Bacillus subtilis SigA ChIP-chip
Ontology highlight
ABSTRACT:
ORGANISM(S): Bacillus subtilis
SUBMITTER: Nathalie Pigeonneau
PROVIDER: E-GEOD-27652 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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. 3 growth phases (exponential, transition, stationary) x 2 biological replicates were analysed on the BsubT2 tiling array.
2012-01-01 | E-GEOD-27665 | 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. 3 growth phases (exponential, transition, stationary) x 2 biological replicates were analysed on the BsubT1 tiling array.
2012-01-01 | E-GEOD-27650 | biostudies-arrayexpress
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
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.
2013-01-15 | E-GEOD-38897 | biostudies-arrayexpress
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.
2015-01-26 | E-GEOD-65272 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in a E. coli fatty acid overproducing strain with or without heterologous expression of the M. luteus FabH. The strain expressing M. luteus FabH produces more methyl ketones. This study will be further described in Goh, E.B., E.E.K. Baidoo, J.D. Keasling, and H.R. Beller. Engineering of bacterial methyl ketone synthesis for biofuels. A 11 microarray study using total RNA recovered from six separate control cultures of Escherichia coli K-12 DH1 fatty acid overproducing strain with empty vector and five separate cultures of test strain, Escherichia coli K-12 DH1 fatty acid overproducing strain with vector overexpressing M. luteus FabH. Each chip measures the expression level of 4,254 genes from Escherichia coli K-12 with eight 60-mer probe pairs (PM/MM) per gene, with 2-fold technical redundancy.
2012-01-26 | E-GEOD-32561 | biostudies-arrayexpress
Project description:Identification of the major PEP-phosphotransferase systems (PTS) for glucose, mannose and cellobiose of Listeria monocytogenes, and their significance for extra- and intracellular growth. Transcriptional profile of prfA, the dependent genes and the PTS genes after growth in MM (minimal medium (Premaratne et al. 2001)) (supplemented with 10 mM Glucose). Listeria monocytogenes EGD-e possesses 86 pts genes encoding 29 complete and several incomplete PEP-dependent phosphotransferase systems (PTS) for the transport of carbohydrates and sugar alcohols. By a systematic deletion analysis we identified the major PTS involved in glucose, mannose and cellobiose transport, when L. monocytogenes grows in a defined minimal medium in the presence of either of these carbohydrates. Under these conditions two of the four PTSMan and at least one of the five PTSGlc function as glucose transporter with different affinities. Cellobiose is transported (with different efficiencies) mainly by two of the six PTSLac and by a PTSGlc that also transports glucose. One of the PTSMan and both PTSLac are regulated by LevR-homologous PRD containing transcriptional activators, detected with PRD deletion mutants. The growth rates of mutants that are lacking these PTS are drastically reduced compared to the wild-type strain upon growth in a defined medium with low concentrations of glucose and cellobiose, respectively. In contrast, replication of these PTS mutants within epithelial cells or macrophages is as efficient as that of the wild-type strain. Keywords: pts and prd deletion mutants A total of three independently isolated RNA samples from each condition were used for the analysis. PTS Samples: GSM458191-GSM458208 PRD Samples: GSM458209-GSM458214
2010-05-19 | E-GEOD-18363 | biostudies-arrayexpress
Project description:Strains devoid of ppGpp (ΔrelA ΔspoT; called ppGpp0), and ppGpp0 dksA- exhibit several amino acid requirements for growth on minimal media. We found that overexpression of DksA can complement some of those requirements. Since DksA is a factor that binds to the RNA polymerase secondary channel, we wondered if other secondary channel proteins might also exert a similar role with respect to growth on minimal media. In our study we found that GreA and partially GreB can in fact complement these requirements under certain conditions. Here, we wished to investigate a broader effect of GreA and GreB on ppGpp0 and ppGpp0 dksA- strains. Since the parent strains are unable to grow in minimal media, we had to supplement the M9 glucose medium with a set of amino acids (DFHILQSTV). We found that both, GreA and GreB can affect a much larger set of genes in the absence of dksA, than in its presence. Also, GreA seems to affect more genes than GreB, under both conditions. We used microarrays to detail the effects of overproducing either GreA or GreB in cells devoid of ppGpp, in the dksA+ or dksA- background E. coli cells harbouring plasmids carrying either greA (pA = pHM1873) or greB (pB = pHM1874) genes, or vector control (pGB2), were monitored in an effort to elucidate the effects of their protein products. This was done in two backgrounds- either in E. coli ppGpp0 cells (ΔrelA, ΔspoT) carrying wt dksA gene or a dksA deletion.
2011-10-26 | E-GEOD-28795 | biostudies-arrayexpress
Project description:Antitoxins are becoming recognized as proteins that regulate more than their own synthesis; for example, we found previously that antitoxin MqsA represses the gene encoding the stationary phase sigma factor RpoS. Here, we investigated the physiological role of antitoxin DinJ of the DinJ/YafQ toxin/antitoxin system and found DinJ also affects the general stress response by decreasing RpoS levels. Corroborating the reduced RpoS levels upon producing DinJ, catalase activity, cell adhesins, and cyclic diguanylate decreased while swimming increased. Using a transcriptome search and DNA-binding assays, we determined that the mechanism by which DinJ reduces RpoS is by repressing cspE which encodes cold-shock protein CspE that inhibits translation of rpoS mRNA. Hence, DinJ influences the general stress response indirectly by regulating cspE. strain: E.coli MG1655M-NM-^T6/pCA24N-dinJ vs MG1655M-NM-^T6/pCA24N treatment:erythromycin Medium:LB low salt Time:10 min Temp: 37M-BM-0C
2012-07-08 | E-GEOD-30692 | biostudies-arrayexpress
Project description:In mycobacteria, SigA is the primary sigma factor. This essential protein binds to RNA polymerase (RNAP) and is responsible for initiating transcription of housekeeping genes. Our knowledge about this factor in medicinally important mycobacteria is limited. Here, we performed an unbiased search for interacting partners of Mycobacterium smegmatis SigA. The search revealed a number of proteins; prominent among them was MoaB2. The SigA-MoaB2 interaction was validated and characterized by several approaches, revealing that it does not require RNAP and is highly specific, as alternative sigma factors did not interact with MoaB2. The structure of MoaB2 was solved by crystallography and the unique, unstructured N-terminal domain of SigA was identified to play a role in the SigA-MoaB2 interaction. Functional experiments showed that MoaB2 inhibits SigA-dependent transcription and increases biological stability of SigA. We propose that MoaB2, by sequestering SigA, exerts a dual effect on the transcription apparatus, and has the potential to modulate gene expression. In summary, this study has uncovered a new binding partner of mycobacterial SigA, paving the way for future research of this phenomenon.
2024-11-11 | PXD039468 | Pride