Translational activation by an alternative sigma factor in Bacillus subtilis
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ABSTRACT:
PROVIDER: PRJNA707207 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13870586_1.fastq.gz | Fastqsanger.gz | |||
| SRR13870586_2.fastq.gz | Fastqsanger.gz | |||
| SRR13870587_1.fastq.gz | Fastqsanger.gz | |||
| SRR13870587_2.fastq.gz | Fastqsanger.gz | |||
| SRR13870588_1.fastq.gz | Fastqsanger.gz |
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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:Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in B. subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history, and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.
2021-04-10 | GSE171761 | GEO
Project description:Bacillus subtilis encodes seven extracytoplasmic function (ECF) σ factors, σM, σW, σX, σY, σZ, σV and σYlaC, that mediate response to cell envelop-active compounds. In this study, we aimed to define the transcriptomic differences between B. subtilis W168 wild type and the derivative 168 Δ7ECF mutant lacking seven ECF sigma factors under unstressed condition, which allows to identify the genes under control of these seven ECF sigma factors. 168 Δ7ECF mutant was as well treated with cell wall-targeting antibiotics, vancomycin and tunicamycin, in order to unravel the genes that respond to these two compounds, however are not under the seven ECF sigma regulon.
2025-10-28 | GSE160347 | GEO
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, σB, 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, σA, owing to extended RNA secondary structures as determined in vivo using DMS-MaPseq. Transcription from σB-dependent promoters ablates the secondary structures and activates translation, leading to dual induction. Translation efficiencies between σB- and σA-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.
| S-EPMC8208050 | biostudies-literature
Project description:6S RNA is a small RNA with specific secondary structure that associates with the complex of RNA polymerase (RNAP) and the primary sigma factor in majority of bacteria. Bacillus subtilis has two 6S RNAs. To compare both 6S RNAs and to identify RNAs that might have a similar functions, we sequenced RNAs that co-immunoprecipitated with RNAP or the primary sigma factor (sigma A). We also sequenced total RNA isolated from the lysate (input sample). We expect that putative 6S RNA-like molecules are enriched in RNA polymerase or sigma A samples compared to the inputs. We performed the experiment both in exponential and stationary phase of growth.
2024-02-09 | E-MTAB-11693 | biostudies-arrayexpress
Project description:Genes encoding the alternative sigma factor SigmaB, involved in the general stress response in firmicutes, as well as its regulators are present in the genome of the enteropathogen Clostridium difficile. We inactivated the sigB gene using the ClosTron technology in order to identify the role of this sigma factor in the physiology of this bacterium. Transcriptomic experiments showed that SigB positively and negatively controlls several genes involved in different cellular processes such as metabolism, sporulation and stress response.
2017-07-07 | GSE85981 | GEO
Project description:The sigma(B)-dependent general stress response in the common soil bacterium Bacillus subtilis can be elicited by a range of stress factors, such as starvation or an ethanol-, salt-, or heat-shock, via a complex upstream signaling cascade. Additionally, sigma(B) can be activated by blue light, via the phototropin homologue YtvA, a component of the environmental branch of the signaling cascade. The genome-wide transcriptomes of B. subtilis reported here show that sigma(B) can activated by blue as well as red light via RsbP/RspQ, the energy branch of sigma(B) upstream signaling cascade.
2009-12-21 | GSE19464 | GEO
Project description:Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit
| PRJNA720823 | ENA
Project description:Laboratory strains of Bacillus subtilis encodes as many as 16 alternative sigma factors, each dedicated to expressing a unique regulon such as those involved in stress resistance, sporulation, and motility. The ancestral strain of B. subtilis also encodes an additional sigma factor homolog, ZpdN, not found in lab strains due to it being encoded on the large, low copy number plasmid pBS32 that was lost during domestication. DNA damage triggers pBS32 hyper-replication and cell death in a manner that depends on ZpdN but how ZpdN mediates these effects was unknown. Here we show that ZpdN is a bona fide sigma factor that can direct RNA polymerase to transcribe ZpdN-dependent genes and we rename ZpdN to SigN accordingly. Rend-seq analysis was used to determine the SigN regulon on pBS32, and the 5’ ends of transcripts were used to predict the SigN consensus sequence. Finally, we characterize the regulation of SigN itself, and show that it is transcribed by at least three promoters: PsigN1, a strong SigA-dependent LexA-repressed promoter, PsigN2, a weak SigA-dependent constitutive promoter, and PsigN3, a SigN-dependent promoter. Thus, in response to DNA damage LexA is derepressed, SigN is expressed and then experiences positive feedback. How cells die in a pBS32-dependent manner remains unknown, but we predict that death is the product of expressing one or more genes in the SigN regulon.
2019-08-22 | GSE134424 | GEO
Project description:The sigma(B)-dependent general stress response in the common soil bacterium Bacillus subtilis can be elicited by a range of stress factors, such as starvation or an ethanol-, salt-, or heat-shock, via a complex upstream signaling cascade. Additionally, sigma(B) can be activated by blue light, via the phototropin homologue YtvA, a component of the environmental branch of the signaling cascade. The genome-wide transcriptomes of B. subtilis reported here show that sigma(B) can activated by blue as well as red light via RsbP/RspQ, the energy branch of sigma(B) upstream signaling cascade. A 16 chip genome-wide expression study using RNA recovered from B.subtilis strain PB565/pYtvA under light and dark conditions before and after induction with IPTG, and from B.subtilis strain PB565 under light and dark conditions. Each B.subtilis subsp. subtilis strain 168 NC_000964 chip measures the expression level of 4,104 genes in two-fold from with eight 60-mer probe pairs (PM/MM) per gene.
2010-05-16 | E-GEOD-19464 | biostudies-arrayexpress