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Title: Structural and phylogenetic diversity of anaerobic carbon-monoxide dehydrogenases
Authors: Inoue, Masao
Nakamoto, Issei
Omae, Kimiho
Oguro, Tatsuki
Ogata, Hiroyuki
Yoshida, Takashi
Sako, Yoshihiko
Author's alias: 井上, 真男
大前, 公保
緒方, 博之
吉田, 天士
左子, 芳彦
Keywords: carbon-monoxide dehydrogenase
genomic context
structural prediction
functional prediction
molecular evolution
horizontal gene transfer
Issue Date: 17-Jan-2019
Publisher: Frontiers Media SA
Journal title: Frontiers in Microbiology
Volume: 9
Thesis number: 3353
Abstract: Anaerobic 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.
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.
DOI(Published Version): 10.3389/fmicb.2018.03353
PubMed ID: 30705673
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