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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional profiling of R. sphaeroides Δirr

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE33533: R. sphaeroides Δirr -Fe vs. R. sphaeroides Δirr +Fe under microaerobic conditions GSE33534: R. sphaeroides Δirr vs. R. sphaeroides 2.4.1 under microaerobic conditions Refer to individual Series

ORGANISM(S): Rhodobacter sphaeroides 2.4.1

SUBMITTER: Verena Peuser

PROVIDER: E-GEOD-33535 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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R. sphaeroides Δirr -Fe vs. R. sphaeroides Δirr +Fe under microaerobic conditions

Project description:Transcriptional profiling of R. sphaeroides Δirr under iron limitation (-Fe) compared to control R. sphaeroides Δirr under normal growth conditions (+Fe). Two strain experiment under normal iron (+Fe) and iron limitation (-Fe) conditions. 6 Biological replicates, independently grown and harvested at OD660=0,4; 1-3 pooled in replicate 1, 4-6 pooled in replicate 2

2011-11-09 | E-GEOD-33533 | biostudies-arrayexpress

R. sphaeroides Δirr vs. R. sphaeroides 2.4.1 under microaerobic conditions

Project description:Transcriptional profiling of R. sphaeroides Δirr compared to control R. sphaeroides 2.4.1 under microaerobic conditions. Two strain experiment under microarobic conditions (30 µM). 6 Biological replicas, independetly grown and harvested at OD660=0,4; 1-3 pooled in replicate 1, 4-6 pooled in replicate 2

2011-11-09 | E-GEOD-33534 | biostudies-arrayexpress

R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 (singlet oxygen stress, aerobic conditions)

Project description:Transcriptional profiling of R. sphaeroides Δlov compared to control R. sphaeroides 2.4.1 under singlet oxygen stress, aerobic conditions Two-strain experiment with overnight cultures of the wild type 2.4.1 and the Δlov mutant. Both were diluted to an OD660 of 0.2 and gassed to adjust aerobic conditions (≈ 170 µM O2). 0.2 µM of methylene blue was added to the cultures to act as photosensitizer. After one doubling time of growth in the darkness cells were illuminated with 800 W m-2 of white light for 7 min.

2011-10-25 | E-GEOD-33260 | biostudies-arrayexpress

Comparative analysis of the response to iron-limitation in the absence of oxygen in R. sphaeroides [Microarray]

Project description:High intracellular levels of unbound iron can contribute to the production of reactive oxygen species (ROS) in the Fenton reaction, while depletion of iron limits the availability of iron containing proteins, some of which have important functions in the oxidative stress defense. Vice versa increased ROS levels lead to damage of proteins with iron sulfur centers. Thus organisms have to coordinate and balance their responses to oxidative stress and iron availability. Our knowledge on the molecular mechanisms underlying the coregulation of these responses is still limited. To discriminate between a direct cellular response to iron limitation and indirect responses, which are the consequence of increased levels of ROS, we compared the response of the alpha proteobacterium Rhodobacter sphaeroides to iron limitation in presence or absence of oxygen. While some genes respond to iron limitation exclusively or much stronger in presence of oxygen, other genes show much stronger response in anaerobic conditions. Remarkably few genes show even opposite response to iron depletion in presence or absence of iron. RNA samples collected from anaerobically grown cultures in presence or absence of iron were analyzed by two-color microarrays

2013-05-23 | E-GEOD-47182 | 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

R. sphaeroides pRPcrZ vs. R. sphaeroides pR4352 under low oxygen conditions

Project description:Transcriptional profiling of R. sphaeroides pRPcrZ compared to control R. sphaeroides pR4352 under low oxygen conditions. In this study we compared the transcriptome of a PcrZ over-expression strain to a control strain. PcrZ is the first small non-coding RNA, which is involved in the complex regulatory network of photosynthesis gene regulation in Rhodobacter sphaeroides. It counteracts the formation of photosynthetic complexes in a redox dependent manner. Two-strain experiment at low oxygen conditions (0.5 mg/L O2)

2012-08-14 | E-GEOD-37381 | biostudies-arrayexpress

R. sphaeroides delta-cryB

Project description:This SuperSeries is composed of the following subset Series: GSE33553: R. sphaeroides delta-cryB vs. R. sphaeroides 2.4.1 photo-oxidative stress, aerobic conditions GSE33554: R. sphaeroides delta-CryB vs. R. sphaeroides 2.4.1 microarobic conditions GSE33555: R. sphaeroides delta-cryB vs. R. sphaeroides 2.4.1 under blue light, semiaerobic conditions Refer to individual Series

2011-11-09 | E-GEOD-33556 | biostudies-arrayexpress

R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 (blue light, semiaerobic conditions)

Project description:Transcriptional profiling of R. sphaeroides Δlov compared to control R. sphaeroides 2.4.1 under blue light, semiaerobic conditions. Two-strain experiment under blue light illumination (20µmol m-2 s-1) and semiaerobic (90 µM O2) conditions

2011-10-25 | E-GEOD-33259 | biostudies-arrayexpress

R. sphaeroides delta-cryB vs. R. sphaeroides 2.4.1 under blue light, semiaerobic conditions

Project description:Transcriptional profiling of R. sphaeroides delta-cryB compared to control R. sphaeroides 2.4.1 under blue light, semiaerobic conditions. Two-strain experiment under blue light illumination (20µmol m-2 s-1) and semiaerobic (90 µM) conditions

2011-11-09 | E-GEOD-33555 | biostudies-arrayexpress

R. sphaeroides delta-cryB vs. R. sphaeroides 2.4.1 photo-oxidative stress, aerobic conditions

Project description:Transcriptional profiling of R. sphaeroides delta-cryB compared to control R. sphaeroides 2.4.1 under photo-oxidative stress, aerobic conditions. Two-strain experiment under 20' photo-oxidative stress (singlet oxygen generated by methylene blue under high light illumination) and aerobic (180 µM) conditions

2011-11-09 | E-GEOD-33553 | biostudies-arrayexpress

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