Identification of HP0244 regulon at different pH conditions
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ABSTRACT:
PROVIDER: PRJNA110897 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptional profiling of Helicobacter pylori comparing 26695 wild-type strain and a HP0244-deficient mutant 26695/∆HP0244::km treated at three different pH conditions (pH 7.4, pH 4.5 without urea, or pH 2.5 with 30 mM urea) for 30 min to define the HP0244 acid-responsive regulon Keywords: Genetic modification and stress response
2009-09-14 | GSE12900 | GEO
Project description:Transcriptional profiling of Helicobacter pylori comparing 26695 wild-type strain and a HP0244-deficient mutant 26695/âHP0244::km treated at three different pH conditions (pH 7.4, pH 4.5 without urea, or pH 2.5 with 30 mM urea) for 30 min to define the HP0244 acid-responsive regulon Keywords: Genetic modification and stress response Wild type vs HP0244-deficient mutant at three different pH conditions (pH7.4, pH4.5 without urea, and pH2.5 with 30 mM urea). Three biological replicates for each pH condition: 3 wild type and 3 mutant, independently grown, pH treated, and harvested.
2010-05-05 | E-GEOD-12900 | biostudies-arrayexpress
Project description:Microbial Interaction of Reductive Dechlorination Consortia under Different pH Conditions
| PRJEB29882 | ENA
Project description:Helicobacter pylori encounters a wide range of pH within the human stomach. In a comparison of H. pylori cultured in vitro under neutral or acidic conditions, about 15% of genes are26 differentially expressed, and corresponding changes are detectable for many of the encoded proteins. The ArsRS two-component system (TCS), comprised of the sensor kinase ArsS and its cognate response regulator ArsR, has an important role in mediating pH-responsive changes in H. pylori gene expression. In this study, we sought to delineate the pH-responsive ArsRS regulon and further define the role of ArsR in pH-responsive gene expression. We compared H. pylori strains containing an intact ArsRS system with an arsS null mutant or strains containing site32 specific mutations of a conserved aspartate residue (D52) in ArsR, which is phosphorylated in response to signals relayed by the cognate sensor kinase ArsS. We identified 178 genes that were pH-responsive in strains containing an intact ArsRS system but not in ∆arsS or arsR mutants. These constituents of the pH-responsive ArsRS regulon include genes involved in acid acclimatization (ureAB, amidases), oxidative stress responses (katA, sodB), transcriptional regulation related to iron or nickel homeostasis (fur, nikR), and genes encoding outer membrane proteins [including sabA, alpA, alpB, hopD (labA), and horA]. When comparing H. pylori strains containing an intact ArsRS TCS with arsRS mutants, each cultured at neutral pH, relatively few genes are differentially expressed. Collectively, these data suggest that ArsRS41 mediated gene regulation has an important role in H. pylori adaptation to changing pH conditions.
2022-02-16 | PXD023679 | Pride
Project description:Proteomic analysis of a commensal Staphylococcus epidermidis strain in different pH conditions for describing the molecular players involved in the skin-to-blood adaptation of the bacterium.
2023-03-11 | PXD034825 | Pride
Project description:The human gastric pathogen Helicobacter pylori is extremely well adapted to the highly acidic conditions encountered in the stomach. The pronounced acid resistance of H. pylori relies mainly on the ammonia-producing enzyme urease, however, urease-independent mechanisms are likely to contribute to acid adaptation. Acid-responsive gene regulation is mediated at least in part by the ArsRS two-component system consisting of the essential OmpR-like response regulator ArsR and the non-essential cognate histidine kinase ArsS whose autophosphorylation is triggered in response to low pH. In this study by global transcriptional profiling of an ArsS-deficient H. pylori mutant grown at pH 5.0 we define the ArsR~P- dependent regulon consisting of 110 genes including the urease gene cluster, the genes encoding the aliphatic amidases AmiE and AmiF and the rocF gene encoding arginase. Keywords: Identification of an ArsRS-Regulon
2006-04-01 | GSE4293 | GEO
Project description:We revealed that an enhancement of rice growth by 2'-deoxymugineic acid (DMA) application was observed not only under high pH conditions where iron availability for plant uptake was reduced but also under normal pH conditions. This result indicates that DMA application improves not only Fe availability for plants but also plant productivity. To explain a mechanism caused by the DMA application, molecular regulation in rice treated with or without DMA was analyzed using microarray analysis and qRT-PCR. Results provide insight into advantages of DMA application in rice seedlings.
2015-04-10 | GSE56455 | GEO
Project description:We revealed that an enhancement of rice growth by 2'-deoxymugineic acid (DMA) application was observed not only under high pH conditions where iron availability for plant uptake was reduced but also under normal pH conditions. This result indicates that DMA application improves not only Fe availability for plants but also plant productivity. To explain a mechanism caused by the DMA application, molecular regulation in rice treated with or without DMA was analyzed using microarray analysis and qRT-PCR. Results provide insight into advantages of DMA application in rice seedlings. Gene expression patterns induced by DMA and EDTA in root and shoot were analyzed with control experiment (no chelator). One independent experiment was performed at each pH (pH 5.8 or pH 8.0).
2015-04-10 | E-GEOD-56455 | biostudies-arrayexpress
Project description:The conditions of the tumor microenvironment, such as hypoxia and nutrient starvation, play critical roles in cancer progression. However, the role of acidic extracellular pH in cancer progression is not studied as extensively as that of hypoxia. Here, we show that extracellular acidic pH (pH 6.8) triggered activation of sterol regulatory element-binding protein 2 (SREBP2) by stimulating nuclear translocation and promoter binding to its targets along with intracellular acidification. Interestingly, inhibition of SREBP2, but not SREBP1, suppressed the upregulation of low pH-induced cholesterol biosynthesis-related genes. Moreover, acyl-CoA synthetase short-chain family member 2 (ACSS2), a direct SREBP2 target, provided a growth advantage to cancer cells under acidic pH. Furthermore, acidic pH-responsive SREBP2 target genes were associated with reduced overall survival of cancer patients. Thus, our findings show that SREBP2 is a key transcriptional regulator of metabolic genes and progression of cancer cells, partly in response to extracellular acidification.
2017-01-25 | GSE93980 | GEO
Project description:Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH. Cultures were grown with aeration to an optical density at 600 nm of 0.3 in potassium-modified Luria-Bertani medium buffered at pH 5.0, 7.0, and 8.7. For each of the three pH conditions, cDNA from RNA of five independent cultures was hybridized to Affymetrix E. coli arrays. Analysis of variance with a significance level of 0.001 resulted in 98% power to detect genes showing a twofold difference in expression. Normalized expression indices were calculated for each gene and intergenic region (IG). Differential expression among the three pH classes was observed for 763 genes and 353 IGs. Hierarchical clustering yielded six well-defined clusters of pH profiles, designated Acid High (highest expression at pH 5.0), Acid Low (lowest expression at pH 5.0), Base High (highest at pH 8.7), Base Low (lowest at pH 8.7), Neutral High (highest at pH 7.0, lower in acid or base), and Neutral Low (lowest at pH 7.0, higher at both pH extremes). Flagellar and chemotaxis genes were repressed at pH 8.7 (Base Low cluster), where the cell's transmembrane proton potential is diminished by the maintenance of an inverted pH gradient. High pH also repressed the proton pumps cytochrome o (cyo) and NADH dehydrogenases I and II. By contrast, the proton-importing ATP synthase F1Fo and the microaerophilic cytochrome d (cyd), which minimizes proton export, were induced at pH 8.7. These observations are consistent with a model in which high pH represses synthesis of flagella, which expend proton motive force, while stepping up electron transport and ATPase components that keep protons inside the cell. Acid-induced genes, on the other hand, were coinduced by conditions associated with increased metabolic rate, such as oxidative stress. All six pH-dependent clusters included envelope and periplasmic proteins, which directly experience external pH. Overall, this study showed that (i) low pH accelerates acid consumption and proton export, while coinducing oxidative stress and heat shock regulons; (ii) high pH accelerates proton import, while repressing the energy-expensive flagellar and chemotaxis regulons; and (iii) pH differentially regulates a large number of periplasmic and envelope proteins. Experiment Overall Design: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH. Overnight cultures were diluted 1:1000 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.0, pH 7.0, and pH 8.7. Bacteria were cultured in baffled flasks (less than 10% volume filled) with rotation at 240 rpm, incubated at 37°C to an optical density at 600 nm of 0.3. For each of the three pH conditions, RNA was isolated from five independent cultures. Labeled cDNA was hybridized to Affymetrix antisense arrays according to standard procedures. To analyze the expression levels, Dchip software was used to generate model-based expression indices normalized to sample pH 7 replicate 1. ANOVA was used to identify genes with sitnificant expression differences among the three pH classes (p = 0.001). For genes showing significant differences, the Log2 expression ratios were determined for each pair of pH classes, and significance was determined by Tukey's test (p = 0.001).
2007-09-21 | E-GEOD-4511 | biostudies-arrayexpress