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.

Kinetics of CO conversion into H2 by Carboxydothermus hydrogenoformans

“…Indeed, a CODH enzyme complex purified from C. hydrogenoformans showed maximal CO-oxidizing:H 2 -evolving activity at a CO level in the headspace as low as 5% (0.03 mM at 70°C) as well (Soboh et al 2002). However, the analysis of the genome of C. hydrogenoformans revealed the remarkable presence of at least five highly differentiated CODH complexes (Wu et al 2005). This likely explains in part why this species was able to grow more rapidly on CO and to exhibit more resistance to the CO toxicity than other hydrogenogenic carboxydotrophic species.…”

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

“…audaxviator appears to have two CODH systems, one in operon CF2 that is similar to the CODH-III carbon fixation system of C. hydrogenoformans (52), and another system present in operon CF1 with formate dehydrogenase that resembles archaeal CODH (see Figure S7 below).…”

“…Desulforudis audaxviator has two CODH gene clusters, each with a phylogenetically distinct catalytic subunit. The first, with Daud0870, corresponds to COG 1151 (cooS) and is in the acetogenic CODH-III family of Carboxydothermus hydrogenoformans (52). COG 1151 is a fairly broad family but, with the additional requirement that cdhC/acsB was found in the neighborhood, the CODH-III type of cooS was only found in the sequenced bacterial genomes at the time of this analysis.…”

[FeFe] hydrogenases and their evolution: a genomic perspective

“…Some genomes (Carboxydothermus hydrogenoformans [51] and Geobacter [52], not included in Table 1) may at first sight appear to encode [FeFe] H 2 ases. However, these sequences are in fact sigma-54-dependent transcriptional regulators having an [FeFe] H 2 ase-like sensory module.…”