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Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres

1
Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
2
Univ Brest, CNRS, Ifremer, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, F-29280 Plouzané, France
*
Author to whom correspondence should be addressed.
Genes 2019, 10(11), 849; https://doi.org/10.3390/genes10110849
Received: 1 October 2019 / Revised: 22 October 2019 / Accepted: 23 October 2019 / Published: 26 October 2019
(This article belongs to the Section Microbial Genetics and Genomics)
Information on the biochemical pathways of carbon and energy metabolism in representatives of the deep lineage bacterial phylum Deferribacteres are scarce. Here, we report the results of the sequencing and analysis of the high-quality draft genome of the thermophilic chemolithoautotrophic anaerobe Deferribacter autotrophicus. Genomic data suggest that CO2 assimilation is carried out by recently proposed reversible tricarboxylic acid cycle (“roTCA cycle”). The predicted genomic ability of D. autotrophicus to grow due to the oxidation of carbon monoxide was experimentally proven. CO oxidation was coupled with the reduction of nitrate to ammonium. Utilization of CO most likely involves anaerobic [Ni, Fe]-containing CO dehydrogenase. This is the first evidence of CO oxidation in the phylum Deferribacteres. The genome of D. autotrophicus encodes a Nap-type complex of nitrate reduction. However, the conversion of produced nitrite to ammonium proceeds via a non-canonical pathway with the participation of hydroxylamine oxidoreductase (Hao) and hydroxylamine reductase. The genome contains 17 genes of putative multiheme c-type cytochromes and “e-pilin” genes, some of which are probably involved in Fe(III) reduction. Genomic analysis indicates that the roTCA cycle of CO2 fixation and putative Hao-enabled ammonification may occur in several members of the phylum Deferribacteres. View Full-Text
Keywords: autotrophic; thermophile; roTCA cycle; CO oxidation; Fe(III)-reduction; nitrate reduction autotrophic; thermophile; roTCA cycle; CO oxidation; Fe(III)-reduction; nitrate reduction
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Slobodkin, A.; Slobodkina, G.; Allioux, M.; Alain, K.; Jebbar, M.; Shadrin, V.; Kublanov, I.; Toshchakov, S.; Bonch-Osmolovskaya, E. Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres. Genes 2019, 10, 849.

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