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RpoE regulon in Rhodobacter sphaeroides

ABSTRACT: In Rhodobacter sphaeroides a transcriptional response to the reactive oxygen species singlet oxygen is controlled by the group IV sigma factor RpoE and the anti-sigma factor ChrR. In this study, we integrated various large datasets to identify genes within the singlet oxygen stress response that contain RpoE-dependent promoters within R. sphaeroides. Transcript pattern clustering and a RpoE-binding sequence model were used to predict candidate promoters that respond to singlet oxygen stress in R. sphaeroides. These candidate promoters were experimentally validated to nine R. sphaeroides RpoE-dependent promoters that control the transcription of 15 genes activated by singlet oxygen.

ORGANISM(S): Cereibacter sphaeroides 2.4.1

PROVIDER: GSE22576 | GEO | 2010/07/01

SECONDARY ACCESSION(S): PRJNA128415

REPOSITORIES: GEO

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RpoE regulon in Rhodobacter sphaeroides

Project description:In Rhodobacter sphaeroides a transcriptional response to the reactive oxygen species singlet oxygen is controlled by the group IV sigma factor RpoE and the anti-sigma factor ChrR. In this study, we integrated various large datasets to identify genes within the singlet oxygen stress response that contain RpoE-dependent promoters within R. sphaeroides. Transcript pattern clustering and a RpoE-binding sequence model were used to predict candidate promoters that respond to singlet oxygen stress in R. sphaeroides. These candidate promoters were experimentally validated to nine R. sphaeroides RpoE-dependent promoters that control the transcription of 15 genes activated by singlet oxygen. DNA immunoprecipitated with polyclonal antibodies against RpoE 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.

2010-06-30 | E-GEOD-22576 | biostudies-arrayexpress

Rhodobacter sphaeroides 2.4.1 pPos19 versus pBBR under singlet oxygen stress

Project description:To learn more about the function of Pos19, we constructed an over-expression strain. For this purpose, the Pos19 gene together with its native RpoE promoter was cloned into the middle-copy plasmid pBBR1 and expressed in the R. sphaeroides wild-type 2.4.1 background. The corresponding strain consequently exhibits a singlet oxygen-induced Pos19 over-expression compared to an empty vector control. Total RNA from the over-expression (pPos19) and from the empty vector control (pBBR) strain was extracted after 7 min of singlet oxygen stress and used for microarray analysis to investigate Pos19-induced changes on transcriptome level.

2017-02-09 | GSE81718 | GEO

Rhodobacter sphaeroides 2.4.1 pSurS versus pBBR under singlet oxygen stress.

Project description:To learn more about the function of SurS, we constructed an over-expression strain. For this purpose, the surS gene together with its native RpoE promoter was cloned into the middle-copy plasmid pBBR1 and expressed in the R. sphaeroides wild-type 2.4.1 background. The corresponding strain consequently exhibits a singlet oxygen-induced SurS over-expression compared to an empty vector control. Total RNA from the over-expression (pSurS) and from the empty vector control (pBBR) strain was extracted after 7 min of singlet oxygen stress and used for microarray analysis to investigate SurS-induced changes on transcriptome level. RNA samples collected after 7 min of singlet oxygen stress were analyzed by two-color microarrays. Each microarray contains a pool of three independent biological replicates for each sample.

2014-07-04 | E-GEOD-59046 | biostudies-arrayexpress

Role of a short LOV protein in blue light- and singlet oxygen-dependent gene regulation in Rhodobacter sphaeroides

Project description:The facultatively photosynthetic bacterium Rhodobacter sphaeroides harbors an unusual LOV (light, oxygen, voltage) domain protein, RsLOV. While showing a characteristic photocycle, the protein misses a C - terminal output domain, similar to PpSB2 in Pseudomonas putida. Oxygen tension and light quantity are the two main responsible factors controlling the expression of photosynthesis genes in Rhodobacter sphaeroides. Two photoreceptor proteins are known to be involved in this regulation: the intensively studied AppA protein and the more recently identified cryptochrome-like protein CryB. Here we show by transcriptome and physiological studies that RsLOV is also involved in the regulation of photosynthetic gene expression. Our data further hint to a connection between RsLOV and the carbon hydrate metabolism, chemotaxis, as well as to the cellular response to photooxidative stress. RsLOV does not only affect blue light dependent gene expression but also redox-dependent regulation. This SuperSeries is composed of the following subset Series: GSE33194: R. sphaeroides ?lov vs. R. sphaeroides 2.4.1 (microarobic conditions) GSE33259: R. sphaeroides ?lov vs. R. sphaeroides 2.4.1 (blue light, semiaerobic conditions) GSE33260: R. sphaeroides ?lov vs. R. sphaeroides 2.4.1 (singlet oxygen stress, aerobic conditions)

2011-10-25 | E-GEOD-33261 | biostudies-arrayexpress

Rhodobacter sphaeroides WT 2.4.1 under singlet oxygen stress

Project description:Transcriptional and translational profiling of R. sphaeroides WT 2.4.1 under singlet oxygen stress compared to control (no stress) conditions

2012-11-14 | GSE42244 | GEO

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.

2012-08-03 | GSE39711 | GEO

Rhodobacter sphaeroides WT 2.4.1 under singlet oxygen stress

Project description:Transcriptional and translational profiling of R. sphaeroides WT 2.4.1 under singlet oxygen stress compared to control (no stress) conditions RNA samples collected at time-point zero and at different time-points after singlet oxygen stress were analyzed by two-color microarrays

2012-11-14 | E-GEOD-42244 | biostudies-arrayexpress

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

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, Entner–Doudoroff 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.

2014-11-18 | GSE63328 | GEO

Rhodobacter capsulatus SB1003 under singlet oxygen stress

Project description:Global transcriptome analyses at growth before and after 10 min of photooxidative stress were applied to monitor stress dependent gene expression in the alpha-proteobacterium Rhodobacter capsulatus. Transcriptome profiles of pigmented cultures with high aeration were monitored before and after the onset of singlet oxygen stress.

2020-01-24 | GSE134200 | GEO

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