Role of Hog1 in oxygen regulation of gene expression
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae S288C Saccharomyces cerevisiae
PROVIDER: GSE26593 | GEO | 2011/01/13
SECONDARY ACCESSION(S): PRJNA136189
REPOSITORIES: GEO
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Project description:Expression microarrays of WT vs. hog1D cells in aerobic or 5 hours of hypoxic growth (100% nitrogen gas). Two strains (WT vs. hog1 deletion), two conditions (aerobic vs. 5 hours hypoxic), two biological replicates each strain/condition.
2011-01-13 | E-GEOD-26593 | biostudies-arrayexpress
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Project description:To test the effects of hypoxia on transcription in Caulobacter crescentus, we cultured cells in a New Brunswick bioreactor under controlled conditions. Prior to innoculation, the medium was bubbled with laboratory air at maximum flow and stirred at 300 rpm for 2 hours. After this period, the medium was considered saturated with air and the oxygen probe was set to 100%. Untreated cultures were grown in air-saturated complex medium at 30 degrees C to OD660=0.5 at pH=7 (continuous air-bubbling; 300 rpm stirring). At cell harvest in aerated culture, the dissolved oxygen probe remained above 98%. To subject cells to hypoxia, culture at OD660=0.5, pH=7 was sparged continuously with nitrogen gas; the dissolved oxygen level as measured by the gas probe dropped from 100% to 0% over the course of 5 minutes under this condition. Hypoxic cultures were continually stirred and bubbled with nitrogen for another 20 minutes after the dissolved gas probe read 0%. Hypoxic cells were then harvested for RNA isolation.
2010-06-21 | GSE21127 | GEO
Project description:To test the effects of hypoxia on transcription in Caulobacter crescentus, we cultured cells in a New Brunswick bioreactor under controlled conditions. Prior to innoculation, the medium was bubbled with laboratory air at maximum flow and stirred at 300 rpm for 2 hours. After this period, the medium was considered saturated with air and the oxygen probe was set to 100%. Untreated cultures were grown in air-saturated complex medium at 30 degrees C to OD660=0.5 at pH=7 (continuous air-bubbling; 300 rpm stirring). At cell harvest in aerated culture, the dissolved oxygen probe remained above 98%. To subject cells to hypoxia, culture at OD660=0.5, pH=7 was sparged continuously with nitrogen gas; the dissolved oxygen level as measured by the gas probe dropped from 100% to 0% over the course of 5 minutes under this condition. Hypoxic cultures were continually stirred and bubbled with nitrogen for another 20 minutes after the dissolved gas probe read 0%. Hypoxic cells were then harvested for RNA isolation. Four independent biological samples are included in this study. Two batches of cells were subjected to 20 minutes of hypoxia in a bioreactor; two cell batches were highly aerated.
2010-06-21 | E-GEOD-21127 | biostudies-arrayexpress
Project description:Using strain NCTC 11168 in carbon (serine)-limited continuous cultures we report the first detailed examination of oxygen-dependent changes in gene and protein expression in Campylobacter jejuni under conditions where the growth rate is fixed. We show that in steady-states established at μ = 0.2 h-1 over a wide-range of oxygen inputs, a perceived aerobiosis scale can be calibrated by the acetate excretion flux, which becomes zero when metabolism is fully aerobic (100% aerobiosis = 5% v/v oxygen in the gas inflow). A label-free proteomic analysis compared protein abundance (reported as the emPAI ratio) at 40% aerobiosis (= 1.88% v/v oxygen in the gas inflow) and 150% aerobiosis (= 7.5% v/v oxygen in the gas inflow) aerobiosis. This identified 857 proteins. Of 223 proteins more abundant at 40% aerobiosis, those involved in host colonisation and alternative pathways of electron transport were prominent. At 150% aerobiosis, 129 proteins were more abundant, including those involved in oxidative stress protection, citric-acid cycle, lactate and proline oxidation.
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Project description:Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in Evans media containing 2 mM glucose as the sole and limiting source of energy and carbon. The working volume was 200 ml, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 0.1 l/min, and the dissolved oxygen tension was maintained at ~7% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode. For anaerobic growth, cells are grown on 100 % nitrogen gas bubbled at 0.1 l/min Cells were grown as above to steady-state, At steady-state, CO gas was bubbled through the culture at 0.1L/min. Samples were taken immediately prior to the addition of CO gas and over a time course of 2.5, 5, 10, 20, 40 and 80 min exposure to CO gas for subsequent analysis using microarrays. Cells were harvested directly into phenol:ethanol to stabilize RNA, and total RNA was purified using Qiagenâ??s RNeasy Mini kit as recommended by the suppliers. Time course experiment with samples taken immediately prior to or 2.5, 5, 10, 20, 40 or 80 minutes after addition of CO gas under either 0 or 100 % perceived aerobiosis. 2 biological repeats were performed for the aerobic condition with 2 technical (dye swap) repeats per biological repeat, and three biological repeats were perfomed for the anaerobic condition with 2 technical (dye swap) repeats per biological repeat.
2016-09-01 | E-GEOD-50713 | biostudies-arrayexpress
Project description:The R. delemar strain ATCC 20344 was cultured under nitrogen starvation conditions with varied oxygen availability to induce high (aerobic) and low (anaerobic) fumarate production.
2017-02-15 | PXD004600 | Pride
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