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Research

Characterization of Anaerobic Catabolism of p-Coumarate in Rhodopseudomonas palustris by Integrating Transcriptomics and Quantitative Proteomics^*,S

Chongle Pan^,, Yasuhiro Oda^¶, Patricia K. Lankford^||, Bing Zhang^,**, Nagiza F. Samatova^,, Dale A. Pelletier^||,, Caroline S. Harwood^¶,¶¶ and Robert L. Hettich^,||||

From the Chemical Sciences Division, Computer Science and Mathematics Division, and ^|| Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Computer Science, North Carolina State University, Raleigh, North Carolina 27695, and ^¶ Department of Microbiology, University of Washington, Seattle, Washington 98195

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 the 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 used as the transcriptomics provided near-full genome coverage of gene expression profiles and the quantitative proteomics ascertained abundance changes of over 1600 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 β-oxidation route and a non-β-oxidation route, are possible. The integrated gene expression data provided strong support for the non-β-oxidation route in R. palustris. A putative gene was proposed for every step in the non-β-oxidation route.

^¶¶ To whom correspondence may be addressed for questions on aromatic catabolism: Dept. of Microbiology, University of Washington, Box 357242, 1959 N. E. Pacific St., Seattle, WA 98195. Tel.: 206-221-2848; Fax: 206-221-5041; E-mail: csh5{at}u.washington.edu

^|||| To whom correspondence should be addressed for questions on proteomics: Oak Ridge National Laboratory, P. O. Box 2008, Oak Ridge, TN 37831. Tel.: 865-574-4968; Fax: 865-576-8559; E-mail: hettichrl{at}ornl.gov