Genome-wide identification of Bacillus subtilis Zur-binding sites.
ABSTRACT: The transcriptional factor Zur plays a key role in regulating zinc homeostasis in Bacillus subtilis. The genomic sites bound by Zur were mapped using a chromatine immunoprecipitation approach. This allowed the identification of 80 inter- and intragenic chromosomal sites bound by Zur. This data set contains 2 samples. Immunoprecipitated (IP) DNA from Bacillus subtilis BSAS36 strain (BSB1, a tryptophan-prototrophic derivative 168 strain expressing a SPA-tagged Zur protein) were extracted from bacterial cells in the exponential growth phase. IP and whole-cell extract DNA were hybridized on tiling array to generate ChIP-on-chip profiles. Two biological replicates were anlyzed.
Project description:The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress. Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished. Wild-type strain and spx mutant cells exposed or not to diamide stress were subjected to tiling array gene expression analysis. To distinguish direct and indirect effects, the genomic sites bound by the Spx-RNAP complex were mapped using a chromatine immunoprecipitation approach. This allowed the identification of 144 transcription units comprising 275 genes under direct Spx regulation. This data set contains 4 samples. Immunoprecipitated (IP) DNA from Bacillus subtilis Bas044 strain (BSB1, a tryptophan-prototrophic derivative 168 strain expressing a SPA-tagged Spx protein) were extracted from bacterial cultures in absence or presence of diamide. IP and whole cell extract DNA were hybridized on tiling array to generate ChIP-on-chip profiles. Two biological replicates were analyzed.
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.
Project description:AbrB is a global gene regulator involved in transition phase phenomena in Bacillus subtilis. It participates in a complex regulatory network governing the expression of stationary phase functions. AbrB was previously found to be phosphorylated on serine 86 located close to its C-terminal oligomerization domain. Here we report that AbrB can be phosphorylated by three B. subtilis serine/threonine kinases expressed during the transition and stationary phase: PrkC, PrkD and YabT. Our in vitro findings suggest that AbrB phosphorylation impedes its DNA binding and abolishes binding cooperativity. In vivo we established that a phospho-mimetic mutation abrB S86D leads to a significant loss of AbrB control over several key target functions: exoprotease production, competence development and sporulation. A wider transcriptome analysis of abrB S86D and S86A mutant strains revealed deregulation of a large number of target genes. We therefore propose that AbrB phosphorylation serves as an additional input for fine-tuning the activity of this ambiactive gene regulator. A 6 arrays study of the transcriptome profiles of B. subtilis strain 168, abrB-S86A and abrB-S86D mutant strains. Compared to the wild-type strain the mutant strains were used to test the effect of the phosphorylation of AbrB on ser-86 (using a phosphomimetic of AbrB (abrB-S86D strain) or its absence (abrB-S86A strain) on transcript profiles.
Project description:Comprison of the transcriptome of wild type Bacillus subtilis to the mutants sigW, rasP and prsW to select all candidate sigW regulated genes. We identified 89 genes as being sigW regulated, including several non-coding RNA's. The effects of rasP and prsW mutations on sigW regulated genes were relatively mild, implying that RasP or PrsW are not strictly required for sigW activation. The rasP mutant has a peliotropic phenotype, affecting competence development, protein secretion and membrane protein production. We show that these are not mirrored in the transcriptome, suggesting that RasP exerts its effects at the post transcriptional level. RNA samples prepared from B. subtilis 168 and mutants sigW, rasP, and prsW were grown in Luria Bertani broth to O.D 600nm 1.0 were reverse transcribed, labeled and hybridized to tiling arrays. All hybridizations (except prsW which was in duplicate) were performed in triplicate using RNA isolated from independent cultures.
Project description:This analysis is part of the study GSE27219, The condition-dependent transcriptome of Bacillus subtilis 168. In this study, 120 transcription units where identified for which transcription did not terminate at any specific site, leading to mRNA extension over long distances with slowly decreasing signal intensity. In most cases, lack of termination and read-through generated antisense transcripts. These findings together with the lack of intrinsic terminators suggested that transcription termination of the 120 transcription units could be mediated by the transcription termination factor Rho. In order to investigate the impact of Rho-mediated termination, tiling array hybridizations using RNA samples of a B. subtilis rho-null mutant and its parental strain were performed. B. subtilis 1012 wild-type and rho-mutant cells were grown in LB medium. Samples for tiling array analysis were taken during exponential growth phase. Hybridizations were performed in triplicate using RNA isolated from independent cultures.
Project description:Bacillus subtilis mutants lacking the SMC-ScpAB complex are severely impaired for chromosome condensation and partitioning, DNA repair, and cells are not viable under standard laboratory conditions. We isolated suppressor mutations that restored the capacity of a smc deletion mutant (Δsmc) to grow under standard conditions. These suppressor mutations reduced chromosome segregation defects and abrogated hypersensitivity to gyrase inhibitors of Δsmc. Three suppressor mutations were mapped in genes involved in tRNA aminoacylation and maturation pathways. A transcriptomic survey of isolated suppressor mutations pointed to a potential link between suppression of Δsmc and induction of the stringent response. This link was confirmed by (p)ppGpp quantification which indicated a constitutive induction of the stringent response in multiple suppressor strains. Furthermore, sublethal concentrations of arginine hydroxamate (RHX), a potent inducer of stringent response, restored growth of Δsmc under non permissive conditions. We showed that production of (p)ppGpp alone was sufficient to suppress the thermosensitivity exhibited by the Δsmc mutant. Our findings shed new light on the coordination between chromosome dynamics mediated by SMC-ScpAB and other cellular processes during rapid bacterial growth. A 7 array study of the transcriptome profiles of B. subtilis strain 168, CB167 and CB169: ylbM and ywlC mutant strains. Compared to the wild-type strain the mutant strains were used to characterize the effect of the mutation on transcript profiles in order to understand the suppression of the SMC deletion.
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.
Project description:This SuperSeries is composed of the following subset Series: GSE27650: Bacillus subtilis SigA ChIP-chip (BsubT1 array) GSE27665: Bacillus subtilis SigA ChIP-chip (BsubT2 array) Refer to individual Series
Project description:Identification of the specific WalR (YycF) binding regions on the B. subtilis chromosome during exponential and phosphate starvation growth phases. The data serves to extend the WalRK regulon in Bacillus subtilis and its role in 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 WalR-SPA protein as well as from wild-type (168) without a tagged WalR. 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.
Project description:RNase Y is an essential endoribonuclease affecting global mRNA stability in Bacillus subtilis. We used high-resolution tiling arrays to analyze the effect of RNase Y depletion on RNA abundance covering the entire genome. The data confirm that this endoribonuclease plays a key role in initiating the decay of a large number of mRNAs as well as non coding RNAs. Comparison of the data with that of two other recent studies revealed very significant differences. About two thirds of the mRNAs upregulated following RNase Y depletion were different when compared to either one of these studies and only about 10% of were in common in all three studies.Our data confirmed already known RNase Y substrates and due to the precision and reproducibility of the profiles allows an exceptionally detailed view of the turnover of hundreds of new RNA substrates. A four arrays study of the transcriptome profiles of the B. subtilis RNase Y depletion strain SSB447 (Shahbabian et al., 2009) in which the gene rny is under the control of an IPTG inducible promoter. Rnase Y depleted cells (IPTG-) are compared to the transcript profiles of non depleted cells (IPTG+). As the rny gene is essential, depletion can only be partial. Here we carefully selected the time point for taking the sample in order to minimize growth rate effects and to obtain an highly reproducible data set.