RNA-Seq provides insights into the novel carbon monoxide metabolism in Carboxydothermus pertinax
1Kyoto univ. agri., 2AIST
[Introduction] Anaerobic carboxydotroph can use carbon monoxide (CO), which is well-known toxic gas for most organisms, as energy and/or carbon source for their growth. In particular, hydrogenogenic carboxydotroph produce H2 via CO oxidization by CO dehydrogenases (CODHs) as key enzymes. In hydrogengenic carboxydotroph Carboxydothermus hydrogenoformas that possesses 5 CODH-encoding genes, CODH-I (cooS-I) coupled with hydrogenase is responsible for this CO metabolism. However, Carboxydothermus pertinax lacks CooS-I and its transcriptional regulator encoded in CODH-I/hydrogenase gene cluster. We aimed to reveal the novel CO metabolism in C. pertinax, using RNA-Seq.
[Materials and Methods] At the late exponential phase, the cells were collected from C. pertinax grown on pyruvate in the presence and absence of CO and total RNA was extracted. Total RNA was removed rRNA using Ribo-ZeroTM Magnetic Kits (Epicentre) and synthesized to cDNA. cDNA was sequenced on MiSeq (Illumina).
[Results and Discussion] RNA-Seq data show that 413 genes were up-regulated and 442 genes were down-regulated by more than two fold in CO metabolism. These genes accounted for about 35 % of 2588 genes in the C. pertinax draft genome. Among the up-regulated genes, H2-evolving hydrogenase related genes and genes in a cluster including CODH-II, which is considered to regenerate NAD (P) H via CO oxidation were up-regulated remarkably (50-1400 folds change) in CO metabolism. These imply that C. pertinax can couple CO oxidation by CODH-II with H2 production by H2-evolving hydrogenase. Most of the down-regulated genes were located in prophage regions of C. pertinax, suggesting that the lysis of temperate phages was repressed in CO metabolism. In generally, temperate phages enter into lytic phase when DNA damages or SOS response occur in the host cell. These results suggest that C. pertinax prefers CO metabolism to heterotrophic metabolism.
keywords:Carbon monoxide,carboxydotroph,CO metabolism,RNA-Seq,CO dehydrogenase