Genomic adaptation of the thermophilic hydrogenogenic carboxydotrophic bacterium from marine sediment, Calderihabitans maritimus KKC1, driven by carbon monoxide dehydrogenases
1Kyoto univ. agri., 2AIST
A novel thermophile Calderihabitans maritimus KKC1 (KKC1) isolated from a submerged marine caldera (Kikai caldera) can grow on carbon monoxide (CO) (carboxydotrophic) and produce hydrogen as a byproduct (hydrogenogenic). KKC1 was phylogenetically related to thermophiles of the genus Moorella, one of which produces acetate in carboxydotrophic growth. In this study, we determined the genome sequence of KKC1 and compared it with two genomes from different strains of Moorella, in order to reveal the relationships between the genomic contents and the variations of carboxydotrophy. By genome-wide phylogenetic analysis, it was strongly suggested that KKC1 and Moorella strains evolved from a common ancestor. KKC1 shared genes related to information process and basic metabolism with Moorella strains. On the other hand, many genes involved in energy production and conversion were found only in KKC1 genome. In particular, KKC1 genome harbored six genes encoding catalytic subunit (CooS) of [Ni,Fe]-carbon monoxide dehydrogenase ([Ni,Fe]-CODH) that are the key enzymes for carboxydotrophic growth, while Moorella strains had only two. Both Moorella strains possessed the well characterized cooS within acetyl-CoA synthase gene clusters, and each strain had additional CooS genes adjacent to either the well-studied energy-converting hydrogenase gene cluster or the gene encoding cysteine synthase. KKC1 conserved all these types of CooS genes. Additionally, KKC1 had one previously reported cooS clustered with nitrite reductase and ferredoxin genes, and two CooS genes in novel genomic contexts which had never been reported; They were adjacent to 1) 2-oxoglutarate:ferredoxin oxidoreductase and ferredoxin genes, 2) 4-hydroxy-3-methylbut-2-enyl diphosphate reductase gene, respectively. These suggest KKC1 can couple CO oxidation to TCA cycle and isoprenoid synthesis. Compared to Moorella strains, KKC1 might have flexible CO metabolism and adapt to high concentration of CO.