Plasmid-Based Machinery Which Promotes Conjugative Exchange Generates Stress Responses in E. coli

ABSTRACTσE, an alternative σ factor that governs a major signaling pathway in envelope stress responses in Gram-negative bacteria, is essential for growth ofEscherichia colinot only under stressful conditions, such as elevated temperature, but also under normal laboratory conditions. A mutational inactivation of thehicBgene has been reported to suppress the lethality caused by the loss of σE.hicBencodes the antitoxin of the HicA-HicB toxin-antitoxin (TA) system; overexpression of the HicA toxin, which exhibits mRNA interferase activity, causes cleavage of mRNAs and an arrest of cell growth, while simultaneous expression of HicB neutralizes the toxic effects of overproduced HicA. To date, however, how the loss of HicB rescues the cell lethality in the absence of σEand, more specifically, whether HicA is involved in this process remain unknown. Here we showed that simultaneous disruption ofhicAabolished suppression of the σEessentiality in the absence ofhicB, while ectopic expression of wild-type HicA, but not that of its mutant forms without mRNA interferase activity, restored the suppression. Furthermore, HicA and two other mRNA interferase toxins, HigB and YafQ, suppressed the σEessentiality even in the presence of chromosomally encoded cognate antitoxins when these toxins were overexpressed individually. Interestingly, when the growth media were supplemented with low levels of antibiotics that are known to activate toxins,E. colicells with no suppressor mutations grew independently of σE. Taken together, our results indicate that the activation of TA system toxins can suppress the σEessentiality and affect the extracytoplasmic stress responses.IMPORTANCEσEis an alternative σ factor involved in extracytoplasmic stress responses. Unlike other alternative σ factors, σEis indispensable for the survival ofE. colieven under unstressed conditions, although the exact reason for its essentiality remains unknown. Toxin-antitoxin (TA) systems are widely distributed in prokaryotes and are composed of two adjacent genes, encoding a toxin that exerts harmful effects on the toxin-producing bacterium itself and an antitoxin that neutralizes the cognate toxin. Curiously, it is known that inactivation of an antitoxin rescues the σEessentiality, suggesting a connection between TA systems and σEfunction. We demonstrate here that toxin activation is necessary for this rescue and suggest the possible involvement of TA systems in extracytoplasmic stress responses.

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The efficacy of long-lasting residual drinking water disinfectants based on hydrogen peroxide and silver

Water Science & Technology ◽

10.2166/wst.2000.0328 ◽

2000 ◽

Vol 42 (1-2) ◽

pp. 293-298 ◽

Cited By ~ 16

Author(s):

R. Pedahzur ◽

D. Katzenelson ◽

N. Barnea ◽

O. Lev ◽

H.I. Shuval ◽

...

Keyword(s):

Hydrogen Peroxide ◽

Heat Shock ◽

Stress Responses ◽

Heat Shock Response ◽

Chemical Properties ◽

Bactericidal Effect ◽

Physiological Effects ◽

Mechanisms Of Toxicity ◽

E Coli ◽

Shock Response

The aim of the present work was to evaluate the disinfectant capacity and the possible fields of application of a combined silver and hydrogen peroxide (HP) water disinfectant. The findings demonstrated the high bactericidal action of silver (on E. coli) and its relatively ineffective virucidal effect (on MS-2 phage). HP was found to have a small bactericidal effect and a mild virucidal one. When combined, silver and HP usually exhibited a synergistic action on the viability of E. coli and on the luminescence of recombinant luminescent E. coli. In some instances, the combined bactericidal effects were 1000-fold higher than the sum of the separate ones. No increased virucidal action was observed. The biocidal action of the combination generally increased with increasing temperature and pH, and decreased in secondary and tertiary effluents. The physiological effects and mechanisms of toxicity of HP, silver and their combinations, were assessed by monitoring the induction of stress promoters upon exposure to the active agents, and by assessing the sensitivity of E. coli mutated in major stress responses to HP, silver and their combinations. The results showed that HP induced a wide array of stress responses, that both silver and HP induced promoters regulated by the heat shock response, and that the dnaK promoter (regulated by the heat shock response) was synergistically induced. The mutant sensitivity tests showed that bacteria deficient in the ability to activate central cellular stress responses (SOS, heat shock, stationary phase, oxidative) were hypersensitive to both HP and silver. These results imply that cellular proteins, and possibly the DNA, are the cellular moieties chiefly affected. The above findings suggest that the potentiated effect of HP and silver is a metabolically dependant/related process that stems from a combination and/or accumulation of physiological effects exerted by the active ingredients. The physico-chemical properties of the combined disinfectant, and its disinfection capacity, points to its potential application as a long-term secondary residual disinfectant for water of relatively high quality.

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Transcriptome Analysis of Escherichia coli during dGTP Starvation

Journal of Bacteriology ◽

10.1128/jb.00218-16 ◽

2016 ◽

Vol 198 (11) ◽

pp. 1631-1644 ◽

Cited By ~ 5

Author(s):

Mark Itsko ◽

Roel M. Schaaper

Keyword(s):

Escherichia Coli ◽

Dna Replication ◽

Stress Responses ◽

De Novo ◽

Replication Stress ◽

Building Blocks ◽

Content Type ◽

Final Cause ◽

E Coli ◽

Genome Wide

ABSTRACTOur laboratory recently discovered thatEscherichia colicells starved for the DNA precursor dGTP are killed efficiently (dGTP starvation) in a manner similar to that described for thymineless death (TLD). Conditions for specific dGTP starvation can be achieved by depriving anE. colioptA1 gptstrain of the purine nucleotide precursor hypoxanthine (Hx). To gain insight into the mechanisms underlying dGTP starvation, we conducted genome-wide gene expression analyses of actively growingoptA1 gptcells subjected to hypoxanthine deprivation for increasing periods. The data show that upon Hx withdrawal, theoptA1 gptstrain displays a diminished ability to derepress thede novopurine biosynthesis genes, likely due to internal guanine accumulation. The impairment in fully inducing thepurRregulon may be a contributing factor to the lethality of dGTP starvation. At later time points, and coinciding with cell lethality, strong induction of the SOS response was observed, supporting the concept of replication stress as a final cause of death. No evidence was observed in the starved cells for the participation of other stress responses, including therpoS-mediated global stress response, reinforcing the lack of feedback of replication stress to the global metabolism of the cell. The genome-wide expression data also provide direct evidence for increased genome complexity during dGTP starvation, as a markedly increased gradient was observed for expression of genes located near the replication origin relative to those located toward the replication terminus.IMPORTANCEControl of the supply of the building blocks (deoxynucleoside triphosphates [dNTPs]) for DNA replication is important for ensuring genome integrity and cell viability. When cells are starved specifically for one of the four dNTPs, dGTP, the process of DNA replication is disturbed in a manner that can lead to eventual death. In the present study, we investigated the transcriptional changes in the bacteriumE. coliduring dGTP starvation. The results show increasing DNA replication stress with an increased time of starvation, as evidenced by induction of the bacterial SOS system, as well as a notable lack of induction of other stress responses that could have saved the cells from cell death by slowing down cell growth.

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BaeSR, Involved in Envelope Stress Response, Protects against Lysogenic Conversion by Shiga Toxin 2-Encoding Phages

Infection and Immunity ◽

10.1128/iai.02916-14 ◽

2015 ◽

Vol 83 (4) ◽

pp. 1451-1457 ◽

Cited By ~ 3

Author(s):

Lejla Imamovic ◽

Alexandre Martínez-Castillo ◽

Carmen Benavides ◽

Maite Muniesa

Keyword(s):

Stress Responses ◽

Shiga Toxin ◽

Phage Infection ◽

Bacterial Cells ◽

Content Type ◽

Signaling Systems ◽

E Coli ◽

Envelope Stress ◽

Lysogenic Conversion

Infection and lysogenic conversion with Shiga toxin-encoding bacteriophages (Stx phages) drive the emergence of new Shiga toxin-producingEscherichia colistrains. Phage attachment to the bacterial surface is the first stage of phage infection. Envelope perturbation causes activation of envelope stress responses in bacterial cells. Although many external factors are known to activate envelope stress responses, the role of these responses in the phage-bacterium interaction remains unexplored. Here, we investigate the link between three envelope signaling systems inE. coli(RcsBC, CpxAR, and BaeSR) and Stx2 phage infection by determining the success of bacterial lysogenic conversion. For this purpose,E. coliDH5α wild-type (WT) and mutant strains lacking RcsBC, CpxAR, or BaeSR signaling systems were incubated with a recombinant Stx2 phage (933W). Notably, the number of lysogens obtained with the BaeSR mutant was 5 log10units higher than with the WT, and the same differences were observed when using 7 different Stx2 phages. To assess whether the membrane receptor used by Stx phages, BamA, was involved in the differences observed,bamAgene expression was monitored by reverse transcription-quantitative PCR (RT-qPCR) in all host strains. A 4-fold-higherbamAexpression level was observed in the BaeSR mutant than in the WT strain, suggesting that differential expression of the receptor used by Stx phages accounted for the increase in the number of lysogenization events. Establishing the link between the role of stress responses and phage infection has important implications for understanding the factors affecting lysogenic conversion, which drives the emergence of new pathogenic clones.

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The ferric iron uptake regulator (Fur) from the extreme acidophile Acidithiobacillus ferrooxidans

Microbiology ◽

10.1099/mic.0.27581-0 ◽

2005 ◽

Vol 151 (6) ◽

pp. 2005-2015 ◽

Cited By ~ 27

Author(s):

R. Quatrini ◽

C. Lefimil ◽

D. S. Holmes ◽

E. Jedlicki

Keyword(s):

Gene Expression ◽

Stress Responses ◽

Acidithiobacillus Ferrooxidans ◽

Iron Uptake ◽

Ferric Iron ◽

Sequence Similarity ◽

Cross Reactivity ◽

Mobility Shift ◽

E Coli ◽

Protein Levels

Acidithiobacillus ferrooxidans is a Gram-negative bacterium that lives at pH 2 in high concentrations of soluble ferrous and ferric iron, making it an interesting model for understanding the biological mechanisms of bacterial iron uptake and homeostasis in extremely acid conditions. A candidate fur AF (Ferric Uptake Regulator) gene was identified in the A. ferrooxidans ATCC 23270 genome. FurAF has significant sequence similarity, including conservation of functional motifs, to known Fur orthologues and exhibits cross-reactivity to Escherichia coli Fur antiserum. The fur AF gene is able to complement fur deficiency in E. coli in an iron-responsive manner. FurAF is also able to bind specifically to E. coli Fur regulatory regions (Fur boxes) and to a candidate Fur box from A. ferrooxidans, as judged by electrophoretic mobility shift assays. FurAF represses gene expression from E. coli Fur-responsive promoters fiu and fhuF when expressed at high protein levels. However, it increases gene expression from these promoters at low concentrations and possibly from other Fur-regulated promoters involved in iron-responsive oxidative stress responses.

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Analysis of Serial Isolates of mcr-1-Positive Escherichia coli Reveals a Highly Active ISApl1 Transposon

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00056-17 ◽

2017 ◽

Vol 61 (5) ◽

Cited By ~ 40

Author(s):

Erik Snesrud ◽

Ana C. Ong ◽

Brendan Corey ◽

Yoon I. Kwak ◽

Robert Clifford ◽

...

Keyword(s):

Escherichia Coli ◽

Stress Responses ◽

Single Copy ◽

The United States ◽

Content Type ◽

E Coli ◽

Highly Active ◽

Copy Numbers ◽

Genes Encoding

ABSTRACT The emergence of a transferable colistin resistance gene (mcr-1) is of global concern. The insertion sequence ISApl1 is a key component in the mobilization of this gene, but its role remains poorly understood. Six Escherichia coli isolates were cultured from the same patient over the course of 1 month in Germany and the United States after a brief hospitalization in Bahrain for an unconnected illness. Four carried mcr-1 as determined by real-time PCR, but two were negative. Two additional mcr-1-negative E. coli isolates were collected during follow-up surveillance 9 months later. All isolates were analyzed by whole-genome sequencing (WGS). WGS revealed that the six initial isolates were composed of two distinct strains: an initial ST-617 E. coli strain harboring mcr-1 and a second, unrelated, mcr-1-negative ST-32 E. coli strain that emerged 2 weeks after hospitalization. Follow-up swabs taken 9 months later were negative for the ST-617 strain, but the mcr-1-negative ST-32 strain was still present. mcr-1 was associated with a single copy of ISApl1, located on a 64.5-kb IncI2 plasmid that shared >95% homology with other mcr-1 IncI2 plasmids. ISApl1 copy numbers ranged from 2 for the first isolate to 6 for the final isolate, but ISApl1 movement was independent of mcr-1. Some movement was accompanied by gene disruption, including the loss of genes encoding proteins involved in stress responses, arginine catabolism, and l-arabinose utilization. These data represent the first comprehensive analysis of ISApl1 movement in serial clinical isolates and reveal that, under certain conditions, ISApl1 is a highly active IS element whose movement may be detrimental to the host cell.

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Genetic Analysis of Activation of the Vibrio cholerae Cpx Pathway

Journal of Bacteriology ◽

10.1128/jb.00406-09 ◽

2009 ◽

Vol 191 (16) ◽

pp. 5044-5056 ◽

Cited By ~ 30

Author(s):

Leyla Slamti ◽

Matthew K. Waldor

Keyword(s):

Vibrio Cholerae ◽

Stress Responses ◽

Disulfide Bonds ◽

Chloride Ions ◽

Mammalian Host ◽

Two Component System ◽

E Coli ◽

Cpx Pathway ◽

Sense And Respond ◽

Molecular Signals

ABSTRACT The Cpx two-component system is thought to mediate envelope stress responses in many gram-negative bacteria and has been implicated in the pathogenicity of several enteric pathogens. While cues that activate the Escherichia coli Cpx system have been identified, the nature of the molecular signals that stimulate this pathway is not well understood. Here, we investigated stimuli that trigger this system in Vibrio cholerae, a facultative pathogen that adapts to various niches during its life cycle. In contrast to E. coli, there was no basal activity of the V. cholerae Cpx pathway under standard laboratory conditions. Furthermore, several known stimuli of the E. coli pathway did not induce expression of this system in V. cholerae. There were no defects in intestinal growth in V. cholerae cpx mutants, arguing against the idea that this pathway promotes V. cholerae adaptation to conditions in the mammalian host. We discovered that chloride ions activate the V. cholerae Cpx pathway, raising the possibility that this signal transduction system provides a means for V. cholerae to sense and respond to alterations in salinity. We used a genetic approach to screen for mutants in which the Cpx pathway is activated. We found that mutations in genes whose products are required for periplasmic disulfide bond isomerization result in activation of the Cpx pathway, suggesting that periplasmic accumulation of proteins with aberrant disulfide bonds triggers the V. cholerae Cpx pathway.

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Genotoxic, Metabolic, and Oxidative Stresses Regulate the RNA Repair Operon ofSalmonella entericaSerovar Typhimurium

Journal of Bacteriology ◽

10.1128/jb.00476-18 ◽

2018 ◽

Vol 200 (23) ◽

Cited By ~ 5

Author(s):

Jennifer E. Kurasz ◽

Christine E. Hartman ◽

David J. Samuels ◽

Bijoy K. Mohanty ◽

Anquilla Deleveaux ◽

...

Keyword(s):

Nucleic Acid ◽

Stress Responses ◽

Nitrogen Limitation ◽

Selective Advantage ◽

Stress Conditions ◽

Rna Repair ◽

Content Type ◽

E Coli ◽

Oxidative Stresses

ABSTRACTThe σ54regulon inSalmonella entericaserovar Typhimurium includes a predicted RNA repair operon encoding homologs of the metazoan Ro60 protein (Rsr), Y RNAs (YrlBA), RNA ligase (RtcB), and RNA 3′-phosphate cyclase (RtcA). Transcription from σ54-dependent promoters requires that a cognate bacterial enhancer binding protein (bEBP) be activated by a specific environmental or cellular signal; the cognate bEBP for the σ54-dependent promoter of thersr-yrlBA-rtcBAoperon is RtcR. To identify conditions that generate the signal for RtcR activation inS. Typhimurium, transcription of the RNA repair operon was assayed under multiple stress conditions that result in nucleic acid damage. RtcR-dependent transcription was highly induced by the nucleic acid cross-linking agents mitomycin C (MMC) and cisplatin, and this activation was dependent on RecA. Deletion ofrtcRorrtcBresulted in decreased cell viability relative to that of the wild type following treatment with MMC. Oxidative stress from peroxide exposure also induced RtcR-dependent transcription of the operon. Nitrogen limitation resulted in RtcR-independent increased expression of the operon; the effect of nitrogen limitation required NtrC. The adjacent toxin-antitoxin module,dinJ-yafQ, was cotranscribed with the RNA repair operon but was not required for RtcR activation, although YafQ endoribonuclease activated RtcR-dependent transcription. Stress conditions shown to induce expression the RNA repair operon ofEscherichia coli(rtcBA) did not stimulate expression of theS. Typhimurium RNA repair operon. Similarly, MMC did not induce expression of theE. colirtcBAoperon, although when expressed inS. Typhimurium,E. coliRtcR responds effectively to the unknown signal(s) generated there by MMC exposure.IMPORTANCEHomologs of the metazoan RNA repair enzymes RtcB and RtcA occur widely in eubacteria, suggesting a selective advantage. Although the enzymatic activities of the eubacterial RtcB and RtcA have been well characterized, the physiological roles remain largely unresolved. Here we report stress responses that activate expression of the σ54-dependent RNA repair operon (rsr-yrlBA-rtcBA) ofS. Typhimurium and demonstrate that expression of the operon impacts cell survival under MMC-induced stress. Characterization of the requirements for activation of this tightly regulated operon provides clues to the possible functions of operon componentsin vivo, enhancing our understanding of how this human pathogen copes with environmental stressors.

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Overlapping stimulons arising in response to divergent stresses in Escherichia coli

10.1101/2021.12.17.473201 ◽

2021 ◽

Author(s):

Huijing Wang ◽

GW McElfresh ◽

Nishantha Wijesuriya ◽

Adam Podgorny ◽

Andrew D Hecht ◽

...

Keyword(s):

Escherichia Coli ◽

Stress Response ◽

Stress Responses ◽

Differential Expression Analysis ◽

Stringent Response ◽

Coli Strain ◽

Growth Media ◽

Overflow Metabolism ◽

Rna Seq ◽

E Coli

Cellular responses to stress can cause a similar change in some facets of fitness even if the stresses are different. Lactose as a sole carbon source for Escherichia coli is an established example: too little causes starvation while excessive lactose import causes toxicity as a side-effect. In an E. coli strain that is robust to osmotic and ionic differences in growth media, B REL606, the rate of antibiotic-tolerant persister formation is elevated in both starvation-inducing and toxicity-inducing concentrations of lactose in comparison to less stressful intermediate concentrations. Such similarities between starvation and toxification raise the question of how much the global stress response stimulon differs between them. We hypothesized that a common stress response is conserved between the two conditions, but that a previously shown threshold driving growth rate heterogeneity in a lactose-toxifying medium would reveal that the growing fraction of cells in that medium to be missing key stress responses that curb growth. To test this, we performed RNA-seq in three representative conditions for differential expression analysis. In comparison to nominally unstressed cultures, both stress conditions showed global shifts in gene expression, with informative similarities and differences. Functional analysis of pathways, gene ontology terms, and clusters of orthogonal groups revealed signatures of overflow metabolism, membrane component shifts, and altered cytosolic and periplasmic contents in toxified cultures. Starving cultures showed an increased tendency toward stringent response-like regulatory signatures. Along with other emerging evidence, our results show multiple possible pathways to stress responses, persistence, and possibly other phenotypes. These results suggest a set of overlapping responses that drives emergence of stress-tolerant phenotypes in diverse conditions.

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Complex Physiology and Compound Stress Responses during Fermentation of Alkali-Pretreated Corn Stover Hydrolysate by an Escherichia coli Ethanologen

Applied and Environmental Microbiology ◽

10.1128/aem.07329-11 ◽

2012 ◽

Vol 78 (9) ◽

pp. 3442-3457 ◽

Cited By ~ 44

Author(s):

Michael S. Schwalbach ◽

David H. Keating ◽

Mary Tremaine ◽

Wesley D. Marner ◽

Yaoping Zhang ◽

...

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Amino Acids ◽

Stationary Phase ◽

Gene Expression Profiling ◽

Stress Responses ◽

Expression Profiling ◽

Content Type ◽

E Coli ◽

Cell Maintenance

ABSTRACTThe physiology of ethanologenicEscherichia coligrown anaerobically in alkali-pretreated plant hydrolysates is complex and not well studied. To gain insight into howE. coliresponds to such hydrolysates, we studied anE. coliK-12 ethanologen fermenting a hydrolysate prepared from corn stover pretreated by ammonia fiber expansion. Despite the high sugar content (∼6% glucose, 3% xylose) and relatively low toxicity of this hydrolysate,E. coliceased growth long before glucose was depleted. Nevertheless, the cells remained metabolically active and continued conversion of glucose to ethanol until all glucose was consumed. Gene expression profiling revealed complex and changing patterns of metabolic physiology and cellular stress responses during an exponential growth phase, a transition phase, and the glycolytically active stationary phase. During the exponential and transition phases, high cell maintenance and stress response costs were mitigated, in part, by free amino acids available in the hydrolysate. However, after the majority of amino acids were depleted, the cells entered stationary phase, and ATP derived from glucose fermentation was consumed entirely by the demands of cell maintenance in the hydrolysate. Comparative gene expression profiling and metabolic modeling of the ethanologen suggested that the high energetic cost of mitigating osmotic, lignotoxin, and ethanol stress collectively limits growth, sugar utilization rates, and ethanol yields in alkali-pretreated lignocellulosic hydrolysates.

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