Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris

ABSTRACT: To address the question of how photosynthetic bacterium Rhodopseudomonas palustris metabolize lignin derived compound p-coumarate, transcriptomics and quantitative proteomics were combined to characterize gene expression profiles at both the mRNA level and protein level in Rhodopseudomonas palustris grown with succinate, benzoate, and p-coumarate as the carbon source. Transcriptome profiles among Rhodopseudomonas palustris cells grown with succinate, benzoate, and p-coumarate as the carbon source were compared.

ORGANISM(S): Rhodopseudomonas palustris

SUBMITTER: Yasuhiro Oda

PROVIDER: E-GEOD-6221 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

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

Pan Chongle C Oda Yasuhiro Y Lankford Patricia K PK Zhang Bing B Samatova Nagiza F NF Pelletier Dale A DA Harwood Caroline S CS Hettich Robert L RL

Molecular & cellular proteomics : MCP 20071220 5

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 (15)N metabolic labeling. Protein relative abundances, along with their confidence intervals ...[more]

PMID: 18156135

Similar Datasets

Project description:Peripheral light harvesting (LH) antenna complexes have been studied extensively in the purple nonsulfur bacterium Rhodopseudomonas palustris because it produces different types of LH complexes under high light intensities (LH2 complex) and low light intensities (LH3 and LH4 complex). The ability of R. palustris to alter its peripheral LH complexes in response to changes in light intensity is attributed to the multiple operons that encode the a and b peptides that make up these complexes, whose expression is affected by light intensity, light quality, and oxygen tension. However, low resolution structures, amino acid similarities between the complexes, and a lack of transcriptional analysis made it difficult to determine the LH complexes composition and functions under different light intensities. It was also unclear how much diversity of the R. palustris LH complexes exists in nature.Results: To gain insight into the composition of the LH complexes, their function under high light intensities and low light intensities, and their prevalence in the environment we undertook an integrative genomics approach using 15 closely related R. palustris strains isolated from the environment and 5 R. palustris ecotypes whose genomes have been sequenced. We sequenced the genomes for the 15 closely related strains and using RNA-seq carried out transcriptomic analysis on all 20 strains grown under high light intensity and low light intensity. We were able to determine that even closely related R. palustris strains had differences in their pucBA gene content and expression, even under the same growth conditions. We also found that the LH2 complex could compensate for the lack of an LH4 complex under LL intensities but not under extremely LL intensities. Conclusions: This is the first time an integrative genomics approach has been used to study light harvesting in the environment. The variation observed in LH gene composition and expression in environmental isolates of R. palustris likely reflects how these strains have adapted to specific light conditions in the environment. We have also shown that there is redundancy between some of the LH complexes under certain light intensities, which may partially explain why multiple operons encoding LH complexes have evolved and been maintained in R. palustris. Examing the variation observed in LH gene composition and expression in various environmental isolates

Dataset Information

Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure