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A genome-wide analysis of PhoP~P binding to chromosomal DNA reveals several novel features of the PhoPR-mediated phosphate limitation response in Bacillus subtilis

ABSTRACT: Identification of the specific PhoP binding regions on the B. subtilis chromosome during exponential and phosphate starvation growth phases. The data serves to extend the PhoPR regulon in Bacillus subtilis and its role in adaptation to phosphate-limiting conditions and cell wall metabolism, as well as implying a role in several other cellular processes.

ORGANISM(S): Bacillus subtilis Bacillus subtilis subsp. subtilis str. 168

PROVIDER: GSE65273 | GEO | 2015/03/05

SECONDARY ACCESSION(S): PRJNA273594

REPOSITORIES: GEO

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A genome-wide analysis of PhoP~P binding to chromosomal DNA reveals several novel features of the PhoPR-mediated phosphate limitation response in Bacillus subtilis

Project description:Identification of the specific PhoP binding regions on the B. subtilis chromosome during exponential and phosphate starvation growth phases. The data serves to extend the PhoPR regulon in Bacillus subtilis and its role in adaptation to phosphate-limiting conditions and cell wall metabolism, as well as implying a role in several other cellular processes. For each sample analyzed in this study three biological replicates were performed. Three different samples were taken from a strain expressing the PhoP-SPA protein as well as from wild-type (168) without a tagged PhoP. Samples were taken from exponentially growing cells in low phosphate medium (LPDM) as well as from phosphate-limited cells (T2). Each sample compares ChIP DNA vs. Total DNA from the same cells.

2015-03-05 | E-GEOD-65273 | biostudies-arrayexpress

Cell envelope metabolism in phosphate limited Bacillus subtilis cells

2011-07-13 | GSE23164 | GEO

Cell envelope metabolism in phosphate limited Bacillus subtilis cells

Project description:Investigation of the whole genome expression level changes in phosphate limited Bacillus subtilis wild-type and delta-phoPR cells Investigation of the whole genome expression level changes of wild-type and delta-phoPR Bacills subtilis cells comparing high and low phosphate medium For each sample analyzed in this study 3 technical replicates were performed. 3 different samples were taken for wild-type cell and delta-phoPR cell, respectively. Samples were taken from exponentially growing cells in high and low phosphate medium as well as from phosphate-limited cells.

2011-07-12 | E-GEOD-23164 | biostudies-arrayexpress

A genome-wide analysis of PhoP~P binding to chromosomal DNA reveals several novel features of the PhoPR-mediated phosphate limitation response in Bacillus subtilis

Project description:A genome-wide analysis of PhoP~P binding to chromosomal DNA reveals several novel features of the PhoPR-mediated phosphate limitation response in Bacillus subtilis

| PRJNA273594 | ENA

Genome-wide transcriptional analysis of the phosphate starvation stimulon of Bacillus subtilis

Project description:Bacillus subtilis responds to phosphate starvation stress by inducing the PhoP and SigB regulons. While the PhoP regulon provides a specific response to phosphate starvation stress, maximizing the acquisition of phosphate (Pi) from the environment and reducing the cellular requirement for this essential nutrient, the SigB regulon provide non-specific resistance to stress by protecting essential cellular components such as DNA and membranes. We have characterized the phosphate starvation stress response of B. subtilis at a genome-wide level using DNA macroarrays. A combination of outlier and cluster analyses identified putatively new members of the PhoP regulon, namely yfkN (2',3'-cyclic-nucleotide 2'-phosphodiesterase), yurI (ribonuclease), yjdB (unknown) and vpr (extracellular serine protease). YurI is thought to be responsible for the non-specific degradation of RNA, whilst the activity of YfkN on various nucleotide phosphates suggests that it could act on substrates liberated by YurI which produces 3` or 5` phosphoribonucleotides. The putative new PhoP regulon members are either known or predicted to be secreted and are likely to be important for the recovery of inorganic phosphate from a variety of organic sources of phosphate in the environment. Keywords: other

2005-11-16 | GSE2667 | GEO

Genome-wide analysis of phosphorylated PhoP binding to chromosomal DNA reveals several novel features of the PhoPR-mediated phosphate limitation response in Bacillus subtilis.

Project description: Not available

| S-EPMC4372752 | biostudies-literature

M. tuberculosis phoP mutant lacking mcr7

Project description:The PhoPR two-component system is essential for virulence in Mycobacterium tuberculosis where it controls expression of approximately 2% of the genes, including those for the ESX-1 secretion apparatus, a major virulence determinant. Mutations in phoP lead to compromised production of pathogen-specific cell wall components and attenuation both ex vivo and in vivo. The PhoP regulon comprises several transcriptional regulators as well as genes for polyketide synthases and PE/PPE proteins. The most prominent site of PhoP regulation was located in the intergenic region between rv2395 and PE_PGRS41, where the mcr7 gene codes for a small non-coding RNA (ncRNA). Our prediction suggested that Mcr7 might regulate tatC at the post-transcriptional level by occlusion of the RBS and the consequent translational arrest. Consequently, we studied the secretome from exponentially grown cultures of strain H37Rv, its phoP mutant and a phoP complemented mutant by in-depth proteomics. The results are consistent with a regulatory model involving PhoP, Mcr7 and tatC mRNA since the absence of Mcr7 in the phoP mutant would result in more efficient TatC translation and therefore increased secretion.

2018-08-29 | PXD000698 | Pride

Chromatin immunoprecipitation of Streptomyces coelicolor wild type and phP-null mutants during phosphate starvation to determine binding locations of PhoP

Project description:S. coelicolor was grown in low-phosphate concentration R5 liquid medium which facilitated the transition to a phosphate starvation induced stationary phase and the subsequent induction of the PhoP regulon. The genome wide binding locations of PhoP during phosphate starvation were determined by chromatin-immunopreciptiation followed by hybridisation to high density S. coelicolor DNA microarrays. The use of both wild-type S. coelicolor and phoP-null mutant strains allowed the identification of specific PhoP binding locations.

2012-08-30 | E-MAXD-50 | biostudies-arrayexpress

Evolutionary conserved mutations in PhoPR attenuate the virulence of animal-adapted tuberculosis strains for humans

Project description:By genome comparison of 30 MTBC strains, we identified three SNPs affecting the phoPR genes of members of the animal and M. africanum lineages that were not seen in the M. tuberculosis sensu-stricto genomes. The genes phoPR encode a two component regulatory system that is known for its strong impact on virulence and immunogenicity of M. tuberculosis due to its key role in the regulation of genes involved in lipid synthesis and secretion of the 6 kDa secreted antigenic target ESAT-6. To explore whether these SNPs affect the expression of the PhoP regulon, we compared the transcriptome of M. tuberculosis mutants lacking the endogenous phoPR genes (ΔphoPR) and their complemented derivatives expressing either the M. bovis or M. tuberculosis allele of phoPR (phoPR-bovis and phoPR-TB respectively). These comparisons were performed in parallel in two M. tuberculosis strains from distinct genetic backgrounds, i.e. strain GC1237 from lineage 2 (also named East-Asia or Beijing cluster) and the H37Rv reference strain from lineage 4 (also named Euro-American cluster).

2014-07-07 | GSE54421 | GEO

Natural mutations in the sensor kinase of the PhoPR two-component regulatory system modulate virulence of ancestor-like tuberculosis bacilli

Project description:In Mycobacterium tuberculosis, the PhoPR two-component regulatory system controls production and secretion of proteins and lipid virulence effectors. Several mutations, present in phoR of Mycobacterium canettii relative to M. tuberculosis, impact the expression of the PhoP regulon and the pathogenicity of the strains. Here, we analyse by RNA-seq the expression profile of PhoP-regulated genes between the two M. tuberculosis strains H37Rv and HN878 and the two M. canettii isolates STB-Ks and STB-Kr.

2023-05-24 | GSE229680 | GEO

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