scholarly journals Glucose Induces ECF Sigma Factor Genes, sigX and sigM, Independent of Cognate Anti-sigma Factors through Acetylation of CshA in Bacillus subtilis

2016 ◽  
Vol 7 ◽  
Author(s):  
Mitsuo Ogura ◽  
Kei Asai
Keyword(s):  
Bacillus Subtilis ◽  
Sigma Factor ◽  
Sigma Factors ◽  
Ecf Sigma Factor

scholarly journals Transcriptional Regulation and Mechanism of SigN (ZpdN), a pBS32-Encoded Sigma Factor in Bacillus subtilis

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Aisha T. Burton ◽  
Aaron DeLoughery ◽  
Gene-Wei Li ◽  
Daniel B. Kearns
Keyword(s):  
Dna Damage ◽  
Bacillus Subtilis ◽  
Sigma Factor ◽  
Consensus Sequence ◽  
Sigma Factors ◽  
Sequencing Analysis ◽  
Dependent Manner ◽  
Content Type ◽  
Alternative Sigma Factors ◽  
Bona Fide

ABSTRACT Laboratory strains of Bacillus subtilis encode many 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 being encoded on the large, low-copy-number plasmid pBS32, which was lost during domestication. DNA damage triggers pBS32 hyperreplication and cell death in a manner that depends on ZpdN, but how ZpdN mediates these effects is 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 SigN accordingly. Rend-seq (end-enriched transcriptome sequencing) 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 SigN is derepressed 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. IMPORTANCE Sigma factors are utilized by bacteria to control and regulate gene expression. Some sigma factors are activated during times of stress to ensure the survival of the bacterium. Here, we report the presence of a sigma factor that is encoded on a plasmid that leads to cellular death after DNA damage.

scholarly journals Translational activation by an alternative sigma factor in Bacillus subtilis

2021 ◽  
Author(s):  
Dylan M. McCormick ◽  
Jean-Benoît Lalanne ◽  
Tammy C. T. Lan ◽  
Silvi Rouskin ◽  
Gene-Wei Li
Keyword(s):  
Bacillus Subtilis ◽  
Sigma Factor ◽  
Rna Folding ◽  
Secondary Structures ◽  
Sigma Factors ◽  
Bacterial Transcription ◽  
Regulate Protein ◽  
Transcriptional Induction

ABSTRACTSigma 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 liberates 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.

scholarly journals Replacement of Vegetative ςA by Sporulation-Specific ςF as a Component of the RNA Polymerase Holoenzyme in Sporulating Bacillus subtilis

1999 ◽  
Vol 181 (8) ◽  
pp. 2346-2350 ◽  
Author(s):  
Matthew Lord ◽  
Daniela Barillà ◽  
Michael D. Yudkin
Keyword(s):  
Bacillus Subtilis ◽  
Rna Polymerase ◽  
Western Blotting ◽  
Sigma Factor ◽  
Sigma Factors ◽  
Relative Affinity ◽  
Rna Polymerase Holoenzyme ◽  
Quantitative Western Blotting

ABSTRACT Soon after asymmetric septation in sporulating Bacillus subtilis cells, ςF is liberated in the prespore from inhibition by SpoIIAB. To initiate transcription from its cognate promoters, ςF must compete with ςA, the housekeeping sigma factor in the predivisional cell, for binding to core RNA polymerase (E). To estimate the relative affinity of E for ςA and ςF, we made separate mixtures of E with each of the two sigma factors, allowed reconstitution of the holoenzyme, and measured the concentration of free E remaining in each mixture. The affinity of E for ςF was found to be about 25-fold lower than that for ςA. We used quantitative Western blotting to estimate the concentrations of E, ςA, and ςF in sporulating cells. The cellular concentrations of E and ςA were both about 7.5 μM, and neither changed significantly during the first 3 h of sporulation. The concentration of ςF was extremely low at the beginning of sporulation, but it rose rapidly to a peak after about 2 h. At its peak, the concentration of ςF was some twofold higher than that of ςA. This difference in concentration cannot adequately account for the replacement of ςA holoenzyme by ςF holoenzyme in the prespore, and it seems that some further mechanism—perhaps the synthesis or activation of an anti-ςA factor—must be responsible for this replacement.

scholarly journals The Single Extracytoplasmic-Function Sigma Factor of Xylella fastidiosa Is Involved in the Heat Shock Response and Presents an Unusual Regulatory Mechanism

2006 ◽  
Vol 189 (2) ◽  
pp. 551-560 ◽  
Author(s):  
José F. da Silva Neto ◽  
Tie Koide ◽  
Suely L. Gomes ◽  
Marilis V. Marques
Keyword(s):  
Heat Shock ◽  
Sigma Factor ◽  
Xylella Fastidiosa ◽  
Expression Profiles ◽  
Consensus Sequence ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Sigma Factors ◽  
Bacterial Cells ◽  
Ecf Sigma Factor

ABSTRACT Genome sequence analysis of the bacterium Xylella fastidiosa revealed the presence of two genes, named rpoE and rseA, predicted to encode an extracytoplasmic function (ECF) sigma factor and an anti-sigma factor, respectively. In this work, an rpoE null mutant was constructed in the citrus strain J1a12 and shown to be sensitive to exposure to heat shock and ethanol. To identify the X. fastidiosa σE regulon, global gene expression profiles were obtained by DNA microarray analysis of bacterial cells under heat shock, identifying 21 σE-dependent genes. These genes encode proteins belonging to different functional categories, such as enzymes involved in protein folding and degradation, signal transduction, and DNA restriction modification and hypothetical proteins. Several putative σE-dependent promoters were mapped by primer extension, and alignment of the mapped promoters revealed a consensus sequence similar to those of ECF sigma factor promoters of other bacteria. Like other ECF sigma factors, rpoE and rseA were shown to comprise an operon in X. fastidiosa, together with a third open reading frame (XF2241). However, upon heat shock, rpoE expression was not induced, while rseA and XF2241 were highly induced at a newly identified σE-dependent promoter internal to the operon. Therefore, unlike many other ECF sigma factors, rpoE is not autoregulated but instead positively regulates the gene encoding its putative anti-sigma factor.

scholarly journals Dual Control of Sinorhizobium meliloti RpoE2 Sigma Factor Activity by Two PhyR-Type Two-Component Response Regulators

2010 ◽  
Vol 192 (8) ◽  
pp. 2255-2265 ◽  
Author(s):  
Bénédicte Bastiat ◽  
Laurent Sauviac ◽  
Claude Bruand
Keyword(s):  
Sigma Factor ◽  
Sinorhizobium Meliloti ◽  
Regulatory System ◽  
Sigma Factors ◽  
Response Regulators ◽  
Methylobacterium Extorquens ◽  
General Stress Response ◽  
Ecf Sigma Factor ◽  
Proposed Model ◽  
Response To Stress

ABSTRACT RpoE2 is an extracytoplasmic function (ECF) sigma factor involved in the general stress response of Sinorhizobium meliloti, the nitrogen-fixing symbiont of the legume plant alfalfa. RpoE2 orthologues are widely found among alphaproteobacteria, where they play various roles in stress resistance and/or host colonization. In this paper, we report a genetic and biochemical investigation of the mechanisms of signal transduction leading to S. meliloti RpoE2 activation in response to stress. We showed that RpoE2 activity is negatively controlled by two paralogous anti-sigma factors, RsiA1 (SMc01505) and RsiA2 (SMc04884), and that RpoE2 activation by stress requires two redundant paralogous PhyR-type response regulators, RsiB1 (SMc01504) and RsiB2 (SMc00794). RsiB1 and RsiB2 do not act at the level of rpoE2 transcription but instead interact with the anti-sigma factors, and we therefore propose that they act as anti-anti-sigma factors to relieve RpoE2 inhibition in response to stress. This model closely resembles a recently proposed model of activation of RpoE2-like sigma factors in Methylobacterium extorquens and Bradyrhizobium japonicum, but the existence of two pairs of anti- and anti-anti-sigma factors in S. meliloti adds an unexpected level of complexity, which may allow the regulatory system to integrate multiple stimuli.

scholarly journals Role of autoregulation and relative synthesis of operon partners in alternative sigma factor networks

2015 ◽  
Author(s):  
Jatin Narula ◽  
Abhinav Tiwari ◽  
Oleg A. Igoshin
Keyword(s):  
Bacillus Subtilis ◽  
Stress Response ◽  
Negative Feedback ◽  
Sigma Factor ◽  
Critical Role ◽  
Sigma Factors ◽  
Alternative Sigma Factor ◽  
Negative Feedback Regulation ◽  
Alternative Sigma Factors

SummaryDespite the central role of alternative sigma factors in bacterial stress response and virulence their regulation remains incompletely understood. Here we investigate one of the best-studied examples of alternative sigma factors: the σBnetwork that controls the general stress response ofBacillus subtilisto uncover widely relevant general design principles that describe the structure-function relationship of alternative sigma factor regulatory networks. We show that the relative stoichiometry of the synthesis rates of σB, its anti-sigma factor RsbW and the anti-anti-sigma factor RsbV plays a critical role in shaping the network behavior by forcing the σBnetwork to function as an ultrasensitive negative feedback loop. We further demonstrate how this negative feedback regulation insulates alternative sigma factor activity from competition with the housekeeping sigma factor for RNA polymerase and allows multiple stress sigma factors to function simultaneously with little competitive interference.Major Subject Areas:Computational and systems biology, Microbiology & Infectious diseaseResearch Organism:Bacillus subtilis

scholarly journals Complementation of a temperature sensitive Escherichia coli rpoD mutation using Lactobacillus sigma factors

2014 ◽  
Author(s):  
James Winkler ◽  
Katy Kao
Keyword(s):  
Escherichia Coli ◽  
Bacillus Subtilis ◽  
Sigma Factor ◽  
Lactobacillus Brevis ◽  
Sigma Factors ◽  
Model Organisms ◽  
Temperature Sensitive ◽  
Genomic Libraries ◽  
E Coli ◽  
Rna Polymerase Holoenzyme

Housekeeping sigma factors in the σ70 family, as components of the RNA polymerase holoenzyme, are responsible for regulating transcription of genes related to vegetative growth. While these factors are well understood in model organisms such asEscherichia coliandBacillus subtilis, little experimental work has focused on the sigma factors in members of theLactobacillusgenus such asLactobacillus brevisandLactobacillus plantarum. This study evaluates the ability of putative σ70 proteins fromL. brevis(σ70-Lb) andL. plantarum(σ70-Lp) to complement a temperature sensitive mutation in theE. coli285c σ70 protein. This report is the first to show that these heterologous sigma factors were capable of restoring the viability ofE. coli285c for growth at 40-43.5 °C, indicating the σ70-Lb and σ70-Lp are capable of initiating transcription in a complex with theE. coli285c RNA polymerase.These heterologous sigma factors may therefore be useful for improving biochemical knowledge of the sigma factor family or for use in the expression of hetereologous genomic libraries.

scholarly journals A Mycobacterial Extracytoplasmic Sigma Factor Involved in Survival following Heat Shock and Oxidative Stress

1999 ◽  
Vol 181 (14) ◽  
pp. 4266-4274 ◽  
Author(s):  
Norvin D. Fernandes ◽  
Qi-long Wu ◽  
Dequan Kong ◽  
Xiaoling Puyang ◽  
Sumeet Garg ◽  
...  
Keyword(s):  
Heat Shock ◽  
Sigma Factor ◽  
Transcriptional Start Site ◽  
Cumene Hydroperoxide ◽  
Single Copy ◽  
Sigma Factors ◽  
Gene Encoding ◽  
Promoter Sequences ◽  
Ecf Sigma Factor

ABSTRACT Extracytoplasmic function (ECF) sigma factors are a heterogeneous group of alternative sigma factors that regulate gene expression in response to a variety of conditions, including stress. We previously characterized a mycobacterial ECF sigma factor, SigE, that contributes to survival following several distinct stresses. A gene encoding a closely related sigma factor, sigH, was cloned fromMycobacterium tuberculosis and Mycobacterium smegmatis. A single copy of this gene is present in these and other fast- and slow-growing mycobacteria, including M. fortuitum and M. avium. While the M. tuberculosis and M. smegmatis sigH genes encode highly similar proteins, there are multiple differences in adjacent genes. The single in vivo transcriptional start site identified inM. smegmatis and one of two identified in M. bovis BCG were found to have −35 promoter sequences that match the ECF-dependent −35 promoter consensus. Expression from these promoters was strongly induced by 50°C heat shock. In comparison to the wild type, an M. smegmatis sigH mutant was found to be more susceptible to cumene hydroperoxide stress but to be similar in logarithmic growth, stationary-phase survival, and survival following several other stresses. Survival of an M. smegmatis sigH sigE double mutant was found to be markedly decreased following 53°C heat shock and following exposure to cumene hydroperoxide. Expression of the second gene in the sigH operon is required for complementation of the sigH stress phenotypes. SigH is an alternative sigma factor that plays a role in the mycobacterial stress response.

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