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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: 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

PROVIDER: PRJNA273594 | ENA |

REPOSITORIES: ENA

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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

2015-03-05 | GSE65273 | GEO

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

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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

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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

Responses of Pelagibacterales strains to phosphate limitation

Project description:Responses of Pelagibacterales strains to phosphate limitation

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Time series expression data during phosphate limitation for E. coli K12 JP6015/pMU91

Project description:A fermentation strategies with phosphate feeding was applied to elongate transition inti phosphate limitation for an tryptophan overproducing E. coli strain High frequency sampling together with the applied fermentation strategy should provide high resolution insights into regulatory regimes involved in phosphate response

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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

A conserved two-component signal transduction system controls the response to phosphate starvation in Bifidobacterium breve UCC2003

Project description:This work reports on the identification and molecular characterization of a two-component regulatory system (2CRS), encoded by phoRP in Bifidobacterium breve UCC2003, which controls the response to phosphate (Pi) starvation. The response regulator PhoP was shown to bind to the promoter region of pstSCAB, specifying a predicted Pi transporter system, as well as that of phoU, which specifies a putative Pi-responsive regulatory protein. This interaction is assumed to cause transcriptional activation under conditions of Pi limitation. The phoRP genes appear to be subject to positive auto-regulation, and with pstSCAB and phoU, represent the complete regulon controlled by the phoRP-encoded 2CRS in B. breve UCC2003. Determination of the minimal PhoP binding region combined with bioinformatic analysis revealed the probable recognition sequence of PhoP, designated here as the PHO box, which together with phoRP is conserved among many high GC-content Gram+ bacteria. The importance of the phoRP 2CRS in the response of B. breve to Pi starvation conditions was confirmed by generating a B. breve::phoP insertion mutant which exhibited decreased growth under phosphate-limiting conditions as compared to its parent strain UCC2003.

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Systems analysis of phosphate-limitation induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides

Project description:Lipid accumulation by oleaginous microorganisms is of great scientific interest and biotechnological potential. While nitrogen limitation has been routinely employed, low-cost raw materials usually contain rich nitrogenous components, thus preventing from efficient lipid production. Inorganic phosphate (Pi) limitation has been found sufficient to promote conversion of sugars into lipids, yet the molecular basis of cellular response to Pi-limitation and concurrent lipid accumulation remains elusive. Here we performed multi-omic analyses of the oleaginous yeast Rhodosporidium toruloides to shield lights on Pi-limitation induced lipid accumulation. Samples were prepared under Pi-limited as well as Pi-replete chemostat conditions, and subjected to analysis at the transcriptomic, proteomic and metabolomic level. In total, 7970 genes, 4212 proteins and 123 metabolites were identified. Results showed that Pi-limitation facilitates up-regulation of Pi-associated metabolism, RNA degradation and triacylglycerol biosynthesis, while down-regulation of ribosome biosynthesis and tricarboxylic acid cycle. Pi-limitation leads to de-phosphorylation of adenosine monophosphate, the allosteric activator of isocitrate dehydrogenase key to lipid biosynthesis. It was found that NADPH, the key cofactor for fatty acid biosynthesis, is limited due to reduced flux through the pentose phosphate pathway and transhydrogenation cycle, and that this can be overcomed by overexpression of an endogenous malic enzyme. These phenomena are found distinctive from those under nitrogen-limitation. The information greatly enriches our understanding on microbial oleaginicity and Pi-related metabolism. Importantly, systems data may facilitate designing advanced cell factories for production of lipids and related oleochemicals.

2018-05-31 | GSE113097 | GEO

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