Abstract
Benzoyl-CoA is the signature central metabolite associated with the anaerobic metabolism of a diverse range of compounds such as humic acid, lignin, amino acids, and industrial chemicals. Aromatic chemicals with different upstream degradation pathways all funnel into the downstream benzoyl-CoA pathway. Different genes encoding enzymes of the benzoyl-CoA pathway could be used as biomarkers for the anaerobic benzoyl-CoA pathway, however, the ring opening hydrolase, encoded by the bamA gene, is ideal because it is detected under a range of respiratory conditions, including under denitrifying, iron-reducing, sulfate-reducing, and fermentative conditions. This work evaluated DNA samples from six diverse environments for the presence of the bamA gene, and had positive results for every sample. Individual bamA gene clones from these sites were compared to published genome sequences. The clone sequences were distributed amongst the genome sequences, although there were clone sequences from two of the analyzed sites that formed a unique clade. Clone sequences were then grouped by site and analyzed with a functional operational taxonomic unit based clustering program to compare the bamA gene diversity of these sites to that of several locations reported in the literature. The results showed that the sequence diversity of the sites separated into two clusters, but there was no clear trend that could be related to the site characteristics. Interestingly, two pristine freshwater sites formed a subgroup within one of the larger clusters. Thus far the bamA gene has only been examined within the context of contaminated environments, however, this study demonstrates that the bamA gene is also detected in uncontaminated sites. The widespread presence of the bamA gene in diverse environments suggests that the anaerobic benzoyl-CoA pathway plays an important role in the global carbon cycle that has thus far been understudied.
Highlights
Aromatic compounds are commonly found in the environment as components in petroleum, industrial contaminants, amino acids, or as humic acids and lignins
The T. aromatica Oah amino acid sequence shared 82% identity with the Geobacter bemidjiensis Bem BamA amino acid sequence over the 100 residue region analyzed in this study
Our analysis of the individual BamA hydrolase amino acid sequence diversity is based upon environmental clones from our laboratory and from the limited number of characterized anaerobic aromatic hydrocarbon-degrading isolates
Summary
Aromatic compounds are commonly found in the environment as components in petroleum, industrial contaminants, amino acids, or as humic acids and lignins. In the absence of oxygen, anaerobes have had to evolve different strategies in order to attack these aromatic rings and utilize the available carbon. Benzoyl-CoA degradation involves an initial systematic reduction of the benzene ring (Figure 1, structures II and III), followed by the hydrolysis of 6-oxocyclohex-1-ene-1-carbonyl-CoA (Figure 1, structure IV) to 3-hydroxypimelyl-CoA (Figure 1, structure V) by 6-oxocyclohex1-ene-1-carbonyl-CoA hydrolase. This latter enzyme is encoded by the bamA gene and its homologs oah and bzdY, which were previously described in Thauera aromatica (Laempe et al, 1999) and Azoarcus strain CIB (López Barragán et al, 2004), respectively
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