一酸化炭素酸化菌の分子生物学的研究

概要

令和 4 年度

京都大学化学研究所 スーパーコンピュータシステム 利用報告書
一酸化炭素酸化菌の分子生物学的研究
Molecular biology of carboxydotrophs

Kyoto University, Graduate School of Agriculture, Division of Applied Biosciences,
Laboratory of Marine Microbiology, Takashi Yoshida
研究成果概要
Prokaryotes called carbon monoxide (CO) oxidizers use CO as carbon or energy sources with
CO dehydrogenases (CODHs), which are divided into nickel-containing CODH (Ni-CODH)
sensitive to O2 and aerotolerant molybdenum-containing CODH (Mo-CODH). For CO oxidizers,
redox state of surrounding environments may be a limiting factor to utilize CO because known CO
oxidizers have either Ni- or Mo-CODH. However, genome and phylogenetic analyses of our new
thermophilic bacterial isolate, strain G301, revealed that it is Parageobacillus sp. that has genes for
both Ni-CODH and Mo-CODH. By comparison of the G301 genome with its close relatives,

G301 was appeared to be the only isolate possessing both Ni-CODH and Mo-CODH genes
while its close relatives have either or none of them. Reconstruction of the respiratory
machinery indicated that CO oxidation by Ni-CODH was coupled with H2 production, and CO
oxidation by Mo-CODH was coupled with reduction of O2 and nitrate. Our genome comparison
revealed no significant differences in genome structures and cellular functions between the CO
oxidizers and the non-CO oxidizers of Parageobacillus, suggesting that genes encoding CODHs

would be retained exclusively for anaerobic and aerobic CO metabolisms and their related
respirations in this genus.
To expand diversity of CO oxidizers, we cultured sediment of Jiunji-onsen of Shizuoka
with CO and conducted metagenome analyses. We obtained Metagenomic Assembled Genomes
(MAGs) of Thermolithobacter ferrireducens as a newly hydrogenogenic CO oxidizers. Further
we successfully isolated the hydrogenogenic CO oxidizers from some aquatic environments and
sequenced their genomes.
Anaerobic CO oxidizers bearing Ni-CODH gain carbon and energy from CO with
metabolic pathways such as Wood-Ljungdahl pathway (WLP). WLP consists of two branches:
methyl branch that uptakes CO2 and H2 by formate dehydrogenase (Fdh) and carbonyl branch
that uptakes CO or CO2 by Ni-CODH/acetyl CoA synthase. To gain insight into microbial
contributions to CO metabolisms in the human gut, we analyzed prokaryotic MAGs in a gut
microbiome dataset. We identified 1,302 potential CO oxidizers (4.3%) out of 30,609 MAGs.
Majority of them belong to orders Oscillospirales (31.6%), Lachnospirales (29.1%), and
Veillonellales (26.3%) of phylum Bacillota. MASs of Oscillospirales and Lachnospirales
possessed incomplete WLP pathway. These MAGs lacked genes related to utilization of CO2 +

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H2 for formate synthesis but possessed genes for utilization of formate derived from glycolysis.
Veillonella MAGs possessed gene clusters possibly related to CO oxidization coupled with
oxaloacetate production and/or nitrate respiration.
CO is also occurred in the ocean. Aerobic CO oxidizers are predicted to consume over 80%
of oceanic CO. Although aerobic CO oxidizers are presumably to be ubiquitous in the ocean,
global distribution and diversity of them remain unknown. Thus, we investigated 52,325
marine MAGs to identify aerobic CO oxidizers bearing Mo-CODH and biogeographic
distribution of them. As a result, 1,792 MAGs belonging to 274 species in nine phyla were
identified as aerobic CO oxidizers. Depth, temperature, dissolved oxygen (DO), and salinity of
environments where MAGs of CO oxidizers and non-CO oxidizers distributed were not
significantly different (p>0.05), thus niche partitioning was not suggested.
発表論文（謝辞あり）
・Isolation and genomic and physiological characterization of Parageobacillus sp. ...