Carbon monoxide-dependent transcriptional changes in a thermophilic, carbon monoxide-utilizing, hydrogen-evolving bacterium Calderihabitans maritimus KKC1 revealed by transcriptomic analysis

Abstract

Calderihabitans maritimus KKC1 is a thermophilic, carbon monoxide (CO)-utilizing, hydrogen-evolving bacterium that harbors seven cooS genes for anaerobic CO dehydrogenases and six hyd genes for [NiFe] hydrogenases and capable of using a variety of electron acceptors coupled to CO oxidation. To understand the relationships among these unique features and the transcriptional adaptation of the organism to CO, we performed a transcriptome analysis of C. maritimus KKC1 grown under 100% CO and N 2 conditions. Of its 3114 genes, 58 and 32 genes were significantly upregulated and downregulated in the presence of CO, respectively. A cooS-ech gene cluster, an "orphan" cooS gene, and bidirectional hyd genes were upregulated under CO, whereas hydrogen-uptake hyd genes were downregulated. Transcriptional changes in anaerobic respiratory genes supported the broad usage of electron acceptors in C. maritimus KKC1 under CO metabolism. Overall, the majority of the differentially expressed genes were oxidoreductase-like genes, suggesting metabolic adaptation to the cellular redox change upon CO oxidation. Moreover, our results suggest a transcriptional response mechanism to CO that involves multiple transcription factors, as well as a CO-responsive transcriptional activator (CooA). Our findings shed light on the diverse mechanisms for transcriptional and metabolic adaptations to CO in CO-utilizing and hydrogen-evolving bacteria.

Biome-specific distribution of Ni-containing carbon monoxide dehydrogenases

“…Some anaerobic carboxydotrophs have multiple gene clusters, of which Ni-CODHs belong to different phylogenetic clades. The expression of these Ni-CODH gene clusters is regulated differently in the presence or absence of CO in some carboxydotrophs (Fukuyama et al 2019 ; Inoue et al 2020a ).…”

“…Furthermore, many carboxydotrophs have been isolated from CO-emitting volcanic environments (Fukuyama et al 2020). However, some carboxydotrophs have also been isolated from samples not related to CO-emitting environments, suggesting their ubiquitous distribution (Inoue et al 2019b(Inoue et al , 2020b. Ni-CODH genes have been identified in metagenome-assembled genomes (MAGs) from various environmental samples (Evans et al 2015;Adam et al 2018;Inoue et al 2019a;Mu et al 2020).…”