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17 results for “mitochondrion”
Supplementary data for: Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochondrion
<p><span>DNA polymerases (DNAPs) synthesize DNA from deoxyribonucleotides in a semi-conservative manner and serve as the core of DNA replication and repair machinery. In eukaryotic cells, there are two genome-containing organelles, mitochondria and plastids, that were derived from an α-proteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNAPs that localize and work in them to maintain their genomes. The evolution of organellar DNAPs has yet to be fully understood because of two unsettled issues. First, the diversity of organellar DNAPs has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNAPs that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNAPs known to date show no phylogenetic affinity to those of the extant α-proteobacteria or cyanobacteria. </span><span>In this study, we identified from diverse eukaryotes 134</span> <span>family A DNAP sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNAPs were further examined experimentally. The results presented here suggest that the diversity of organellar DNAPs has been shaped by multiple transfers of the Pol</span><span>I</span><span> 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 two mitochondrial DNAPs, POP and a candidate of the direct descendant of the proto-mitochondrial DNAP, rdxPolA, identified in this study.</span></p>
Rapid evolution of mitochondrion-related genes in haplodiploid arthropods
<p>Amino acid sequences of orthologous groups that are available on https://i5k.gitlab.io/ArthroFam/arthropoda.html</p> <p>1. Zipped file of amino acid sequences</p> <p>arthropoda-seqs-all.zip</p> <p> </p> <p>2. Information of orthologous groups, gene names, and species names</p> <p>arthropoda-ortho-groups.txt</p> <p> </p> <p>3. MD5 values of the above files</p> <p>md5.txt</p>
Secretome dataset for: The ESCRT protein CHMP5 restricts bone formation by controlling endolysosome-mitochondrion-mediated cell senescence
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Supplementary data for: Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochondrion
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Proteomic dataset for: The ESCRT protein CHMP5 restricts bone formation by controlling endolysosome-mitochondrion-mediated cell senescence
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Transcriptome dataset for: The ESCRT protein CHMP5 restricts bone formation by controlling endolysosome-mitochondrion-mediated cell senescence
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Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids
<p>Mitochondria retain their own genomes as other bacterial endosymbiont-derived organelles. Nevertheless, no protein for DNA replication and repair is encoded in any mitochondrial genomes (mtDNAs) assessed to date, suggesting the nucleus primarily governs the maintenance of mtDNA. As the proteins of diverse evolutionary origins occupy a large proportion of the current mitochondrial proteomes, we anticipate finding the same evolutionary trend in the nucleus-encoded machinery for mtDNA maintenance. Indeed, none of the DNA polymerases (DNAPs) in the mitochondrial endosymbiont, a putative α-proteobacterium, seemingly had been inherited by their descendants (mitochondria), as none of the known types of mitochondrion-localized DNAP showed a specific affinity to the α-proteobacterial DNAPs. Nevertheless, we currently have no concrete idea of how and when the known types of mitochondrion-localized DNAPs emerged. We here explored the origins of mitochondrion-localized DNAPs after the improvement of the samplings of DNAPs from bacteria and phages/viruses. Past studies revealed that a set of mitochondrion-localized DNAPs in kinetoplastids and diplonemids, namely PolIB, PolIC, PolID, PolI-Perk1/2, and PolI-dipl (henceforth designated collectively as "PolIBCD+") have emerged from a single DNAP. In this study, we recovered an intimate connection between PolIBCD+ and the DNAPs found in a particular group of phages. Thus, the common ancestor of kinetoplastids and diplonemids most likely converted a laterally acquired phage DNAP into a mitochondrion-localized DNAP that was ancestral to PolIBCD+. The phage origin of PolIBCD+ hints at a potentially large contribution of proteins acquired via non-vertical processes to the machinery for mtDNA maintenance in kinetoplastids and diplonemids.</p>
Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids
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Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP
<p>We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. <em>Barthelona </em>spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one <em>Barthelona </em>strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. We here propose that strain PAP020 is incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substratelevel phosphorylation were detected. Instead, we detected the putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.</p>
Mitochondrion
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Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP
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Subcellular genomics shows pervasive within-mitochondrion single nucleotide variant heteroplasmy as revealed by single mitochondrion sequencing
GEO Series GSE107115. Mus musculus. 158 samples. Type: Expression profiling by high throughput sequencing.
MAVI1, an Endoplasmic Reticulum-localized Microprotein, Suppresses Antiviral Innate Immune Response by Targeting MAVS on Mitochondrion
GEO Series GSE221218. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Single-Mitochondrion Sequencing Uncovers Distinct Mutational Patterns and Heteroplasmy Landscape in Mouse Astrocytes and Neurons
GEO Series GSE218122. Mus musculus. 179 samples. Type: Other.
Data for "Hypotheses on the extended phenotype of the mitochondrion"
<p>Mitochondrial genome data associated with the manuscript "Hypotheses on the extended phenotype of the mitochondrion".</p> <p>This is simply a particular RefSeq mitochondrial data release. Note that NCBI does not appear to maintain an archive of past RefSeq mitochondrial data files.<br> </p>
Mitophagy and mitochondrion-related expression profiles in response to physiological and pathological hypoxia in the corneal epithelium
GEO Series GSE218718. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Disruption of mitochondrion-to-nucleus interaction in deceased cloned piglets
GEO Series GSE68877. Sus scrofa. 44 samples. Type: Expression profiling by array.
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OpenNeuro
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