Transcriptomic study of Bacillus subtilis lacking seven extracytoplasmic function (ECF) σ factors
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ABSTRACT:
ORGANISM(S): Bacillus subtilis
PROVIDER: GSE160347 | GEO | 2025/10/28
REPOSITORIES: GEO
Similar Datasets
Project description:The extracytoplasmic function (ECF) σ factors are fundamental for bacterial adaptation to distinct environments and for survival under different stress conditions. The emerging pathogen Arcobacter butzleri possesses seven putative pairs of σ/anti-σ factors belonging to the ECF family. Here, we report the identification of the genes regulated by five out of the seven A. butzleri ECF σ factors. Three of the ECF σ factors play an apparent role in transport, energy generation and the maintainance of redox balance. Several genes like the nap, sox and tct genes are regulated by more than one ECF σ factor indicating that the A. butzleri ECF σ factors form a network of overlapping regulons. In contrast to other eubacteria, these A. butzleri ECF regulons appear to primarily regulate responses to changing environments in order to meet metabolic needs instead of an obvious role in stress adaptation.
2011-12-31 | GSE34089 | 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: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:Transcriptomic study of Bacillus subtilis lacking seven extracytoplasmic function (ECF) σ factors
| PRJNA672979 | ENA
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. Strains WT vs. ΔMWX, WT vs. Δ7ECF, Δ7ECF vs. ΔMWX. Each experiment was conducted three times using three independent total RNA preparations (biological triplicates). For each paried comparison, one sample was was labeled with Alexa Fluor 555 and the other was with Alexa Fluor 647. For each comparison, one replicate was performed with dyewap with the same RNA preparation.
2010-07-21 | E-GEOD-22930 | biostudies-arrayexpress
Project description:Next to the two-component and quorum sensing systems, cell-surface signaling (CSS) has been recently identified as an important regulatory system in Pseudomonas aeruginosa. CSS senses signals from outside the cell and transmits them into the cytoplasm. It consists of a TonB-dependent outer membrane receptor, a cytoplasmic membrane-localized sigma factor regulator (or anti-sigma factor), and an extracytoplasmic function (ECF) sigma factor. Upon perception of the extracellular signal by the receptor the ECF sigma factor is activated and promotes the transcription of a specific set of gene(s). Although most P. aeruginosa ECF sigma factors are involved in the regulation of iron uptake, we have identified a novel ECF sigma factor (PA0675) involved in the regulation of virulence. By microarray analysis of cells overexpressing PA0675 from the pMUM3 plasmid we have identified the genes regulated by this sigma factor.
2009-04-21 | GSE15697 | GEO
Project description:To define the ECF sigma sigV - regulated genes during log growth phase in LB media under induction conditions for sigV The seven extracytoplasmic function (ECF) sigma (σ) factors of Bacillus subtilis are broadly implicated in resistance to antibiotics and other cell envelope stressors mediated, in part, by regulation of cell envelope synthesis and modification enzymes. We here define the regulon of σV as including at least 20 operons many of which are also regulated by σM, σX, or σW. The σV regulon is strongly and specifically induced by lysozyme and this induction is key to the intrinsic resistance of B. subtilis to lysozyme. Strains with null mutations in either sigV or in all seven ECF σ factor genes (Δ7ECF) have essentially equal increases in sensitivity to lysozyme. Induction of σV in the Δ7ECF background restores lysozyme resistance, whereas induction of σM, σX or σW does not. Lysozyme resistance results from the ability of σV to activate the transcription of two operons: the autoregulated sigV-rsiV-oatA-yrhK operon and dltABCDE. Genetic analyses reveal that oatA and dlt are largely redundant with respect to lysozyme sensitivity: single mutants are not affected in lysozyme sensitivity whereas a double oatA dltA mutant is as sensitive as a sigV null strain. Moreover, the triple sigV oatA dltA mutant is no more sensitive than the oatA dltA double mutant, indicating that there are no other σV-dependent genes necessary for lysozyme resistance. Thus, σV confers lysozyme resistance by activation of two cell wall modification pathways: O-acetylation of peptidoglycan catalyzed by OatA and D-alanylation of teichoic acids by DltABCDE. Strains Δ7Pxyl-sigV + xylose vs. Δ7Pxyl-sigV - xylose, 168 + lysozyme vs. 168 - lysozyme. Each experiment was conducted 6 times using three independent total RNA preparations (biologlical triplicates). For each paired comparison, one sample was labeled with Alexa Fluor 555 and the other was with Alexa Fluor 647. For each comparison, three replicates were performed with dyeswap with the same RNA preparation.
2011-08-22 | E-GEOD-31563 | biostudies-arrayexpress
Project description:Extracytoplasmic function (ECF) sigma factors are known to play an important role in the bacterial response to various environmental stresses. Porphyromonas gingivalis, a prominent etiological agent in human periodontitis, possesses six putative ECF sigma factors. So far, information is limited on an ECF sigma factor, PGN_0319. It has been recently reported that the expression of genes encoding some of the ECF sigma factors including PGN_0319 was affected by hemin availability. The aim of this study was to evaluate the role of PGN_0319 in hemin utilization by P. gingivalis. We evaluated the gene expression profile of the PGN_0319 mutant by DNA microarray, and then real-time reverse transcription PCR analysis was performed to assess genes with altered expression levels. The expressions level of hmuY and hmuR, which encode an outer-membrane protein involved in hemin utilization, and cdhR, a transcriptional regulator of hmuYR, were significantly decreased in the PGN_0319 mutant. The transcription of these genes was restored in the PGN_0319 complemented strain. We observed that the PGN_0319 mutant showed reduced growth in log phase compared with wild type under hemin-limiting condition. By electrophoretic mobility shift assay we demonstrated the recombinant PGN_0319 protein bound to the promoter region of hmuY and cdhR. In addition, we observed that PGN_0319 gene was upregulated in response to low cell density. These results demonstrate that PGN_0319 play an important role in the early growth of P. gingivalis, and directly regulates hmuYR and cdhR, thereby plays a role in the mechanisms involved in hemin utilization by P. gingivalis.
2017-01-01 | GSE78048 | GEO
Project description:Next to the two-component and quorum sensing systems, cell-surface signaling (CSS) has been recently identified as an important regulatory system in Pseudomonas aeruginosa. CSS senses signals from outside the cell and transmits them into the cytoplasm. It consists of a TonB-dependent outer membrane receptor, a cytoplasmic membrane-localized sigma factor regulator (or anti-sigma factor), and an extracytoplasmic function (ECF) sigma factor. Upon perception of the extracellular signal by the receptor the ECF sigma factor is activated and promotes the transcription of a specific set of gene(s). Although most P. aeruginosa ECF sigma factors are involved in the regulation of iron uptake, we have identified a novel ECF sigma factor (PA0675) involved in the regulation of virulence. By microarray analysis of cells overexpressing PA0675 from the pMUM3 plasmid we have identified the genes regulated by this sigma factor. Two different samples are analyzed namely P. aeruginosa (pMMB67EH) (control/reference sample) and P. aeruginosa (pMUM3) (overexpressing the PA0675 ECF sigma factor). Two different replicates per sample are included.
2009-04-21 | E-GEOD-15697 | biostudies-arrayexpress
Project description:To define the ECF sigma sigV - regulated genes during log growth phase in LB media under induction conditions for sigV The seven extracytoplasmic function (ECF) sigma (σ) factors of Bacillus subtilis are broadly implicated in resistance to antibiotics and other cell envelope stressors mediated, in part, by regulation of cell envelope synthesis and modification enzymes. We here define the regulon of σV as including at least 20 operons many of which are also regulated by σM, σX, or σW. The σV regulon is strongly and specifically induced by lysozyme and this induction is key to the intrinsic resistance of B. subtilis to lysozyme. Strains with null mutations in either sigV or in all seven ECF σ factor genes (Δ7ECF) have essentially equal increases in sensitivity to lysozyme. Induction of σV in the Δ7ECF background restores lysozyme resistance, whereas induction of σM, σX or σW does not. Lysozyme resistance results from the ability of σV to activate the transcription of two operons: the autoregulated sigV-rsiV-oatA-yrhK operon and dltABCDE. Genetic analyses reveal that oatA and dlt are largely redundant with respect to lysozyme sensitivity: single mutants are not affected in lysozyme sensitivity whereas a double oatA dltA mutant is as sensitive as a sigV null strain. Moreover, the triple sigV oatA dltA mutant is no more sensitive than the oatA dltA double mutant, indicating that there are no other σV-dependent genes necessary for lysozyme resistance. Thus, σV confers lysozyme resistance by activation of two cell wall modification pathways: O-acetylation of peptidoglycan catalyzed by OatA and D-alanylation of teichoic acids by DltABCDE.
2011-08-23 | GSE31563 | GEO