Peripheral pathways of anaerobic benzoate degradation in Rhodopseudomonas palustris

Use of the recently completed Rhodopseudomonas palustris genome sequence and a mini-Tn5 library of R. palustris mutant strains has facilitated studies of physiological processes including photosynthesis and organic acid degradation in R. palustris. In an examination of genes involved in photosynthesis, two mutant strains in two closely related genes (ppsR1 and ppsR2) were identified in a visual screen of the mutant library, indicating that each gene encodes a functional protein. The sequence and role of the R. palustris PpsR homologues was compared to those of other photosynthetic bacteria. A separate screen of the mutant library for R. palustris strains impaired in growth with p-coumarate, resulted in the identification of a mutant strain that displayed a growth defect when various aromatic and alicyclic compounds were supplied as sole carbon sources. The transposon insertion mapped to a gene encoding a possible oxidoreductase and a potential role for this enzyme in anaerobic aromatic degradation is described.; An R. palustris microarray was used to identify genes that increased in expression in cells grown with p-coumarate compared to cells grown with succinate. Results from the microarray experiment provided information about the physiology of R. palustris cells growing with p-coumarate. Potential genes for p-coumarate degradation were identified and examined for a role in p-coumarate acyl-side chain removal.; Pimelyl-coenzyme A (CoA) is the product of ring cleavage during anaerobic benzoate degradation. The further metabolism of pimelyl-CoA to central metabolites is catalyzed by a cluster of beta-oxidation genes named the pim genes. A mutant strain in which the entire pim cluster was deleted from the chromosome was impaired in growth with dicarboxylic acids containing 7--14 carbons and benzoate. The acyl-CoA ligase encoded by pimA was purified and activity of the ligase was measured with a range of dicarboxylic and fatty acid substrates. Results from studies of the pim cluster show that the Pim enzymes catalyze the metabolism of medium chain-length dicarboxylic acids. However R. palustris must also encode other enzymes for dicarboxylic acid degradation because the Pim operon deletion strain can still grow slowly with these substrates.