Bacillus subtilis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA329126 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The objective of the study was to determine the role of dnaA in regulating gene expression, and the extent to which the effects are mediated by sda and spo0A.
2018-02-16 | GSE84421 | GEO
Project description:This project is about the proteomes of wild type cells (WT) and spo0A-null strain of B. subtilis during exponential growth in mannose medium. B2 & B4 corresponds to the wild type cells (two biological replicate samples) and B6 & B8 corresponds to spo0A-null data (two biological replicate samples).
2023-05-10 | PXD039192 | Pride
Project description:The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing transcription of genes in the DnaA regulon. We report here that simply growing B. subtilis in LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA, and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA in Bacillus subtilis encodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB but not in LB supplemented with manganese, and induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress. Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays).
2010-06-12 | E-GEOD-22296 | biostudies-arrayexpress
Project description:The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing transcription of genes in the DnaA regulon. We report here that simply growing B. subtilis in LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA, and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA in Bacillus subtilis encodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB but not in LB supplemented with manganese, and induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress.
2010-06-12 | GSE22296 | GEO
Project description:Transcriptome comparison of Bacillus subtilis Natto under sliding permissive (0.7% agar) and restrictive (1.5% agar or spo0A mutant strain) conditions.
2015-08-04 | GSE43840 | GEO
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.
2015-01-26 | GSE65272 | GEO
Project description:Transcriptome comparison of Bacillus subtilis Natto under sliding permissive (0.7% agar) and restrictive (1.5% agar or spo0A mutant strain) conditions. B subtilis Natto wild type cells were grown on the top of LB solid medium with 1.5% and 0.7% agar concentration (samples 1-4). B subtilis Natto wild type and spo0A derivative were grown on top of LB solid medium with 0.7% agar concentration (Sample 5-7). In first experiment, 4 biological replicates were used, while in the second experiment 3 biological replicates included. Dye swaps are included in both experiments.
2015-08-04 | E-GEOD-43840 | biostudies-arrayexpress
Project description:Identification of the specific SigA binding regions on the B. subtilis chromosome during exponential, transition and stationary growth phases. The data served to help the analysis of the repertoire of B. subtilis promoters established from transcriptome profiles.
2012-01-01 | GSE27665 | GEO
Project description:Identification of the specific SigA binding regions on the B. subtilis chromosome during exponential, transition and stationary growth phases. The data served to help the analysis of the repertoire of B. subtilis promoters established from transcriptome profiles.
2012-01-01 | GSE27650 | GEO
Project description:Initiation of bacterial DNA replication takes place at the origin of replication (oriC), a region characterized by the presence of multiple DnaA boxes that serve as the binding sites for the master initiator protein DnaA. The absence or failure of DNA replication can result in bacterial cell growth arrest or death. Here, we aimed to uncover the physiological and molecular consequences of stopping replication in the model bacterium Bacillus subtilis. For this purpose, DNA replication was blocked using a CRISPRi approach specifically targeting DnaA boxes 6 and 7, which are essential for replication initiation. We characterized the phenotype of these cells and analyzed the overall changes in the proteome using quantitative mass spectrometry. Cells with arrested replication were elongating and not dividing but showed no evidence of DNA damage response (DDR). Moreover, these cells did not cease translation over time. This study sets the ground for future research on non-replicating but translationally active B. subtilis, which might be valuable for biotechnological applications.
2024-03-26 | PXD036876 | Pride