Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics

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.