Project description:Facultative phototrophic bacteria are excellent models for analyzing the coordination of major metabolic traits including oxidative phosphorylation, photophosphorylation, carbon dioxide fixation and nitrogen fixation. In Rhodobacter sphaeroides and R. capsulatus, a two-component system called RegBA (PrrBA) controls these functions and it has been thought that this redox sensing regulatory system was essential for coordinating electron flow and could not be easily replaced in facultative phototrophs. Here we show that this is not the case and that the oxygen-sensing FixlJ-K system, initially described in rhizobia, controls microaerobic respiration, photophosphorylation and several other metabolic traits in Rhodopseudomonas palustris. A R. palustris fixK mutant grew normally aerobically but was impaired in microaerobic growth. It was also severely impaired in photosynthetic growth and has very little bacteriochlorophyll. Transcriptome analyses indicated that FixK positively regulates heme and bacteriochlorophyll biosynthesis, cbb3 oxidase and NADH dehydrogenase genes, as well as genes for hydrogen uptake, iron oxidation, and aromatic compound degradation. Electrophoretic mobility shift assays showed that FixK binds directly to the promoters of a bacteriochlorophyll biosynthesis operon, a bacteriophytochrome-histidine kinase gene and the fnr-type regulatory gene, aadR. AadR is likely responsible for mediating some indirect effects of FixK on expression of anaerobic genes. These results underscore that physiologically similar bacteria can use very different regulatory strategies to control common major metabolisms. Comparison of transcription profiles of Rhodopseudomonas palustris wild type and fixK mutant grown microaerobically.
Project description:Facultative phototrophic bacteria are excellent models for analyzing the coordination of major metabolic traits including oxidative phosphorylation, photophosphorylation, carbon dioxide fixation and nitrogen fixation. In Rhodobacter sphaeroides and R. capsulatus, a two-component system called RegBA (PrrBA) controls these functions and it has been thought that this redox sensing regulatory system was essential for coordinating electron flow and could not be easily replaced in facultative phototrophs. Here we show that this is not the case and that the oxygen-sensing FixlJ-K system, initially described in rhizobia, controls microaerobic respiration, photophosphorylation and several other metabolic traits in Rhodopseudomonas palustris. A R. palustris fixK mutant grew normally aerobically but was impaired in microaerobic growth. It was also severely impaired in photosynthetic growth and has very little bacteriochlorophyll. Transcriptome analyses indicated that FixK positively regulates heme and bacteriochlorophyll biosynthesis, cbb3 oxidase and NADH dehydrogenase genes, as well as genes for hydrogen uptake, iron oxidation, and aromatic compound degradation. Electrophoretic mobility shift assays showed that FixK binds directly to the promoters of a bacteriochlorophyll biosynthesis operon, a bacteriophytochrome-histidine kinase gene and the fnr-type regulatory gene, aadR. AadR is likely responsible for mediating some indirect effects of FixK on expression of anaerobic genes. These results underscore that physiologically similar bacteria can use very different regulatory strategies to control common major metabolisms.
Project description:The redox-sensing two-component signal transduction system, RegSR, in Rhodopseudomonas palustris has been shown to regulate an uptake hydrogenase in response to varying cellular redox states; however, its role is still largely undefined. Here, we used RNA sequencing to compare gene expression patterns in wild type R. palustris strain CGA010 to a ΔregSR derivative, CGA2023, under varying metabolic conditions. Growth conditions were chosen to utilize the different metabolic capabilites of R. palustris and, thus, present a variety of different redox challenges to the cell.
Project description: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. Keywords: Comparison of transcriptome profiles
Project description: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.
Project description:The purple bacterium Rhodopseudomonas palustris is a model organism for dissecting the energy and electron transfer processes that have evolved in phototrophic organisms. This bacterium is of particular interest because, in addition to driving its metabolism via solar energy capture, it is capable of nitrogen and carbon dioxide fixation, producing hydrogen and utilising a wide range of organic compounds. Understanding these processes underpins the potential exploitation of Rhodopseudomonas palustris for synthetic biology, biohydrogen production and bioremediation, for example. Like other purple bacteria, Rhodopseudomonas palustris has 2 light-harvesting (LH) systems: LH1 and LH2. The former has already been extensively characterised by X-ray crystallography and cryo-EM. The aim of this proteomics project is to provide complementary information to support the cryo-EM mapping of LH2 structure.
Project description:To address the question of how photosynthetic bacterium Rhodopseudomonas palustris differentially regulates gene expression of three nitrogenase isozymes (Mo, V, and Fe nitrogenases), we constructed Mo strain (Mo nitrogenase only strain), V strain (V nitrogenase only strain), and Fe strain (Fe nitrogenase only strain), and analyzed the whole genome transcriptome profiles of each mutant and wild-type cells grown under nitrogen-fixing conditions. Keywords: Genetic modification
Project description:In this paper, we present the first comparative transcriptome profiles with ARR treated and control of R. palustris. Moreover, putative two ARR biotransformation mechanisms in R. palustris were first given. All of these provided a valuable genomic resource for further studying molecular mechanism of biotransformation and genetic modification of R. palustris.
