Bacillus subtilis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA286854 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To identify potential targets of co-regulation by DnaA and Rok, we compared the transcriptional profiles of dnaA null, rok null, and dnaA null rok null mutants. Because a dnaA null mutant requires an oriC- strain background, we used an oriC- oriN+ background for all strains, to allow direct comparisons.
2015-06-13 | GSE69788 | GEO
Project description:To identify potential targets of co-regulation by DnaA and Rok, we compared the transcriptional profiles of dnaA null, rok null, and dnaA null rok null mutants. Because a dnaA null mutant requires an oriC- strain background, we used an oriC- oriN+ background for all strains, to allow direct comparisons. We compared biological triplicates for each of the following strains: dnaA null (CAL2074), rok null (CAS196), dnaA null rok null (CAS192), and dnaA+ rok+ (CAL2083; control).
2015-06-13 | E-GEOD-69788 | biostudies-arrayexpress
Project description:The Rok protein of Bacillus subtilis was identified as a negative regulator of competence development. Here we show that Rok binds to extended areas of the B. subtilis genome that are characterized by a high A+T content and are known or believed to have been acquired by horizontal gene transfer, e.g. mobile elements. A deletion of rok results in higher excision of one such element, ICEBs1. The preferential association of Rok with DNA with a high A+T content is also observed in a Gram-negative host, E. coli, and depends on a conserved C-terminal region of the protein. Based on our findings, we propose that Rok is a nucleoid-associated protein that fulfills a function analogous to H-NS, a protein absent from most Gram-positive bacteria. The genome-wide binding profile of the transcription factor Rok and the nucleoid-binding protein HBsu were determined. Three biological replicates were analyzed per strain (one per array). Binding profiles were determined in exponentially growing cells. Enrichment in immunoprecipitated samples versus total genomic DNA were determined.
2011-01-01 | E-GEOD-23199 | biostudies-arrayexpress
Project description:Initiation of DNA replication requires binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC. In low G+C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase at oriC, and this depends on DnaA. DnaD and DnaB are also required to load the replicative helicase outside of oriC during replication restart, in a DnaA-independent manner. DnaA also binds to many sites around the chromosome, outside of oriC, and acts as a transcription factor at several of these. Using chromatin immunoprecipitation, we found that DnaD and DnaB, but not the replicative helicase, are associated with many of the chromosomal regions bound by DnaA in vivo in Bacillus subtilis. This association was dependent on DnaA and the order of recruitment was the same as that at oriC, but was independent of a functional oriC. The presence of DnaD and DnaB at the secondary (non-oriC) targets of DnaA in the absence of helicase loading indicates a possible role for DnaD and DnaB in modulating the activity of DnaA. The genome-wide binding profiles of DnaA, DnaD, DnaB and DnaC were determined. Binding profiles were determined in exponentially growing cells with and without HPUra treatment. Three biological replicates were analyzed per protein/treatment (one per array). Enrichment in immunoprecipitated samples versus total genomic DNA were determined.
2010-12-07 | E-GEOD-23686 | biostudies-arrayexpress
Project description:Comparison of the B subtilis rok mutant vs wild type (sample 1-4) and rok-comK mutant vs comK mutant (sample 5-8)
2011-02-01 | GSE22370 | GEO
Project description:The Rok protein of Bacillus subtilis was identified as a negative regulator of competence development. Here we show that Rok binds to extended areas of the B. subtilis genome that are characterized by a high A+T content and are known or believed to have been acquired by horizontal gene transfer, e.g. mobile elements. A deletion of rok results in higher excision of one such element, ICEBs1. The preferential association of Rok with DNA with a high A+T content is also observed in a Gram-negative host, E. coli, and depends on a conserved C-terminal region of the protein. Based on our findings, we propose that Rok is a nucleoid-associated protein that fulfills a function analogous to H-NS, a protein absent from most Gram-positive bacteria.
2011-01-01 | GSE23199 | GEO
Project description:Initiation of DNA replication requires binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC. In low G+C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase at oriC, and this depends on DnaA. DnaD and DnaB are also required to load the replicative helicase outside of oriC during replication restart, in a DnaA-independent manner. DnaA also binds to many sites around the chromosome, outside of oriC, and acts as a transcription factor at several of these. Using chromatin immunoprecipitation, we found that DnaD and DnaB, but not the replicative helicase, are associated with many of the chromosomal regions bound by DnaA in vivo in Bacillus subtilis. This association was dependent on DnaA and the order of recruitment was the same as that at oriC, but was independent of a functional oriC. The presence of DnaD and DnaB at the secondary (non-oriC) targets of DnaA in the absence of helicase loading indicates a possible role for DnaD and DnaB in modulating the activity of DnaA.
2010-12-07 | GSE23686 | GEO
Project description:Comparison of the B subtilis rok mutant vs wild type (sample 1-4) and rok-comK mutant vs comK mutant (sample 5-8) One condition design comparision of (rok vs wt) and (rok-comK vs comK) including a dye swap, 4 biological replicate
2011-02-01 | E-GEOD-22370 | biostudies-arrayexpress
Project description:Expression of ykrL of Bacillus subtilis, encoding a close homologue of the Escherichia coli membrane protein quality control protease HtpX, was shown to be upregulated under membrane protein overproduction stress. Using DNA affinity chromatography, two proteins were found to bind to the promoter region of ykrL: Rok, known as a repressor of competence and genes for extracytoplasmic functions, and YkrK, a novel type of regulator encoded by the gene adjacent to ykrL, but divergently transcribed. Electrophoretic mobility shift assays showed Rok and YkrK binding to the ykrL promoter region as well as YkrK binding to the ykrK promoter region. Comparative bioinformatic analysis of the ykrL promoter regions in related Bacillus species revealed a consensus motif, which was demonstrated to be the binding site of YkrK. Deletion of rok and ykrK in a PykrL-gfp reporter strain showed that both proteins are repressors of ykrL expression. In addition, conditions which activated PykrL (membrane protein overproduction, dissipation of the membrane potential, salt- and phenol stress) point to the involvement of YkrL in membrane protein quality control.
2012-04-04 | GSE33456 | 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