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dc.contributor.authorInoue, Masaoen
dc.contributor.authorNakamoto, Isseien
dc.contributor.authorOmae, Kimihoen
dc.contributor.authorOguro, Tatsukien
dc.contributor.authorOgata, Hiroyukien
dc.contributor.authorYoshida, Takashien
dc.contributor.authorSako, Yoshihikoen
dc.contributor.alternative井上, 真男ja
dc.contributor.alternative大前, 公保ja
dc.contributor.alternative緒方, 博之ja
dc.contributor.alternative吉田, 天士ja
dc.contributor.alternative左子, 芳彦ja
dc.date.accessioned2019-05-14T04:24:46Z-
dc.date.available2019-05-14T04:24:46Z-
dc.date.issued2019-01-17-
dc.identifier.issn1664-302X-
dc.identifier.urihttp://hdl.handle.net/2433/241359-
dc.description.abstractAnaerobic Ni-containing carbon-monoxide dehydrogenases (Ni-CODHs) catalyze the reversible conversion between carbon monoxide and carbon dioxide as multi-enzyme complexes responsible for carbon fixation and energy conservation in anaerobic microbes. However, few biochemically characterized model enzymes exist, with most Ni-CODHs remaining functionally unknown. Here, we performed phylogenetic and structure-based Ni-CODH classification using an expanded dataset comprised of 1942 non-redundant Ni-CODHs from 1375 Ni-CODH-encoding genomes across 36 phyla. Ni-CODHs were divided into seven clades, including a novel clade. Further classification into 24 structural groups based on sequence analysis combined with structural prediction revealed diverse structural motifs for metal cluster formation and catalysis, including novel structural motifs potentially capable of forming metal clusters or binding metal ions, indicating Ni-CODH diversity and plasticity. Phylogenetic analysis illustrated that the metal clusters responsible for intermolecular electron transfer were drastically altered during evolution. Additionally, we identified novel putative Ni-CODH-associated proteins from genomic contexts other than the Wood–Ljungdahl pathway and energy converting hydrogenase system proteins. Network analysis among the structural groups of Ni-CODHs, their associated proteins and taxonomies revealed previously unrecognized gene clusters for Ni-CODHs, including uncharacterized structural groups with putative metal transporters, oxidoreductases, or transcription factors. These results suggested diversification of Ni-CODH structures adapting to their associated proteins across microbial genomes.en
dc.format.mimetypeapplication/pdf-
dc.language.isoeng-
dc.publisherFrontiers Media SAen
dc.rights© 2019 Inoue, Nakamoto, Omae, Oguro, Ogata, Yoshida and Sako. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.en
dc.subjectcarbon-monoxide dehydrogenaseen
dc.subjectgenomic contexten
dc.subjectstructural predictionen
dc.subjectfunctional predictionen
dc.subjectmolecular evolutionen
dc.subjecthorizontal gene transferen
dc.titleStructural and phylogenetic diversity of anaerobic carbon-monoxide dehydrogenasesen
dc.typejournal article-
dc.type.niitypeJournal Article-
dc.identifier.jtitleFrontiers in Microbiologyen
dc.identifier.volume9-
dc.relation.doi10.3389/fmicb.2018.03353-
dc.textversionpublisher-
dc.identifier.artnum3353-
dc.addressGraduate School of Agriculture, Kyoto Universityen
dc.addressGraduate School of Agriculture, Kyoto Universityen
dc.addressGraduate School of Agriculture, Kyoto Universityen
dc.addressGraduate School of Agriculture, Kyoto Universityen
dc.addressInstitute for Chemical Research, Kyoto Universityen
dc.addressGraduate School of Agriculture, Kyoto Universityen
dc.addressGraduate School of Agriculture, Kyoto Universityen
dc.identifier.pmid30705673-
dcterms.accessRightsopen access-
datacite.awardNumber16H06381-
jpcoar.funderName日本学術振興会ja
jpcoar.funderName.alternativeJapan Society for the Promotion of Science (JSPS)en
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