Proteolysis of σS (RpoS) and the general stress response in Escherichia coli

Protein degradation by a component of the chaperonin-linked protease ClpP

In cells, proteins are synthesized, function, and degraded (dead). Protein synthesis (spring) is important for the life of proteins. However, how proteins die is equally important for organisms. Proteases are secreted from cells and used as nutrients to break down external proteins. Proteases degrade unwanted and harmful cellular proteins. In eukaryotes, a large enzyme complex called the proteasome is primarily responsible for cellular protein degradation. Prokaryotes, such as bacteria, have similar protein degradation systems. In this review, we describe the structure and function of the ClpXP complex in the degradation system, which is an ATP-dependent protease in bacterial cells, with a particular focus on ClpP.

The regulatory network comprising ArcAB-RpoS-RssB influences motility in Vibrio cholerae

The diarrheal disease cholera is caused by the versatile and responsive bacterium Vibrio cholerae, which is capable of adapting to environmental changes. Among others, the alternative sigma factor RpoS activates response pathways, including regulation of motility- and chemotaxis-related genes under nutrient-poor conditions in V. cholerae. Although RpoS has been well characterised, links between RpoS and other regulatory networks remain unclear. In this study, we identified the ArcAB two-component system to control rpoS transcription and RpoS protein stability in V. cholerae. In a manner similar to that seen in Escherichia coli, the ArcB kinase not only activates the response regulator ArcA but also RssB, the anti-sigma factor of RpoS. Our results demonstrated that, in V. cholerae, RssB is phosphorylated by ArcB, which subsequently activates RpoS proteolysis. Furthermore, ArcA acts as a repressor of rpoS transcription. Additionally, we determined that the cysteine residue at position 180 of ArcB is crucial for signal recognition and activity. Thus, our findings provide evidence linking RpoS response to the anoxic redox control system ArcAB in V. cholerae.

Phenolic compounds induce ferroptosis-like death by promoting hydroxyl radical generation in the Fenton reaction

Phenolic compounds are industrially versatile chemicals, also the most ubiquitous pollutants. Recently, biosynthesis and biodegradation of phenols has attracted increasing attention, while phenols' toxicity is a major issue. Here, we evolved phloroglucinol-tolerant Escherichia coli strains via adaptive evolution, and three mutations (ΔsodB, ΔclpX and fetAB overexpression) prove of great assistance in the tolerance improvement. We discover that phloroglucinol complexes with iron and promotes the generation of hydroxyl radicals in Fenton reaction, which leads to reducing power depletion, lipid peroxidation, and ferroptosis-like cell death of E. coli. Besides phloroglucinol, various phenols can trigger ferroptosis-like death in diverse organisms, from bacteria to mammalian cells. Furthermore, repressing this ferroptosis-like death improves phloroglucinol production and phenol degradation by corresponding strains respectively, showing great application potential in microbial degradation or production of desired phenolic compounds, and phloroglucinol-induced ferroptosis suppresses tumor growth in mice, indicating phloroglucinol as a promising drug for cancer treatment.

[Protein degradation in bacteria: focus on the ClpP protease]

Proteins in the cells are born (synthesized), work, and die (decomposed). In the life of a protein, its birth is obviously important, but how it dies is equally important in living organisms. Proteases secreted into the outside of cells are used to decompose the external proteins and the degradation products are taken as the nutrients. On the other hand, there are also proteases that decompose unnecessary or harmful proteins which are generated in the cells. In eukaryotes, a large enzyme complex called the proteasome is primarily responsible for degradation of such proteins. Bacteria, which are prokaryotes, have a similar system as the proteasome. We would like to explain the bacterial degradation system of proteins or the death of proteins, which is performed by ATP-dependent protease Clp, with a particular focus on the ClpXP complex, and with an aspect as a target for antibiotics against bacteria.

Broad time-dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature

In the current study, metabolic genes and networks that influence the persistence of pathogenic Escherichia coli O104:H4 strain C227/11Φcu in agricultural soil microenvironments at low temperature were investigated. The strain was incubated in alluvial loam (AL) and total RNA was prepared from samples at time point 0, and after 1 and 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes for either time point comparison. The two lists of differentially expressed genes were then subjected to gene set enrichment of Gene Ontology terms. In total, 17 GO gene sets and 3 Pfam domains were found to be enriched after 1 week. After 4 weeks, 17 GO gene sets and 7 Pfam domains were statistically enriched. Especially stress response genes and genes of the primary metabolism were particularly affected at both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment. The results of this transcriptome analysis show that persistence of C227/11Φcu in soils is associated with a complex interplay of metabolic networks.

Multicopy expression of sigma factor RpoH reduces prodigiosin biosynthesis in Serratia marcescens FS14

Regulation of prodigiosin biosynthesis is received wide attention due to the antimicrobial, immunosuppressive and anticancer activities of prodigiosin. Here, we constructed a transposon mutant library in S. marcescens FS14 to identify genes involved in the regulation of prodigiosin biosynthesis. 62 strains with apparently different colors were obtained. Identification of the transposon insertion sites revealed that they are classified into three groups: the coding region of cyaA and two component system eepS/R and the promoter region of rpoH. Since the effect of cyaA and eepS/R genes on prodigiosin was extensively investigated in Serratia marcescens, we chose the mutant of rpoH for further investigation. Further deletion mutation of rpoH gene showed no effect on prodigiosin production suggesting that the effect on prodigiosin production caused by transposon insertion is not due to the deletion of RpoH. We further demonstrated that multicopy expression of RpoH reduced prodigiosin biosynthesis indicating that transposon insertion caused RpoH enhanced expression. Previous results indicate that RpoS is the sigma factor for transcription of pig gene cluster in FS14, to test whether the enhanced expression of RpoH prevents prodigiosin by competing with RpoS, we found that multicopy expression of RpoS could alleviate the prodigiosin production inhibition by enhanced RpoH. We proposed that multicopy expressed RpoH competes with RpoS for core RNA polymerase (RNAP) resulting in decreased transcription of pig gene cluster and prodigiosin production reduction. We also demonstrated that RpoH is not directly involved in prodigiosin biosynthesis. Our results suggest that manipulating the transcription level of sigma factors may be applied to regulate the production of secondary metabolites.

Past, Present, and Future of Extracytoplasmic Function σ Factors: Distribution and Regulatory Diversity of the Third Pillar of Bacterial Signal Transduction

Responding to environmental cues is a prerequisite for survival in the microbial world. Extracytoplasmic function σ factors (ECFs) represent the third most abundant and by far the most diverse type of bacterial signal transduction. While archetypal ECFs are controlled by cognate anti-σ factors, comprehensive comparative genomics efforts have revealed a much higher abundance and regulatory diversity of ECF regulation than previously appreciated. They have also uncovered a diverse range of anti-σ factor-independent modes of controlling ECF activity, including fused regulatory domains and phosphorylation-dependent mechanisms. While our understanding of ECF diversity is comprehensive for well-represented and heavily studied bacterial phyla-such as Proteobacteria, Firmicutes, and Actinobacteria (phylum Actinomycetota)-our current knowledge about ECF-dependent signaling in the vast majority of underrepresented phyla is still far from complete. In particular, the dramatic extension of bacterial diversity in the course of metagenomic studies represents both a new challenge and an opportunity in expanding the world of ECF-dependent signal transduction.

DegS protease regulates the motility, chemotaxis, and colonization of Vibrio cholerae

In bacteria, DegS protease functions as an activating factor of the σ^E envelope stress response system, which ultimately activates the transcription of stress response genes in the cytoplasm. On the basis of high-throughput RNA sequencing, we have previously found that degS knockout inhibits the expression of flagellum synthesis- and chemotaxis-related genes, thereby indicating that DegS may be involved in the regulation of V. cholerae motility. In this study, we examined the relationships between DegS and motility in V. cholerae. Swimming motility and chemotaxis assays revealed that degS or rpoE deletion promotes a substantial reduction in the motility and chemotaxis of V. cholerae, whereas these activities were restored in ΔdegS::degS and ΔdegSΔrseA strains, indicating that DegS is partially dependent on σ^E to positively regulate V. cholerae activity. Gene-act network analysis revealed that the cAMP-CRP-RpoS signaling pathway, which plays an important role in flagellar synthesis, is significantly inhibited in ΔdegS mutants, whereas in response to the overexpression of cyaA/crp and rpoS in the ΔdegS strain, the motility and chemotaxis of the ΔdegS + cyaA/crp and ΔdegS + rpoS strains were partially restored compared with the ΔdegS strain. We further demonstrated that transcription levels of the flagellar regulatory gene flhF are regulated by DegS via the cAMP-CRP-RpoS signaling pathway. Overexpression of the flhF gene in the ΔdegS strain partially restored motility and chemotaxis. In addition, suckling mouse intestinal colonization experiments indicated that the ΔdegS and ΔrpoE strains were characterized by the poor colonization of mouse intestines, whereas colonization efficacy was restored in the ΔdegSΔrseA, ΔdegS + cyaA/crp, ΔdegS + rpoS, and ΔdegS + flhF strains. Collectively, our findings indicate that DegS regulates the motility and chemotaxis of V. cholerae via the cAMP-CRP-RpoS-FlhF pathway, thereby influencing the colonization of suckling mouse intestines.

Bacterial degrons in synthetic circuits

Bacterial proteases are a promising post-translational regulation strategy in synthetic circuits because they recognize specific amino acid degradation tags (degrons) that can be fine-tuned to modulate the degradation levels of tagged proteins. For this reason, recent efforts have been made in the search for new degrons. Here we review the up-to-date applications of degradation tags for circuit engineering in bacteria. In particular, we pay special attention to the effects of degradation bottlenecks in synthetic oscillators and introduce mathematical approaches to study queueing that enable the quantitative modelling of proteolytic queues.

Cooperative Interaction between Acid and Copper Resistance in Escherichia coli

The persistence of pathogenic Escherichia coli under acidic conditions poses a serious risk to food safety, especially in acidic foods such as kimchi. To identify the bacterial factors required for acid resistance, transcriptomic analysis was conducted on an acid-resistant enterotoxigenic E. coli strain and the genes with significant changes in their expression under acidic pH were selected as putative resistance factors against acid stress. These genes included those associated with a glutamatedependent acid resistance (GDAR) system and copper resistance. E. coli strains lacking GadA, GadB, or YbaST, the components of the GDAR system, exhibited significantly attenuated growth and survival under acidic stress conditions. Accordantly, the inhibition of the GDAR system by 3-mercaptopropionic acid and aminooxyacetic acid abolished bacterial adaptation and survival under acidic conditions, indicating the indispensable role of a GDAR system in acid resistance. Intriguingly, the lack of cueR encoding a transcriptional regulator for copper resistance genes markedly impaired bacterial resistance to acid stress as well as copper. Conversely, the absence of YbaST severely compromised bacterial resistance against copper, suggesting an interplay between acid and copper resistance. These results suggest that a GDAR system can be a promising target for developing control measures to prevent E. coli resistance to acid and copper treatments.

New Global Insights on the Regulation of the Biphasic Life Cycle and Virulence Via ClpP-Dependent Proteolysis in Legionella pneumophila

Legionella pneumophila, an environmental bacterium that parasitizes protozoa, causes Legionnaires’ disease in humans that is characterized by severe pneumonia. This bacterium adopts a distinct biphasic life cycle consisting of a nonvirulent replicative phase and a virulent transmissive phase in response to different environmental conditions. Hence, the timely and fine-tuned expression of growth and virulence factors in a life cycle–dependent manner is crucial for survival and replication. Here, we report that the completion of the biphasic life cycle and bacterial pathogenesis is greatly dependent on the protein homeostasis regulated by caseinolytic protease P (ClpP)-dependent proteolysis. We characterized the ClpP-dependent dynamic profiles of the regulatory and substrate proteins during the biphasic life cycle of L. pneumophila using proteomic approaches and discovered that ClpP-dependent proteolysis specifically and conditionally degraded the substrate proteins, thereby directly playing a regulatory role or indirectly controlling cellular events via the regulatory proteins. We further observed that ClpP-dependent proteolysis is required to monitor the abundance of fatty acid biosynthesis–related protein Lpg0102/Lpg0361/Lpg0362 and SpoT for the normal regulation of L. pneumophila differentiation. We also found that the control of the biphasic life cycle and bacterial virulence is independent. Furthermore, the ClpP-dependent proteolysis of Dot/Icm (defect in organelle trafficking/intracellular multiplication) type IVB secretion system and effector proteins at a specific phase of the life cycle is essential for bacterial pathogenesis. Therefore, our findings provide novel insights on ClpP-dependent proteolysis, which spans a broad physiological spectrum involving key metabolic pathways that regulate the transition of the biphasic life cycle and bacterial virulence of L. pneumophila, facilitating adaptation to aquatic and intracellular niches.

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ClpP is the major determinant of biphasic life cycle–dependent protein turnover.

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ClpP-dependent proteolysis monitors SpoT abundance for cellular differentiation.

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ClpP-dependent regulation of life cycle and bacterial virulence is independent.

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ClpP-dependent proteolysis of T4BSS and effector proteins is vital for virulence.

Sequence-dependent model of genes with dual σ factor preference

Escherichia coli uses σ factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single σ factor, approximately 5% of them have dual σ factor preference. The most common are those responsive to both σ⁷⁰, which controls housekeeping genes, and σ³⁸, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that 'σ⁷⁰⁺³⁸ genes' are nearly as upregulated in stationary growth as 'σ³⁸ genes'. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in σ³⁸ levels. We then propose and validate a sequence dependent model of σ⁷⁰⁺³⁸ genes, with dual sensitivity to σ³⁸ and σ⁷⁰, that is applicable in the exponential and stationary growth phases, as well in the transient period in between. We further propose a general model, applicable to other stresses and σ factor combinations. Given this, promoters controlling σ⁷⁰⁺³⁸ genes (and variants) could become important building blocks of synthetic circuits with predictable, sequence-dependent sensitivity to transitions between the exponential and stationary growth phases.

ClpX/P-Dependent Degradation of Novel Substrates in Streptococcus mutans

Regulated proteolysis is where AAA+ ATPases (ClpX, ClpC, and ClpE) are coupled to a protease subunit (ClpP) to facilitate degradation of misfolded and native regulatory proteins in the cell. The process is intricately linked to protein quality control and homeostasis and modulates several biological processes. In streptococci, regulated proteolysis is vital to various functions, including virulence expression, competence development, bacteriocin production, biofilm formation, and stress responses. Among the various Clp ATPases, ClpX is the major one that recognizes specific amino acid residues in its substrates and delivers them to the ClpP proteolytic chamber for degradation. While multiple ClpX substrates have been identified in Escherichia coli and other bacteria, little is known about the identity of these substrates in streptococci. Here, we used a preliminary proteomic analysis to identify putative ClpX substrates using Streptococcus mutans as a model organism. SMU.961 is one such putative substrate where we identified the Glu-Lue-Gln (ELQ) motif at the C terminus that is recognized by ClpX/P. We identified several other proteins, including MecA, which also harbor ELQ and are degraded by ClpX/P. This is surprising since MecA is known to be degraded by ClpC/P in Bacillus subtilis; however, ClpX/P-mediated MecA degradation is unknown. We also identified Glu and Gln as the crucial residues for ClpX recognition. Our data indicate a species and perhaps strain-specific recognition of ELQ by streptococcal ClpX/P. At present, we do not know whether this species-dependent degradation by ClpX/P is unique to S. mutans, and we are currently examining the phenomenon in other pathogenic streptococci. IMPORTANCE ClpX/P is a major intracellular proteolytic complex that is responsible for protein quality control in the cell. ClpX, an AAA+ ATPase, distinguishes the potential substrates by recognizing short motifs at the C-terminal end of proteins and delivers the substrates for degradation by ClpP protease. The identity of these ClpX substrates, which varies greatly among bacteria, is known only for a few well-studied species. Here, we used Streptococcus mutans as a model organism to identify ClpX substrates. We found that a short motif of three residues is successfully recognized by ClpX/P. Interestingly, the motif is not present at the ultimate C-terminal end; rather it is present close to the end. This result suggests that streptococcal ClpX ATPase can recognize internal motifs.

Survival of Enterohemorrhagic Escherichia coli O104:H4 Strain C227/11Φcu in Agricultural Soils Depends on rpoS and Environmental Factors

The consumption of contaminated fresh produce caused outbreaks of enterohemorrhagic (EHEC) Escherichia coli. Agricultural soil might be a reservoir for EHEC strains and represent a contamination source for edible plants. Furthermore, the application of manure as fertilizer is an important contamination route. Thus, the German fertilizer ordinance prohibits the use of manure 12 weeks before crop harvest to avoid pathogen transmission into the food chain. In this study, the survival of E. coli O104:H4 strain C227/11Φcu in soil microenvironments with either diluvial sand or alluvial loam at two temperatures was investigated for more than 12 weeks. It was analyzed whether the addition of cattle manure extends EHEC survival in these microenvironments. The experiments were additionally performed with isogenic ΔrpoS and ΔfliC deletion mutants of C227/11Φcu. The survival of C227/11Φcu was highest at 4 °C, whereas the soil type had a minor influence. The addition of cattle manure increased the survival at 22 °C. Deletion of rpoS significantly decreased the survival period under all cultivation conditions, whereas fliC deletion did not have any influence. The results of our study demonstrate that EHEC C227/11Φcu is able to survive for more than 12 weeks in soil microenvironments and that RpoS is an important determinant for survival.

Increase in SARS-CoV-2 infected biomedical waste among low middle-income countries: environmental sustainability and impact with health implications

Studies have shown that severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) is a highly infectious disease, with global deaths rising to about 360,438 as of 28 May 2020. Different countries have used various approaches such as lockdown, social distancing, maintenance of personal hygiene, and increased establishment of testing and isolation centers to manage the pandemic. Poor biomedical waste (BMW) management, treatment, and disposal techniques, especially SARS-CoV-2 infected BMW, may threaten the environmental and public health in most developing countries and, by extension, impact the economic status of individuals and the nation at large. This may increase the potential for the transmission of air/blood body fluid-borne pathogens, increase the growth of microorganisms, risk of mutagenesis, and upsurge of more virulent strain. In contrast, uncontrolled substandard burning could increase the potential spread of nosocomial infection and environmental exposure to toxic organic compounds, heavy metals, radioactive, and genotoxic bio-aerosols which might be present in the gaseous, liquid, and solid by-products. The paucity of understanding of pathophysiology and management of the SARS-CoV-2 pandemic has also necessitated the need to put in place appropriate disposal techniques to cater for the sudden increase in the global demand for personal protective equipment (PPE) and pharmaceutical drugs to manage the pandemic and to reduce the risk of preventable infection by the waste. Therefore, there is a need for adequate sensitization, awareness, and environmental monitoring of the impacts of improper handling of SARS-CoV-2 infected BMWs. Hence, this review aimed to address the issues relating to the improper management of increased SARS-CoV-2 infected BMW in low middle-income countries (LMICs).

Impact of the Resistance Responses to Stress Conditions Encountered in Food and Food Processing Environments on the Virulence and Growth Fitness of Non-Typhoidal Salmonellae

The success of Salmonella as a foodborne pathogen can probably be attributed to two major features: its remarkable genetic diversity and its extraordinary ability to adapt. Salmonella cells can survive in harsh environments, successfully compete for nutrients, and cause disease once inside the host. Furthermore, they are capable of rapidly reprogramming their metabolism, evolving in a short time from a stress-resistance mode to a growth or virulent mode, or even to express stress resistance and virulence factors at the same time if needed, thanks to a complex and fine-tuned regulatory network. It is nevertheless generally acknowledged that the development of stress resistance usually has a fitness cost for bacterial cells and that induction of stress resistance responses to certain agents can trigger changes in Salmonella virulence. In this review, we summarize and discuss current knowledge concerning the effects that the development of resistance responses to stress conditions encountered in food and food processing environments (including acid, osmotic and oxidative stress, starvation, modified atmospheres, detergents and disinfectants, chilling, heat, and non-thermal technologies) exerts on different aspects of the physiology of non-typhoidal Salmonellae, with special emphasis on virulence and growth fitness.

Role of Regulated Proteolysis in the Communication of Bacteria With the Environment

For bacteria to flourish in different niches, they need to sense signals from the environment and translate these into appropriate responses. Most bacterial signal transduction systems involve proteins that trigger the required response through the modification of gene transcription. These proteins are often produced in an inactive state that prevents their interaction with the RNA polymerase and/or the DNA in the absence of the inducing signal. Among other mechanisms, regulated proteolysis is becoming increasingly recognized as a key process in the modulation of the activity of these signal response proteins. Regulated proteolysis can either produce complete degradation or specific cleavage of the target protein, thus modifying its function. Because proteolysis is a fast process, the modulation of signaling proteins activity by this process allows for an immediate response to a given signal, which facilitates adaptation to the surrounding environment and bacterial survival. Moreover, regulated proteolysis is a fundamental process for the transmission of extracellular signals to the cytosol through the bacterial membranes. By a proteolytic mechanism known as regulated intramembrane proteolysis (RIP) transmembrane proteins are cleaved within the plane of the membrane to liberate a cytosolic domain or protein able to modify gene transcription. This allows the transmission of a signal present on one side of a membrane to the other side where the response is elicited. In this work, we review the role of regulated proteolysis in the bacterial communication with the environment through the modulation of the main bacterial signal transduction systems, namely one- and two-component systems, and alternative σ factors.

The DNA Damage Inducible SOS Response Is a Key Player in the Generation of Bacterial Persister Cells and Population Wide Tolerance

Population-wide tolerance and persisters enable susceptible bacterial cells to endure hostile environments, including antimicrobial exposure. The SOS response can play a significant role in the generation of persister cells, population-wide tolerance, and shielding. The SOS pathway is an inducible DNA damage repair system that is also pivotal for bacterial adaptation, pathogenesis, and diversification. In addition to the two key SOS regulators, LexA and RecA, some other stressors and stress responses can control SOS factors. Bacteria are exposed to DNA-damaging agents and other environmental and intracellular factors, including cigarette smoke, that trigger the SOS response at a number of sites within the host. The Escherichia coli TisB/IstR module is as yet the only known SOS-regulated toxin–antitoxin module involved in persister formation. Nevertheless, the SOS response plays a key role in the formation of biofilms that are highly recalcitrant to antimicrobials and can be abundant in persisters. Furthermore, the dynamic biofilm environment generates DNA-damaging factors that trigger the SOS response within the biofilm, fueling bacterial adaptation and diversification. This review highlights the SOS response in relation to antimicrobial recalcitrance to antimicrobials in four clinically significant species, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Mycobacterium tuberculosis.

DksA plays an essential role in regulating the virulence of Borrelia burgdorferi

The RNA polymerase-binding protein DksA, together with the alarmone nucleotides (p)ppGpp, mediates the stringent response to nutrient starvation in Borrelia burgdorferi. To date, the contribution of DksA to B. burgdorferi infection remains unknown. We report here that DksA is essential for B. burgdorferi to infect a mammalian host. dksA expression was highly induced during infection. Moreover, a dksA-deficient mutant was incapable of infecting mice. The mutant displayed growth defects when cultured in vitro and resistance to osmotic pressure was markedly reduced. These phenotypes were fully restored to those of the wild type when dksA mutation was complemented. We further showed that DksA controlled the expression of virulence-associated lipoprotein OspC, likely via the central alternative sigma factor RpoS. Synthesis of RpoS was abolished in the dksA mutant, but rpoS transcription remained unaffected. Additionally, we found that the expression of clpX, clpA, clpP, and clpP2 was significantly increased in the mutant, suggesting that DksA may post-transcriptionally regulate rpoS expression via its effect on ClpXP and/or ClpAP proteases. These combined data demonstrate that DksA regulates B. burgdorferi virulence at least partially through its influence on RpoS and OspC. This study thus elucidates that, in addition to function as a stringent response regulator, DksA promotes the transcription and/or translation of genes contributing to B. burgdorferi infectivity.

Small RNAs OmrA and OmrB promote class III flagellar gene expression by inhibiting the synthesis of anti-Sigma factor FlgM

Bacteria can move by a variety of mechanisms, the best understood being flagella-mediated motility. Flagellar genes are organized in a three-tiered cascade allowing for temporally regulated expression that involves both transcriptional and post-transcriptional control. The class I operon encodes the master regulator FlhDC that drives class II gene transcription. Class II genes include fliA and flgM, which encode the Sigma factor σ²⁸, required for class III transcription, and the anti-Sigma factor FlgM, which inhibits σ²⁸ activity, respectively. The flhDC mRNA is regulated by several small regulatory RNAs (sRNAs). Two of these, the sequence-related OmrA and OmrB RNAs, inhibit FlhD synthesis. Here, we report on a second layer of sRNA-mediated control downstream of FhlDC in the flagella pathway. By mutational analysis, we confirm that a predicted interaction between the conserved 5ʹ seed sequences of OmrA/B and the early coding sequence in flgM mRNA reduces FlgM expression. Regulation is dependent on the global RNA-binding protein Hfq. In vitro experiments support a canonical mechanism: binding of OmrA/B prevents ribosome loading and decreases FlgM protein synthesis. Simultaneous inhibition of both FlhD and FlgM synthesis by OmrA/B complicated an assessment of how regulation of FlgM alone impacts class III gene transcription. Using a combinatorial mutation strategy, we were able to uncouple these two targets and demonstrate that OmrA/B-dependent inhibition of FlgM synthesis liberates σ²⁸ to ultimately promote higher expression of the class III flagellin gene fliC.

The Temporal Expression of Global Regulator Protein CsrA Is Dually Regulated by ClpP During the Biphasic Life Cycle of Legionella pneumophila

Legionella pneumophila, an environmental bacterium that parasitizes protozoa, is the causative pathogen of Legionnaires' disease. L. pneumophila adopts a distinct biphasic life cycle that allows it to adapt to environmental conditions for survival, replication, and transmission. This cycle consists of a non-virulent replicative phase (RP) and a virulent transmissive phase (TP). Timely and fine-tuned expression of growth and virulence factors in a life cycle-dependent manner is crucial. Herein, we report evidence that CsrA, a key regulator of the switch between the RP and the TP, is dually regulated in a ClpP-dependent manner during the biphasic life cycle of L. pneumophila. First, we show that the protein level of CsrA is temporal during the life cycle and is degraded by ClpP during the TP. The ectopic expression of CsrA in a ΔclpP mutant, but not in the wild type, inhibits both the initiation of the RP in vitro and the invasiveness to Acanthamoeba castellanii, indicating that the ClpP-mediated proteolytic pathway regulates the CsrA protein level. We further show that the temporally expressed IHFB is the transcriptional inhibitor of csrA and is degraded via a ClpP-dependent manner during the RP. During the RP, the level of CsrA is increased by promoting the degradation of IHFB and reducing the degradation of the accumulated CsrA via a ClpP-dependent manner. During the TP, the level of CsrA is decreased by inhibiting the degradation of IHFB and promoting the degradation of the accumulated CsrA via a ClpP-dependent manner as well. In conclusion, our results show that the growth-stage-specific expression level of CsrA is dually regulated by ClpP-dependent proteolysis at both the transcription and protein levels during the biphasic life cycle of L. pneumophila.

Adaptation of the Alphaproteobacterium Rhodobacter sphaeroides to stationary phase

Exhaustion of nutritional resources stimulates bacterial populations to adapt their growth behaviour. General mechanisms are known to facilitate this adaptation by sensing the environmental change and coordinating gene expression. However, the existence of such mechanisms among the Alphaproteobacteria remains unclear. This study focusses on global changes in transcript levels during growth under carbon-limiting conditions in a model Alphaproteobacterium, Rhodobacter sphaeroides, a metabolically diverse organism capable of multiple modes of growth including aerobic and anaerobic respiration, anaerobic anoxygenic photosynthesis and fermentation. We identified genes that showed changed transcript levels independently of oxygen levels during the adaptation to stationary phase. We selected a subset of these genes and subjected them to mutational analysis, including genes predicted to be involved in manganese uptake, polyhydroxybutyrate production and quorum sensing and an alternative sigma factor. Although these genes have not been previously associated with the adaptation to stationary phase, we found that all were important to varying degrees. We conclude that while R. sphaeroides appears to lack a rpoS-like master regulator of stationary phase adaptation, this adaptation is nonetheless enabled through the impact of multiple genes, each responding to environmental conditions and contributing to the adaptation to stationary phase.

DNA supercoiling and transcription in bacteria: a two-way street

BACKGROUND

The processes of DNA supercoiling and transcription are interdependent because the movement of a transcription elongation complex simultaneously induces under- and overwinding of the DNA duplex and because the initiation, elongation and termination steps of transcription are all sensitive to the topological state of the DNA.

RESULTS

Policing of the local and global supercoiling of DNA by topoisomerases helps to sustain the major DNA-based transactions by eliminating barriers to the movement of transcription complexes and replisomes. Recent data from whole-genome and single-molecule studies have provided new insights into how interactions between transcription and the supercoiling of DNA influence the architecture of the chromosome and how they create cell-to-cell diversity at the level of gene expression through transcription bursting.

CONCLUSIONS

These insights into fundamental molecular processes reveal mechanisms by which bacteria can prevail in unpredictable and often hostile environments by becoming unpredictable themselves.

Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth

Mycobacterial σ^B belongs to the group II family of sigma factors, which are widely considered to transcribe genes required for stationary-phase survival and the response to stress. Here we explored the mechanism underlying the observed hypersensitivity of ΔsigB deletion mutants of Mycobacterium smegmatis, M. abscessus, and M. tuberculosis to rifampin (RIF) and uncovered an additional constitutive role of σ^B during exponential growth of mycobacteria that complements the function of the primary sigma factor, σ^A Using chromatin immunoprecipitation sequencing (ChIP-Seq), we show that during exponential phase, σ^B binds to over 200 promoter regions, including those driving expression of essential housekeeping genes, like the rRNA gene. ChIP-Seq of ectopically expressed σ^A-FLAG demonstrated that at least 61 promoter sites are recognized by both σ^A and σ^B These results together suggest that RNA polymerase holoenzymes containing either σ^A or σ^B transcribe housekeeping genes in exponentially growing mycobacteria. The RIF sensitivity of the ΔsigB mutant possibly reflects a decrease in the effective housekeeping holoenzyme pool, which results in susceptibility of the mutant to lower doses of RIF. Consistent with this model, overexpression of σ^A restores the RIF tolerance of the ΔsigB mutant to that of the wild type, concomitantly ruling out a specialized role of σ^B in RIF tolerance. Although the properties of mycobacterial σ^B parallel those of Escherichia coli σ³⁸ in its ability to transcribe a subset of housekeeping genes, σ^B presents a clear departure from the E. coli paradigm, wherein the cellular levels of σ³⁸ are tightly controlled during exponential growth, such that the transcription of housekeeping genes is initiated exclusively by a holoenzyme containing σ⁷⁰ (E.σ⁷⁰).IMPORTANCE All mycobacteria encode a group II sigma factor, σ^B, closely related to the group I principal housekeeping sigma factor, σ^A Group II sigma factors are widely believed to play specialized roles in the general stress response and stationary-phase transition in the bacteria that encode them. Contrary to this widely accepted view, we show an additional housekeeping function of σ^B that complements the function of σ^A in logarithmically growing cells. These findings implicate a novel and dynamic partnership between σ^A and σ^B in maintaining the expression of housekeeping genes in mycobacteria and can perhaps be extended to other bacterial species that possess multiple group II sigma factors.

The SOS system: A complex and tightly regulated response to DNA damage

Genomes of all living organisms are constantly threatened by endogenous and exogenous agents that challenge the chemical integrity of DNA. Most bacteria have evolved a coordinated response to DNA damage. In Escherichia coli, this inducible system is termed the SOS response. The SOS global regulatory network consists of multiple factors promoting the integrity of DNA as well as error-prone factors allowing for survival and continuous replication upon extensive DNA damage at the cost of elevated mutagenesis. Due to its mutagenic potential, the SOS response is subject to elaborate regulatory control involving not only transcriptional derepression, but also post-translational activation, and inhibition. This review summarizes current knowledge about the molecular mechanism of the SOS response induction and progression and its consequences for genome stability. Environ. Mol. Mutagen. 60:368-384, 2019. © 2018 The Authors. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.

Resonance assignments of sigma factor S binding protein Crl from Escherichia coli

During bacterial transcription, sigma (σ) factors reversibly bind to RNA polymerase (RNAP) and recognize specific promoter sequences to initiate the process. While different sigma factors are utilized under different external conditions, Sigma S (RpoS, σ^S), a stress-responding sigma factor, is activated when bacteria face external threats. σ^S, which has a much lower affinity to RNAP compared with sigma D (RpoD, σ⁷⁰), is controlled by a very complex network of regulatory factors. Crl protein, a transcriptional factor from Escherichia coli (E. coli, Ec), stimulates σ^S-dependent transcription by promoting the association of σ^S with core RNA polymerase. As an important regulator for σ^S, Crl is induced by low temperature, leading to an increased transcription rate of a subset of genes of the rpoS regulon under stress conditions or in stationary phase of growth. However, the underlying molecular mechanism for Crl/σ^S remains elusive. Here we describe the complete ¹H, ¹³C and ¹⁵N chemical shift assignments of Crl as the basis for NMR structure determination and interaction studies.

Physiological, Genetic, and Transcriptomic Analysis of Alcohol-Induced Delay of Escherichia coli Death

When Escherichia coli K-12 is inoculated into rich medium in batch culture, cells experience five phases. While the lag and logarithmic phases are mechanistically fairly well defined, the stationary phase, death phase, and long-term stationary phase are less well understood. Here, we characterize a mechanism of delaying death, a phenomenon we call the "alcohol effect," where the addition of small amounts of certain alcohols prolongs stationary phase for at least 10 days longer than in untreated conditions. We show that the stationary phase is extended when ethanol is added above a minimum threshold concentration. Once ethanol levels fall below a threshold concentration, cells enter the death phase. We also show that the effect is conferred by the addition of straight-chain alcohols 1-propanol, 1-butanol, 1-pentanol, and, to a lesser degree, 1-hexanol. However, methanol, isopropanol, 1-heptanol, and 1-octanol do not delay entry into death phase. Though modulated by RpoS, the alcohol effect does not require RpoS activity or the activities of the AdhE or AdhP alcohol dehydrogenases. Further, we show that ethanol is capable of extending the life span of stationary-phase cultures for non-K-12 E. coli strains and that this effect is caused in part by genes of the glycolate degradation pathway. These data suggest a model where ethanol and other shorter 1-alcohols can serve as signaling molecules, perhaps by modulating patterns of gene expression that normally regulate the transition from stationary phase to death phase.IMPORTANCE In one of the most well-studied organisms in the life sciences, Escherichia coli, we still do not fully understand what causes populations to die. This is largely due to the technological difficulties of studying bacterial cell death. This study provides an avenue to studying how and why E. coli populations, and perhaps other microbes, transition from stationary phase to death phase by exploring how ethanol and other alcohols delay the onset of death. Here, we demonstrate that alcohols are acting as signaling molecules to achieve the delay in death phase. This study not only offers a better understanding of a fundamental process but perhaps also provides a gateway to studying the dynamics between ethanol and microbes in the human gastrointestinal tract.

Early Response of Sulfolobus acidocaldarius to Nutrient Limitation

In natural environments microorganisms encounter extreme changes in temperature, pH, osmolarities and nutrient availability. The stress response of many bacterial species has been described in detail, however, knowledge in Archaea is limited. Here, we describe the cellular response triggered by nutrient limitation in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. We measured changes in gene transcription and protein abundance upon nutrient depletion up to 4 h after initiation of nutrient depletion. Transcript levels of 1118 of 2223 protein coding genes and abundance of approximately 500 proteins with functions in almost all cellular processes were affected by nutrient depletion. Our study reveals a significant rerouting of the metabolism with respect to degradation of internal as well as extracellular-bound organic carbon and degradation of proteins. Moreover, changes in membrane lipid composition were observed in order to access alternative sources of energy and to maintain pH homeostasis. At transcript level, the cellular response to nutrient depletion in S. acidocaldarius seems to be controlled by the general transcription factors TFB2 and TFEβ. In addition, ribosome biogenesis is reduced, while an increased protein degradation is accompanied with a loss of protein quality control. This study provides first insights into the early cellular response of Sulfolobus to organic carbon and organic nitrogen depletion.

Enteropathogens: Tuning Their Gene Expression for Hassle-Free Survival

Enteropathogenic bacteria have been the cause of the majority of foodborne illnesses. Much of the research has been focused on elucidating the mechanisms by which these pathogens evade the host immune system. One of the ways in which they achieve the successful establishment of a niche in the gut microenvironment and survive is by a chain of elegantly regulated gene expression patterns. Studies have shown that this process is very elaborate and is also regulated by several factors. Pathogens like, enteropathogenic Escherichia coli (EPEC), Salmonella Typhimurium, Shigellaflexneri, Yersinia sp. have been seen to employ various regulated gene expression strategies. These include toxin-antitoxin systems, quorum sensing systems, expression controlled by nucleoid-associated proteins (NAPs), several regulons and operons specific to these pathogens. In the following review, we have tried to discuss the common gene regulatory systems of enteropathogenic bacteria as well as pathogen-specific regulatory mechanisms.

ATP reduction by MgtC and Mg2+ homeostasis by MgtA and MgtB enables Salmonella to accumulate RpoS upon low cytoplasmic Mg2+ stress

RpoS is one of several alternative sigma factors known to alter gene expression profiles by RpoS-associated RNA polymerase in response to a variety of stresses. The enteric bacteria Salmonella enterica and Escherichia coli accumulate RpoS under low Mg²⁺ concentrations via a common mechanism in which the PhoP regulator activates expression of antiadaptor proteins that, by sequestering the adaptor RssB, prevent RpoS degradation by the protease ClpXP. Here, we demonstrate that this genetic program alone does not fully support RpoS accumulation when cytoplasmic Mg²⁺ concentration drops to levels that impair protein synthesis. Under these circumstances, only S. enterica continues RpoS accumulation in a manner dependent on other PhoP-activated programs (i.e. ATP reduction by the MgtC protein and Mg²⁺ import by the MgtA and MgtB transporters) that maintain translation homeostasis. Moreover, we provide evidence that the mgtC gene, which is present in S. enterica but not in E. coli, is responsible for the differences in RpoS accumulation between these two bacterial species. Our results suggest that bacteria possess a mechanism to control RpoS accumulation responding to cytoplasmic Mg²⁺ levels, the difference of which causes distinct RpoS accumulation in closely related bacterial species.

Regulated Proteolysis in Bacteria

Regulated proteolysis is a vital process that affects all living things. Bacteria use energy-dependent AAA+ proteases to power degradation of misfolded and native regulatory proteins. Given that proteolysis is an irreversible event, specificity and selectivity in degrading substrates are key. Specificity is often augmented through the use of adaptors that modify the inherent specificity of the proteolytic machinery. Regulated protein degradation is intricately linked to quality control, cell-cycle progression, and physiological transitions. In this review, we highlight recent work that has shed light on our understanding of regulated proteolysis in bacteria. We discuss the role AAA+ proteases play during balanced growth as well as how these proteases are deployed during changes in growth. We present examples of how protease selectivity can be controlled in increasingly complex ways. Finally, we describe how coupling a core recognition determinant to one or more modifying agents is a general theme for regulated protein degradation.

Transfer RNA instability as a stress response in Escherichia coli: Rapid dynamics of the tRNA pool as a function of demand

Production of the translation apparatus of E. coli is carefully matched to the demand for protein synthesis posed by a given growth condition. For example, the fraction of RNA polymerases that transcribe rRNA and tRNA drops from 80% during rapid growth to 24% within minutes of a sudden amino acid starvation. We recently reported in Nucleic Acids Research that the tRNA pool is more dynamically regulated than previously thought. In addition to the regulation at the level of synthesis, we found that tRNAs are subject to demand-based regulation at the level of their degradation. In this point-of-view article we address the question of why this phenomenon has not previously been described. We also present data that expands on the mechanism of tRNA degradation, and we discuss the possible implications of tRNA instability for the ability of E. coli to cope with stresses that affect the translation process.

Regulation of σ factors by conserved partner switches controlled by divergent signalling systems

Partner-Switching Systems (PSS) are widespread regulatory systems, each comprising a kinase-anti-σ, a phosphorylatable anti-σ antagonist and a phosphatase module. The anti-σ domain quickly sequesters or delivers the target σ factor according to the phosphorylation state of the anti-σ antagonist induced by environmental signals. The PSS components are proteins alone or merged to other domains probably to adapt to the input signals. PSS are involved in major cellular processes including stress response, sporulation, biofilm formation and pathogenesis. Surprisingly, the target σ factors are often unknown and the sensing modules acting upstream from the PSS diverge according to the bacterial species. Indeed, they belong to either two-component systems or complex pathways as the stressosome or Chemosensory Systems (CS). Based on a phylogenetic analysis, we propose that the sensing module in Gram-negative bacteria is often a CS.

Evolutionary Remodeling of Bacterial Motility Checkpoint Control

Regulatory networks play a central role in the relationship between genotype and phenotype in all organisms. However, the mechanisms that underpin the evolutionary plasticity of these networks remain poorly understood. Here, we used experimental selection for enhanced bacterial motility in a porous environment to explore the adaptability of one of the most complex networks known in bacteria. We found that the resulting phenotypic changes are mediated by adaptive mutations in several functionally different proteins, including multiple components of the flagellar motor. Nevertheless, this evolutionary adaptation could be explained by a single mechanism, namely remodeling of the checkpoint regulating flagellar gene expression. Supported by computer simulations, our findings suggest that the specific “bow-tie” topology of the checkpoint facilitates evolutionary tuning of the cost-benefit trade-off between motility and growth. We propose that bow-tie regulatory motifs, which are widespread in cellular networks, play a general role in evolutionary adaptation.

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Multiple mutations enhance swimming behavior under selection

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A universal trade-off relationship between motility and growth is observed

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Checkpoint remodeling provides a mechanism of evolutionary adaptation

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Bow-tie topology facilitates evolvability of the motility network

Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli

Here, we investigated novel interactions of three global regulators of the network that controls biofilm formation in the model bacterium Escherichia coli using computational network analysis, an in vivo reporter assay and physiological validation experiments. We were able to map critical nodes that govern planktonic to biofilm transition and identify 8 new regulatory interactions for CRP, IHF or Fis responsible for the control of the promoters of rpoS, rpoE, flhD, fliA, csgD and yeaJ. Additionally, an in vivo promoter reporter assay and motility analysis revealed a key role for IHF as a repressor of cell motility through the control of FliA sigma factor expression. This investigation of first stage and mature biofilm formation indicates that biofilm structure is strongly affected by IHF and Fis, while CRP seems to provide a fine-tuning mechanism. Taken together, the analysis presented here shows the utility of combining computational and experimental approaches to generate a deeper understanding of the biofilm formation process in bacteria.

Osmosensing by the bacterial PhoQ/PhoP two-component system

The PhoQ/PhoP two-component system plays an essential role in the response of enterobacteria to the environment of their mammalian hosts. It is known to sense several stimuli that are potentially associated with the host, including extracellular magnesium limitation, low pH, and the presence of cationic antimicrobial peptides. Here, we show that the PhoQ/PhoP two-component systems of Escherichia coli and Salmonella can also perceive an osmotic upshift, another key stimulus to which bacteria become exposed within the host. In contrast to most previously established stimuli of PhoQ, the detection of osmotic upshift does not require its periplasmic sensor domain. Instead, we show that the activity of PhoQ is affected by the length of the transmembrane (TM) helix as well as by membrane lateral pressure. We therefore propose that osmosensing relies on a conformational change within the TM domain of PhoQ induced by a perturbation in cell membrane thickness and lateral pressure under hyperosmotic conditions. Furthermore, the response mediated by the PhoQ/PhoP two-component system was found to improve bacterial growth recovery under hyperosmotic stress, partly through stabilization of the sigma factor RpoS. Our findings directly link the PhoQ/PhoP two-component system to bacterial osmosensing, suggesting that this system can mediate a concerted response to most of the established host-related cues.

Backbone resonance assignments of the Escherichia coli 62 kDa protein, Hsp31

Dimeric Hsp31 protein was first characterized as a holding chaperone of Escherichia coli (E. coli), and has been suggested as having protease activity due to the presence of a potential catalytic triad, Cys185, His186, and Asp214. However, it has recently been reported that Hsp31 displays a relatively strong glyoxalase III activity that can decompose reactive carbonyl species (methylglyoxal and glyoxal) in the absence of additional cofactor. Hsp31 is a representative member of the DJ-1/ThiJ/PfpI protein superfamily, and the importance of DJ-1 protein in Parkinson's disease has been well known. The structural flexibility of the long loop region, which encompasses from the P- to the A-domain, is important for the chaperone activity of Hsp31. The backbone chemical shifts (CSs) would be useful for studying the structural changes of Hsp31 that are critical for the holding chaperone activity, and also for deciphering the switching mechanism between the glyoxalase III and the chaperone. Here, we report the backbone CSs (H^N, N, CO, C_α, and C_β) of the deuterated Hsp31 protein (62 kDa). The CS analysis showed that the predicted regions of secondary structures are in good agreement with those observed in the previous crystal structure of Hsp31.

Protection of the general stress response σS factor by the CrsR regulator allows a rapid and efficient adaptation of Shewanella oneidensis

To cope with environmental stresses, bacteria have evolved various strategies, including the general stress response (GSR). GSR is governed by an alternative transcriptional σ factor named σ^S (RpoS) that associates with RNA polymerase and controls the expression of numerous genes. Previously, we have reported that posttranslational regulation of σ^S in the aquatic bacterium Shewanella oneidensis involves the CrsR-CrsA partner-switching regulatory system, but the exact mechanism by which CrsR and CrsA control σ^S activity is not completely unveiled. Here, using a translational gene fusion, we show that CrsR sequesters and protects σ^S during the exponential growth phase and thus enables rapid gene activation by σ^S as soon as the cells enter early stationary phase. We further demonstrate by an in vitro approach that this protection is mediated by the anti-σ domain of CrsR. Structure-based alignments of CsrR orthologs and other anti-σ factors identified a CsrR-specific region characteristic of a new family of anti-σ factors. We found that CrsR is conserved in many aquatic proteobacteria, and most of the time it is associated with CrsA. In conclusion, our results suggest that CsrR-mediated protection of σ^S during exponential growth enables rapid adaptation of S. oneidensis to changing and stressful growth conditions, and this ability is probably widespread among aquatic proteobacteria.

Functional Diversity of AAA+ Protease Complexes in Bacillus subtilis

Here, we review the diverse roles and functions of AAA+ protease complexes in protein homeostasis, control of stress response and cellular development pathways by regulatory and general proteolysis in the Gram-positive model organism Bacillus subtilis. We discuss in detail the intricate involvement of AAA+ protein complexes in controlling sporulation, the heat shock response and the role of adaptor proteins in these processes. The investigation of these protein complexes and their adaptor proteins has revealed their relevance for Gram-positive pathogens and their potential as targets for new antibiotics.

The regulatory significance of tag recycling in the mycobacterial Pup-proteasome system

Pup, a ubiquitin analog, tags proteins for degradation by the bacterial proteasome. As an intracellular proteolytic system, the Pup-proteasome system (PPS) must be carefully regulated to prevent excessive protein degradation. Currently, those factors underlying PPS regulation remain poorly understood. Here, experimental analysis combined with theoretical modeling of in vivo protein pupylation revealed how the basic PPS design allows stable and controlled protein pupylation. Specifically, the recycling of Pup when targets are degraded allows the PPS to maintain steady-state levels of protein pupylation and degradation at a rate limited by proteasome function, and at a pupylome level limited by Pup concentrations. This design allows the Pup-ligase, a highly promiscuous enzyme, to act in a controlled manner without causing damage, and the PPS to be effectively tuned to control protein degradation. This study thus provides understanding of how the inherent design of an intracellular proteolytic system serves crucial regulatory purposes.

Hydrophobicity of Residue 128 of the Stress-Inducible Sigma Factor RpoS Is Critical for Its Activity

RpoS is a key stress-inducible sigma factor that regulates stress resistance genes in Escherichia coli, such as the katE gene encoding catalase HPII and the glg genes encoding glycogen synthesis proteins. Monitoring RpoS activity can provide information on the stress sensitivity of E. coli isolates in clinical settings because the RpoS in these isolates is often mutated. In the present study, we found a novel, missense point mutation at RpoS residue 128 in a clinical Shiga toxin-producing E. coli (STEC) isolate. This mutation caused RpoS dysfunction and increased stress sensitivity. A mutant rpoS was cloned from a clinical STEC that is vulnerable to cold temperature and oxidative stresses. Mutant RpoS protein expression was detected in the clinical isolate, and this RpoS was non-functional according to HPII activity and glycogen levels, which are positively regulated by RpoS and thus are used as indicators for RpoS function. A reporter assay with β-galactosidase indicated that the dysfunction occurred at the transcriptional level of genes regulated by RpoS. Furthermore, substitution analysis indicated that the hydrophobicity of the amino acid at residue 128 was critical for RpoS activity; the simulation analysis indicated that the amino acids of RNA polymerase (RNAP) that interact with RpoS residue 128 are hydrophobic, suggesting that this hydrophobic interaction is critical for RpoS activity. In addition, substitution of Ile128 to Pro128 abolished RpoS activity, possibly as a result of disruption of the secondsary structure around residue 128, indicating that the structure is also a crucial factor for RpoS activity. These results indicate that only one point mutation at a hydrophobic residue of the complex formed during transcription leads to a critical change in RpoS regulation. Moreover, we found that Ile128 is widely conserved among various bacteria: several bacterial strains have Met128 or Leu128, which are hydrophobic residues, and these strains had similar or higher RpoS activity than that observed with Ile128 in this study. These data indicate that the hydrophobicity of the amino acid at residue 128 is critical for RpoS activity and is consequently important for bacterial survival. Taken together, these findings may contribute to a deeper understanding of protein functional mechanisms and bacterial stress responses.

Tail-Anchored Inner Membrane Protein ElaB Increases Resistance to Stress While Reducing Persistence in Escherichia coli

Host-associated bacteria, such as Escherichia coli, often encounter various host-related stresses, such as nutritional deprivation, oxidative stress, and temperature shifts. There is growing interest in searching for small endogenous proteins that mediate stress responses. Here, we characterized the small C-tail-anchored inner membrane protein ElaB in E. coli ElaB belongs to a class of tail-anchored inner membrane proteins with a C-terminal transmembrane domain but lacking an N-terminal signal sequence for membrane targeting. Proteins from this family have been shown to play vital roles, such as in membrane trafficking and apoptosis, in eukaryotes; however, their role in prokaryotes is largely unexplored. Here, we found that the transcription of elaB is induced in the stationary phase in E. coli and stationary-phase sigma factor RpoS regulates elaB transcription by binding to the promoter of elaB Moreover, ElaB protects cells against oxidative stress and heat shock stress. However, unlike membrane peptide toxins TisB and GhoT, ElaB does not lead to cell death, and the deletion of elaB greatly increases persister cell formation. Therefore, we demonstrate that disruption of C-tail-anchored inner membrane proteins can reduce stress resistance; it can also lead to deleterious effects, such as increased persistence, in E. coliIMPORTANCEEscherichia coli synthesizes dozens of poorly understood small membrane proteins containing a predicted transmembrane domain. In this study, we characterized the function of the C-tail-anchored inner membrane protein ElaB in E. coli ElaB increases resistance to oxidative stress and heat stress, while inactivation of ElaB leads to high persister cell formation. We also demonstrated that the transcription of elaB is under the direct regulation of stationary-phase sigma factor RpoS. Thus, our study reveals that small inner membrane proteins may have important cellular roles during the stress response.

Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12

The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcriptional responses remains unclear. We investigated the effect of RpoS concentration on the transcriptome during stationary phase in rich media. We found that 23% of genes in the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed genes and promoters. We observed three distinct classes of response to RpoS by genes in the regulon: genes whose expression changes linearly with increasing RpoS level, genes whose expression changes dramatically with the production of only a little RpoS ("sensitive" genes), and genes whose expression changes very little with the production of a little RpoS ("insensitive"). We show that sequences outside the core promoter region determine whether an RpoS-regulated gene is sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes and that the sensitivity of a gene to RpoS corresponds to the timing of induction as cells enter stationary phase. Thus, promoter sensitivity to RpoS is a mechanism to coordinate specific cellular processes with growth phase and may also contribute to the diversity of stress responses directed by RpoS.IMPORTANCE The sigma factor RpoS is a global regulator that controls the response to many stresses in Escherichia coli Different stresses result in different levels of RpoS production, but the consequences of this variation are unknown. We describe how changing the level of RpoS does not influence all RpoS-regulated genes equally. The cause of this variation is likely the action of transcription factors that bind the promoters of the genes. We show that the sensitivity of a gene to RpoS levels explains the timing of expression as cells enter stationary phase and that genes with different RpoS sensitivities are enriched for specific functional groups. Thus, promoter sensitivity to RpoS is a mechanism that coordinates specific cellular processes in response to stresses.

Stringent factor and proteolysis control of sigma factor RpoS expression in Vibrio cholerae

Vibrio cholerae can colonize the gastrointestinal track of humans and cause the disease cholera. During colonization, the alternative sigma factor, RpoS, controls a process known as "mucosal escape response," defining a specific spatial and temporal response and effecting chemotaxis and motility. In this report, the expression and proteolytic control of RpoS in V. cholerae was characterized. To date, aspects of proteolysis control, the involved components, and proteolysis regulation have not been addressed for RpoS in V. cholerae. Similar to Escherichia coli, we find that the RpoS protein is subjected to regulated intracellular proteolysis, which is mediated by homologues of the proteolysis-targeting factor RssB and the protease complex ClpXP. As demonstrated, RpoS expression transiently peaks after cells are shifted from rich to minimal growth medium. This peak level is dependent on (p)ppGpp-activated rpoS transcription and controlled RpoS proteolysis. The RpoS peak level also correlates with induction of a chemotaxis gene, encoding a methyl-accepting chemotaxis protein, earlier identified to belong to the mucosal escape response pathway. These results suggest that the RpoS expression peak is linked to (p)ppGpp alarmone increase, leading to enhanced motility and chemotaxis, and possibly contributing to the mucosal escape response.

Transcriptomic Analysis of Laribacter hongkongensis Reveals Adaptive Response Coupled with Temperature

Bacterial adaptation to different hosts requires transcriptomic alteration in response to the environmental conditions. Laribacter hongkongensis is a gram-negative, facultative anaerobic, urease-positive bacillus caused infections in liver cirrhosis patients and community-acquired gastroenteritis. It was also found in intestine from commonly consumed freshwater fishes and drinking water reservoirs. Since L. hongkongensis could survive as either fish or human pathogens, their survival mechanisms in two different habitats should be temperature-regulated and highly complex. Therefore, we performed transcriptomic analysis of L. hongkongensis at body temperatures of fish and human in order to elucidate the versatile adaptation mechanisms coupled with the temperatures. We identified numerous novel temperature-induced pathways involved in host pathogenesis, in addition to the shift of metabolic equilibriums and overexpression of stress-related proteins. Moreover, these pathways form a network that can be activated at a particular temperature, and change the physiology of the bacteria to adapt to the environments. In summary, the dynamic of transcriptomes in L. hongkongensis provides versatile strategies for the bacterial survival at different habitats and this alteration prepares the bacterium for the challenge of host immunity.

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.

Antibiotics and iron-limiting conditions and their effect on the production and composition of outer membrane vesicles secreted from clinical isolates of extraintestinal pathogenic E. coli

PURPOSE

The focus of this study was to characterize the effect of clinically relevant stress-inducing conditions on the production and composition of proinflammatory outer membrane vesicles (OMVs) produced from ST131 extraintestinal pathogenic Escherichia coli (ExPEC) clinical isolates.

EXPERIMENTAL DESIGN

A label-free method (relative normalized spectral index quantification, SINQ) was used to identify changes in the respective OMV proteomes following exposure of the ExPEC strains to antibiotics and low iron. Nanoparticle tracking analysis was used to quantify changes in abundance and size of OMVs produced by the gentamicin-resistant (GenR) and gentamicin-sensitive (GenS) ExPEC strains.

RESULTS

Up to a 13.1-fold increase in abundance of particles were detected when the gentamicin-sensitive strain was exposed to a range of gentamicin concentrations. In contrast, no increase was observed for the gentamicin-resistant strain. Iron-limiting conditions had minimal effect on OMV production for either strain. Marked changes in the OMV proteome were observed for both strains including increases in Hsp100/Clp proteins, ATP-dependent ClpP protease, and regulatory proteins.

CONCLUSION

These data provide information on changes in the composition of OMV particles derived from ExPEC strains generated in response to clinically relevant conditions. We show that the levels of the proinflammatory OMVs increase for gentamicin-sensitive ExPEC exposed to the antibiotic.