Acscodh Genes in Bacteria

8.2.1. Clostridia

The clostridia are anaerobic heterotrophs that can oxidize or ferment a wide variety of organic substrates [94]. Acetogenesis, the formation of acetyl-CoA by

CO2 fixation, was first elaborated in Clostridium thermoaceticum (now Moorella thermoacetica) [95] and the Wood-Ljungdahl pathway was first discovered in this organism. Because this pathway requires an ACS/CODH enzyme to catalyze acetyl-CoA biosynthesis, the ACS/CODH protein from M. thermoacetica has been well studied and serves as a model system [96].

Besides M. thermoacetica, clostridial genomes that encode a complete ACS/ CODH complex include Alkaliphilus metalliredigenes, Carboxydothermus hydrogenoformans, Clostridium difficile and Desulfitobacterium hafniense. ACS/CODH genes from these bacteria often cluster with cooC genes and genes encoding other proteins in the Wood-Ljungdahl pathway.

While most clostridia do not have an ACS/CODH complex (or use the Wood-Ljungdahl pathway), numerous clostridial genomes encode homologs of the single subunit CODH protein. Pathogenic clostridia (Clostridium botulinum, Clostridium difficile, and Clostridium tetani) contain one or more copies of the CODH gene, as do environmental and solvent-producing clostridia such as Clostridium acetobutylicum, M. thermoacetica, and Ruminococcus albus. These bacteria are phylogenetically scattered throughout the clostridia. Therefore we may infer that the ancestor of the clostridia encoded a similar protein and that the CODH enzyme is quite old.

Carboxydothermus hydrogenoformans is a hydrogen-producing, carbon monoxide-oxidizing bacterium that can use CO as a primary carbon source. The genome sequence of the microbe revealed one ACS/CODH and four CODH enzymes [97]. The bacterium uses the ACS/CODH complex (called CODH-III) in the Wood-Ljungdahl pathway to fix CO. One CODH enzyme (CODH-I) is genetically linked to a hydrogenase gene cluster, suggesting that it forms the CO-oxidizing:H2-evolving complex that was previously isolated from C. hydrogenoformans [98]. This complex is similar to the well-studied Rhodospirillum rub-rum complex that is described in Section 8.2.2.

Two of the remaining CODH proteins (CODH-II and CODI-IV) are associated with CooF proteins and have been proposed to support oxidative stress response or anabolic electron transfer processes [97]. The fifth homolog (CODH-V) represents the CODH-like group of bacterial and archaeal proteins with modified C- and D-cluster residues and no known function. Desulfitobacterium hafniense, another member of the Peptococcaceae family, has a similar complement of ACS/CODH and CODH proteins — all are most closely related to orthologs in C. hydrogenoformans.

Dehalococcoides ethenogenes is a tetrachloroethene-dechlorinating member of the green nonsulfur bacteria that grows on acetate. Its genome encodes homologs of the a, y and 8 subunits of an ACS/CODH complex (all in a gene cluster with other Wood-Ljungdahl pathway genes), yet there is no apparent homolog of the p subunit in this genome [99]. The genome is also missing methyl-ene-tetrahydrofolate reductase and methyltetrahydrofolate:cob(I)alamin methyl-transferase genes. It is not clear how any of the identified components of this pathway could function without these essential proteins. These genes were almost certainly acquired by horizontal gene transfer, but we do not know whether the missing genes were not transferred or lost subsequent to the transfer event.

8.2.2. Proteobacteria

Only one of the many sequenced proteobacterial genomes encodes homologs of all four ACS/CODH/CoFeSP subunits. This strict anaerobe, Syntrophobacter fumaroxidans, grows syntrophically with hydrogen- and formate-consuming methanogens in a propionate-oxidizing coculture [100]. Originally isolated from an upflow anaerobic sludge bed, S. fumaroxidans cells oxidize propionate using the methylmalonyl-CoA pathway, releasing hydrogen and formate that is consumed by methanogens. This organism can also be grown in pure culture by fumarate fermentation. Enzyme activities of the Wood-Ljungdahl pathway (including CODH) were found in extracts of fumarate-grown cells. This pathway was suggested to be reversible, functioning as an anaplerotic reaction in propionate catabolism, and an aceticlastic reaction during fumarate fermentation [101].

S. fumaroxidans was grown in pure culture on propionate and sulfate, but could not be grown on acetate and sulfate. Other syntrophically grown bacteria can grow on acetate in coculture with a methanogen using the Wood-Ljungdahl pathway [102,103]. While there is ample opportunity for gene acquisition by horizontal gene transfer in these consortia, the phylogeny of the ACS/CODH genes indicates the S. fumaroxidans genes were recruited from the clostridia, not from methanogens. Its genome contains a second CODH gene that is associated with other oxidoreductase genes.

Rhodospirillum rubrum is a purple nonsulfur photosynthetic bacterium that oxidizes CO. The CooA heme protein senses redox state and CO, activating transcription of CODH during anaerobic photosynthetic growth [104]. CO oxidation by CODH is coupled to hydrogenase activity by the ferredoxin-like electron transfer protein CooF [105,106]. Tight regulation of CODH expression is probably important in this organism because it can also grow heterotrophically as a facultative aerobe. A similar set of genes is found in the genome sequence of another a-proteobacterium, Rhodopseudomonas palustris str. BisB18, although these genes are missing from sequences of five other R. palustris strains. This distribution may have arisen from a recent gene transfer event. The sulfate-reducing 8-proteobacterium Desulfovibrio vulgaris also has homologous CODH and hydrogenase genes that were probably acquired by horizontal gene transfer.

Several S-proteobacterial genomes have homologs of the R. rubrum CODH, but are missing the associated hydrogenase genes. These organisms include De-sulfovibrio desulfuricans, Geobacter metallireducens, Geobacter sulfurreducens, and Pelobacter carbinolicus. Similarly, the green sulfur bacterium Chlorobium phaeobacteroides DSM 266T has an unassociated CODH gene, while other Chlo-robium species have no homologs. CODH genes in these genomes are usually associated with cooC and cooF genes. These organisms may couple CO oxidation to unknown reductive processes.

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