scholarly journals Structural basis for sigma factor mimicry in the general stress response of Alphaproteobacteria

2012 ◽  
Vol 109 (21) ◽  
pp. E1405-E1414 ◽  
Author(s):  
S. Campagne ◽  
F. F. Damberger ◽  
A. Kaczmarczyk ◽  
A. Francez-Charlot ◽  
F. H.- T. Allain ◽  
...  
Keyword(s):  
Stress Response ◽  
Sigma Factor ◽  
Structural Basis ◽  
General Stress Response ◽  
General Stress

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.

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 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 Genome-Wide Analysis of the General Stress Response Network in Escherichia coli: σS-Dependent Genes, Promoters, and Sigma Factor Selectivity

2005 ◽  
Vol 187 (5) ◽  
pp. 1591-1603 ◽  
Author(s):  
Harald Weber ◽  
Tino Polen ◽  
Johanna Heuveling ◽  
Volker F. Wendisch ◽  
Regine Hengge
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Rna Polymerase ◽  
Sigma Factor ◽  
Regulatory Network ◽  
Cell Physiology ◽  
Data Set ◽  
General Stress Response ◽  
General Stress ◽  
Genome Wide

ABSTRACT The σS (or RpoS) subunit of RNA polymerase is the master regulator of the general stress response in Escherichia coli. While nearly absent in rapidly growing cells, σS is strongly induced during entry into stationary phase and/or many other stress conditions and is essential for the expression of multiple stress resistances. Genome-wide expression profiling data presented here indicate that up to 10% of the E. coli genes are under direct or indirect control of σS and that σS should be considered a second vegetative sigma factor with a major impact not only on stress tolerance but on the entire cell physiology under nonoptimal growth conditions. This large data set allowed us to unequivocally identify a σS consensus promoter in silico. Moreover, our results suggest that σS-dependent genes represent a regulatory network with complex internal control (as exemplified by the acid resistance genes). This network also exhibits extensive regulatory overlaps with other global regulons (e.g., the cyclic AMP receptor protein regulon). In addition, the global regulatory protein Lrp was found to affect σS and/or σ70 selectivity of many promoters. These observations indicate that certain modules of the σS-dependent general stress response can be temporarily recruited by stress-specific regulons, which are controlled by other stress-responsive regulators that act together with σ70 RNA polymerase. Thus, not only the expression of genes within a regulatory network but also the architecture of the network itself can be subject to regulation.

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.

Structure of the RsbX phosphatase involved in the general stress response ofBacillus subtilis

2015 ◽  
Vol 71 (6) ◽  
pp. 1392-1399 ◽  
Author(s):  
Aik-Hong Teh ◽  
Masatomo Makino ◽  
Takeshi Hoshino ◽  
Seiki Baba ◽  
Nobutaka Shimizu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Stress Response ◽  
Metal Binding ◽  
Sigma Factor ◽  
Phosphorylation Sites ◽  
Ofbacillus Subtilis ◽  
Metal Binding Site ◽  
General Stress Response ◽  
General Stress ◽  
Helical Turn

In the general stress response ofBacillus subtilis, which is governed by the sigma factor σB, stress signalling is relayed by a cascade of Rsb proteins that regulate σBactivity. RsbX, a PPM II phosphatase, halts the response by dephosphorylating the stressosome composed of RsbR and RsbS. The crystal structure of RsbX reveals a reorganization of the catalytic centre, with the second Mn2+ion uniquely coordinated by Gly47 O from the β4–α1 loop instead of a water molecule as in PPM I phosphatases. An extra helical turn of α1 tilts the loop towards the metal-binding site, and the β2–β3 loop swings outwards to accommodate this tilting. The residues critical for this defining feature of the PPM II phosphatases are highly conserved. Formation of the catalytic centre is metal-specific, as crystallization with Mg2+ions resulted in a shift of the β4–α1 loop that led to loss of the second ion. RsbX also lacks the flap subdomain characteristic of PPM I phosphatases. On the basis of a stressosome model, the activity of RsbX towards RsbR-P and RsbS-P may be influenced by the different accessibilities of their phosphorylation sites.

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