The Complete Genome Sequence of Clostridium aceticum: a Missing Link between Rnf- and Cytochrome-Containing Autotrophic Acetogens

Abstract

Clostridium aceticum was the first isolated autotrophic acetogen, converting CO2 plus H2 or syngas to acetate. Its genome has now been completely sequenced and consists of a 4.2-Mbp chromosome and a small circular plasmid of 5.7 kbp. Sequence analysis revealed major differences from other autotrophic acetogens. C. aceticum contains an Rnf complex for energy conservation (via pumping protons or sodium ions). Such systems have also been found in C. ljungdahlii and Acetobacterium woodii. However, C. aceticum also contains a cytochrome, as does Moorella thermoacetica, which has been proposed to be involved in the generation of a proton gradient. Thus, C. aceticum seems to represent a link between Rnf- and cytochrome-containing autotrophic acetogens. In C. aceticum, however, the cytochrome is probably not involved in an electron transport chain that leads to proton translocation, as no genes for quinone biosynthesis are present in the genome.

Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov.

“…DSM 2634=ATCC 13726). Subsequent analyses of 16S rRNA gene sequences showed that members of three proposed genera (listed as genera 6, 7 and 8 in Collins et al , 1994), namely ‘ C. aminobutyricum’ , Clostridium felsineum , Clostridium formicaceticum , and Clostridium halophilum , along with the more recently described Clostridium caminithermale , form a relatively compact separate group that also includes Clostridium aceticum and Anaerovirgula multivorans (Brisbarre et al , 2003; Chen et al , 2006; Pikuta et al , 2006; Gerritsen et al , 2014; Poehlein et al , 2015; Lawson et al , 2016). In the 2009 edition of Bergey’s, these species were assigned to Clostridiaceae 2, a sister group to Peptostreptococcaceae (Ludwig et al , 2009b), and are listed the same way in the SILVA database (Yilmaz et al , 2014).…”

“…Also, aside from the genome of C. aceticum (Poehlein et al , 2015), there was almost no sequence data to verify the 16S rRNA gene-based tree. Therefore, these organisms were excluded from further analysis.…”

First Insights into the Genome Sequence of the Strictly Anaerobic Homoacetogenic Sporomusa sphaeroides Strain E (DSM 2875)

“…The cluster of genes encoding enzymes of the methyl and carbonyl branches of the Wood-Ljungdahl pathway is present in the genome and showed the same organization as described for S. ovata DSM 2662 (6). The genome contains genes encoding for enzymes involved in the metabolism of one-carbon compounds, including cooS for the putative synthesis of the carbon monoxide dehydrogenase (CODH) required for growing on CO. Five genes of the formate dehydrogenase ( fdhs ) complex involved in the oxidation of formate were also detected.…”

Genome Sequence of the Acetogenic Bacterium Butyribacterium methylotrophicum DSM 3468 T

“…Genes encoding enzymes of the methyl and carbonyl branches of the Wood-Ljungdahl pathway are conserved within acetogenic bacteria (11). Correspondingly, the genome of B. methylotrophicum harbors a gene cluster that is highly similar to the respective cluster of E. limosum ATCC 8486 T and harbors genes encoding the Rnf complex.…”