Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Effects of the Fnr homologue AadR on global gene expression

ABSTRACT: In order to define the AadR regulon we did transcriptome analysis of an aadR in frame-deletion mutant and compared to that of wild type. We found that AadR positively modulated expression of 43 genes, most of which are involved in degradation of aromatic acids under anaerobic conditions. It also activated expression of four genes encoding for unknown proteins and a possible DNA-binding stress protein. Furthermore, AadR repressed the expression of 100 genes, including fixK and many genes controlled by FixK, mainly those involved in a microaerobic lifestyle R. palustris strains were grown in defined medium anaerobically in light (photosynthetically) in sealed tubes with nitrogen gas in the headspace. Succinate and p-coumarate were provided as carbon sources.

ORGANISM(S): Rhodopseudomonas palustris

SUBMITTER: Yasuhiro Oda

PROVIDER: E-GEOD-19093 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

FixK, a global regulator of microaerobic growth, controls photosynthesis in Rhodopseudomonas palustris.

Rey Federico E FE Harwood Caroline S CS

Molecular microbiology 20100201 4

Purple non-sulphur phototrophic bacteria (PNSB) are excellent models for analysing the co-ordination of major metabolisms, including oxidative phosphorylation, photophosphorylation, carbon dioxide fixation and nitrogen fixation. In species studied to date, a two-component system called RegBA controls these functions and it has been thought that this redox sensing regulatory system is essential for co-ordinating electron flow and cannot be easily replaced. Here we show that this is not the case f ...[more]

PMID: 20487293

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Project description:Photosynthetic microbes can produce the clean-burning fuel hydrogen using one of natureâ??s most plentiful resources, sunlight 1,2. Anoxygenic photosynthetic bacteria generate hydrogen and ammonia during a process known as biological nitrogen fixation. This reaction is catalyzed by the enzyme nitrogenase and consumes nitrogen gas, ATP and electrons 3. One bacterium, Rhodopseudomonas palustris, has a remarkable ability to obtain electrons from green plant-derived material 4,5 and to efficiently absorb both high and low intensity light energy to form ATP 6. Manipulating R. palustris or a similar organism to produce hydrogen commercially will require us to identify all its genes that contribute to hydrogen production and to understand how this process is regulated in cells. Here we describe mutant strains in which metabolism is redirected such that hydrogen production is uncoupled from nitrogen fixation. Our data indicate that three different single amino acid changes in the transcriptional regulator NifA each yielded strains that produced hydrogen even in the presence of the repressing nitrogen source ammonium and in the absence of specific inducing metabolic signals. We used the mutants to show that, in addition to nitrogenase genes, 18 genes outside of the nitrogenase gene cluster may contribute to hydrogen production. Some of these genes are likely involved in efficient ATP acquisition and in channeling electrons to nitrogenase for reduction of protons to molecular hydrogen. Our results demonstrate that photosynthetic bacteria can be genetically manipulated for sustained production of pure hydrogen in a variety of cultivation conditions in the absence of oxygen, nitrogen or other gases as long as light and an electron donor are supplied. Transcriptome profile of wild type (CGA009) growing photosynthetically in the presence of amonium an acetate was compare with that of 4 different mutants (CGA570, CGA571, CGA572 and CGA574). We did 2 biological replicates per strain.

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

Effects of the Fnr homologue AadR on global gene expression

Publications

FixK, a global regulator of microaerobic growth, controls photosynthesis in Rhodopseudomonas palustris.

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