Submitted on April 2, 2007
Revised on December 7, 2007
Accepted on December 20, 2007
Characterization of anaerobic catabolism of p-coumarate in rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics
Chongle Pan, Yasuhiro Oda, Patricia K. Lankford, Bing Zhang, Nagiza F. Samatova, Dale A. Pelletier, Caroline S. Harwood, and Robert L. Hettich
Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6131
Corresponding Author: hettichrl{at}ornl.gov
In this study, the pathway for anaerobic catabolism of p-coumarate by a model bacterium, Rhodopseudomonas palustris, was characterized by comparing the gene expression profiles of cultures grown in presence of p-coumarate, benzoate or succinate as the sole carbon sources. Gene expression was quantified at the mRNA level with transcriptomics and at the protein level with quantitative proteomics using 15N metabolic labeling. Protein relative abundances, along with their confidence intervals for statistical significance evaluation, were estimated with the software ProRata. Both -omics measurements were needed, since the transcriptomics provided near-full genome coverage of gene expression profiles and the quantitative proteomics ascertained abundance changes of over 1,600 proteins. The integrated gene expression data are consistent with the hypothesis that p-coumarate is converted to benzoyl-CoA, which is then degraded via a known aromatic ring reduction pathway. For the metabolism of p-coumarate to benzoyl-CoA, two alternative routes, a ß-oxidation route and a non-ß-oxidation route, are possible. The integrated gene expression data provided strong support for the non-ß-oxidation route in R. palustris. A putative gene was proposed for every step in the non-ß-oxidation route.