Transcriptomic analysis of Helicobacter pylori 26695 exposed to lethal concentration of a bactericidal inhibitor of the essential response regulator HsrA
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ABSTRACT:
PROVIDER: PRJEB77837 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13382336_1.fastq.gz | Fastqsanger.gz | |||
| ERR13382336_2.fastq.gz | Fastqsanger.gz | |||
| ERR13382337_1.fastq.gz | Fastqsanger.gz | |||
| ERR13382337_2.fastq.gz | Fastqsanger.gz | |||
| ERR13382338_1.fastq.gz | Fastqsanger.gz |
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Project description:Helicobacter pylori, a pathogenic member of phylum Campylobacterota (formerly Epsilonproteobacteria), is recognized as the leading cause of several human gastric pathologies, including acute and chronic gastritis, peptic ulcer disease, gastric adenocarcinoma, and gastric mucosa-associated lymphoid tissue (MALT) lymphoma. In the last two decades, the alarming increase of the antibiotic resistance levels to first-line and even “rescue” antibiotics, especially clarithromycin, metronidazole and levofloxacin, has led to a marked decrease of the eradication rates of traditional therapies. In previous works, we have validated the essential protein HsrA as an effective therapeutic target for H. pylori infection. HsrA is an OmpR/PhoB-type orphan response regulator, unique and highly conserved in members of phylum Campylobacterota, which appears involved in a variety of crucial physiological processes. In the present work, we carried out a transcriptomic analysis in order to discern the global effects of lethal concentrations of a bactericidal HsrA inhibitor on the H. pylori physiology. Treatment with the bactericidal HsrA inhibitor significantly changed the transcript levels of 367 open reading frames (ORF), of which 212 genes appeared upregulated and 155 genes resulted in downregulation, as compared with control samples. Thus, in vivo HsrA inhibition influenced, directly or indirectly, the expression of 23% of ORFs encoded by the H. pylori 26696 genome. Among the 268 differentially expressed genes (DEGs) with defined functions, two functional categories were highly enriched with downregulated genes involved in essential physiological processes: (1) ribosome biogenesis, and (2) electron transfer and oxidative phosphorylation.
2024-09-21 | E-MTAB-14255 | biostudies-arrayexpress
Project description:Helicobacter pylori 26695 Genome sequencing
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Project description:Helicobacter pylori strain:26695-1MET Genome sequencing
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Project description:RNA-seq to investigate regulatory roles of DNA methyltransferases in Helicobacter pylori strain 26695.
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Project description:To further examine the roles of DppA, we performed RNA-seq analysis and investigated the genes expressed differentially between H. pylori 26695 and a ΔdppA strain.We found that 253 genes were differentially expressed with a |Log2 (fold change)| > 1, including 116 genes that were upregulated and 137 genes that were downregulated in ∆dppA (P < 0.05). We also performed functional classification of the genes upregulated and downregulated in ∆dppA. We found that those genes involved in energy metabolism, transportation, and translation were significantly downregulated in ∆dppA, which might contribute to the decreased growth rate of H. pylori in this genetic background. Genes involved in DNA metabolism, bacterial pathogenesis, and motility were upregulated in this strain, and they might contribute to the virulence of H. pylori.
2021-01-05 | GSE164216 | GEO
Project description:Dear Sir or Madam, we report an in-depth proteogenomics study of Helicobacter pylori strain 26695 and provide the supporting MS data via ProteomExchange. The study includes 2 biological replicates with 6 different datasets: G1: in-gel digestion with trypsin, replicate 1 G2: in-gel digestion with trypsin, replicate 2 T1: SEC fractionation of low molecular weight (LMW) proteins and subsequent trypsin digestion, replicate 1 T2: SEC fractionation of LMW proteins and subsequent trypsin digestion, replicate 2 A1: SEC fractionation of LMW proteins and subsequent AspN digestion, replicate 1 A2: SEC fractionation of LMW proteins and subsequent AspN digestion, replicate 2 L1: SEC fractionation of LMW proteins and subsequent LysC digestion, replicate 1 L2: SEC fractionation of LMW proteins and subsequent LysC digestion, replicate 2 In our proteogenomics approach, we could identify four previously missing protein annotations and were able to correct sequences of six protein coding regions. Furthermore we identified signal peptidase cleavage sites for 72 different proteins. MGFs were generated by Maxquant 1.1 [1] using recalibration of peptide parent masses. For PRIDE (http://www.ebi.ac.uk/pride) submission, we made an additional database search with Mascot and X!Tandem using the SearchGUI [2]. Therefore we searched against a NCBI database of H. pylori strain 26695 complemented with the sequence corrections, signal peptide cleavage sites and missing annotations with the same configurations as described in materials and methods. For pride xml export we used the software PeptideShaker (http://code.google.com/p/peptide-shaker/). The complemented database has entries which will be submitted to the UniProtKB via SPIN. The entries have the according SPIN number as accession number. The NCBI accession numbers for the shortened sequences due to signal peptide cleavage are extended with “_1”. The fasta database is added to the submission. For additional information, please contact me: stephan.mueller@ufz.de Yours sincerely, Stephan Mueller References: [1] Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. Journal of proteome research. 2011;10:1794-805. [2] Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L. SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics. 2011;11:996-9.
2013-08-01 | PXD000054 | Pride
Project description:The bactericidal function of neutrophils are dependent on myriad intrinsic and extrinsic stimuli. Using systems immunology approaches we identified microbiome- and infection-induced changes in neutrophils. We focused on investigating the Prenylcysteine oxidase 1 like (Pcyox1l) protein function. Murine and human Pcyox1l proteins share ninety four percent aminoacid homology revealing significant evolutionary conservation and implicating Pcyox1l in mediating important biological functions. Here we show that the loss of Pcyox1l protein results in significant reductions in the mevalonate pathway impacting autophagy and cellular viability under homeostatic conditions. Concurrently, Pcyox1l CRISPRed-out neutrophils exhibit deficient bactericidal properties. Pcyox1l knock-out mice demonstrate significant susceptibility to infection with the gram-negative pathogen P. aeruginosa exemplified through increased neutrophil infiltrates, hemorrhaging, and reduced bactericidal functionality. Cumulatively, we ascribe a function to Pcyox1l protein as a fundamental regulator of the prenylation pathway and suggest connections beween metabolic responses and neutrophil functionality. Anastasia Petenkova , Shelby A. Auger, Jeffrey Lamb, Daisy Quellier, Cody Carter, On TakTo, Jelena Milosevic, Rana Barghout, Abirami Kugadas, Xiaoxiao Lu, Jennifer Geddes-McAlister, Raina Fichorova, David B. Sykes, Mark D. Distefano, and Mihaela Gadjeva. 2023. Prenylcysteine oxidase 1 like protein is required for neutrophil bactericidal activities. Nat.Comm.
2023-04-14 | PXD031115 | Pride
Project description:To determine dose-dependent effects of metal exposure we performed microarray hybridizations with RNA isolated from Daphnia magna following Cu, Cd, and Zn exposures over a range of concentrations that included a tolerated concentration, a sublethal concentration, and a highly toxic concentration. The gene expression profiles revealed effects to digestion related genes, immune related genes, metallothioneins, and oxidative stress genes at the higher concentrations. We also observed that the highest concentrations produced less specific gene expression profiles than the lower concentrations suggesting a more general stress response at the higher concentrations. The lowest concentration tested, representing tolerated concentrations of the metals, caused differential expression of only a few genes and were distinct from the expression profiles of the higher concentrations. This result provides support for the presence of a No Observed Transcriptional Effect Level (NOTEL) for metal exposure in D. magna and suggests that gene expression analysis may offer a strategy for distinguishing between toxic and nontoxic concentrations of metals in the environment. Keywords: ecotoxicogenomic exposure study
2008-06-09 | GSE7668 | GEO