountains of the Southern Levant, with more than 400 km gap to other Elaphe populations. This population has been known to science for only 50 years and is virtually unstudied due to its extreme rarity. We studied these snakes' morphological and genetic variation from the three countries where they are known to occur, i.e., Israel (Hermon, the Israeli-controlled Golan Heights), Lebanon, and Syria. We used nine mitochondrial and nuclear genes, complete mitogenome sequences, and a comprehensive morphological examination including published data, our own field observations, and museum specimens, to study its relationship to other species in the group. The three currently recognized species of the group (E. quatuorlineata, E. sauromates, E. urartica), and the Levant population, form four deeply divergent, strongly supported clades. Three of these clades correspond to the abovementioned species while the Southern Levant clade, which is genetically and morphologically distinct from all named congeners, is described here as a new species, Elaphe druzei sp. nov. The basal divergence of this group is estimated to be the Late Miocene with subsequent radiation from 5.1 to 3.9 Mya. The revealed biogeography of the E. quatuorlineata group supports the importance of the Levant as a major center of endemism and diversity of biota in Eurasia. The new species is large-sized and is one of the rarest snakes in the Western Palearctic. Because of its small mountain distribution range, in an area affected by land use and climate change, the new Elaphe urgently needs strict protection. Despite political issues, we hope this will be based on the cooperation of all countries where the new species occurs.},
}
@article {pmid36951086,
year = {2023},
author = {Sloan, DB and DeTar, RA and Warren, JM},
title = {Aminoacyl-tRNA Synthetase Evolution within the Dynamic Tripartite Translation System of Plant Cells.},
journal = {Genome biology and evolution},
volume = {15},
number = {4},
pages = {},
pmid = {36951086},
issn = {1759-6653},
mesh = {Animals ; *Amino Acyl-tRNA Synthetases/genetics/metabolism ; Plant Cells/metabolism ; Amino Acid Sequence ; Cytosol/metabolism ; RNA, Transfer/genetics/metabolism ; },
abstract = {Eukaryotes maintain separate protein translation systems for nuclear and organellar genes, including distinct sets of tRNAs and aminoacyl-tRNA synthetases (aaRSs). In animals, mitochondrial-targeted aaRSs are expressed at lower levels and are less conserved in sequence than cytosolic aaRSs involved in translation of nuclear mRNAs, likely reflecting lower translational demands in mitochondria. In plants, translation is further complicated by the presence of plastids, which share most aaRSs with mitochondria. In addition, plant mitochondrial tRNA pools have a dynamic history of gene loss and functional replacement by tRNAs from other compartments. To investigate the consequences of these distinctive features of translation in plants, we analyzed sequence evolution in angiosperm aaRSs. In contrast to previously studied eukaryotic systems, we found that plant organellar and cytosolic aaRSs exhibit only a small difference in expression levels, and organellar aaRSs are slightly more conserved than cytosolic aaRSs. We hypothesize that these patterns result from high translational demands associated with photosynthesis in mature chloroplasts. We also investigated aaRS evolution in Sileneae, an angiosperm lineage with extensive mitochondrial tRNA replacement and aaRS retargeting. We predicted positive selection for changes in aaRS sequence resulting from these recent changes in subcellular localization and tRNA substrates but found little evidence for accelerated sequence divergence. Overall, the complex tripartite translation system in plant cells appears to have imposed more constraints on the long-term evolutionary rates of organellar aaRSs compared with other eukaryotic lineages, and plant aaRS protein sequences appear largely robust to more recent perturbations in subcellular localization and tRNA interactions.},
}
@article {pmid36949187,
year = {2023},
author = {Mühleip, A and Flygaard, RK and Baradaran, R and Haapanen, O and Gruhl, T and Tobiasson, V and Maréchal, A and Sharma, V and Amunts, A},
title = {Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex.},
journal = {Nature},
volume = {615},
number = {7954},
pages = {934-938},
pmid = {36949187},
issn = {1476-4687},
support = {MR/M00936X/1/MRC_/Medical Research Council/United Kingdom ; MR/T032154/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Cryoelectron Microscopy ; Electron Transport ; *Electron Transport Complex III/chemistry/metabolism/ultrastructure ; *Electron Transport Complex IV/chemistry/metabolism/ultrastructure ; *Mitochondria/chemistry/enzymology/metabolism/ultrastructure ; *Mitochondrial Membranes/chemistry/enzymology/metabolism/ultrastructure ; *Electron Transport Complex II/chemistry/metabolism/ultrastructure ; *Electron Transport Complex I/chemistry/metabolism/ultrastructure ; Protein Multimerization ; Protein Subunits/chemistry/metabolism ; Molecular Dynamics Simulation ; Binding Sites ; Evolution, Molecular ; },
abstract = {Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane[1]. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III2-IV2 supercomplex that contributes to the