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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Rhodobacter sphaeroides respiration and photosynthesis

ABSTRACT: This series contains two subsets of samples not being directly compared. The two subsets are: GSE2145: 30% O2 vs PS 10W/m2 GSE2146: CT01 vs wild-type at 3% O2 Below results represent the K-means (K=4) clustering analysis using GeneSpring software. The list contains genes/ORFs contained in each of the 4 clusters. Keywords: other

ORGANISM(S): Rhodobacter sphaeroides

SUBMITTER: Timothy Donohue

PROVIDER: E-GEOD-2150 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of genes required for recycling reducing power during photosynthetic growth.

Tavano Christine L CL Podevels Angela M AM Donohue Timothy J TJ

Journal of bacteriology 20050801 15

Photosynthetic organisms have the unique ability to transform light energy into reducing power. We study the requirements for photosynthesis in the alpha-proteobacterium Rhodobacter sphaeroides. Global gene expression analysis found that approximately 50 uncharacterized genes were regulated by changes in light intensity and O\2 tension, similar to the expression of genes known to be required for photosynthetic growth of this bacterium. These uncharacterized genes included RSP4157 to -4159, which ...[more]

PMID: 16030219

Similar Datasets

Rhodobacter sphaeroides respiration and photosynthesis

Project description:This series contains two subsets of samples not being directly compared. The two subsets are: GSE2145: 30% O2 vs PS 10W/m2 GSE2146: CT01 vs wild-type at 3% O2 Below results represent the K-means (K=4) clustering analysis using GeneSpring software. The list contains genes/ORFs contained in each of the 4 clusters. Keywords: other

2005-04-01 | GSE2150 | GEO

30% O2 vs PS 10W/m2

Project description:Comparison of wild-type (2.4.1) R. sphaeroides gene expression in 30% O2 aerobic respiration vs. photosynthesis 10W/m2 light, to identify candidate photosynthesis genes. RNA preparation: pellet cells from exponential phase cultures using 5% phenol in ethanol stop solution; lysozyme + SDS to lyse; phenol/chloroform extraction + DNase treatment + RNeasy kit clean up. Manuscript in preparation. The below normalized data was generated using GeneSpring software with the following settings: A data: Data Transformation: set all values less than 0.01 to 0.01 Per Chip: normalize to 50th percentile, and then Per Gene: normalize to median B data: Data Transformation: set all values less than 0.01 to 0.01 Per Chip: normalize to 50th percentile Values from independent replicates were averaged Keywords = Rhodobacter sphaeroides Keywords = photosynthesis Keywords = purple bacteria Keywords: other

2010-06-10 | E-GEOD-2145 | biostudies-arrayexpress

CT01 vs wild-type at 3% O2

Project description:Comparison of wild-type (2.4.1) and CT01 (contains an omega Spr/Smr insertion in RSP4157) gene expression; growth condition is (3% O2 + 96%N2 + 1%CO2) semi-aerobic growth in the dark. Manuscript in preparation. The below normalized data was generated using GeneSpring software with the following settings: A data: Data Transformation: set all values less than 0.01 to 0.01 Per Chip: normalize to 50th percentile, and then Per Gene: normalize to median B data: Data Transformation: set all values less than 0.01 to 0.01 Per Chip: normalize to 50th percentile Values from independent replicates were averaged Keywords = Rhodobacter sphaeroides Keywords = photosynthesis Keywords = semi-aerobic Keywords = purple bacteria Keywords: other

2010-06-10 | E-GEOD-2146 | biostudies-arrayexpress

Oxygen-dependent transcriptome profiling in R.sphaeroides 2.4.1 in the dark

Project description:Wild type (2.4.1) strain, dark conditions, controlled oxtgen concentration in the growth medium (achieved by constant sparging with a gas mixture containing 1% CO2, variable - indicated for every sample - concentration O2 and balance N2). Keywords: dose response Cells were harvested at OD 0.16-0.18 after rapid addition of rifampicin, spun down and frozen for subsequent RNA isolation. RNA was isolated using bead beater and RNeasy kit. Traces of DNA were removed by DNAse I treatment until level non-detectable by 33-36 cycles of real-time PCR. Further sample preparaton -according Affymetrix protocols. Data processing: MAS 5.0 values are deposited here (for compatability with other submitted samples), values used in the publications are obtained with RMA and may be recreated using the supplied CEL files.

2010-06-11 | E-GEOD-7004 | biostudies-arrayexpress

Cereibacter sphaeroides

Project description:30% O2 vs PS 10W/m2

| PRJNA91399 | ENA

Effect of oligomycin on transcript levels in Arabidopsis seedling cultures

Project description:To understand how an inhibition of the mitochondrial ATP synthase affects transcriptional programming and to identify potential candidates of the signaling machinery involved in ATP synthase deficiency responses, we used oligomycin on seedling liquid cultures. Seedlings were harvested at time points 0, 1 and 4 h after the start of oligomycin and control (EtOH) treatments. Already 1 h after addition of oligomycin a total of 102 genes were more than threefold up-regulated and 14 genes were repressed, with most of them showing persistent changes. After 4 h, 580 additional genes were more than threefold up-regulated, and 152 genes were repressed by oligomycin. Several genes for alternative NAD(P)H dehydrogenases and alternative oxidases (AOX1a, AOX1d and NDA1) were up-regulated early, and additional homologs (NDA2, NDB2, NDB4 and AOX1b) followed 4 h after the start of treatment. Several genes for subunits of complex I, complex IV and the ATP synthase were induced whereas hardly any genes encoding enzymes of glycolysis and the TCA cycle changed. Additionally, four of five hallmark genes for oxidative stress were increased by oligomycin. These genes are At2g21640 (UPOX), At1g19020, At1g05340 and At1g57630 and code for proteins of unknown function. Among oxidative stress proteins with known functions, several H2O2-responsive Glutathione-S-transferases and BCS1 (CYTOCHROME BC1 SYNTHESIS) were strongly up-regulated already after 1 h. BCS1 is induced by salicylic acid and independent of other reactive oxygen signaling (ROS) pathways, such as H2O2. The results indicate that several different ROS and defense signaling pathways were induced simultaneously by oligomycin. This is further corroborated by induction of several transcription factors of the WRKY and NAC families, which have been previously implicated in coordinating cellular defense signaling. Three replicates for each treatment including oligomycin and control (EtOH) samples.

2012-06-27 | E-GEOD-38965 | biostudies-arrayexpress

Pseudomonas aeruginosa PA14 wild-type vs the tpbA (PA14_13660) mutant

Project description:Microarray analysis for the biofilm cells of Pseudomonas aeruginosa PA14 wild-type vs the tpbA (PA14_13660) mutant in LB medium at 4 and 7 h at 37C Microarray analysis for the biofilm cells of Pseudomonas aeruginosa PA14 wild-type vs the tpbA (PA14_13660) mutant in LB medium at 4 and 7 h at 37C.

2009-05-23 | E-GEOD-13871 | biostudies-arrayexpress

The scr circuit in Vibrio parahaemolyticus: output targets and transcriptional regulation by a c-di-GMP responsive protein

Project description:Vibrio parahaemolyticus scr genes modulate expression of gene sets pertinent to swarming and biofilm formation. They do so by affecting the level of the second messenger c-di-GMP. Here we explore the extent of this regulation by comparing the transcriptomes of a scrABC mutant and its wild-type parental strain. The scope of transcriptional effects modulated by c-di-GMP includes ~100 genes that are positively and negatively regulated. An elevated cellular level of c-di-GMP represses the surface sensing regulon including the genes encoding the lateral flagellar and type three secretion systems while inducing expression of genes encoding cell surface molecules and capsular polysaccharide. Expression of a few transcriptional regulators was also affected, and here we describe the role of one, CpsQ. CpsQ is one of four V. parahaemolyticus homologs in the CsgD/VpsT family of regulators, members of which have been implicated in c-di-GMP signaling. Mutations in cpsQ, like defects in another previously identified capsule regulator, cpsR, suppress the sticky phenotype of scr mutants. By using a combination of mutant and reporter analyses in Vibrio and E. coli, CpsQ is shown to be the direct positive regulator of cpsA transcription and its cpsA-activating ability is found to be responsive to the cellular level of c-di-GMP. Unexpectedly, we find that a low level of this nucleotide diminishes the stability of CpsQ. The molecular interplay in this signaling circuit is further defined by demonstrating that CpsQ is epistatic to CpsS, a negative regulator of capsule. CpsR activates cpsQ, and CpsQ can also regulate its own transcription. Wildtype Vibrio parahaemolyticus (LM5674) and scrABC mutant (LM6567) were grown on rich mediim agar plates and gene expression profiles were compared.

2011-12-31 | E-GEOD-30508 | biostudies-arrayexpress

P. aeruginosa PA14 WT in LB medium vs in LB with 10 mM adenosine medium

Project description:To investigate the impact of adenosine on gene expression of wild-type PA14. To investigate the impact of adenosine on gene expression of wild-type PA14, cells were harvested after incubating for 7 h in LB medium and LB with 10 mM adenosine medium, and RNA was extracted with the RNeasy Mini Kit (Qiagen, Valencia, CA) using a bead beater (Biospec, Bartlesville, OK ) with RNAlater buffer (Applied Biosystems, Foster City, CA) to stabilize the RNA.

2012-05-22 | E-GEOD-29665 | biostudies-arrayexpress

Transcription profiling of human skeletal muscle from males with type 2 diabetes to identify genes involved in oxidative phosphorylation

Project description:DNA microarrays can be used to discover gene expression changes characteristic of human disease. This is challenging, however, when relevant differences are subtle at the level of individual genes. We introduce an analytical strategy, Gene Set Enrichment Analysis, designed to detect modest but coordinate changes in the expression of groups of functionally related genes. Using this approach, we identify a set of genes involved in oxidative phosphorylation whose expression is coordinately decreased in human diabetic muscle. Expression of these genes is high at sites of insulin-mediated glucose disposal, activated by PGC-1a, and correlated with total-body aerobic capacity. Our results associate this gene set with clinically important variation in human metabolism, and illustrate the value of pathway relationships in the analysis of genomic profiling experiments.

2007-07-17 | E-CBIL-30 | biostudies-arrayexpress

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