Rhodopseudomonas palustris
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PROVIDER: PRJNA120515 | ENA |
REPOSITORIES: ENA
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Project description:Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris
| PRJNA94739 | ENA
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.
2010-08-16 | GSE6742 | GEO
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.
2010-08-15 | E-GEOD-6742 | biostudies-arrayexpress
Project description:Rhodopseudomonas palustris CGA009 Transcriptome or Gene expression
| PRJNA976412 | ENA
Project description:Rhodopseudomonas palustris, a nonsulphur purple photosynthetic bacteria, has been extensively investigated for its metabolic versatility including ability to produce hydrogen gas from sunlight and biomass. The availability of the finished genome sequences of six R. palustris strains (BisA53, BisB18, BisB5, CGA009, HaA2 and TIE-1) combined with online bioinformatics software for integrated analysis presents new opportunities to determine the genomic basis of metabolic versatility and ecological lifestyles of the bacteria species. The purpose of this investigation was to compare the functional annotations available for multiple R. palustris genomes to identify annotations that can be further investigated for strain-specific or uniquely shared phenotypic characteristics. A total of 2,355 protein family Pfam domain annotations were clustered based on presence or absence in the six genomes. The clustering process identified groups of functional annotations including those that could be verified as strain-specific or uniquely shared phenotypes. For example, genes encoding water/glycerol transport were present in the genome sequences of strains CGA009 and BisB5, but absent in strains BisA53, BisB18, HaA2 and TIE-1. Protein structural homology modeling predicted that the two orthologous 240 aa R. palustris aquaporins have water-specific transport function. Based on observations in other microbes, the presence of aquaporin in R. palustris strains may improve freeze tolerance in natural conditions of rapid freezing such as nitrogen fixation at low temperatures where access to liquid water is a limiting factor for nitrogenase activation. In the case of adaptive loss of aquaporin genes, strains may be better adapted to survive in conditions of high-sugar content such as fermentation of biomass for biohydrogen production. Finally, web-based resources were developed to allow for interactive, user-defined selection of the relationship between protein family annotations and the R. palustris genomes.
| S-EPMC3201837 | biostudies-literature
Project description:Anthropogenic carbon dioxide (CO2) release in the atmosphere from fossil fuel combustion has inspired scientists to study CO2 to biofuel conversion. Oxygenic phototrophs such as cyanobacteria have been used to produce biofuels using CO2. However, oxygen generation during oxygenic photosynthesis adversely affects biofuel production efficiency. To produce n-butanol (biofuel) from CO2, here we introduce an n-butanol biosynthesis pathway into an anoxygenic (non-oxygen evolving) photoautotroph, Rhodopseudomonas palustris TIE-1 (TIE-1). Using different carbon, nitrogen, and electron sources, we achieve n-butanol production in wild-type TIE-1 and mutants lacking electron-consuming (nitrogen-fixing) or acetyl-CoA-consuming (polyhydroxybutyrate and glycogen synthesis) pathways. The mutant lacking the nitrogen-fixing pathway produce the highest n-butanol. Coupled with novel hybrid bioelectrochemical platforms, this mutant produces n-butanol using CO2, solar panel-generated electricity, and light with high electrical energy conversion efficiency. Overall, this approach showcases TIE-1 as an attractive microbial chassis for carbon-neutral n-butanol bioproduction using sustainable, renewable, and abundant resources.
| S-EPMC8566592 | biostudies-literature
Project description:The biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris on a local scale was investigated. Thirty clones of phototrophic bacteria were isolated from each of five unevenly spaced sampling locations in freshwater marsh sediments along a linear 10-m transect, and a total of 150 clones were characterized by BOX-PCR genomic DNA fingerprinting. Cluster analysis of 150 genomic fingerprints yielded 26 distinct genotypes, and 106 clones constituted four major genotypes that were repeatedly isolated. Representatives of these four major genotypes were tentatively identified as R. palustris based on phylogentic analyses of 16S rRNA gene sequences. The differences in the genomic fingerprint patterns among the four major genotypes were accompanied by differences in phenotypic characteristics. These phenotypic differences included differences in the kinetics of carbon source use, suggesting that there may be functional differences with possible ecological significance among these clonal linages. Morisita-Horn similarity coefficients (C(MH)), which were used to compare the numbers of common genotypes found at pairs of sampling locations, showed that there was substantial similarity between locations that were 1 cm apart (C(MH), >/=0.95) but there was almost no similarity between locations that were >/=9 m apart (C(MH), </=0.25). These calculations showed there was a gradual decrease in similarity among the five locations as a function of distance and that clones of R. palustris were lognormally distributed along the linear 10-m transect. These data indicate that natural populations of R. palustris are assemblages of genetically distinct ecotypes and that the distribution of each ecotype is patchy.
| S-EPMC194913 | biostudies-literature
Project description:Rhodopseudomonas palustris is an alphaproteobacterium that has served as a model organism for studies of photophosphorylation, regulation of nitrogen fixation, production of hydrogen as a biofuel, and anaerobic degradation of aromatic compounds. This bacterium is able to transition between anaerobic photoautotrophic growth, anaerobic photoheterotrophic growth, and aerobic heterotrophic growth. As a starting point to explore the genetic basis for the metabolic versatility of R. palustris, we used transposon mutagenesis and Tn-seq to identify 552 genes as essential for viability in cells growing aerobically on semirich medium. Of these, 323 have essential gene homologs in the alphaproteobacterium Caulobacter crescentus, and 187 have essential gene homologs in Escherichia coli. There were 24 R. palustris genes that were essential for viability under aerobic growth conditions that have low sequence identity but are likely to be functionally homologous to essential E. coli genes. As expected, certain functional categories of essential genes were highly conserved among the three organisms, including translation, ribosome structure and biogenesis, secretion, and lipid metabolism. R. palustris cells divide by budding in which a sessile cell gives rise to a motile swarmer cell. Conserved cell cycle genes required for this developmental process were essential in both C. crescentus and R. palustris. Our results suggest that despite vast differences in lifestyles, members of the alphaproteobacteria have a common set of essential genes that is specific to this group and distinct from that of gammaproteobacteria like E. coli.Essential genes in bacteria and other organisms are those absolutely required for viability. Rhodopseudomonas palustris has served as a model organism for studies of anaerobic aromatic compound degradation, hydrogen gas production, nitrogen fixation, and photosynthesis. We used the technique of Tn-seq to determine the essential genes of R. palustris grown under heterotrophic aerobic conditions. The transposon library generated in this study will be useful for future studies to identify R. palustris genes essential for viability under specialized growth conditions and also for survival under conditions of stress.
| S-EPMC4810602 | biostudies-literature
Project description:The purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris strain CGA009 uses the three-carbon dicarboxylic acid malonate as the sole carbon source under phototrophic conditions. However, this bacterium grows extremely slowly on this compound and does not have operons for the two pathways for malonate degradation that have been detected in other bacteria. Many bacteria grow on a spectrum of carbon sources, some of which are classified as poor growth substrates because they support low growth rates. This trait is rarely addressed in the literature, but slow growth is potentially useful in biotechnological applications where it is imperative for bacteria to divert cellular resources to value-added products rather than to growth. This prompted us to explore the genetic and physiological basis for the slow growth of R. palustris with malonate as a carbon source. There are two unlinked genes annotated as encoding a malonyl coenzyme A (malonyl-CoA) synthetase (MatB) and a malonyl-CoA decarboxylase (MatA) in the genome of R. palustris, which we verified as having the predicted functions. Additionally, two tripartite ATP-independent periplasmic transporters (TRAP systems) encoded by rpa2047 to rpa2049 and rpa2541 to rpa2543 were needed for optimal growth on malonate. Most of these genes were expressed constitutively during growth on several carbon sources, including malonate. Our data indicate that R. palustris uses a piecemeal approach to growing on malonate. The data also raise the possibility that this bacterium will evolve to use malonate efficiently if confronted with an appropriate selection pressure.IMPORTANCE There is interest in understanding how bacteria metabolize malonate because this three-carbon dicarboxylic acid can serve as a building block in bioengineering applications to generate useful compounds that have an odd number of carbons. We found that the phototrophic bacterium Rhodopseudomonas palustris grows extremely slowly on malonate. We identified two enzymes and two TRAP transporters involved in the uptake and metabolism of malonate, but some of these elements are apparently not very efficient. R. palustris cells growing with malonate have the potential to be excellent biocatalysts, because cells would be able to divert cellular resources to the production of value-added compounds instead of using them to support rapid growth. In addition, our results suggest that R. palustris is a candidate for directed evolution studies to improve growth on malonate and to observe the kinds of genetic adaptations that occur to make a metabolic pathway operate more efficiently.
| S-EPMC7237771 | biostudies-literature
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
2008-05-07 | GSE6221 | GEO