A Genomic and Biochemical Characterization of Carbon Monoxide Utilizing Thermophilic Bacteria

Abstract

Carbon monoxide (CO), while being a potent toxin to many organisms, serves as an essential metabolite of some microorganisms. CO-utilizing prokaryotes form a substantial microbial subgroup in most thermophilic ecosystems and are increasingly recognized as important members of microbial consortia. One subgroup of CO-utilizers, hydrogenogens, couples the oxidation of CO to hydrogen production. Hydrogenogens are significant ecologically, medically, and biotechnologically. Thermophilic hydrogenogens occupy a truly extreme niche. They thrive at temperatures that are prohibitive to the growth of most organisms by using CO, a substrate with only modest energy returns. The genomes of two hydrogenogens have been sequenced to understand the genomic determinants allowing these organisms to prosper in such a habitat. A comparison of the genome sequences of Carboxydothermus hydrogenoformans and Thermosinus carboxydivorans revealed the presences of novel CO-sensing mechanisms and a unique protein-folding system. C. hydrogenoformans encodes five CO-dehydrogenases (CODH) and two CO-responsive transcriptional activators (CooA). The multiplicity of CODHs and CooAs points to a possible crosstalk between these activators enabling efficient use of CO through multiple CODHs. CooA-1 was found to activate gene expression under higher CO concentrations, regulating the genes involved in coupling CO oxidation to hydrogen production. CooA-2 was activated under lower CO levels, regulating both hydrogen production and carbon fixation. This unique cooperation between CooAs helps to explain the hydrogenogens' ability to grow efficiently on a minimal carbon source. Many carbon monoxide utilizing bacteria also possess novel protein folding systems. The genomes of C. hydrogenoformans and T. carboxydivorans encode a unique chaperonin (Hsp60), with higher similarity to the archaeal and eukaryotic chaperonins than to the bacterial chaperonins. Homologs of this novel chaperonin were found in five additional bacterial genomes, four of which were CO-utilizers. These chaperonins share many structural and functional qualities with the Group II chaperonins and occur in separate gene clusters than the GroEL/ES chaperonins. This finding represents the discovery of a novel third group of chaperonins, which may represent an ancestor of the archaeal and eukaryotic chaperonins. A thorough study of these novel chaperonins provides insights into the evolution and function of this essential and medically relevant protein family.