Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

Abstract

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a “minimal” model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously. Carboxydothermus hydrogenoformans, a bacterium isolated from a Russian hotspring, is studied for three major reasons: it grows at very high temperature, it lives almost entirely on a diet of carbon monoxide (CO), and it converts water to hydrogen gas as part of its metabolism. Understanding this organism's unique biology gets a boost from the decoding of its genome, reported in this issue of PLoS Genetics. For example, genome analysis reveals that it encodes five different forms of the protein machine carbon monoxide dehydrogenase (CODH). Most species have no CODH and even species that utilize CO usually have only one or two. The five CODH in C. hydrogenoformans likely allow it to both use CO for diverse cellular processes and out-compete for it when it is limiting. The genome sequence also led the researchers to experimentally document new aspects of this species' biology including the ability to form spores. The researchers then used comparative genomic analysis to identify conserved genes found in all spore-forming species, including Bacillus anthracis, and not in any other species. Finally, the genome sequence and analysis reported here will aid in those trying to develop this and other species into systems to biologically produce hydrogen gas from water.