Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1 from gene expression profiling

ABSTRACT: In this study, we performed expression profiling experiments to determine the respective regulons of RpoHI and RpoHII in Rhodobacter sphaeroides. We grew R. sphaeroides in aerobic conditions and induced either proteins ectopically and compared the global gene expression profiles. The expression profiles of R. sphaeroides strains lacking either RpoHI or RpoHII were compered to strains expressing RpoHI or RpoHII ectopically from a plasmid to detect gene differentially expressed. Three biological replicates were performed for each strain.

ORGANISM(S): Rhodobacter sphaeroides 2.4.1

SUBMITTER: Yann Dufour

PROVIDER: E-GEOD-39712 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1

Project description:This SuperSeries is composed of the following subset Series: GSE39711: RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1 from chromatin immuno-precipitation GSE39712: RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1 from gene expression profiling Refer to individual Series

2012-08-02 | E-GEOD-39806 | biostudies-arrayexpress

Expression data from H2-producing Rhodobacter sphaeroides cultures fed different organic substrates

Project description:Rhodobacter sphaeroides produces hydrogen gas (H2) via its nitrogenase enzyme during photoheterotrophic growth under nitrogen-limited conditions. We find that cells produce different amounts of H2 and show different growth rates, depending on the organic substrate provided (lactate, succinate, glucose, xylose, or glycerol). We used global transcript analyses to determine what genes are involved in the onset of H2 production, and those that lead to different H2 production capacities in cells fed different organic substrates. Growth and real-time H2 production were followed for photoheterotrophically grown Rhodobacter sphaeroides cultures (19 mL test tube cultures) fed one of five different organic substrates (lactate, succinate, glucose, xylose, or glycerol) and provided glutamate as the sole nitrogen source. Cells were harvested for RNA extraction during early post-exponential growth, at points near the maximum H2 production rates of the cultures. Non-H2-producing cells (500 mL cultures) fed succinate and provided NH4+ as nitrogen source were also harvested for RNA extraction as reference samples. At least two samples for every given set of conditions were analyzed.

2011-08-21 | E-GEOD-29811 | biostudies-arrayexpress

RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1 from chromatin immuno-precipitation

Project description:In this study, we performed a ChIP-chip experiment to determine the respective regulons of RpoHI and RpoHII in Rhodobacter sphaeroides. We grew R. sphaeroides in aerobic conditions and induced either proteins ectopically and immuno-precipitated the regions of the genomic DNA interacting with the sigma factors. DNA immunoprecipitated with antibodies against RpoHI or RpoHII was labelled with Cy5 and hybridized on two-color tilling arrays (triplicates for each) with genomic DNA as an input control labelled with Cy3.

2012-08-02 | E-GEOD-39711 | biostudies-arrayexpress

Microarray analysis of Rhodobacter sphaeroides CceR and AkgR deletion strains

Project description:To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides global gene expression analysis was used to determine genes under the regulatory influence of 2 transcription factors: CcmR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulation of central carbon and energy metabolism. Microarray analysis conducted for deletion strains of 2 transcription factors known or predicted to be involved in the regulation of central carbon metabolism 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.

2015-02-02 | E-GEOD-63448 | biostudies-arrayexpress

RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1 from gene expression profiling

Project description:In this study, we performed expression profiling experiments to determine the respective regulons of RpoHI and RpoHII in Rhodobacter sphaeroides. We grew R. sphaeroides in aerobic conditions and induced either proteins ectopically and compared the global gene expression profiles.

2012-08-03 | GSE39712 | GEO

RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1 from chromatin immuno-precipitation

2012-08-03 | GSE39711 | GEO

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

Project description:Rhodobacter sphaeroides is the best studied photosynthetic bacterium, yet much remains unknown about its transcriptional regulatory processes on a genome-scale. We developed a work-flow for genome-scale reconstruction of transcriptional regulatory networks and applied it to sequence and gene expression data sets available for R. sphaeroides. To assess the predictive performance of our reconstructed model, we generated global transcript level and/or protein-DNA interaction data for 3 transcription factors (PpsR, RSP_0489 and RSP_3341). This dataset contains global transcript level analyses for RSP_0489 and RSP_3341 deletion strains, as well as matching wild type controls. Microarray analysis conducted for deletion strains of 2 previously uncharacterized transcription factors predicted to be involved in the regulation of carbon metabolism and iron homeostasis in R. 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.

2014-06-17 | E-GEOD-58553 | biostudies-arrayexpress

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

The sRNA SorY confers resistance during photooxidative stress by affecting a metabolite transporter in Rhodobacter sphaeroides

Project description:Exposure to oxygen and light generates photooxidative stress by the bacteriochlorophyll a mediated formation of singlet oxygen (1O2) in the facultative photosynthetic bacterium Rhodobacter sphaeroides. We have identified SorY as an sRNA, which is induced under several stress conditions and confers increased resistance against 1O2. SorY by direct interaction decreases the levels of takP mRNA, encoding a TRAP-T transporter. A takP mutant shows higher resistance to 1O2 than the wild type, which is no longer affected by SorY. We present a model in which SorY reduces the metabolite flux into the TCA cycle by reducing malate import through TakP. It was previously shown that oxidative stress in bacteria leads to switch from glycolysis to the pentose phosphate cycle and to reduced activity of the tricaboxylic acid cycle. As a consequence the production of the prooxidant NADH is reduced and production of the protective NADPH is enhanced. In R. sphaeroides enzymes for glycolysis, pentose phosphate pathway, EntnerM-bM-^@M-^SDoudoroff pathway and gluconeogenesis are induced in response to 1O2 by the alternative sigma factor RpoHII. The same is true for the sRNA SorY. By limiting malate import SorY thus contributes to the balance of the metabolic fluxes under photooxidative stress conditions. This assigns a so far unknown function to an sRNA in oxidative stress response. RNA samples collected from a control strain harbouring an empty vector (2.4.1pBBR) and of the SorY overexpressing strain (2.4.1pBBRSorYi) after 10 min of 1O2 stress were analyzed by two-color microarrays

2014-11-18 | E-GEOD-63328 | biostudies-arrayexpress

Growth-phase dependent gene regulation in the alpha-proteobacterium Rhodobacter sphaeroides

Project description:Global transcriptome analyses at different stages of growth were applied to monitor growth phase-dependent gene expression in the alpha-proteobacterium Rhodobacter sphaeroides. Low aerated cultures with strong changes in levels of dissolved oxygen during growth, were compared to aerated cultures showing little variation in oxygen levels. Cells were in stationary phase for 12 h or for 57 h before dilution into fresh medium. The majority of genes (78-86%) were not differentially expressed across growth phases. Gene expression in outgrowth phase was strongly influenced by the length of the preceding stationary phase. After 57 h in stationary phase a much larger number of genes was induced after dilution, 39% of which are known to be controlled by the alternative sigma factors RpoHI and/or RpoHII. Growth experiments with mutant strains assign an important function in stationary phase and especially in outgrowth to these sigma factors and genes for both sigma factors showed growth phase-dependent expression. Besides the known consensus sequences for the RpoH sigma factors, some new consensus sequences were identified in subsets of growth phase-dependent genes. Genes for several predicted regulatory proteins exhibited growth phase-specific expression implying a role in growth phase adaptation in alpha-proteobacteria, which needs verification in the future. RNA samples collected from R. sphaeroides 2.4.1 wild type cells in several growth phases were analyzed by two-color microarrays Please note that each sample represents biological triplicates.

2015-11-26 | E-GEOD-75345 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data