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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Identification of HP0244 regulon at different pH conditions

ABSTRACT: 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.

ORGANISM(S): Helicobacter pylori

SUBMITTER: George Sachs

PROVIDER: E-GEOD-12900 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The pH-responsive regulon of HP0244 (FlgS), the cytoplasmic histidine kinase of Helicobacter pylori.

Wen Yi Y Feng Jing J Scott David R DR Marcus Elizabeth A EA Sachs George G

Journal of bacteriology 20081031 2

Helicobacter pylori colonizes the acidic gastric environment, in contrast to all other neutralophiles, whose acid resistance and tolerance responses allow only gastric transit. This acid adaptation is dependent on regulation of gene expression in response to pH changes in the periplasm and cytoplasm. The cytoplasmic histidine kinase, HP0244, which until now was thought only to regulate flagellar gene expression via its cognate response regulator, HP0703, was found to generate a response to decli ...[more]

PMID: 18978046

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Identification of HP0244 regulon at different pH conditions

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

Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori

Project description:In this study transcriptional start sites (TSS) for H. pylori 26695 were determined To detect the complement of transcripts expressed from H. pylori, we collected three independent biological replicates (B1 – B3) from 26695 wild type strain grown to mid-exponential (OD 600 ~0.6) phase under microaerophilic conditions at 37°C in BHI medium. For all three samples, total RNA was extracted and subjected to differential RNA-seq (dRNA-seq) library preparation for primary transcriptome analysis as described previously (Sharma et al., 2010). Specifically, prior to cDNA library construction half of each RNA sample was treated with 5’ terminator exonuclease (+TEX samples), which degrades RNAs containing a 5’-monophosphate (5’-P) and, thus, enriches for primary transcripts containing 5’-triphosphates (5’-PPP). The other half of each sample was left untreated (-TEX samples) and thus contains both primary transcripts (5’-PPP) and processed RNAs (5’-P).

2015-07-01 | E-GEOD-67564 | biostudies-arrayexpress

Biological cost of rifampicin resistance in Helicobacter pylori

Project description:The present study was aimed at analyzing (i) the biological cost of RNA polymerase (rpoB) mutations conferring rifampin resistance on H.pylori, (ii) the relationship between the cost of rpoB mutations and the chromosomal mutaion, (iii) the relationship between the cost of rpoB mutations and the transcription profile of sensitive and resistantrif strains of H.pylori (iv) and rpoB mutations in view of the possible fitness burden associated with resistance to another antibiotics. H.pylori reference strain 26695 was routinely maintained on Columbia agar plates and H. pylori-selective antibiotic mix Dent. Liquid culture was grown in BHI broth. Both plates and broth cultures were incubated at 37C under atmosphere enriched with 5% CO2 for 2-3 days . Mutant strains were selected by culturing H. pylori 26695 on selective plates containing rifampicin. In 5 days resistant colonies were picked up and passed under rifampicin pressure. RNA isolated was reverse transcribed and used to probe H. pylori home-made arrays

2010-11-30 | E-GEOD-25333 | biostudies-arrayexpress

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2015-06-13 | E-GEOD-69847 | biostudies-arrayexpress

Helicobacter pylori pathogenic mechanism

Project description:Helicobacter pylori infection reprograms host gene expression and influences various cellular processes, which have been investigated by cDNA microarray in vitro culture cells and in vivo patients of the chronic abdominal complaint. In this study，the effects of H. pylori infection on host gene expression in the gastric antral mucosa of patients with chronic gastritis were examined. The gastric antral mucosa was obtained from a total of 6 untreated patients undergoing gastroscopic and pathologic confirmation of chronic superficial gastritis. Three patients infected by H. pylori and 3 patients uninfected were used to cDNA microarray experiment.

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Salt regulated gene expression in Helicobacter pylori

Project description:In this study, we tested the hypothesis that high salt concentrations might alter gene expression in H. pylori. Analysis here provides into the role that salt may play in H. pylori pathogenesis. . H. pylori strain 26695 (SC#7) was grown for 15 h in BB-FBS medium containing 0.5% sodium chloride (i.e. BB-FBS-0.5%) The bacterial cells were then grown for 10 h, in fresh brucella broth at either 0.25% or 1.5% salt, harvested by centrifugation, and frozen at -80oC. RNA isolated was reverse transcribed and used to probe H. pylori Panorama arrays

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RNA-seq analysies of pH-responsive gene expression in Helicobacter pylori

Project description:Purpose: Next-generation sequencing (NGS) was used to analyze pH-responsive gene expression in H. pylori. The goals of this study are to compare H. pylori pH-responsive gene expression in H. pylori strain 26695 and 26695 dervatives containing mutations to the ArsRS two component system.

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RNA-seq analysis of pH-responsive gene expression in Helicobacter pylori [ArsS]

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Proteomic anlaysis of Fabry iPSC derived cardiomyocytes treated with GLA modRNA

Project description:Recent studies in non-human model systems have shown therapeutic potential of modified mRNA (modRNA) treatments for lysosomal storage diseases. Here, we assessed the efficacy of a modRNA treatment to restore the expression of the ÃŽÂ±-galactosidase (GLA) gene in a human cardiac model generated from induced-pluripotent stem cell-derived from two patients with Fabry disease. In line with the clinical phenotype, cardiomyocytes from Fabry patientÃ¢â‚¬â„¢s induced pluripotent stem cells show accumulation of the glycosphinolipid Globotriaosylceramide (GB3), which is an ÃŽÂ±-galactosidase substrate. Further, the patient-specific cardiomyocytes have significant upregulation of lysosomal associated proteins. Upon modRNA treatment, a subset of lysosomal proteins were partially restored to wildtype levels, implying the rescue of the molecular phenotype associated with the Fabry genotype. Importantly, a significant reduction of GB3 levels was observed in GLA modRNA treated cardiomyocytes demonstrating that ÃŽÂ±-galactosidase enzymatic activity was restored. Together, our results validate the utility of patient IPSC-derived cardiomyocytes as a model to study disease processes in Fabry disease and the therapeutic potential of GLA modRNA treatment to reduce GB3 accumulation in the heart.

2023-07-20 | PXD038361 | Pride

The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori

Project description:We performed a transcriptome analysis of two Helicobacter pylori wild-type strains and their corresponding mutants lacking a highly conserved GCGC-specific m5C-MTase (JHP1050) that was predicted to be active in all of 459 H. pylori genome sequences analyzed. Transcriptome data revealed that m5C-methylation modifies the transcription of multiple genes related to adherence to host cells, natural competence for DNA uptake or susceptibility to copper.

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