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Digging deeper into the PpsR regulon of Rhodobacter sphaeroides

ABSTRACT: The expression of genes involved in photosystem development in Rhodobacter sphaeroides is dependent upon three major regulatory networks: FnrL, the PrrBA two-component system and the AppA-PpsR pathway. A PrrA- mutant strain of R. sphaeroides is unable to develop under photosynthetic conditions, but when combined with a ppsR mutation, is able to resume growth. In an effort to better characterize the ppsR regulon and to unravel the relationship between the PrrBA and the AppA-PpsR networks, we compared transcriptome profiles from the wild type, PrrA- and PrrA-PpsR- strains under a permissive, common, growth condition: anaerobic-dark-DMSO. Here is stored the microarray data for the PrrA-PpsR- double mutant strain grown under this condition. Keywords: transcriptome profile

ORGANISM(S): Cereibacter sphaeroides 2.4.1

PROVIDER: GSE9534 | GEO | 2008/08/31

SECONDARY ACCESSION(S): PRJNA103343

REPOSITORIES: GEO

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Digging deeper into the PpsR regulon of Rhodobacter sphaeroides

Project description:The expression of genes involved in photosystem development in Rhodobacter sphaeroides is dependent upon three major regulatory networks: FnrL, the PrrBA two-component system and the AppA-PpsR pathway. A PrrA- mutant strain of R. sphaeroides is unable to develop under photosynthetic conditions, but when combined with a ppsR mutation, is able to resume growth. In an effort to better characterize the ppsR regulon and to unravel the relationship between the PrrBA and the AppA-PpsR networks, we compared transcriptome profiles from the wild type, PrrA- and PrrA-PpsR- strains under a permissive, common, growth condition: anaerobic-dark-DMSO. Here is stored the microarray data for the PrrA-PpsR- double mutant strain grown under this condition. Keywords: transcriptome profile Rhodobacter sphaeroides PrrA-PpsR- grown under anaerobic dark DMSO conditions. Sparged with 95% N2, 5% CO2 in sistrom minimal medium A supplemented with final concentration 0.1% YE, 0.5% DMSO. The total RNA from three independent cultures of R. sphaeroides PrrA-PpsR- grown under anaerobic-dark-DMSO conditions was used. cDNA synthesis, fragmentation, labeling and hybridization are described elsewhere (Roh et al., 2004).

2010-06-20 | E-GEOD-9534 | biostudies-arrayexpress

FnrL regulon in Rhodobacter sphaeroides

2010-07-01 | GSE22027 | GEO

PpsR regulon in Rhodobacter sphaeroides

Project description:mRNA levels were measured in Rhodobacter sphaeroides 2.4.1 at 20% O2 and 0.5% O2, Rhodobacter sphaeroides 2.4.1 App11 (AppA-null), Rhodobacter sphaeroides 2.4.1 (pPNs) and PpsR mutant PPS2-4. The mRNA samples were prepared from cultures supplied with 20% O2, 1% CO2, and 79% N2, and grown in the dark to an OD of 0.18. The mRNA levels for each strain was measured three times. Keywords: repeat sample

2004-07-03 | GSE1515 | GEO

FnrL regulon in Rhodobacter sphaeroides

Project description:In this study, we performed a ChIP-chip experiment to determine the regulon of FnrL in Rhodobacter sphaeroides. We grew R. sphaeroides under anaerobic photosnthetic conditions, in which FnrL is expected to bind DNA and contol gene expression, and immuno-precipitated FnrL, but also sigma70 and the Beta' subunits of RNA polymerase to determine transcription activity. DNA immunoprecipitated with polyclonal antibodies against FnrL, sigma70, or the Beta' subunit of RNA polymerase was labelled with Cy5 and hybridized on two-color tilling arrays (triplicates for each) with genomic DNA as an input control labelled with Cy3.

2010-07-01 | E-GEOD-22027 | biostudies-arrayexpress

Global analysis of photosynthesis transcriptional regulatory networks [ChIP-seq]

2014-12-15 | GSE58716 | GEO

Global analysis of photosynthesis transcriptional regulatory networks [ChIP-seq]

Project description:To gain a deeper understanding of the transcription factors that regulate photosynthesis in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 4 transcription factors (FnrL, PrrA, CrpK and RSP_2888) known or predicted to be involved in the regulation of photosynthesis. Genome-wide protein-DNA interaction analysis of 4 transcription factors known or predicted to be involved in the regulation of photosynthesis in Rhodobacter sphaeroides, using ChIP-seq and complementary assays.

2014-12-15 | E-GEOD-58716 | biostudies-arrayexpress

Global analysis of photosynthesis transcriptional regulatory networks [Expression profiling]

2014-12-15 | GSE58554 | GEO

Global analysis of photosynthesis transcriptional regulatory networks [Expression profiling]

Project description:To gain a deeper understanding of the transcription factors that regulate photosynthesis in Rhodobacter sphaeroides global gene expression analysis was used to determine the expression profiles of the deletion mutants of 4 transcription factors (FnrL, PrrA, CrpK and RSP_2888) known or predicted to be involved in the regulation of photosynthesis. Microarray analysis conducted for deletion strains of 4 transcription factors known or predicted to be involved in the regulation of photosynthesis in Rhodobacter sphaeroides using the R. sphaeroides Affymetrix gene chip. These deletion mutant expression profiles were compared to that of wild type cells to determine differentially expressed genes regulated by these transcription factors.

2014-12-15 | E-GEOD-58554 | biostudies-arrayexpress

An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks [ChIP-Seq]

Project description:By integrating sequence information from closely related bacteria with a compendium of high-throughput gene expression datasets, a large-scale transcriptional regulatory networks was constructed for Rhodobacter sphaeroides. Predictions from this network were validated in part using genome-wide analysis for 3 transcription factors (PpsR, RSP_0489 and RSP_3341). Genome-wide protein-DNA interaction analysis of 3 transcription factors predicted to be involved in photosynthesis (PpsR), carbon metabolism (RSP_0489) and iron homeostasis (RSP_3341) were used to validate predictions from a large-scale reconstruction of R. sphaeroides transcriptional regulatory network.

2014-07-01 | E-GEOD-58648 | biostudies-arrayexpress

An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks [ChIP-Seq]

2014-07-01 | GSE58648 | GEO

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