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

Research paper by Faith H FH Harrison, Caroline S CS Harwood

Indexed on: 11 Mar '05Published on: 11 Mar '05Published in: Microbiology (Reading, England)


Bacteria in anoxic environments typically convert aromatic compounds derived from pollutants or green plants to benzoyl-CoA, and then to the C7 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 C14 dicarboxylic acid tetradecanedioate. The mutant was unimpaired in growth on the C8-fatty acid caprylate. The acyl-CoA ligase predicted to be encoded by the pimA gene was purified, and found to be active with C7-C14 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 C7-C14 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.