scholarly journals An Extracytoplasmic Function Sigma Factor Acts as a General Stress Response Regulator in Sinorhizobium meliloti

2007 ◽  
Vol 189 (11) ◽  
pp. 4204-4216 ◽  
Author(s):  
Laurent Sauviac ◽  
Heinui Philippe ◽  
Kounthéa Phok ◽  
Claude Bruand
Keyword(s):  
Stress Response ◽  
Stationary Phase ◽  
Stress Responses ◽  
Sigma Factor ◽  
Sinorhizobium Meliloti ◽  
In Planta ◽  
General Stress Response ◽  
Stress Response Genes ◽  
General Stress

ABSTRACT Sinorhizobium meliloti genes transcriptionally up-regulated after heat stress, as well as upon entry into stationary phase, were identified by microarray analyses. Sixty stress response genes were thus found to be up-regulated under both conditions. One of them, rpoE2 (smc01506), encodes a putative extracytoplasmic function (ECF) sigma factor. We showed that this sigma factor controls its own transcription and is activated by various stress conditions, including heat and salt, as well as entry into stationary phase after either carbon or nitrogen starvation. We also present evidence that the product of the gene cotranscribed with rpoE2 negatively regulates RpoE2 activity, and we therefore propose that it plays the function of anti-sigma factor. By combining transcriptomic, bioinformatic, and quantitative reverse transcription-PCR analyses, we identified 44 RpoE2-controlled genes and predicted the number of RpoE2 targets to be higher. Strikingly, more than one-third of the 60 stress response genes identified in this study are RpoE2 targets. Interestingly, two genes encoding proteins with known functions in stress responses, namely, katC and rpoH2, as well as a second ECF-encoding gene, rpoE5, were found to be RpoE2 regulated. Altogether, these data suggest that RpoE2 is a major global regulator of the general stress response in S. meliloti. Despite these observations, and although this sigma factor is well conserved among alphaproteobacteria, no in vitro nor in planta phenotypic difference from the wild-type strain could be detected for rpoE2 mutants. This therefore suggests that other important actors in the general stress response have still to be identified in S. meliloti.

scholarly journals A Mutant RNA Polymerase Activates the General Stress Response, Enabling Escherichia coli Adaptation to Late Prolonged Stationary Phase

mSphere ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Pabitra Nandy ◽  
Savita Chib ◽  
Aswin Seshasayee
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Stationary Phase ◽  
Sigma Factor ◽  
Slow Growth ◽  
Content Type ◽  
General Stress Response ◽  
E Coli ◽  
General Stress ◽  
Small Colony

ABSTRACT Escherichia coli populations undergo repeated replacement of parental genotypes with fitter variants deep in stationary phase. We isolated one such variant, which emerged after 3 weeks of maintaining an E. coli K-12 population in stationary phase. This variant displayed a small colony phenotype and slow growth and was able to outcompete its ancestor over a narrow time window in stationary phase. The variant also shows tolerance to beta-lactam antibiotics, though not previously exposed to the antibiotic. We show that an RpoC(A494V) mutation confers the slow growth and small colony phenotype on this variant. The ability of this mutation to confer a growth advantage in stationary phase depends on the availability of the stationary-phase sigma factor σS. The RpoC(A494V) mutation upregulates the σS regulon. As shown over 20 years ago, early in prolonged stationary phase, σS attenuation, but not complete loss of activity, confers a fitness advantage. Our study shows that later mutations enhance σS activity, either by mutating the gene for σS directly or via mutations such as RpoC(A494V). The balance between the activities of the housekeeping major sigma factor and σS sets up a trade-off between growth and stress tolerance, which is tuned repeatedly during prolonged stationary phase. IMPORTANCE An important general mechanism of a bacterium’s adaptation to its environment involves adjusting the balance between growing fast and tolerating stresses. One paradigm where this plays out is in prolonged stationary phase: early studies showed that attenuation, but not complete elimination, of the general stress response enables early adaptation of the bacterium E. coli to the conditions established about 10 days into stationary phase. We show here that this balance is not static and that it is tilted back in favor of the general stress response about 2 weeks later. This can be established by direct mutations in the master regulator of the general stress response or by mutations in the core RNA polymerase enzyme itself. These conditions can support the development of antibiotic tolerance although the bacterium is not exposed to the antibiotic. Further exploration of the growth-stress balance over the course of stationary phase will necessarily require a deeper understanding of the events in the extracellular milieu.

General Stress Response Regulator RpoS in Adaptive Mutation and Amplification in Escherichia coli

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 669-680 ◽  
Author(s):  
Mary-Jane Lombardo ◽  
Ildiko Aponyi ◽  
Susan M Rosenberg
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Stationary Phase ◽  
Point Mutation ◽  
Stress Responses ◽  
Genome Rearrangement ◽  
Adaptive Mutation ◽  
Induced Mutations ◽  
General Stress Response ◽  
General Stress

Abstract Microbial cells under growth-limiting stress can generate mutations by mechanisms distinct from those in rapidly growing cells. These mechanisms might be specific stress responses that increase mutation rates, potentially altering rates of evolution, or might reflect non-stress-specific processes in rare growing cells. In an Escherichia coli model system, both frameshift reversion mutations and gene amplifications occur as apparent starvation-induced mutations. Whereas frameshift reversion (“point mutation”) requires recombination proteins, the SOS response, and error-prone DNA polymerase IV (DinB), amplification requires neither SOS nor pol IV. We report that both point mutation and amplification require the stationary-phase and general stress response transcription factor RpoS (σS). Growth-dependent mutation does not. Alternative interpretations are excluded. The results imply, first, that point mutation and amplification are stress responses that occur in differentiated stationary-phase (not rare growing) cells and, second, that transient genetic instability, producing both point mutation and genome rearrangement, may be a previously unrecognized component of the RpoS-dependent general stress response.

scholarly journals A mutant RNA polymerase activates the general stress response, enabling E. coli adaptation to late prolonged stationary phase

2020 ◽  
Author(s):  
Pabitra Nandy ◽  
Savita Chib ◽  
Aswin Seshasayee
Keyword(s):  
Stress Response ◽  
Rna Polymerase ◽  
Stationary Phase ◽  
Sigma Factor ◽  
Slow Growth ◽  
General Mechanism ◽  
General Stress Response ◽  
E Coli ◽  
General Stress ◽  
Small Colony

AbstractEscherichia coli populations undergo repeated replacement of parental genotypes with fitter variants deep in stationary phase. We isolated one such variant, which emerged after three weeks o of maintaining an E. coli K12 population in stationary phase. This variant displayed a small colony phenotype, slow growth and was able to outcompete its ancestor over a narrow time window in stationary phase. The variant also shows tolerance to beta-lactam antibiotics, though not previously exposed to the antibiotic. We show that an RpoC (A494V) mutation confers the slow growth and small colony phenotype to this variant. The ability of this mutation to confer a growth advantage in stationary phase depends on the availability of the stationary phase sigma factor σS. The RpoC (A494V) mutation up-regulates the σS regulon. As shown over 20 years ago, early in prolonged stationary phase, σS attenuation, but not complete loss of activity, confers a fitness advantage. Our study shows that later mutations enhance σS activity, either by mutating the gene for σS directly, or via mutations such as RpoC (A494V). The balance between the activities of the housekeeping major sigma factor and σS sets up a trade-off between growth and stress tolerance, which is tuned repeatedly during prolonged stationary phase.ImportanceAn important general mechanism of bacterial adaptation to its environment involves adjusting the balance between growing fast, and tolerating stresses. One paradigm where this plays out is in prolonged stationary phase: early studies showed that attenuation, but not complete elimination, of the general stress response enables early adaptation of the bacterium E. coli to the conditions established about 10 days into stationary phase. We show here that this balance is not static and that it is tilted back in favour of the general stress response about two weeks later. This can be established by direct mutations in the master regulator of the general stress response, or by mutations in the core RNA polymerase enzyme itself. These conditions can support the development of antibiotic tolerance though the bacterium is not exposed to the antibiotic. Further exploration of the growth-stress balance over the course of stationary phase will necessarily require a deeper understanding of the events in the extracellular milieu.

scholarly journals WrpA Is an Atypical Flavodoxin Family Protein under Regulatory Control of the Brucella abortus General Stress Response System

2016 ◽  
Vol 198 (8) ◽  
pp. 1281-1293 ◽  
Author(s):  
Julien Herrou ◽  
Daniel M. Czyż ◽  
Jonathan W. Willett ◽  
Hye-Sook Kim ◽  
Gekleng Chhor ◽  
...  
Keyword(s):  
Stress Response ◽  
Mouse Model ◽  
Binding Site ◽  
Brucella Abortus ◽  
Chronic Infection ◽  
Content Type ◽  
General Stress Response ◽  
General Stress

ABSTRACTThe general stress response (GSR) system of the intracellular pathogenBrucella abortuscontrols the transcription of approximately 100 genes in response to a range of stress cues. The core genetic regulatory components of the GSR are required forB. abortussurvival under nonoptimal growth conditionsin vitroand for maintenance of chronic infection in anin vivomouse model. The functions of the majority of the genes in the GSR transcriptional regulon remain undefined.bab1_1070is among the most highly regulated genes in this regulon: its transcription is activated 20- to 30-fold by the GSR system under oxidative conditionsin vitro. We have solved crystal structures of Bab1_1070 and demonstrate that it forms a homotetrameric complex that resembles those of WrbA-type NADH:quinone oxidoreductases, which are members of the flavodoxin protein family. However,B. abortusWrbA-relatedprotein (WrpA) does not bind flavin cofactors with a high affinity and does not function as an NADH:quinone oxidoreductasein vitro. Soaking crystals with flavin mononucleotide (FMN) revealed a likely low-affinity binding site adjacent to the canonical WrbA flavin binding site. Deletion ofwrpA(ΔwrpA) does not compromise cell survival under acute oxidative stressin vitroor attenuate infection in cell-based or mouse models. However, a ΔwrpAstrain does elicit increased splenomegaly in a mouse model, suggesting that WrpA modulatesB. abortusinteraction with its mammalian host. Despite high structural homology with canonical WrbA proteins, we propose thatB. abortusWrpA represents a functionally distinct member of the diverse flavodoxin family.IMPORTANCEBrucella abortusis an etiological agent of brucellosis, which is among the most common zoonotic diseases worldwide. The general stress response (GSR) regulatory system ofB. abortuscontrols the transcription of approximately 100 genes and is required for maintenance of chronic infection in a murine model; the majority of GSR-regulated genes remain uncharacterized. We presentin vitroandin vivofunctional and structural analyses of WrpA, whose expression is strongly induced by GSR under oxidative conditions. Though WrpA is structurally related to NADH:quinone oxidoreductases, it does not bind redox cofactors in solution, nor does it exhibit oxidoreductase activityin vitro. However, WrpA does affect spleen inflammation in a murine infection model. Our data provide evidence that WrpA forms a new functional class of WrbA/flavodoxin family proteins.

scholarly journals Global Analysis of the General Stress Response ofBacillus subtilis

2001 ◽  
Vol 183 (19) ◽  
pp. 5617-5631 ◽  
Author(s):  
Anja Petersohn ◽  
Matthias Brigulla ◽  
Stefan Haas ◽  
Jörg D. Hoheisel ◽  
Uwe Völker ◽  
...  
Keyword(s):  
Stress Response ◽  
Stress Resistance ◽  
Sigma Factor ◽  
Global Analysis ◽  
Transcriptional Analysis ◽  
Ethanol Stress ◽  
General Stress Response ◽  
Multiple Stress ◽  
Stress Genes ◽  
General Stress

ABSTRACT Gene arrays containing all currently known open reading frames ofBacillus subtilis were used to examine the general stress response of Bacillus. By proteomics, transcriptional analysis, transposon mutagenesis, and consensus promoter-based screening, 75 genes had previously been described as ςB-dependent general stress genes. The present gene array-based analysis confirmed 62 of these already known general stress genes and detected 63 additional genes subject to control by the stress sigma factor ςB. At least 24 of these 125 ςB-dependent genes seemed to be subject to a second, ςB-independent stress induction mechanism. Therefore, this transcriptional profiling revealed almost four times as many regulon members as the proteomic approach, but failure of confirmation of all known members of the ςB regulon indicates that even this approach has not yet elucidated the entire regulon. Most of the ςB-dependent general stress proteins are probably located in the cytoplasm, but 25 contain at least one membrane-spanning domain, and at least 6 proteins appear to be secreted. The functions of most of the newly described genes are still unknown. However, their classification as ςB-dependent stress genes argues that their products most likely perform functions in stress management and help to provide the nongrowing cell with multiple stress resistance. A comprehensive screening program analyzing the multiple stress resistance of mutants with mutations in single stress genes is in progress. The first results of this program, showing the diminished salt resistance of yjbC and yjbD mutants compared to that of the wild type, are presented. Only a few new ςB-dependent proteins with already known functions were found, among them SodA, encoding a superoxide dismutase. In addition to analysis of the ςB-dependent general stress regulon, a comprehensive list of genes induced by heat, salt, or ethanol stress in a ςB-independent manner is presented. Perhaps the most interesting of the ςB-independent stress phenomena was the induction of the extracytoplasmic function sigma factor ςW and its entire regulon by salt shock.

scholarly journals PhyR Is Involved in the General Stress Response of Methylobacterium extorquens AM1

2007 ◽  
Vol 190 (3) ◽  
pp. 1027-1035 ◽  
Author(s):  
Benjamin Gourion ◽  
Anne Francez-Charlot ◽  
Julia A. Vorholt
Keyword(s):  
Stress Response ◽  
Heat Shock ◽  
Stress Responses ◽  
Target Genes ◽  
Stress Proteins ◽  
Plant Colonization ◽  
Methylobacterium Extorquens ◽  
General Stress Response ◽  
Amino Terminal ◽  
General Stress

ABSTRACTPhyR represents a novel alphaproteobacterial family of response regulators having a structure consisting of two domains; a predicted amino-terminal extracytoplasmic function (ECF) sigma factor-like domain and a carboxy-terminal receiver domain. PhyR was first described inMethylobacterium extorquensAM1, in which it has been shown to be essential for plant colonization, probably due to its suggested involvement in the regulation of a number of stress proteins. Here we investigated the PhyR regulon using microarray technology. We found that the PhyR regulon is rather large and that most of the 246 targets are under positive control. Mapping of transcriptional start sites revealed candidate promoters for PhyR-mediated regulation. One of these promoters, an ECF-type promoter, was identified upstream of one-third of the target genes by in silico analysis. Among the PhyR targets are genes predicted to be involved in multiple stress responses, includingkatE,osmC,htrA,dnaK,gloA,dps, anduvrA. The induction of these genes is consistent with our phenotypic analyses which revealed that PhyR is involved in resistance to heat shock and desiccation, as well as oxidative, UV, ethanol, and osmotic stresses, inM. extorquensAM1. The finding that PhyR is involved in the general stress response was further substantiated by the finding that carbon starvation induces protection against heat shock and that this protection is at least in part dependent on PhyR.

scholarly journals Global Transcriptional Response of Bacillus subtilis to Heat Shock

2001 ◽  
Vol 183 (24) ◽  
pp. 7318-7328 ◽  
Author(s):  
John D. Helmann ◽  
Ming Fang Winston Wu ◽  
Phil A. Kobel ◽  
Francisco-Javier Gamo ◽  
Michael Wilson ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Stress Response ◽  
Heat Shock ◽  
Dna Sequences ◽  
Stress Responses ◽  
Transcriptional Response ◽  
Transcriptional Responses ◽  
General Stress Response ◽  
General Stress ◽  
Induced Genes

ABSTRACT In response to heat stress, Bacillus subtilisactivates the transcription of well over 100 different genes. Many of these genes are members of a general stress response regulon controlled by the secondary sigma factor, ςB, while others are under control of the HrcA or CtsR heat shock regulators. We have used DNA microarrays to monitor the global transcriptional response to heat shock. We find strong induction of known ςB-dependent genes with a characteristic rapid induction followed by a return to near prestimulus levels. The HrcA and CtsR regulons are also induced, but with somewhat slower kinetics. Analysis of DNA sequences proximal to newly identified heat-induced genes leads us to propose ∼70 additional members of the ςB regulon. We have also identified numerous heat-induced genes that are not members of known heat shock regulons. Notably, we observe very strong induction of arginine biosynthesis and transport operons. Induction of several genes was confirmed by quantitative reverse transcriptase PCR. In addition, the transcriptional responses measured by microarray hybridization compare favorably with the numerous previous studies of heat shock in this organism. Since many different conditions elicit both specific and general stress responses, knowledge of the heat-induced general stress response reported here will be helpful for interpreting future microarray studies of other stress responses.

scholarly journals Ensifer aridi LMR001T Symbiosis and Tolerance to Stress Do Not Require the Alternative Sigma Factor RpoE2

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1787
Author(s):  
Meryem Belfquih ◽  
Ilham Sakrouhi ◽  
Hassan Ait-Benhassou ◽  
Emeric Dubois ◽  
Dany Severac ◽  
...  
Keyword(s):  
Stress Response ◽  
Sigma Factor ◽  
A Priori ◽  
Climatic Conditions ◽  
Targeted Mutagenesis ◽  
Alternative Sigma Factor ◽  
Gene Encoding ◽  
General Stress Response ◽  
Stress Genes ◽  
General Stress

The recently proposed species Ensifer aridi represents an interesting model to study adaptive mechanisms explaining its maintenance under stressful pedo-climatic conditions. To get insights into functions associated with hyperosmotic stress adaptation in E. aridi, we first performed RNAseq profiling of cells grown under sub-lethal stresses applied by permeating (NaCl) and non-permeating (PEG8000) solutes that were compared to a transcriptome from unstressed bacteria. Then an a priori approach, consisting of targeted mutagenesis of the gene encoding alternative sigma factor (rpoE2), involved in the General Stress Response combined with phenotyping and promoter gfp fusion-based reporter assays of selected genes was carried out to examine the involvement of rpoE2 in symbiosis and stress response. The majority of motility and chemotaxis genes were repressed by both stresses. Results also suggest accumulation of compatible solute trehalose under stress and other metabolisms such as inositol catabolism or the methionine cycling-generating S-adenosyl methionine appears strongly induced notably under salt stress. Interestingly, many functions regulated by salt were shown to favor competitiveness for nodulation in other rhizobia, supporting a role of stress genes for proper symbiosis’ development and functioning. However, despite activation of the general stress response and identification of several genes possibly under its control, our data suggest that rpoE2 was not essential for stress tolerance and symbiosis’ development, indicating that E. aridi possesses alternative regulatory mechanisms to adapt and respond to stressful environments.

scholarly journals The General Stress Sigma Factor ςS ofEscherichia coli Is Induced during Diauxic Shift from Glucose to Lactose

1998 ◽  
Vol 180 (23) ◽  
pp. 6203-6206 ◽  
Author(s):  
Daniela Fischer ◽  
Antje Teich ◽  
Peter Neubauer ◽  
Regine Hengge-Aronis
Keyword(s):  
Sigma Factor ◽  
Lag Phase ◽  
Diauxic Shift ◽  
Glucose Starvation ◽  
General Stress Response ◽  
General Stress ◽  
Economical System ◽  
Diauxic Lag

ABSTRACT The general stress sigma factor ςS (RpoS) ofEscherichia coli is strongly induced in response to glucose starvation. This increase in the cellular ςS level is due to stabilization of ςS, which under non-stress conditions is subject to rapid proteolysis. In the present study, it is demonstrated that ςS is also induced during the diauxic shift from glucose to lactose, i.e., under conditions of glucose exhaustion in the presence of another, less-preferred carbon source that eventually gets utilized. This ςS induction, which is due to stabilization, is transient and precedes the induction of β-galactosidase. In parallel, ςS-dependent genes are transiently activated, as was shown here for osmY. Although ςS can mediate transcription of lacZ in vitro, ςS does not contribute to the induction of β-galactosidase during the diauxic lag phase. Rather, the induction of ςS and the general stress response during the diauxic shift plays the role of a rapidly activated emergency system, which is shut off again as soon as the cells are able to cope with the stress situation by utilizing a more specific and more economical system.

scholarly journals Crl, a Low Temperature-induced Protein inEscherichia coliThat Binds Directly to the Stationary Phase σ Subunit of RNA Polymerase

2004 ◽  
Vol 279 (19) ◽  
pp. 19540-19550 ◽  
Author(s):  
Alexandre Bougdour ◽  
Cécile Lelong ◽  
Johannes Geiselmann
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Low Temperature ◽  
Rna Polymerase ◽  
Stationary Phase ◽  
Sigma Factor ◽  
Physiological Signals ◽  
Alternative Sigma Factor ◽  
Transcription Rate ◽  
Stress Response Genes

The alternative sigma factor σS(RpoS) ofEscherichia coliRNA polymerase regulates the expression of stationary phase and stress-response genes. σSis also required for the transcription of the cryptic genescsgBAthat encode the subunits of the curli proteins. The expression of thecsgBAgenes is regulated in response to a multitude of physiological signals. In stationary phase, these genes are transcribed by the σSfactor, and expression of the operon is enhanced by the small protein Crl. It has been shown that Crl stimulates the activity of σS, leading to an increased transcription rate of a subset of genes of therpoSregulon in stationary phase. However, the underlying molecular mechanism has remained elusive. We show here that Crl interacts directly with σSand that this interaction promotes binding of the σSholoenzyme (EσS) to thecsgBApromoter. Expression of Crl is increased during the transition from growing to stationary phase. Crl accumulates in stationary phase cells at low temperature (30 °C) but not at 37 °C. We therefore propose that Crl is a second thermosensor, besides DsrA, controlling σSactivity.

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