Effect of hpyAVIBM, a C5 cytosine methyltransferase deletion on the Helicobacter pylori transcriptome
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PROVIDER: PRJNA137815 | ENA |
REPOSITORIES: ENA
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Project description:Helicobacter pylori genome is rich in restriction - modification (R-M) systems. Around 4 % of the genome codes for components of R-M systems. hpyAVIBM, which codes for a putative phase-variable C5 - cytosine methyltransferase (MTase) from H. pylori lacks a cognate restriction enzyme. To analysis the effect of deleting hpyAVIBM on the Helicobacter pylori transcriptome, microarray analysis was done with the wild type strains and corresponding hpyAVIBM deletion strains
2011-03-16 | E-GEOD-27946 | biostudies-arrayexpress
Project description:Helicobacter pylori genome is rich in restriction - modification (R-M) systems. Around 4 % of the genome codes for components of R-M systems. hpyAVIBM, which codes for a putative phase-variable C5 - cytosine methyltransferase (MTase) from H. pylori lacks a cognate restriction enzyme.
2011-03-16 | GSE27946 | GEO
Project description:Helicobacter pylori genome is rich in restriction - modification (R-M) systems. Around 4 % of the genome codes for components of R-M systems. hpyAVIBM, which codes for a putative phase-variable C5 - cytosine methyltransferase (MTase) from H. pylori lacks a cognate restriction enzyme.
2010-12-29 | GSE26340 | GEO
Project description:Helicobacter pylori genome is rich in restriction - modification (R-M) systems. Around 4 % of the genome codes for components of R-M systems. hpyAVIBM, which codes for a putative phase-variable C5 - cytosine methyltransferase (MTase) from H. pylori lacks a cognate restriction enzyme. To analysis the effect of expression of hpyAVIBM on the E. coli transcriptome, microarray analysis was done with the cells expressing wild type MTase with the cells expressing catalytic inactive mutant of the MTase.
2010-12-29 | E-GEOD-26340 | biostudies-arrayexpress
Project description:Bone marrow-derived macrophages from Dhps fl/fl mice and mice with specific deletion of Dhps in myeloid cells were infected with Helicobacter pylori PMSS1 for 24 hours. Cells were washed and lysed. Proteins were analyzed by isobaric tags for relative and absolute quantitation (iTRAQ).
2021-09-09 | PXD018187 | Pride
Project description:5-methylcytosine is one of the major epigenetic modifications of DNA in living organisms. In bacteria, some species possess DNA methyltransferases that produce the cytosine modification in both strands or either strand of its target sequence. The purpose of this study is to characterize BatIM, the orphan cytosine methyltransferase coded on a prophage region of Bacillus anthracis.
2022-03-02 | GSE160371 | GEO
Project description:Helicobacter pylori colonizes the gastric epithelium and is the leading cause of gastric adenocarcinoma. There is increasing evidence that DNA methylation regulates gene expression in addition to its role in genome protection. In this study, we characterize the impact of acidity, the Two-Component System (TCS) ArsRS, Autoinducer-2, and the Type I m6A DNA methyltransferase HsdM1 (HP0463) on the Helicobacter pylori methylome. Transcription of hsdM1 increases at least 4-fold in the absence of the sensory histidine kinase ArsS, the major acid sensing protein of H. pylori. HsdM1 exists in the phase-variable operon hsdR1-hsdM1. Phase-locking hsdR1 (HP0464), the restriction endonuclease gene, has significant impacts on the transcription of hsdM1. To determine the impacts of methyltransferase transcription patterns on the methylome, we conducted methylome sequencing on samples that had undergone prolonged acid-exposure experiment. We found differentially methylated motifs between pH 7 and pH 5 growth conditions, and that deletions of arsS and hsdM1 interfere with the epigenetic acid response. Deletion of arsS leads to altered hsdM1 expression and alters the activity of multiple methyltransferases in both conditions indicating that the ArsRS TCS, in addition to its role in acid acclimation via direct effects on regulon member transcription, may also indirectly impact gene expression via regulation of the methylome. We characterized the target motif of HsdM1 (HP0463) to be (H)HTCAVN6TGY. HsdM1 may hierarchically regulate the Type II m5C DNA methyltransferase HP1121. This complex regulation of DNA methyltransferases, and thus differential methylation patterns, may have implications for the decades-long persistent infection by H. pylori.
2024-01-01 | GSE241991 | GEO
Project description:Characterization of BatIM, the cytosine methyltransferase of Bacillus anthracis
| PRJNA673128 | ENA
Project description:A real-time assay for CpG-specific cytosine-C5 methyltransferase activity has been developed. The assay applies a break light oligonucleotide in which the methylation of an unmethylated 5'-CG-3' site is enzymatically coupled to the development of a fluorescent signal. This sensitive assay can measure rates of DNA methylation down to 0.34 +/- 0.06 fmol/s. The assay is reproducible, with a coefficient of variation over six independent measurements of 4.5%. Product concentration was accurately measured from fluorescence signals using a linear calibration curve, which achieved a goodness of fit (R(2)) above 0.98. The oligonucleotide substrate contains three C5-methylated cytosine residues and one unmethylated 5'-CG-3' site. Methylation yields an oligonucleotide containing the optimal substrate for the restriction enzyme GlaI. Cleavage of the fully methylated oligonucleotide leads to separation of fluorophore from quencher, giving a proportional increase in fluorescence. This method has been used to assay activity of DNMT1, the principle maintenance methyltransferase in human cells, and for the kinetic characterization of the bacterial cytosine-C5 methyltransferase M.SssI. The assay has been shown to be suitable for the real-time monitoring of DNMT1 activity in a high-throughput format, with low background signal and the ability to obtain linear rates of methylation over long periods, making this a promising method of high-throughput screening for inhibitors.
| S-EPMC2875032 | biostudies-literature
Project description:Thiele2005 - Genome-scale metabolic network
of Helicobacter pylori (iIT341)
This model is described in the article:
Expanded metabolic
reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in
silico genome-scale characterization of single- and
double-deletion mutants.
Thiele I, Vo TD, Price ND, Palsson
BØ.
J. Bacteriol. 2005 Aug; 187(16):
5818-5830
Abstract:
Helicobacter pylori is a human gastric pathogen infecting
almost half of the world population. Herein, we present an
updated version of the metabolic reconstruction of H. pylori
strain 26695 based on the revised genome annotation and new
experimental data. This reconstruction, iIT341 GSM/GPR,
represents a detailed review of the current literature about H.
pylori as it integrates biochemical and genomic data in a
comprehensive framework. In total, it accounts for 341
metabolic genes, 476 intracellular reactions, 78 exchange
reactions, and 485 metabolites. Novel features of iIT341
GSM/GPR include (i) gene-protein-reaction associations, (ii)
elementally and charge-balanced reactions, (iii) more accurate
descriptions of isoprenoid and lipopolysaccharide metabolism,
and (iv) quantitative assessments of the supporting data for
each reaction. This metabolic reconstruction was used to carry
out in silico deletion studies to identify essential and
conditionally essential genes in H. pylori. A total of 128
essential and 75 conditionally essential metabolic genes were
identified. Predicted growth phenotypes of single knockouts
were validated using published experimental data. In addition,
in silico double-deletion studies identified a total of 47
synthetic lethal mutants involving 67 different metabolic genes
in rich medium.
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2015-07-30 | MODEL1507180007 | BioModels