Transcriptional Regulation and Mechanism of SigN (ZpdN), a pBS32 encoded Sigma Factor
Ontology highlight
ABSTRACT:
ORGANISM(S): Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10
PROVIDER: GSE134424 | GEO | 2019/08/22
REPOSITORIES: GEO
Similar Datasets
Project description:The extracytoplasmic function sigma factor SigH is responsible for heat and oxidative stress response in a biotechnologically -important bacterium Corynebacterium glutamicum. Due to the hierarchical nature of the regulatory network, it has not been possible to fully determine the SigH regulon by previous transcriptome analyses. Here, we determined the direct genome-wide targets of SigH were determined by ChIP-chip analysis using a deletion mutant of rshA, encoding an anti-sigma factor of SigH. Seventy-five SigH-dependent promoters, including 39 new ones, were identified. Firstly, SigH-dependent heat induction was confirmed for several of the new targets, including two genes (ilvD and lipA) encoding Fe-S cluster containing enzymes. Internal SigH-dependent promoters were found in operon-like gene clusters involved in the pentose phosphate pathway, and riboflavin biosynthesis, and Zn uptake. Accordingly, deletion of rshA resulted in hyperproduction of riboflavin probably due to the coordinated upregulation of these genes. A SigH-dependent promoter was also found upstream of znuC1 in the znuA1C1B1 operon encoding an ABC-type transporter for Zn uptake. Overexpression of znuC1B1 by deletion of rshA and by an IPTG-inducible promoter and similarly affected expression of Zn-responsive genes, indicating that SigH-dependent upregulation of part of the operon potentiates Zn uptake. probably through Zn overload, indicating new physiological roles of SigH. Furthermore, reporter assays demonstrated that rshA in the sigH-rshA operon was heat-inducible under the control of an internal SigH-dependent promoters, identified upstream of rshA within the sigH-rshA operon, while the sigH promoter was independent of SigH, suggesting negative autoregulation of SigH activity. Finally, a SigH-dependent promoter identified and upstream of sigA encoding the primary sigma factor , wereas highly heat-inducible, but much weaker than the known SigA-dependent one.. The promoter upstream of sigH was independent of SigH but showed weak heat-shock response. The known SigA-dependent sigA promoter was much stronger than the SigH-dependent one. Taken together with the fact that SigH also regulates sigB encoding the primary-like sigma factor, Tthese findings uncovered a complicated regulatory network of the sigma factors.
2014-11-25 | GSE52040 | GEO
Project description:The extracytoplasmic function sigma factor SigH is responsible for heat and oxidative stress response in a biotechnologically -important bacterium Corynebacterium glutamicum. Due to the hierarchical nature of the regulatory network, it has not been possible to fully determine the SigH regulon by previous transcriptome analyses. Here, we determined the direct genome-wide targets of SigH were determined by ChIP-chip analysis using a deletion mutant of rshA, encoding an anti-sigma factor of SigH. Seventy-five SigH-dependent promoters, including 39 new ones, were identified. Firstly, SigH-dependent heat induction was confirmed for several of the new targets, including two genes (ilvD and lipA) encoding Fe-S cluster containing enzymes. Internal SigH-dependent promoters were found in operon-like gene clusters involved in the pentose phosphate pathway, and riboflavin biosynthesis, and Zn uptake. Accordingly, deletion of rshA resulted in hyperproduction of riboflavin probably due to the coordinated upregulation of these genes. A SigH-dependent promoter was also found upstream of znuC1 in the znuA1C1B1 operon encoding an ABC-type transporter for Zn uptake. Overexpression of znuC1B1 by deletion of rshA and by an IPTG-inducible promoter and similarly affected expression of Zn-responsive genes, indicating that SigH-dependent upregulation of part of the operon potentiates Zn uptake. probably through Zn overload, indicating new physiological roles of SigH. Furthermore, reporter assays demonstrated that rshA in the sigH-rshA operon was heat-inducible under the control of an internal SigH-dependent promoters, identified upstream of rshA within the sigH-rshA operon, while the sigH promoter was independent of SigH, suggesting negative autoregulation of SigH activity. Finally, a SigH-dependent promoter identified and upstream of sigA encoding the primary sigma factor , wereas highly heat-inducible, but much weaker than the known SigA-dependent one.. The promoter upstream of sigH was independent of SigH but showed weak heat-shock response. The known SigA-dependent sigA promoter was much stronger than the SigH-dependent one. Taken together with the fact that SigH also regulates sigB encoding the primary-like sigma factor, Tthese findings uncovered a complicated regulatory network of the sigma factors.
2014-11-25 | GSE52039 | GEO
Project description:Abstract of associated manuscript: The Bacillus subtilis extracytoplasmic function (ECF) sigma(M) factor is activated by cell envelope stress elicited by antibiotics, and by acid, heat, ethanol and superoxide stresses. Here, we have used several complementary approaches to identify genes controlled by sigma(M). In many cases, expression is only partially dependent on sigma(M) because of both overlapping promoter recognition with other ECF sigma factors and the presence of additional promoter elements. Genes regulated by sigma(M) have a characteristic pattern of induction in response to cell envelope-acting antibiotics as evidenced by hierarchical clustering analysis. sigma(M) also contributes to the expression of the Spx transcription factor and thereby indirectly regulates genes of the Spx regulon. Cell envelope stress responses also include regulons controlled by sigma(W), sigma(B) and several two-component regulatory systems (e.g. LiaRS, YycFG, BceRS). Activation of the sigma(M) regulon increases expression of proteins functioning in transcriptional control, cell wall synthesis and shape determination, cell division, DNA damage monitoring, recombinational repair and detoxification.
2008-12-05 | GSE13820 | GEO
Project description:The ability of bacteria to adapt to stress depends on their ability to conditionally express specific sets of genes. Bacillus subtilis encodes seven extracytoplasmic function (ECF) sigma (σ) factors that regulate functions important for survival under conditions eliciting cell envelope stress. Of these, four have been studied in detail: σM, σW, σX and σV . The regulons of these four σ factors overlap, although the sequences that determine promoter selectivity are incompletely understood. A major role in promoter selectivity has been ascribed to the core promoter -10 and -35recognition elements. Here, we demonstrate that a homopolymeric T-tract motif, proximal to the-35 recognition element, functions in combination with the core promoter sequences to2determine selectivity for ECF sigma factors. This motif is critical for promoter activation by σV, contributes to activation by σM and σX, but has relatively little effect for σW. We propose that this motif, which is a feature of the deduced promoter consensus for a subset of ECF s factors from many species, affects confirmation or curvature of the DNA to influence promoter activity. The differential effect of this region amongst ECF s factors thereby provides a mechanism to modulate the nature and extent of regulon overlap.
2017-02-28 | GSE95393 | GEO
Project description:Abstract of associated manuscript: The Bacillus subtilis extracytoplasmic function (ECF) sigma(M) factor is activated by cell envelope stress elicited by antibiotics, and by acid, heat, ethanol and superoxide stresses. Here, we have used several complementary approaches to identify genes controlled by sigma(M). In many cases, expression is only partially dependent on sigma(M) because of both overlapping promoter recognition with other ECF sigma factors and the presence of additional promoter elements. Genes regulated by sigma(M) have a characteristic pattern of induction in response to cell envelope-acting antibiotics as evidenced by hierarchical clustering analysis. sigma(M) also contributes to the expression of the Spx transcription factor and thereby indirectly regulates genes of the Spx regulon. Cell envelope stress responses also include regulons controlled by sigma(W), sigma(B) and several two-component regulatory systems (e.g. LiaRS, YycFG, BceRS). Activation of the sigma(M) regulon increases expression of proteins functioning in transcriptional control, cell wall synthesis and shape determination, cell division, DNA damage monitoring, recombinational repair and detoxification. WT (-van) vs. WT (+van), sigM (-van) vs. sigM (+van), WT (-van) vs. sigM (-van), WT (+van) vs. sigM (+van), WT (-van) vs. spx (-van), WT (+van) vs. spx (+van). Each experiment was conducted at least twice using two independent total RNA preparations. For vancomycin untreated and treated experiments, untreated samples were labeled with Alexa Fluor 555 and treated samples with Alexa Fluor 647. For WT vs. mutant experiments, wild type was labeled with Alexa Fluor 555 and mutants with Alexa Fluor 647. For dye swap experiment, wild-type was labeled with Alexa Fluor 647 and mutant with Alexa Fluor 555. Bacillus subtilis CU1065, WT (-van) vs. WT (+van), sigM (-van) vs. sigM (+van), WT (-van) vs. sigM (-van), WT (+van) vs. sigM (+van), WT (-van) vs. spx (-van), WT (+van) vs. spx (+van)
2010-05-15 | E-GEOD-13820 | biostudies-arrayexpress
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
2012-01-01 | E-GEOD-27652 | biostudies-arrayexpress
Project description:Sigma factors are an important class of bacterial transcription factors that lend specificity to RNA polymerases by binding to distinct promoter elements for genes in their regulons. Here we show that activation of the general stress sigma factor, B, in Bacillus subtilis paradoxically leads to dramatic induction of translation for a subset of its regulon genes. These genes are translationally repressed when transcribed by the housekeeping sigma factor, A, owing to extended RNA secondary structures as determined in vivo using DMS-MaPseq. Transcription fromB-dependent promoters liberates the secondary structures and activates translation, leading to dual induction. Translation efficiencies between B- and A-dependent RNA isoforms can vary by up to 100-fold, which in multiple cases exceeds the magnitude of transcriptional induction. These results highlight the role of long-range RNA folding in modulating translation and demonstrate that a transcription factor can regulate protein synthesis beyond its effects on transcript levels.
2021-03-06 | GSE168393 | GEO
Project description:Bacillus subtilis encodes seven extracytoplasmic function (ECF) sigma factors. Three (sigma M, sigma W and simga X) mediate responses to cell envelope active antibiotics. The functions of sigma Y, sigma Z, sigma V, and YlaC remain largely unknown, and strong inducers of these sigma factors and their regulons have yet to be defined. Here, we define transcriptomic and phenotypic differences under non-stress conditions between strains carrying deletions in all seven ECF sigma factor genes (Δ7ECF), a sigMWX triple mutant (∆MWX), and the parental 168 strain. Our results identify >80 genes as at least partially dependent on ECF sigma factors and, as expected, most of these are dependent on sigma M, sigma W or sigma X which are active at a significant basal level during growth. Several genes, including the eps operon encoding enzymes for exopolysaccharide (EPS) production, were decreased in expression in Δ7ECF but affected little if at all in ΔMWX. Consistent with this observation, Δ7ECF (but not ∆MWX) showed reduced biofilm formation. Extending previous observations, we also note that ∆MWX is sensitive to a variety of antibiotics and Δ7ECF is either as sensitive as, or slightly more sensitive than, the ΔMWX strain to these stressors. These findings emphasize the overlapping nature of the seven ECF s factor regulons in B. subtilis, confirm that three of these (sigma M, W or X) play the dominant role in conferring intrinsic resistance to antibiotics, and provide initial insights into the roles of the remaining ECF sigma factors.
2010-07-21 | GSE22930 | GEO
Project description:Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. A significant fraction of genes in each regulon are of unknown function and we can propose new candidates for spore coat proteins synthesized under the control of sigmaE and sigmaK among proteins previously detected in the spore proteome (Lawley et al., 2009 (PMID 19542279)). Global analysis of developmental gene expression under the control of these sigma factors indicate deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We show that the expression of the sigmaE regulon in the mother cell is not strictly under the control of sigmaF despite the fact that the forespore product SpoIIR is required for the processing of pro-sigmaE. In addition, the sigmaK regulon is not controlled by sigmaG in C. difficile in connection with the lack of pro-sigmaK processing in this bacterium. However, a control of the forespore on sigmaK targets is maintained through a sigmaF-dependent regulation of sigmaK-controlled genes, a process that bypasses sigmaG. Here, transcriptional profiling of the Clostridium difficile 630E strain vs. a sigE mutant after 24h of growth in MS is performed.
2014-02-20 | GSE43201 | GEO