Role of rpoS in Escherichia coli O157:H7 strain H32 biofilm development and survival

Mechanistic and bibliometric insights into RpoS-mediated biofilm regulation and its strategic role in food safety applications

Biofilm, complex structures formed by microorganisms within an extracellular polymeric matrix, pose significant challenges in the sector by harboring dangerous pathogens and complicating decontamination, thereby increasing the risk of foodborne illnesses. This article provides a comprehensive review of the sigma factor, rpoS's role in biofilm development, specifically in gram-negative bacteria, and how the genetic, environmental, and regulatory elements influence rpoS activity with its critical role in bacterial stress responses. Our findings reveal that rpoS is a pivotal regulator of biofilm formation, enhancing bacterial survival in adverse conditions. Key factors affecting rpoS activity include oxidative and osmotic stress and nutrient availability. Understanding rpoS-mediated regulatory pathways is essential for developing targeted biofilm management strategies to improve food quality and safety. Furthermore, a bibliometric analysis highlights significant research trends and gaps in the literature, guiding future research directions. Future research should focus on detailed mechanistic studies of rpoS-mediated biofilm regulation, the development of specific rpoS inhibitors, and innovative approaches like biofilm-resistant surface coatings. This knowledge can lead to more effective contamination prevention and overall food safety enhancements.

Biofilm-Forming Capacity of Escherichia coli Isolated from Cattle and Beef Packing Plants: Relation to Virulence Attributes, Stage of Processing, Antimicrobial Interventions, and Heat Tolerance

Despite the importance of biofilm formation in the contamination of meat by pathogenic Escherichia coli at slaughter plants, drivers for biofilm remain unclear. To identify selection pressures for biofilm, we evaluated 745 isolates from cattle and 700 generic E. coli isolates from two beef slaughter plants for motility, the expression of curli and cellulose, and biofilm-forming potential. Cattle isolates were also screened for serogroup, stx₁, stx₂, eae, and rpoS. Generic E. coli isolates were compared by source (hide of carcass, hide-off carcass, and processing equipment) before and after the implementation of antimicrobial hurdles. The proportion of E. coli isolates capable of forming biofilms was lowest (7.1%; P < 0.05) for cattle isolates and highest (87.3%; P < 0.05) from equipment. Only one enterohemorrhagic E. coli (EHEC) isolate was an extremely strong biofilm former, in contrast to 73.4% of E. coli isolates from equipment. Isolates from equipment after sanitation had a greater biofilm-forming capacity (P < 0.001) than those before sanitation. Most cattle isolates were motile and expressed curli, although these traits along with the expression of cellulose and the detection of rpoS were not necessary for biofilm formation. In contrast, isolates capable of forming biofilms on equipment were almost exclusively motile and able to express curli. The results of the present study indicate that cattle rarely carry EHEC capable of making strong biofilms in slaughter plants. However, if biofilm-forming EHEC contaminates equipment, current sanitation procedures may not eliminate the most robust biofilm-forming strains. Accordingly, new and effective antibiofilm hurdles for meat-processing equipment are required to reduce future instances of foodborne disease. IMPORTANCE As the majority of enterohemorrhagic E. coli (EHEC) isolates are not capable of forming biofilms, sources were undetermined for biofilm-forming EHEC isolated from "high-event periods" in beef slaughter plants. This study demonstrated that sanitation procedures used on beef-processing equipment may inadvertently lead to the survival of robust biofilm-forming strains of E. coli. Cattle only rarely carry EHEC capable of forming strong biofilms (1/745 isolates evaluated), but isolates with greater biofilm-forming capacity were more likely (P < 0.001) to survive equipment sanitation. In contrast, chilling carcasses for 3 days at 0°C reduced (P < 0.05) the proportion of biofilm-forming E. coli. Consequently, an additional antibiofilm hurdle for meat-processing equipment, perhaps involving cold exposure, is necessary to further reduce the risk of foodborne disease.

Effects of the Quinone Oxidoreductase WrbA on Escherichia coli Biofilm Formation and Oxidative Stress

The effects of natural compounds on biofilm formation have been extensively studied, with the goal of identifying biofilm formation antagonists at sub-lethal concentrations. Salicylic and cinnamic acids are some examples of these compounds that interact with the quinone oxidoreductase WrbA, a potential biofilm modulator and an antibiofilm compound biomarker. However, WrbA’s role in biofilm development is still poorly understood. To investigate the key roles of WrbA in biofilm maturation and oxidative stress, Escherichia coli wild-type and ∆wrbA mutant strains were used. Furthermore, we reported the functional validation of WrbA as a molecular target of salicylic and cinnamic acids. The lack of WrbA did not impair planktonic growth, but rather affected the biofilm formation through a mechanism that depends on reactive oxygen species (ROS). The loss of WrbA function resulted in an ROS-sensitive phenotype that showed reductions in biofilm-dwelling cells, biofilm thickness, matrix polysaccharide content, and H₂O₂ tolerance. Endogenous oxidative events in the mutant strain generated a stressful condition to which the bacterium responded by increasing the catalase activity to compensate for the lack of WrbA. Cinnamic and salicylic acids inhibited the quinone oxidoreductase activity of purified recombinant WrbA. The effects of these antibiofilm molecules on WrbA function was proven for the first time.

Functional investigation of the chromosomal ccdAB and hipAB operon in Escherichia coli Nissle 1917

Toxin-antitoxin systems (TASs) have attracted much attention due to their important physiological functions. These small genetic factors have been widely studied mostly in commensal Escherichia coli strains, whereas the role of TASs in the probiotic E. coli Nissle 1917 (EcN) is still elusive. Here, the physiological role of chromosomally encoded type II TASs in EcN was examined. We showed that gene pair ECOLIN_00240-ECOLIN_00245 and ECOLIN_08365-ECOLIN_08370 were two functional TASs encoding CcdAB and HipAB, respectively. The homologs of CcdAB and HipAB were more conserved in E. coli species belonging to pathogenic groups, suggesting their important roles in EcN. CRISPRi-mediated repression of ccdAB and hipAB significantly reduced the biofilm formation of EcN in the stationary phase. Moreover, ccdAB and hipAB were shown to be responsible for the persister formation in EcN. Biofilm and persister formation of EcN controlled by the ccdAB and hipAB were associated with the expression of genes involved in DNA synthesis, SOS response, and stringent response. Besides, CRISPRi was proposed to be an efficient tool in annotating multiple TASs simultaneously. Collectively, our results advance knowledge and understanding of the role of TASs in EcN, which will enhance the utility of EcN in probiotic therapy.

Key points

• Two TASs in EcN were identified as hipAB and ccdAB.

• Knockdown of HipAB and CcdAB resulted in decreased biofilm formation of EcN.

• Transcriptional silencing of hipAB and ccdAB affected the persister formation of EcN.

• An attractive link between TASs and stress response was unraveled in EcN.

• CRISPRi afforded a fast and in situ annotation of multiple TASs simultaneously.

Reaction of Surrogate Escherichia coli Serotype O157:H7 and Non-O157 Strains to Nutrient Starvation: Variation in Phenotype and Transcription of Stress Response Genes and Behavior on Lettuce Plants in the Field

Preharvest contamination with bacteria borne by irrigation water may result in leafy vegetables serving as vehicles for transmission of Shiga toxin-producing Escherichia coli (STEC) to humans. The influence of starvation-associated stress on the behavior of non-toxin-producing strains of E. coli serotype O157:H7 and serotypes O26, O103, O111, and O145 was examined subsequent to their introduction to the phyllosphere of field-grown romaine lettuce as inocula simulating starved (96 h in sterile deionized water) and nutrient-depleted (24 h broth culture) cells. As with E. coli O157:H7, leaf populations of the non-O157 strains declined rapidly during the first 72 h postinoculation, displaying the biphasic decay curve typical of serotype O157:H7 isolates. Preinoculation treatment appeared not to influence decay rates greatly (P > 0.5), but strain-specific differences (persistence period and attachment proficiency) indicated that serotype O103:H2 strain PARC445 was a better survivor. Also assessed was the impact of preinoculation treatment on phenotypes key to leaf colonization and survival and the expression of starvation stress-associated genes. The 96-h starvation period enhanced biofilm formation in one strain but reduced motility and autoinducer 2 formation in all five study strains relative to those characteristics in stationary-phase cells. Transcription of rpoS, dps, uspA, and gapA was reduced significantly (P < 0.05) in starvation-stressed cells relative to that for exponential- and stationary-phase cultures. Strain-specific differences were observed; serotype O103:H2 PARC445 had greater downturns than did serotype O157:H7 and other non-O157 strains. Within this particular cohort, the behavior of the representative serotype O157:H7 strain, PARC443 (ATCC 700728), was not predictive of behavior of non-O157 members of this STEC group.

Current anti-biofilm strategies and potential of antioxidants in biofilm control

INTRODUCTION

Biofilm formation is a strategy for microorganisms to adapt and survive in hostile environments. Microorganisms that are able to produce biofilms are currently recognized as a threat to human health. Areas covered: Many strategies have been employed to eradicate biofilms, but several drawbacks from these methods had subsequently raised concerns on the need for alternative approaches to effectively prevent biofilm formation. One of the main mechanisms that drives a microorganism to transit from a planktonic to a biofilm-sessile state, is oxidative stress. Chemical agents that could target oxidative stress regulators, for instance antioxidants, could therefore be used to treat biofilm-associated infections. Expert commentary: The focus of this review is to summarize the function and limitation of the current anti-biofilm strategies and will propose the use of antioxidants as an alternative method to treat, prevent and eradicate biofilms. Studies have shown that water-soluble and lipid-soluble antioxidants can reduce and prevent biofilm formation, by influencing the expression of genes associated with oxidative stress. Further in vivo work should be conducted to ensure the efficacy of these antioxidants in a biological environment. Nevertheless, antioxidants are promising anti-biofilm agents, and thus is a potential solution for biofilm-associated infections in the future.

The alternative sigma factor RpoQ regulates colony morphology, biofilm formation and motility in the fish pathogen Aliivibrio salmonicida

Background

Quorum sensing (QS) is a cell-to cell communication system that bacteria use to synchronize activities as a group. LitR, the master regulator of QS in Aliivibrio salmonicida, was recently shown to regulate activities such as motility, rugosity and biofilm formation in a temperature dependent manner. LitR was also found to be a positive regulator of rpoQ. RpoQ is an alternative sigma factor belonging to the sigma −70 family. Alternative sigma factors direct gene transcription in response to environmental signals. In this work we have studied the role of RpoQ in biofilm formation, colony morphology and motility of A. salmonicida LFI1238.

Results

The rpoQ gene in A. salmonicida LFI1238 was deleted using allelic exchange. We found that RpoQ is a strong repressor of rugose colony morphology and biofilm formation, and that it controls motility of the bacteria. We also show that overexpression of rpoQ in a ΔlitR mutant of A. salmonicida disrupts the biofilm produced by the ΔlitR mutant and decreases its motility, whereas rpoQ overexpression in the wild-type completely eliminates the motility.

Conclusion

The present work demonstrates that the RpoQ sigma factor is a novel regulatory component involved in modulating motility, colony morphology and biofilm formation in the fish pathogen A. salmonicida. The findings also confirm that RpoQ functions downstream of the QS master regulator LitR. However further studies are needed to elucidate how LitR and RpoQ work together in controlling phenotypes related to QS in A. salmonicida.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1258-9) contains supplementary material, which is available to authorized users.

Toward a better understanding of the mechanisms of symbiosis: a comprehensive proteome map of a nascent insect symbiont

Symbiotic bacteria are common in insects and can affect various aspects of their hosts’ biology. Although the effects of insect symbionts have been clarified for various insect symbiosis models, due to the difficulty of cultivating them in vitro, there is still limited knowledge available on the molecular features that drive symbiosis. Serratia symbiotica is one of the most common symbionts found in aphids. The recent findings of free-living strains that are considered as nascent partners of aphids provide the opportunity to examine the molecular mechanisms that a symbiont can deploy at the early stages of the symbiosis (i.e., symbiotic factors). In this work, a proteomic approach was used to establish a comprehensive proteome map of the free-living S. symbiotica strain CWBI-2.3^T. Most of the 720 proteins identified are related to housekeeping or primary metabolism. Of these, 76 were identified as candidate proteins possibly promoting host colonization. Our results provide strong evidence that S. symbiotica CWBI-2.3^T is well-armed for invading insect host tissues, and suggest that certain molecular features usually harbored by pathogenic bacteria are no longer present. This comprehensive proteome map provides a series of candidate genes for further studies to understand the molecular cross-talk between insects and symbiotic bacteria.

Comparative gene expression analysis of Porphyromonas gingivalis ATCC 33277 in planktonic and biofilms states

Background and objective

Porphyromonas gingivalis is a keystone pathogen in the onset and progression of periodontitis. Its pathogenicity has been related to its presence and survival within the subgingival biofilm. The aim of the present study was to compare the genome-wide transcription activities of P. gingivalis in biofilm and in planktonic growth, using microarray technology.

Material and methods

P. gingivalis ATCC 33277 was incubated in multi-well culture plates at 37°C for 96 hours under anaerobic conditions using an in vitro static model to develop both the planktonic and biofilm states (the latter over sterile ceramic calcium hydroxyapatite discs). The biofilm development was monitored by Confocal Laser Scanning Microscopy (CLSM) and Scanning Electron Microscopy (SEM). After incubation, the bacterial cells were harvested and total RNA was extracted and purified. Three biological replicates for each cell state were independently hybridized for transcriptomic comparisons. A linear model was used for determining differentially expressed genes and reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to confirm differential expression. The filtering criteria of ≥ ±2 change in gene expression and significance p-values of <0.05 were selected.

Results

A total of 92 out of 1,909 genes (4.8%) were differentially expressed by P. gingivalis growing in biofilm compared to planktonic. The 54 up-regulated genes in biofilm growth were mainly related to cell envelope, transport, and binding or outer membranes proteins. Thirty-eight showed decreased expression, mainly genes related to transposases or oxidative stress.

Conclusion

The adaptive response of P. gingivalis in biofilm growth demonstrated a differential gene expression.

The General Stress Response σS Is Regulated by a Partner Switch in the Gram-negative Bacterium Shewanella oneidensis

Here, we show that a partner-switching system of the aquatic Proteobacterium Shewanella oneidensis regulates post-translationally σ^S (also called RpoS), the general stress response sigma factor. Genes SO2118 and SO2119 encode CrsA and CrsR, respectively. CrsR is a three-domain protein comprising a receiver, a phosphatase, and a kinase/anti-sigma domains, and CrsA is an anti-sigma antagonist. In vitro, CrsR sequesters σ^S and possesses kinase and phosphatase activities toward CrsA. In turn, dephosphorylated CrsA binds the anti-sigma domain of CrsR to allow the release of σ^S This study reveals a novel pathway that post-translationally regulates the general stress response sigma factor differently than what was described for other proteobacteria like Escherichia coli We argue that this pathway allows probably a rapid bacterial adaptation.

Links between Transcription, Environmental Adaptation and Gene Variability in Escherichia coli: Correlations between Gene Expression and Gene Variability Reflect Growth Efficiencies

Gene expression is known to be the principle factor explaining how fast genes evolve. Highly transcribed genes evolve slowly because any negative impact caused by a particular mutation is magnified by protein abundance. However, gene expression is a phenotype that depends both on the environment and on the strains or species. We studied this phenotypic plasticity by analyzing the transcriptome profiles of four Escherichia coli strains grown in three different culture media, and explored how expression variability was linked to gene allelic diversity. Genes whose expression changed according to the media and not to the strains were less polymorphic than other genes. Genes for which transcription depended predominantly on the strain were more polymorphic than other genes and were involved in sensing and responding to environmental changes, with an overrepresentation of two-component system genes. Surprisingly, we found that the correlation between transcription and gene diversity was highly variable among growth conditions and could be used to quantify growth efficiency of a strain in a medium. Genetic variability was found to increase with gene expression in poor growth conditions. As such conditions are also characterized by down-regulation of all DNA repair systems, including transcription-coupled repair, we suggest that gene expression under stressful conditions may be mutagenic and thus leads to a variability in mutation rate among genes in the genome which contributes to the pattern of protein evolution.

Mini-review: Biofilm responses to oxidative stress

Biofilms constitute the predominant microbial style of life in natural and engineered ecosystems. Facing harsh environmental conditions, microorganisms accumulate reactive oxygen species (ROS), potentially encountering a dangerous condition called oxidative stress. While high levels of oxidative stress are toxic, low levels act as a cue, triggering bacteria to activate effective scavenging mechanisms or to shift metabolic pathways. Although a complex and fragmentary picture results from current knowledge of the pathways activated in response to oxidative stress, three main responses are shown to be central: the existence of common regulators, the production of extracellular polymeric substances, and biofilm heterogeneity. An investigation into the mechanisms activated by biofilms in response to different oxidative stress levels could have important consequences from ecological and economic points of view, and could be exploited to propose alternative strategies to control microbial virulence and deterioration.

Fluorescence-based tools for single-cell approaches in food microbiology

The better understanding of the functioning of microbial communities is a challenging and crucial issue in the field of food microbiology, as it constitutes a prerequisite to the optimization of positive and technological microbial population functioning, as well as for the better control of pathogen contamination of food. Heterogeneity appears now as an intrinsic and multi-origin feature of microbial populations and is a major determinant of their beneficial or detrimental functional properties. The understanding of the molecular and cellular mechanisms behind the behavior of bacteria in microbial communities requires therefore observations at the single-cell level in order to overcome "averaging" effects inherent to traditional global approaches. Recent advances in the development of fluorescence-based approaches dedicated to single-cell analysis provide the opportunity to study microbial communities with an unprecedented level of resolution and to obtain detailed insights on the cell structure, metabolism activity, multicellular behavior and bacterial interactions in complex communities. These methods are now increasingly applied in the field of food microbiology in different areas ranging from research laboratories to industry. In this perspective, we reviewed the main fluorescence-based tools used for single-cell approaches and their concrete applications with specific focus on food microbiology.

Natural rpoS mutations contribute to population heterogeneity in Escherichia coli O157:H7 strains linked to the 2006 US spinach-associated outbreak

We previously reported significantly different acid resistance between curli variants derived from the same Escherichia coli O157:H7 strain, although the curli fimbriae were not associated with this phenotypic divergence. Here we investigated the underlying molecular mechanism by examining the genes encoding the common transcriptional regulators of curli biogenesis and acid resistance. rpoS null mutations were detected in all curli-expressing variants of the 2006 spinach-associated outbreak strains, whereas a wild-type rpoS was present in all curli-deficient variants. Consequently curli-expressing variants were much more sensitive to various stress challenges than curli-deficient variants. This loss of general stress fitness appeared solely to be the result of rpoS mutation since the stress resistances could be restored in curli-expressing variants by a functional rpoS. Comparative transcriptomic analyses between the curli variants revealed a large number of differentially expressed genes, characterized by the enhanced expression of metabolic genes in curli-expressing variants, but a marked decrease in transcription of genes related to stress resistances. Unlike the curli-expressing variants of the 1993 US hamburger-associated outbreak strains (Applied Environmental Microbiology 78: 7706-7719), all curli-expressing variants of the 2006 spinach-associated outbreak strains carry a functional rcsB gene, suggesting an alternative mechanism governing intra-strain phenotypic divergence in E. coli O157:H7.

Elucidating the function of the RpoS regulon

ABSTRACT: 

Bacterial adaptation to suboptimal nutrient environments, including host and/or extreme environments, is subject to complex, coordinated control involving many proteins and RNAs. Among the γ-proteobacteria, which includes many pathogens, the RpoS regulon has been a key focus for many years. Although the RpoS regulator was first identified as a growth phase-dependent regulator, our current understanding of RpoS is now more nuanced as this central regulator also has roles in exponential phase, biofilm development, bacterial virulence and bacterial persistence, as well as in stress adaptation. Induction of RpoS can also exert substantial metabolic effects by negatively regulating key systems including flagella biosynthesis, cryptic phage gene expression and the tricarboxylic acid cycle. Although core RpoS-controlled metabolic functions are conserved, there are substantial differences in RpoS regulation even among closely related bacteria, indicating that regulatory plasticity may be an important aspect of RpoS regulation, which is important in evolutionary adaptation to specialized environments.

Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase III modulator

Background

Ribonuclease III (RNase III) activity modulates hundreds of genes in Escherichia coli (E. coli). YmdB, a member of the macrodomain protein family, is one of known trans-acting regulators of RNase III activity; however, the significance of its regulatory role in specific bacterial cellular processes and related genes has not been determined. YmdB overexpression was used to model YmdB-induced RNase III inhibition in vivo, and microarray analysis identified gene targets and cellular processes related to RNase III inhibition.

Results

The expression of >2,000 E. coli genes was modulated by YmdB induction; 129 genes were strongly regulated, of which 80 have not been reported as RNase III targets. Of these, ten are involved in biofilm formation. Significantly, YmdB overexpression also inhibited biofilm formation via a process that is not uniquely dependent upon RNase III inhibition. Moreover, biofilm formation is interdependently regulated by RpoS, a known stress response regulator and biofilm inhibitor, and by YmdB.

Conclusions

This is the first global profile of target genes modulated by YmdB-induced RNase III inhibition in E. coli, and the data reveal a novel, hitherto unrecognized regulatory role for YmdB in biofilm modulation.

PotD protein stimulates biofilm formation by Escherichia coli

In natural environments bacteria often adopt a biofilm-growth mode. PotD is a spermidine/putrescine-binding periplasmic protein belonging to polyamine transport system and we have examined its role during biofilm formation and for planktonic growth in Escherichia coli BL21(DE3) strains that either over-express PotD (PotD+), or under-express it (PotDi) and also in a control strain with vector pET26b(+) (PotD0). The three strains displayed similar growth in planktonic growth-mode, but over expression of PotD protein greatly stimulated the formation of biofilms, while less biofilm formed by strain PotDi in comparison to strain PotD0. The expressions of five genes, recA, sfiA, groEL, groES, and gyrA, were increasingly expressed in PotD+ biofilm cells. Thus, PotD is likely to change the rate of polyamine synthesis, which stimulates the expression of SOS genes and biofilm formation.