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.

scholarly journals DksA and ppGpp Regulate the σS Stress Response by Activating Promoters for the Small RNA DsrA and the Anti-Adapter Protein IraP

2017 ◽  
Vol 200 (2) ◽  
Author(s):  
Mary E. Girard ◽  
Saumya Gopalkrishnan ◽  
Elicia D. Grace ◽  
Jennifer A. Halliday ◽  
Richard L. Gourse ◽  
...  
Keyword(s):  
Stress Response ◽  
Rna Polymerase ◽  
Stationary Phase ◽  
Sigma Factor ◽  
Bacterial Species ◽  
Adaptor Protein ◽  
Large Family ◽  
Alternative Sigma Factor ◽  
Term Survival ◽  
Content Type

ABSTRACT σS is an alternative sigma factor, encoded by the rpoS gene, that redirects cellular transcription to a large family of genes in response to stressful environmental signals. This so-called σS general stress response is necessary for survival in many bacterial species and is controlled by a complex, multifactorial pathway that regulates σS levels transcriptionally, translationally, and posttranslationally in Escherichia coli. It was shown previously that the transcription factor DksA and its cofactor, ppGpp, are among the many factors governing σS synthesis, thus playing an important role in activation of the σS stress response. However, the mechanisms responsible for the effects of DksA and ppGpp have not been elucidated fully. We describe here how DksA and ppGpp directly activate the promoters for the anti-adaptor protein IraP and the small regulatory RNA DsrA, thereby indirectly influencing σS levels. In addition, based on effects of DksAN88I, a previously identified DksA variant with increased affinity for RNA polymerase (RNAP), we show that DksA can increase σS activity by another indirect mechanism. We propose that by reducing rRNA transcription, DksA and ppGpp increase the availability of core RNAP for binding to σS and also increase transcription from other promoters, including PdsrA and PiraP. By improving the translation and stabilization of σS, as well as the ability of other promoters to compete for RNAP, DksA and ppGpp contribute to the switch in the transcription program needed for stress adaptation. IMPORTANCE Bacteria spend relatively little time in log phase outside the optimized environment found in a laboratory. They have evolved to make the most of alternating feast and famine conditions by seamlessly transitioning between rapid growth and stationary phase, a lower metabolic mode that is crucial for long-term survival. One of the key regulators of the switch in gene expression that characterizes stationary phase is the alternative sigma factor σS. Understanding the factors governing σS activity is central to unraveling the complexities of growth, adaptation to stress, and pathogenesis. Here, we describe three mechanisms by which the RNA polymerase binding factor DksA and the second messenger ppGpp regulate σS levels.

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 Crl Facilitates RNA Polymerase Holoenzyme Formation

2006 ◽  
Vol 188 (22) ◽  
pp. 7966-7970 ◽  
Author(s):  
Tamas Gaal ◽  
Mark J. Mandel ◽  
Thomas J. Silhavy ◽  
Richard L. Gourse
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Stationary Phase ◽  
Mechanism Of Action ◽  
Sigma Factor ◽  
Transcriptional Coactivator ◽  
Transcription System ◽  
The Core ◽  
Core Enzyme ◽  
Rna Polymerase Holoenzyme

ABSTRACT The Escherichia coli Crl protein has been described as a transcriptional coactivator for the stationary-phase sigma factor σS. In a transcription system with highly purified components, we demonstrate that Crl affects transcription not only by the EσS RNA polymerase holoenzyme but also by Eσ70 and Eσ32. Crl increased transcription dramatically but only when the σ concentration was low and when Crl was added to σ prior to assembly with the core enzyme. Our results suggest that Crl facilitates holoenzyme formation, the first positive regulator identified with this mechanism of action.

scholarly journals RpoS-Regulated Genes of Escherichia coli Identified by Random lacZ Fusion Mutagenesis

2004 ◽  
Vol 186 (24) ◽  
pp. 8499-8507 ◽  
Author(s):  
Somalinga R. V. Vijayakumar ◽  
Mark G. Kirchhof ◽  
Cheryl L. Patten ◽  
Herb E. Schellhorn
Keyword(s):  
Escherichia Coli ◽  
Sigma Factor ◽  
Genetic Screen ◽  
The Other ◽  
Alternative Sigma Factor ◽  
Gene Fusions ◽  
Wild Type ◽  
Stress Response Genes ◽  
Independent Gene ◽  
Bacterial Genes

ABSTRACT RpoS is a conserved alternative sigma factor that regulates the expression of many stress response genes in Escherichia coli. The RpoS regulon is large but has not yet been completely characterized. In this study, we report the identification of over 100 RpoS-dependent fusions in a genetic screen based on the differential expression of an operon-lacZ fusion bank in rpoS mutant and wild-type backgrounds. Forty-eight independent gene fusions were identified, including several in well-characterized RpoS-regulated genes, such as osmY, katE, and otsA. Many of the other fusions mapped to genes of unknown function or to genes that were not previously known to be under RpoS control. Based on the homology to other known bacterial genes, some of the RpoS-regulated genes of unknown functions are likely important in nutrient scavenging.

scholarly journals Regulation of the Alternative Sigma Factor σE during Initiation, Adaptation, and Shutoff of the Extracytoplasmic Heat Shock Response in Escherichia coli

2003 ◽  
Vol 185 (8) ◽  
pp. 2512-2519 ◽  
Author(s):  
Sarah E. Ades ◽  
Irina L. Grigorova ◽  
Carol A. Gross
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Sigma Factor ◽  
Cell Envelope ◽  
Alternative Sigma Factor ◽  
Shock Response ◽  
Response To Stress ◽  
Temperature Downshift ◽  
The Relationship ◽  
Fine Tune

ABSTRACT The alternative sigma factor σE is activated in response to stress in the extracytoplasmic compartment of Escherichia coli. Here we show that σE activity increases upon initiation of the stress response by a shift to an elevated temperature (43°C) and remains at that level for the duration of the stress. When the stress is removed by a temperature downshift, σE activity is strongly repressed and then slowly returns to levels seen in unstressed cells. We provide evidence that information about the state of the cell envelope is communicated to σE primarily through the regulated proteolysis of the inner membrane anti-sigma factor RseA, as the degradation rate of RseA is correlated with the changes in σE activity throughout the stress response. However, the relationship between σE activity and the rate of degradation of RseA is complex, indicating that other factors may cooperate with RseA and serve to fine-tune the response.

scholarly journals An N-Terminally Truncated RpoS (σS) Protein in Escherichia coli Is Active In Vivo and Exhibits Normal Environmental Regulation Even in the Absence of rpoS Transcriptional and Translational Control Signals

2002 ◽  
Vol 184 (12) ◽  
pp. 3167-3175 ◽  
Author(s):  
K. Rajkumari ◽  
J. Gowrishankar
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Rna Polymerase ◽  
Stationary Phase ◽  
Translational Control ◽  
Sigma Factor ◽  
Receptor Protein ◽  
Wild Type ◽  
Truncated Protein

ABSTRACT RpoS (σS) in Escherichia coli is a stationary-phase-specific primary sigma factor of RNA polymerase which is 330 amino acids long and belongs to the eubacterial σ70 family of proteins. Conserved domain 1.1 at the N-terminal end of σ70 has been shown to be essential for RNA polymerase function, and its deletion has been shown to result in a dominant-lethal phenotype. We now report that a σS variant with a deletion of its N-terminal 50 amino acids (σSΔ1-50), when expressed in vivo either from a chromosomal rpoS::IS10 allele (in rho mutant strains) or from a plasmid-borne arabinose-inducible promoter, is as proficient as the wild type in directing transcription from the proU P1 promoter; at three other σS-dependent promoters that were tested (osmY, katE, and csiD), the truncated protein exhibited a three- to sevenfold reduced range of activities. Catabolite repression at the csiD promoter (which requires both σS and cyclic AMP [cAMP]-cAMP receptor protein for its activity) was also preserved in the strain expressing σSΔ1-50. The intracellular content of σSΔ1-50 was regulated by culture variables such as growth phase, osmolarity, and temperature in the same manner as that described earlier for σS, even when the truncated protein was expressed from a template that possessed neither the transcriptional nor the translational control elements of wild-type rpoS. Our results indicate that, unlike that in σ70, the N-terminal domain in σS may not be essential for the protein to function as a sigma factor in vivo. Furthermore, our results suggest that the induction of σS-specific promoters in stationary phase and during growth under conditions of high osmolarity or low temperature is mediated primarily through the regulation of σS protein degradation.

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.

scholarly journals One of Two OsmC Homologs in Bacillus subtilis Is Part of the ςB-Dependent General Stress Regulon

1998 ◽  
Vol 180 (16) ◽  
pp. 4212-4218 ◽  
Author(s):  
Uwe Völker ◽  
Kasper Krogh Andersen ◽  
Haike Antelmann ◽  
Kevin M. Devine ◽  
Michael Hecker
Keyword(s):  
Escherichia Coli ◽  
Bacillus Subtilis ◽  
Stationary Phase ◽  
Expression Pattern ◽  
Sigma Factor ◽  
Minimal Medium ◽  
Alternative Sigma Factor ◽  
Rich Medium ◽  
E Coli ◽  
Complex Expression

ABSTRACT In this report we present the identification and analysis of twoBacillus subtilis genes, yklA andykzA, which are homologous to the partially RpoS-controlledosmC gene from Escherichia coli. TheyklA gene is expressed at higher levels in minimal medium than in rich medium and is driven by a putative vegetative promoter. Expression of ykzA is not medium dependent but increases dramatically when cells are exposed to stress and starvation. This stress-induced increase in ykzA expression is absolutely dependent on the alternative sigma factor ςB, which controls a large stationary-phase and stress regulon. ykzAis therefore another example of a gene common to the RpoS and ςB stress regulons of E. coli andB. subtilis, respectively. The composite complex expression pattern of the two B. subtilis genes is very similar to the expression profile of osmC in E. coli.

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