Phylogenomic Evidence for a Myxococcal Contribution to the Mitochondrial Fatty Acid Beta-Oxidation
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{"title"=>"Phylogenomic evidence for a Myxococcal contribution to the Mitochondrial Fatty Acid Beta-Oxidation", "type"=>"journal", "authors"=>[{"first_name"=>"Agatha", "last_name"=>"Schlüter", "scopus_author_id"=>"7006811073"}, {"first_name"=>"Iñaki", "last_name"=>"Ruiz-Trillo", "scopus_author_id"=>"6508015789"}, {"first_name"=>"Aurora", "last_name"=>"Pujol", "scopus_author_id"=>"36148296400"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"362094097", "doi"=>"10.1371/journal.pone.0021989", "isbn"=>"1932-6203", "pmid"=>"21760940", "issn"=>"19326203", "scopus"=>"2-s2.0-79960054403", "sgr"=>"79960054403"}, "id"=>"b8ef8862-7ff7-38a7-8206-8f69e2a8858e", "abstract"=>"BACKGROUND: The origin of eukaryotes remains a fundamental question in evolutionary biology. Although it is clear that eukaryotic genomes are a chimeric combination of genes of eubacterial and archaebacterial ancestry, the specific ancestry of most eubacterial genes is still unknown. The growing availability of microbial genomes offers the possibility of analyzing the ancestry of eukaryotic genomes and testing previous hypotheses on their origins.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: Here, we have applied a phylogenomic analysis to investigate a possible contribution of the Myxococcales to the first eukaryotes. We conducted a conservative pipeline with homologous sequence searches against a genomic sampling of 40 eukaryotic and 357 prokaryotic genomes. The phylogenetic reconstruction showed that several eukaryotic proteins traced to Myxococcales. Most of these proteins were associated with mitochondrial lipid intermediate pathways, particularly enzymes generating reducing equivalents with pivotal roles in fatty acid β-oxidation metabolism. Our data suggest that myxococcal species with the ability to oxidize fatty acids transferred several genes to eubacteria that eventually gave rise to the mitochondrial ancestor. Later, the eukaryotic nucleocytoplasmic lineage acquired those metabolic genes through endosymbiotic gene transfer.\\n\\nCONCLUSIONS/SIGNIFICANCE: Our results support a prokaryotic origin, different from α-proteobacteria, for several mitochondrial genes. Our data reinforce a fluid prokaryotic chromosome model in which the mitochondrion appears to be an important entry point for myxococcal genes to enter eukaryotes.", "link"=>"http://www.mendeley.com/research/phylogenomic-evidence-myxococcal-contribution-mitochondrial-fatty-acid-betaoxidation", "reader_count"=>15, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>8, "Medicine and Dentistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>4}}, "reader_count_by_country"=>{"Czech Republic"=>1, "Germany"=>2, "Spain"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/758575"], "description"=>"<p>Symbol corresponds to the human annotation as found in NCBI. Support indicates the statistical support for a monophyletic myxococcal+eukaryotic group as obtained from the 1000-replicate ML bootstrap values (BV, in %) and the Bayesian posterior probability (PP). Localization indicates the localization determined for most of the studied eukaryotes. Taxa shown in the last column are the eukaryotes in which the TargetP program (<a href=\"http://www.cbs.dtu.dk/services/TargetP/\" target=\"_blank\">http://www.cbs.dtu.dk/services/TargetP/</a>) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021989#pone.0021989-Emanuelsson1\" target=\"_blank\">[52]</a> detected a putative mitochondria-targeting peptide. When generic lineage names, such as Archaeplastida, Excavata, Fungi, Metazoa or Trypanosomatids, are shown, at least two different species of this group were found to have a predicted signal peptide.</p>", "links"=>[], "tags"=>["eukaryotic", "proteins", "myxococcal"], "article_id"=>428952, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Agatha Schlüter", "Iñaki Ruiz-Trillo", "Aurora Pujol"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021989.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_eukaryotic_proteins_with_a_predicted_myxococcal_origin_/428952", "title"=>"List of eukaryotic proteins with a predicted myxococcal origin.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-07 02:29:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/758318"], "description"=>"<p>Schematic representation of the acyl-CoA pathway, including the β-oxidation cycle. Enzymes with myxococcal ancestry are indicated in green boxes. Abbreviations: ACS, acyl-CoA synthetase; ACD, acyl-CoA dehydrogenase; ETF, electron transport flavoprotein; ECH, enoyl-CoA hydratase; HADH, hydroxyacyl-CoA dehydrogenase; and TA, thioesterase.</p>", "links"=>[], "tags"=>["acyl-coa"], "article_id"=>428698, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Agatha Schlüter", "Iñaki Ruiz-Trillo", "Aurora Pujol"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021989.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_acyl_CoA_pathway_/428698", "title"=>"The acyl-CoA pathway.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-07 02:24:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/758486"], "description"=>"<p>(1) A hydrogen-consuming methanogenic archaeon established symbiosis with the hydrogen-producing mitochondrial ancestor. Previously, a fatty acid degrading myxococcal species transferred genes to the mitochondrial ancestor before the endosymbiotic event. (2) The methanogenic archaeon engulfed the symbiont that gave rise to the mitochondrion. Over time, genes were transferred to the eukaryotic nuclear genome via endosymbiotic gene transfer. Proteins with myxococcal, mitochondrial and archaeal ancestries are depicted in green, blue and yellow boxes, respectively.</p>", "links"=>[], "tags"=>["myxococcal", "genes"], "article_id"=>428866, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Agatha Schlüter", "Iñaki Ruiz-Trillo", "Aurora Pujol"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021989.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_of_transfer_of_myxococcal_genes_to_eukaryotes_/428866", "title"=>"Model of transfer of myxococcal genes to eukaryotes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-07 02:27:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/381478", "https://ndownloader.figshare.com/files/381513", "https://ndownloader.figshare.com/files/381571", "https://ndownloader.figshare.com/files/381612", "https://ndownloader.figshare.com/files/381791"], "description"=>"<div><h3>Background</h3><p>The origin of eukaryotes remains a fundamental question in evolutionary biology. Although it is clear that eukaryotic genomes are a chimeric combination of genes of eubacterial and archaebacterial ancestry, the specific ancestry of most eubacterial genes is still unknown. The growing availability of microbial genomes offers the possibility of analyzing the ancestry of eukaryotic genomes and testing previous hypotheses on their origins.</p> <h3>Methodology/Principal Findings</h3><p>Here, we have applied a phylogenomic analysis to investigate a possible contribution of the Myxococcales to the first eukaryotes. We conducted a conservative pipeline with homologous sequence searches against a genomic sampling of 40 eukaryotic and 357 prokaryotic genomes. The phylogenetic reconstruction showed that several eukaryotic proteins traced to Myxococcales. Most of these proteins were associated with mitochondrial lipid intermediate pathways, particularly enzymes generating reducing equivalents with pivotal roles in fatty acid β-oxidation metabolism. Our data suggest that myxococcal species with the ability to oxidize fatty acids transferred several genes to eubacteria that eventually gave rise to the mitochondrial ancestor. Later, the eukaryotic nucleocytoplasmic lineage acquired those metabolic genes through endosymbiotic gene transfer.</p> <h3>Conclusions/Significance</h3><p>Our results support a prokaryotic origin, different from α-proteobacteria, for several mitochondrial genes. Our data reinforce a fluid prokaryotic chromosome model in which the mitochondrion appears to be an important entry point for myxococcal genes to enter eukaryotes.</p> </div>", "links"=>[], "tags"=>["phylogenomic", "myxococcal", "mitochondrial", "fatty", "beta-oxidation"], "article_id"=>135358, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Agatha Schlüter", "Iñaki Ruiz-Trillo", "Aurora Pujol"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0021989.s001", "https://dx.doi.org/10.1371/journal.pone.0021989.s002", "https://dx.doi.org/10.1371/journal.pone.0021989.s003", "https://dx.doi.org/10.1371/journal.pone.0021989.s004", "https://dx.doi.org/10.1371/journal.pone.0021989.s005"], "stats"=>{"downloads"=>6, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phylogenomic_Evidence_for_a_Myxococcal_Contribution_to_the_Mitochondrial_Fatty_Acid_Beta_Oxidation/135358", "title"=>"Phylogenomic Evidence for a Myxococcal Contribution to the Mitochondrial Fatty Acid Beta-Oxidation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-07-07 01:29:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/758172"], "description"=>"<p>Bayesian phylogenetic trees of (i) the isocitrate dehydrogenase 3 NAD(+) alpha, beta and gamma genes, (ii) the acyl-CoA dehydrogenase C-2 to C-3 short chain gene (ACADS), and (iii) acetyl-CoA acyltransferase 2 (ACAA2). The Bayesian posterior probability (PP) until convergence diagnostic and 1000-replicate bootstrap values (BV) for ML trees are indicated if they were above 50%. A black dot indicates PP>0.95. Eukaryotic, myxococcal/δ-proteobacterial and α-proteobacterial taxa are highlighted in blue, red and green, respectively.</p>", "links"=>[], "tags"=>["ancestry", "eukaryotic"], "article_id"=>428541, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Agatha Schlüter", "Iñaki Ruiz-Trillo", "Aurora Pujol"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021989.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Myxococcal_ancestry_of_eukaryotic_proteins_/428541", "title"=>"Myxococcal ancestry of eukaryotic proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-07 02:22:21"}

PMC Usage Stats | Further Information

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Relative Metric

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