The pimFABCDE operon from Rhodopseudomonas palustris mediates dicarboxylic acid degradation and participates in anaerobic benzoate degradation

Bacteria in anoxic environments typically convert aromatic compounds derived from pollutants or green plants to benzoyl-CoA, and then to the C-7 dicarboxylic acid derivative 3-hydroxypimelyl-CoA. Inspection of the recently completed genome sequence of the purple nonsulfur phototroph Rhodopseudomonas palustris revealed one predicted cluster of genes for the beta-oxidation of dicarboxylic acids. These genes, annotated as pimFABCDE, are predicted to encode acyl-CoA ligase, enoyl-CoA hydratase, acyl-CoA dehydrogenase and acyl-CoA transferase enzymes, which should allow the conversion of odd-chain dicarboxylic acids to glutaryl-CoA, and even-chain dicarboxylic acids to succinyl-CoA. A mutant strain that was deleted in the pim gene cluster grew at about half the rate of the wild-type parent when benzoate or pimelate was supplied as the sole carbon source. The mutant grew five times more slowly than the wild-type on the C-14 dicarboxylic acid tetradecanedioate. The mutant was unimpaired in growth on the C-8-fatty acid caprylate. The acyl-CoA ligase predicted to be encoded by the pimA gene was purified, and found to be active with C-7-C-14 dicarboxylic and fatty acids. The expression of a pimA-lacZ chromosomal gene fusion increased twofold when cells were grown in the presence of straight-chain C-7-C-14 dicarboxylic and fatty acids. These results suggest that the beta-oxidation enzymes encoded by the pim gene cluster are active with medium-chain-length dicarboxylic acids, including pimelate. However, the finding that the pim operon deletion mutant is still able to grow on dicarboxylic acids, albeit at a slower rate, indicates that R. palustris has additional genes that can also specify the degradation of these compounds.