scholarly journals Extracytoplasmic Function σ Factors as Tools for Coordinating Stress Responses

2021 ◽  
Vol 22 (8) ◽  
pp. 3900
Author(s):  
Rubén de de Dios ◽  
Eduardo Santero ◽  
Francisca Reyes-Ramírez
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Stress Response ◽  
Stress Responses ◽  
Transcription Initiation ◽  
Genomic Context ◽  
General Stress Response ◽  
Functional Studies ◽  
Functional Stress

The ability of bacterial core RNA polymerase (RNAP) to interact with different σ factors, thereby forming a variety of holoenzymes with different specificities, represents a powerful tool to coordinately reprogram gene expression. Extracytoplasmic function σ factors (ECFs), which are the largest and most diverse family of alternative σ factors, frequently participate in stress responses. The classification of ECFs in 157 different groups according to their phylogenetic relationships and genomic context has revealed their diversity. Here, we have clustered 55 ECF groups with experimentally studied representatives into two broad classes of stress responses. The remaining 102 groups still lack any mechanistic or functional insight, representing a myriad of systems yet to explore. In this work, we review the main features of ECFs and discuss the different mechanisms controlling their production and activity, and how they lead to a functional stress response. Finally, we focus in more detail on two well-characterized ECFs, for which the mechanisms to detect and respond to stress are complex and completely different: Escherichia coli RpoE, which is the best characterized ECF and whose structural and functional studies have provided key insights into the transcription initiation by ECF-RNAP holoenzymes, and the ECF15-type EcfG, the master regulator of the general stress response in Alphaproteobacteria.

scholarly journals IraL Is an RssB Anti-adaptor That Stabilizes RpoS during Logarithmic Phase Growth in Escherichia coli and Shigella

mBio ◽  
2014 ◽  
Vol 5 (3) ◽  
Author(s):  
Andrew J. Hryckowian ◽  
Aurelia Battesti ◽  
Justin J. Lemke ◽  
Zachary C. Meyer ◽  
Rodney A. Welch
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Stress Response ◽  
Sigma Factor ◽  
Logarithmic Phase ◽  
Phase Growth ◽  
Content Type ◽  
General Stress Response ◽  
E Coli ◽  
K 12

ABSTRACTRpoS (σS), the general stress response sigma factor, directs the expression of genes under a variety of stressful conditions. Control of the cellular σSconcentration is critical for appropriately scaled σS-dependent gene expression. One way to maintain appropriate levels of σSis to regulate its stability. Indeed, σSdegradation is catalyzed by the ClpXP protease and the recognition of σSby ClpXP depends on the adaptor protein RssB. Three anti-adaptors (IraD, IraM, and IraP) exist inEscherichia coliK-12; each interacts with RssB andinhibitsRssBactivity under different stress conditions, thereby stabilizing σS. Unlike K-12, someE. coliisolates, including uropathogenicE. colistrain CFT073, show comparable cellular levels of σSduring the logarithmic and stationary growth phases, suggesting that there are differences in the regulation of σSlevels amongE. colistrains. Here, we describe IraL, an RssB anti-adaptor that stabilizes σSduring logarithmic phase growth in CFT073 and otherE. coliandShigellastrains. By immunoblot analyses, we show that IraL affects the levels and stability of σSduring logarithmic phase growth. By computational and PCR-based analyses, we reveal thatiraLis found in manyE. colipathotypes but not in laboratory-adapted strains. Finally, by bacterial two-hybrid and copurification analyses, we demonstrate that IraL interacts with RssB by a mechanism distinct from that used by other characterized anti-adaptors. We introduce a fourth RssB anti-adaptor found inE. colispecies and suggest that differences in the regulation of σSlevels may contribute to host and niche specificity in pathogenic and nonpathogenicE. colistrains.IMPORTANCEBacteria must cope with a variety of environmental conditions in order to survive. RpoS (σS), the general stress response sigma factor, directs the expression of many genes under stressful conditions in both pathogenic and nonpathogenicEscherichia colistrains. The regulation of σSlevels and activity allows appropriately scaled σS-dependent gene expression. Here, we describe IraL, an RssB anti-adaptor that, unlike previously described anti-adaptors, stabilizes σSduring the logarithmic growth phase in the absence of additional stress. We also demonstrate thatiraLis found in a large number ofE. coliandShigellaisolates. These data suggest that strains containingiraLare able to initiate σS-dependent gene expression under conditions under which strains withoutiraLcannot. Therefore, IraL-mediated σSstabilization may contribute to host and niche specificity inE. coli.

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 shift to human body temperature (37°C) rapidly reprograms multiple adaptive responses in Escherichia coli that would facilitate niche survival and colonization

2021 ◽  
Author(s):  
Anastasia Gant Kanegusuku ◽  
Isidora N. Stankovic ◽  
Pamela A. Cote-Hammarlof ◽  
Priscilla H. Yong ◽  
Christine A. White-Ziegler
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Stress Response ◽  
Stress Responses ◽  
Anaerobic Respiration ◽  
Acid Resistance ◽  
Adaptive Responses ◽  
E Coli ◽  
Human Host ◽  
Small Regulatory Rnas

One of the first environmental cues sensed by a microbe as it enters a human host is an upshift in temperature to 37°C. In this dynamic timepoint analysis, we demonstrate that this environmental transition rapidly signals a multitude of gene expression changes in Escherichia coli . Bacteria grown at 23°C under aerobic conditions were shifted to 37°C and mRNA expression was measured at timepoints after the shift to 37°C (t=0.5, 1, and 4 hours). The first hour is characterized by a transient shift to anaerobic respiration strategies and stress responses, particularly acid resistance, indicating that temperature serves as a sentinel cue to predict and prepare for various niches within the host. The temperature effects on a subset of stress response genes were shown to be mediated by RpoS, directly correlated with RpoS, DsrA and RprA levels, and increased acid resistance was observed that was dependent on 23°C growth and RpoS. By 4 hours, gene expression shifted to aerobic respiration pathways, decreased stress responses, coupled with increases in genes associated with biosynthesis (amino acid, nucleotides), iron uptake, and host defense. ompT , a gene that confers resistance to antimicrobial peptides, was highly thermoregulated and with a pattern conserved in enteropathogenic and uropathogenic E. coli . An immediate decrease in curli gene expression concomitant with an increase in flagellar gene expression implicates temperature in this developmental decision. Together, our studies demonstrate that temperature signals a reprogramming of gene expression immediately upon an upshift that may predict, prepare, and benefit survival of the bacterium within the host. IMPORTANCE: As one of the first cues sensed by the microbe upon entry into a human host, understanding how bacteria like E. coli modulate gene expression in response to temperature improves our understanding of how bacteria immediately initiate responses beneficial to survival and colonization. For pathogens, understanding the various pathways of thermal regulation could yield valuable targets for anti-infective chemotherapeutic drugs or disinfection measures. In addition, our data provide a dynamic examination of the RpoS stress response, providing genome-wide support for how temperature impacts RpoS through changes in RpoS stability and modulation by small regulatory RNAs.

scholarly journals Cell-to-cell heterogeneity in Escherichia coli stress response originates from pulsatile expression and growth

2020 ◽  
Author(s):  
Nadia M. V. Sampaio ◽  
Caroline M. Blassick ◽  
Jean-Baptiste Lugagne ◽  
Mary J. Dunlop
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Stress Response ◽  
Single Cell ◽  
Phenotypic Variability ◽  
Growth Dynamics ◽  
Time Lapse ◽  
Cell Heterogeneity ◽  
Temporal Expression ◽  
Functional Consequences

AbstractCell-to-cell heterogeneity in gene expression and growth can have critical functional consequences, such as determining whether individual bacteria survive or die following stress. Although phenotypic variability is well documented, the dynamics that underlie it are often unknown. This information is critical because dramatically different outcomes can arise from gradual versus rapid changes in expression and growth. Using single-cell time-lapse microscopy, we measured the temporal expression of a suite of stress response reporters in Escherichia coli, while simultaneously monitoring growth rate. In conditions without stress, we found widespread examples of pulsatile expression. Single-cell growth rates were often anti-correlated with gene expression, with changes in growth preceding changes in expression. These pulsatile dynamics have functional consequences, which we demonstrate by measuring survival after challenging cells with the antibiotic ciprofloxacin. Our results suggest that pulsatile expression and growth dynamics are common in stress response networks and can have direct consequences for survival.

scholarly journals Short- and Long-Term Transcriptomic Responses of Escherichia coli to Biocides: a Systems Analysis

2020 ◽  
Vol 86 (14) ◽  
Author(s):  
Beatriz Merchel Piovesan Pereira ◽  
Xiaokang Wang ◽  
Ilias Tagkopoulos
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Stress Responses ◽  
Zinc Homeostasis ◽  
Cross Resistance ◽  
Transcriptional Responses ◽  
Systematic Analysis ◽  
Content Type ◽  
Short Term Exposure

ABSTRACT The mechanisms of the bacterial response to biocides are poorly understood, despite their broad application. To identify the genetic basis and pathways implicated in the biocide stress response, we exposed Escherichia coli populations to 10 ubiquitous biocides. By comparing the transcriptional responses between a short-term exposure (30 min) and a long-term exposure (8 to 12 h) to biocide stress, we established the common gene and pathway clusters that are implicated in general and biocide-specific stress responses. Our analysis revealed a temporal choreography, starting from the upregulation of chaperones to the subsequent repression of motility and chemotaxis pathways and the induction of an anaerobic pool of enzymes and biofilm regulators. A systematic analysis of the transcriptional data identified a zur-regulated gene cluster to be highly active in the stress response against sodium hypochlorite and peracetic acid, presenting a link between the biocide stress response and zinc homeostasis. Susceptibility assays with knockout mutants further validated our findings and provide clear targets for downstream investigation of the implicated mechanisms of action. IMPORTANCE Antiseptics and disinfectant products are of great importance to control and eliminate pathogens, especially in settings such as hospitals and the food industry. Such products are widely distributed and frequently poorly regulated. Occasional outbreaks have been associated with microbes resistant to such compounds, and researchers have indicated potential cross-resistance with antibiotics. Despite that, there are many gaps in knowledge about the bacterial stress response and the mechanisms of microbial resistance to antiseptics and disinfectants. We investigated the stress response of the bacterium Escherichia coli to 10 common disinfectant and antiseptic chemicals to shed light on the potential mechanisms of tolerance to such compounds.

scholarly journals Fitness, Stress Resistance, and Extraintestinal Virulence in Escherichia coli

2013 ◽  
Vol 81 (8) ◽  
pp. 2733-2742 ◽  
Author(s):  
Alexandre Bleibtreu ◽  
Pierre-Alexis Gros ◽  
Cédric Laouénan ◽  
Olivier Clermont ◽  
Hervé Le Nagard ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Stress Response ◽  
Mouse Model ◽  
Stress Resistance ◽  
Maximum Growth ◽  
Competitive Fitness ◽  
Content Type ◽  
General Stress Response ◽  
E Coli

ABSTRACTThe extraintestinal virulence ofEscherichia coliis dependent on numerous virulence genes. However, there is growing evidence for a role of the metabolic properties and stress responses of strains in pathogenesis. We assessed the respective roles of these factors in strain virulence by developing phenotypic assays for measuringin vitroindividual and competitive fitness and the general stress response, which we applied to 82 commensal and extraintestinal pathogenicE. colistrains previously tested in a mouse model of sepsis. Individual fitness properties, in terms of maximum growth rates in various media (Luria-Bertani broth with and without iron chelator, minimal medium supplemented with gluconate, and human urine) and competitive fitness properties, estimated as the mean relative growth rate per generation in mixed cultures with a reference fluorescentE. colistrain, were highly diverse between strains. The activity of the main general stress response regulator, RpoS, as determined by iodine staining of the colonies, H2O2resistance, andrpoSsequencing, was also highly variable. No correlation between strain fitness and stress resistance and virulence in the mouse model was found, except that the maximum growth rate in urine was higher for virulent strains. Multivariate analysis showed that the number of virulence factors was the only independent factor explaining the virulence in mice. At the species level, growth capacity and stress resistance are heterogeneous properties that do not contribute significantly to the intrinsic virulence of the strains.

scholarly journals Gene Expression in Trypanosomatid Parasites

2010 ◽  
Vol 2010 ◽  
pp. 1-15 ◽  
Author(s):  
Santiago Martínez-Calvillo ◽  
Juan C. Vizuet-de-Rueda ◽  
Luis E. Florencio-Martínez ◽  
Rebeca G. Manning-Cela ◽  
Elisa E. Figueroa-Angulo
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Histone Variants ◽  
Protein Coding ◽  
Functional Studies ◽  
Polycistronic Transcription ◽  
General Transcription Factors ◽  
Genome Wide ◽  
Trypanosomatid Parasites

The parasitesLeishmaniaspp.,Trypanosoma brucei,andTrypanosoma cruziare the trypanosomatid protozoa that cause the deadly human diseases leishmaniasis, African sleeping sickness, and Chagas disease, respectively. These organisms possess unique mechanisms for gene expression such as constitutive polycistronic transcription of protein-coding genes and trans-splicing. Little is known about either the DNA sequences or the proteins that are involved in the initiation and termination of transcription in trypanosomatids.In silicoanalyses of the genome databases of these parasites led to the identification of a small number of proteins involved in gene expression. However, functional studies have revealed that trypanosomatids have more general transcription factors than originally estimated. Many posttranslational histone modifications, histone variants, and chromatin modifying enzymes have been identified in trypanosomatids, and recent genome-wide studies showed that epigenetic regulation might play a very important role in gene expression in this group of parasites. Here, we review and comment on the most recent findings related to transcription initiation and termination in trypanosomatid protozoa.

scholarly journals Deciphering the genetic and transcriptional basis of cross-stress responses in Escherichia coli under complex evolutionary scenarios

2014 ◽  
Author(s):  
Violeta Zorraquino-Salvo ◽  
Semarhy Quinones-Soto ◽  
Minseung Kim ◽  
Navneet Rai ◽  
Ilias Tagkopoulos
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Stress Responses ◽  
Metal Ion ◽  
Cellular Stress Response ◽  
Metal Ion Binding ◽  
Evolutionary Potential ◽  
Specific Expression ◽  
Stress Vulnerability ◽  
Stress Protection

A tantalizing question in microbial physiology is the inter-dependence and evolutionary potential of cellular stress response across multiple environmental dimensions. To address this question, we comprehensively characterized the cross-stress behavior of wild-type and evolved Escherichia coli populations in five abiotic stresses (n-butanol, osmotic, alkaline, acidic, and oxidative) by performing genome-scale genetic, transcriptional and growth profiling, thus identifying 18 cases of cross-stress protection and one case of cross-stress vulnerability. We identified 18 cases of cross-stress protection and one case of cross-stress vulnerability, along with core and stress-specific networks. We tested several hypotheses regarding the effect of the stress order, stress combinations, mutation reversal and varying environments to the evolution and final cellular fitness of the respective populations. Our results argue of a common systems-level core of the stress response with several crucial implicated pathways that include metal ion binding and glycolysis/gluconeogenesis that is further complemented by a stress-specific expression program.

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