ExsA and LcrF recognize similar consensus binding sites, but differences in their oligomeric state influence interactions with promoter DNA

Pathogenicity and virulence of Yersinia

The genus Yersinia includes human, animal, insect, and plant pathogens as well as many symbionts and harmless bacteria. Within this genus are Yersinia enterocolitica and the Yersinia pseudotuberculosis complex, with four human pathogenic species that are highly related at the genomic level including the causative agent of plague, Yersinia pestis. Extensive laboratory, field work, and clinical research have been conducted to understand the underlying pathogenesis and zoonotic transmission of these pathogens. There are presently more than 500 whole genome sequences from which an evolutionary footprint can be developed that details shared and unique virulence properties. Whereas the virulence of Y. pestis now seems in apparent homoeostasis within its flea transmission cycle, substantial evolutionary changes that affect transmission and disease severity continue to ndergo apparent selective pressure within the other Yersiniae that cause intestinal diseases. In this review, we will summarize the present understanding of the virulence and pathogenesis of Yersinia, highlighting shared mechanisms of virulence and the differences that determine the infection niche and disease severity.

The Psychrotrophic Pseudomonas lundensis, a Non-aeruginosa Pseudomonad, Has a Type III Secretion System of the Ysc Family, Which Is Transcriptionally Active at 37°C

The type III secretion system (T3SS) is a needle-like structure found in Gram-negative pathogens that directly delivers virulence factors like toxins and effector molecules into eukaryotic cells. The T3SS is classified into different families according to the type of effector and host. Of these, the Ysc family T3SS, found in Yersinia species and Pseudomonas aeruginosa, confers high virulence to bacteria against eukaryotic hosts. Here, we present the first identification and transcriptional analyses of a Ysc T3SS in a non-aeruginosaPseudomonas species, Pseudomonas lundensis, an environmental psychrotrophic bacterium and important agent of frozen food spoilage. We have identified and sequenced isolates of P. lundensis from three very distinct ecological niches (Antarctic temporary meltwater pond, U.S. supermarket 1% pasteurized milk, and cystic fibrosis lungs) and compared these to previously reported food spoilage isolates in Europe. In this paper, we show that strains of P. lundensis isolated from these diverse environments with ambient temperatures ranging from below freezing to 37°C all possess a Ysc family T3SS secretion system and a T3S effector, ExoU. Using in vitro and in vivo transcriptomics, we show that the T3SS in P. lundensis is transcriptionally active, is expressed more highly at mammalian body temperature (37°C) than 4°C, and has even higher expression levels when colonizing a host environment (mouse intestine). Thus, this Ysc T3SS-expressing psychrotrophic Pseudomonad has an even greater range of growth niches than previously appreciated, including diseased human airways.

Characterization of the binding motif for the T3SS master regulator LcrF in Yersinia pseudotuberculosis

LcrF is the master regulator that positively regulates the Ysc type III secretion system (T3SS) in Yersinia and shares a high similarity with the DNA-binding domain of the T3SS master regulator ExsA in Pseudomonas aeruginosa. Based on these features, bioinformatics analysis has predicted a putative LcrF-binding site in its target promoters. Here, we experimentally characterized its binding motif. An adenine-rich LcrF-binding region in the lcrG promoter sequence, a typical regulatory target of LcrF, was first confirmed. To obtain detailed information, this binding region was cloned into a synthetized promoter and mutations in this region were further constructed. We demonstrated that the 5'-AAAAA-n5-GnCT-3' sequence is required for LcrF regulation and this motif is strictly located 4-bp upstream of a noncanonical promoter, in which the -35 and -10 elements are separated by a 21-bp spacer. Consistently, the putative binding motif was found in promoters of nine T3SS related operons or genes positively regulated by LcrF. Transcriptome analysis further confirmed that LcrF specifically activates T3SS genes in Yersinia. Collectively, our data suggest that LcrF has evolved to be a specific T3SS activator with a stringent sequence requirement for transcriptional regulation.

T3SEpp: an Integrated Prediction Pipeline for Bacterial Type III Secreted Effectors

Many Gram-negative bacteria infect hosts and cause diseases by translocating a variety of type III secreted effectors (T3SEs) into the host cell cytoplasm. However, despite a dramatic increase in the number of available whole-genome sequences, it remains challenging for accurate prediction of T3SEs. Traditional prediction models have focused on atypical sequence features buried in the N-terminal peptides of T3SEs, but unfortunately, these models have had high false-positive rates. In this research, we integrated promoter information along with characteristic protein features for signal regions, chaperone-binding domains, and effector domains for T3SE prediction. Machine learning algorithms, including deep learning, were adopted to predict the atypical features mainly buried in signal sequences of T3SEs, followed by development of a voting-based ensemble model integrating the individual prediction results. We assembled this into a unified T3SE prediction pipeline, T3SEpp, which integrated the results of individual modules, resulting in high accuracy (i.e., ∼0.94) and >1-fold reduction in the false-positive rate compared to that of state-of-the-art software tools. The T3SEpp pipeline and sequence features observed here will facilitate the accurate identification of new T3SEs, with numerous benefits for future studies on host-pathogen interactions.IMPORTANCE Type III secreted effector (T3SE) prediction remains a big computational challenge. In practical applications, current software tools often suffer problems of high false-positive rates. One of the causal factors could be the relatively unitary type of biological features used for the design and training of the models. In this research, we made a comprehensive survey on the sequence-based features of T3SEs, including signal sequences, chaperone-binding domains, effector domains, and transcription factor binding promoter sites, and assembled a unified prediction pipeline integrating multi-aspect biological features within homology-based and multiple machine learning models. To our knowledge, we have compiled the most comprehensive biological sequence feature analysis for T3SEs in this research. The T3SEpp pipeline integrating the variety of features and assembling different models showed high accuracy, which should facilitate more accurate identification of T3SEs in new and existing bacterial whole-genome sequences.

Transcriptional and Post-transcriptional Regulatory Mechanisms Controlling Type III Secretion

Type III secretion systems (T3SSs) are utilized by numerous Gram-negative bacteria to efficiently interact with host cells and manipulate their function. Appropriate expression of type III secretion genes is achieved through the integration of multiple control elements and regulatory pathways that ultimately coordinate the activity of a central transcriptional activator usually belonging to the AraC/XylS family. Although several regulatory elements are conserved between different species and families, each pathogen uses a unique set of control factors and mechanisms to adjust and optimize T3SS gene expression to the need and lifestyle of the pathogen. This is reflected by the complex set of sensory systems and diverse transcriptional, post-transcriptional and post-translational control strategies modulating T3SS expression in response to environmental and intrinsic cues. Whereas some pathways regulate solely the T3SS, others coordinately control expression of one or multiple T3SSs together with other virulence factors and fitness traits on a global scale. Over the past years, several common regulatory themes emerged, e.g., environmental control by two-component systems and carbon metabolism regulators or coupling of T3SS induction with host cell contact/translocon-effector secretion. One of the remaining challenges is to resolve the understudied post-transcriptional regulation of T3SS and the dynamics of the control process.

BfvR, an AraC-Family Regulator, Controls Biofilm Formation and pH6 Antigen Production in Opposite Ways in Yersinia pestis Biovar Microtus

Biofilm formation is critical for blocking flea foregut and hence for transmission of Y. pestis by flea biting. In this study, we identified the regulatory role of the AraC-family transcriptional regulator BfvR (YPO1737 in strain CO92) in biofilm formation and virulence of Yersinia pestis biovar Microtus. Crystal violet staining, Caenorhabditis elegans biofilm assay, colony morphology assay, intracellular c-di-GMP concentration determination, and BALB/c mice challenge were employed to reveal that BfvR enhanced Y. pestis biofilm formation while repressed its virulence in mice. Further molecular biological assays demonstrated that BfvR directly stimulated the expression of hmsHFRS, waaAE-coaD, and hmsCDE, which, in turn, affected the production of exopolysaccharide, LPS, and c-di-GMP, respectively. In addition, BfvR directly and indirectly repressed psaABC and psaEF transcription, respectively. We concluded that the modulation of biofilm- and virulence-related genes by BfvR led to increased biofilm formation and reduced virulence of Y. pestis biovar Microtus.

The Transcriptional Regulator HlyU Positively Regulates Expression of exsA, Leading to Type III Secretion System 1 Activation in Vibrio parahaemolyticus

Vibrio parahaemolyticus is a marine bacterium that is globally recognized as the leading cause of seafood-borne gastroenteritis. V. parahaemolyticus uses various toxins and two type 3 secretion systems (T3SS-1 and T3SS-2) to subvert host cells during infection. We previously determined that V. parahaemolyticus T3SS-1 activity is upregulated by increasing the expression level of the master regulator ExsA under specific growth conditions. In this study, we set out to identify V. parahaemolyticus genes responsible for linking environmental and growth signals to exsA gene expression. Using transposon mutagenesis in combination with a sensitive and quantitative luminescence screen, we identify HlyU and H-NS as two antagonistic regulatory proteins controlling the expression of exsA and, hence, T3SS-1 in V. parahaemolyticus Disruption of hns leads to constitutive unregulated exsA gene expression, consistent with its known role in repressing exsA transcription. In contrast, genetic disruption of hlyU completely abrogated exsA expression and T3SS-1 activity. A V. parahaemolyticushlyU null mutant was significantly deficient for T3SS-1-mediated host cell death during in vitro infection. DNA footprinting studies with purified HlyU revealed a 56-bp protected DNA region within the exsA promoter that contains an inverted repeat sequence. Genetic evidence suggests that HlyU acts as a derepressor, likely by displacing H-NS from the exsA promoter, leading to exsA gene expression and appropriately regulated T3SS-1 activity. Overall, the data implicate HlyU as a critical positive regulator of V. parahaemolyticus T3SS-1-mediated pathogenesis.IMPORTANCE Many Vibrio species are zoonotic pathogens, infecting both animals and humans, resulting in significant morbidity and, in extreme cases, mortality. While many Vibrio species virulence genes are known, their associated regulation is often modestly understood. We set out to identify genetic factors of V. parahaemolyticus that are involved in activating exsA gene expression, a process linked to a type III secretion system involved in host cytotoxicity. We discover that V. parahaemolyticus employs a genetic regulatory switch involving H-NS and HlyU to control exsA promoter activity. While HlyU is a well-known positive regulator of Vibrio species virulence genes, this is the first report linking it to a transcriptional master regulator and type III secretion system paradigm.

Environmental Regulation of Yersinia Pathophysiology

Hallmarks of Yersinia pathogenesis include the ability to form biofilms on surfaces, the ability to establish close contact with eukaryotic target cells and the ability to hijack eukaryotic cell signaling and take over control of strategic cellular processes. Many of these virulence traits are already well-described. However, of equal importance is knowledge of both confined and global regulatory networks that collaborate together to dictate spatial and temporal control of virulence gene expression. This review has the purpose to incorporate historical observations with new discoveries to provide molecular insight into how some of these regulatory mechanisms respond rapidly to environmental flux to govern tight control of virulence gene expression by pathogenic Yersinia.

Yersinia Type III Secretion System Master Regulator LcrF

Many Gram-negative pathogens express a type III secretion (T3SS) system to enable growth and survival within a host. The three human-pathogenic Yersinia species, Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica, encode the Ysc T3SS, whose expression is controlled by an AraC-like master regulator called LcrF. In this review, we discuss LcrF structure and function as well as the environmental cues and pathways known to regulate LcrF expression. Similarities and differences in binding motifs and modes of action between LcrF and the Pseudomonas aeruginosa homolog ExsA are summarized. In addition, we present a new bioinformatics analysis that identifies putative LcrF binding sites within Yersinia target gene promoters.

Inhibition of Pseudomonas aeruginosa ExsA DNA-Binding Activity by N-Hydroxybenzimidazoles

The Pseudomonas aeruginosa type III secretion system (T3SS) is a primary virulence determinant and a potential target for antivirulence drugs. One candidate target is ExsA, a member of the AraC family of DNA-binding proteins required for expression of the T3SS. A previous study identified small molecules based on an N-hydroxybenzimidazole scaffold that inhibit the DNA-binding activity of several AraC proteins, including ExsA. In this study, we further characterized a panel of N-hydroxybenzimidazoles. The half-maximal inhibitory concentrations (IC50s) for the tested N-hydroxybenzimidazoles ranged from 8 to 45 μM in DNA-binding assays. Each of the N-hydroxybenzimidazoles protected mammalian cells from T3SS-dependent cytotoxicity, and protection correlated with reduced T3SS gene expression in a coculture infection model. Binding studies with the purified ExsA DNA-binding domain (i.e., lacking the amino-terminal self-association domain) confirmed that the activity of N-hydroxybenzimidazoles results from interactions with the DNA-binding domain. The interaction is specific, as an unrelated DNA-binding protein (Vfr) was unaffected by N-hydroxybenzimidazoles. ExsA homologs that control T3SS gene expression in Yersinia pestis, Aeromonas hydrophila, and Vibrio parahaemolyticus were also sensitive to N-hydroxybenzimidazoles. Although ExsA and Y. pestis LcrF share 79% sequence identity in the DNA-binding domain, differential sensitivities to several of the N-hydroxybenzimidazoles were observed. Site-directed mutagenesis based on in silico docking of inhibitors to the DNA-binding domain, and on amino acid differences between ExsA and LcrF, resulted in the identification of several substitutions that altered the sensitivity of ExsA to N-hydroxybenzimidazoles. Development of second-generation compounds targeted to the same binding pocket could lead to drugs with improved pharmacological properties.

Transcriptional profiling of Vibrio parahaemolyticus exsA reveals a complex activation network for type III secretion

Vibrio parahaemolyticus (Vp) is a marine halophilic bacterium that is commonly associated with oysters and shrimp. Human consumption of contaminated shellfish can result in Vp mediated gastroenteritis and severe diarrheal disease. Vp encodes two type 3 secretion systems (T3SS-1 and T3SS2) that have been functionally implicated in cytotoxicity and enterotoxicity respectively. In this study, we profiled protein secretion and temporal promoter activities associated with exsA and exsB gene expression. exsA is an AraC-like transcriptional activator that is critical for activating multiple operons that encode T3SS-1 genes, whereas exsB is thought to encode an outer membrane pilotin component for T3SS-1. The exsBA genetic locus has two predicted promoter elements. The predicted exsB and exsA promoters were individually cloned upstream of luxCDABE genes in reporter plasmid constructs allowing for in situ, real-time quantitative light emission measurements under many growth conditions. Low calcium growth conditions supported maximal exsB and exsA promoter activation. exsB promoter activity exhibited high basal activity and resulted in an exsBA co-transcript. Furthermore, a separate proximal exsA promoter showed initial low basal activity yet eventually exceeded that of exsB and reached maximal levels after 2.5 h corresponding to an entry into early log phase. exsA promoter activity was significantly higher at 30°C than 37°C, which also coincided with increased secretion levels of specific T3SS-1 effector proteins. Lastly, bioinformatic analyses identified a putative expanded ExsA binding motif for multiple transcriptional operons. These findings suggest a two wave model of Vp T3SS-I induction that integrates two distinct promoter elements and environmental signals into a complex ExsA activation framework.

The RNA Helicase DeaD Stimulates ExsA Translation To Promote Expression of the Pseudomonas aeruginosa Type III Secretion System

The Pseudomonas aeruginosa type III secretion system (T3SS) is a primary virulence factor important for phagocytic avoidance, disruption of host cell signaling, and host cell cytotoxicity. ExsA is the master regulator of T3SS transcription. The expression, synthesis, and activity of ExsA is tightly regulated by both intrinsic and extrinsic factors. Intrinsic regulation consists of the well-characterized ExsECDA partner-switching cascade, while extrinsic factors include global regulators that alter exsA transcription and/or translation. To identify novel extrinsic regulators of ExsA, we conducted a transposon mutagenesis screen in the absence of intrinsic control. Transposon disruptions within gene PA2840, which encodes a homolog of the Escherichia coli RNA-helicase DeaD, significantly reduced T3SS gene expression. Recent studies indicate that E. coli DeaD can promote translation by relieving inhibitory secondary structures within target mRNAs. We report here that PA2840, renamed DeaD, stimulates ExsA synthesis at the posttranscriptional level. Genetic experiments demonstrate that the activity of an exsA translational fusion is reduced in a deaD mutant. In addition, exsA expression in trans fails to restore T3SS gene expression in a deaD mutant. We hypothesized that DeaD relaxes mRNA secondary structure to promote exsA translation and found that altering the mRNA sequence of exsA or the native exsA Shine-Dalgarno sequence relieved the requirement for DeaD in vivo. Finally, we show that purified DeaD promotes ExsA synthesis using in vitro translation assays. Together, these data reveal a novel regulatory mechanism for P. aeruginosa DeaD and add to the complexity of global regulation of T3SS.

IMPORTANCE

Although members of the DEAD box family of RNA helicases are appreciated for their roles in mRNA degradation and ribosome biogenesis, an additional role in gene regulation is now emerging in bacteria. By relaxing secondary structures in mRNAs, DEAD box helicases are now thought to promote translation by enhancing ribosomal recruitment. We identify here an RNA helicase that plays a critical role in promoting ExsA synthesis, the central regulator of the Pseudomonas aeruginosa type III secretion system, and provide additional evidence that DEAD box helicases directly stimulate translation of target genes. The finding that DeaD stimulates exsA translation adds to a growing list of transcriptional and posttranscriptional regulatory mechanisms that control type III gene expression.

The Yersinia pestis type III secretion system: expression, assembly and role in the evasion of host defenses

Yersinia pestis, the etiologic agent of plague, utilizes a type III secretion system (T3SS) to subvert the defenses of its mammalian hosts. T3SSs are complex nanomachines that allow bacterial pathogens to directly inject effector proteins into eukaryotic cells. The Y. pestis T3SS is not expressed during transit through the flea vector, but T3SS gene expression is rapidly thermoinduced upon entry into a mammalian host. Assembly of the T3S apparatus is a highly coordinated process that requires the homo- and hetero-oligomerization over 20 Yersinia secretion (Ysc) proteins, several assembly intermediates and the T3S process to complete the assembly of the rod and external needle structures. The activation of effector secretion is controlled by the YopN/TyeA/SycN/YscB complex, YscF and LcrG in response to extracellular calcium and/or contact with a eukaryotic cell. Cell contact triggers the T3S process including the secretion and assembly of a pore-forming translocon complex that facilitates the translocation of effector proteins, termed Yersinia outer proteins (Yops), across the eukaryotic membrane. Within the host cell, the Yop effector proteins function to inhibit bacterial phagocytosis and to suppress the production of pro-inflammatory cytokines.

Self-association is required for occupation of adjacent binding sites in Pseudomonas aeruginosa type III secretion system promoters

ExsA is a member of the AraC/XylS family of transcriptional regulators and is required for expression of the Pseudomonas aeruginosa type III secretion system (T3SS). All P. aeruginosa T3SS promoters contain two adjacent binding sites for monomeric ExsA. The amino-terminal domain of ExsA (NTD) is thought to mediate interactions between the ExsA monomers bound to each site. Threading the NTD onto the AraC backbone revealed an α-helix that likely serves as the primary determinant for dimerization. In this study, we performed alanine scanning mutagenesis of the ExsA α-helix (residues 136 to 152) to identify determinants required for self-association. Residues L137, C139, L140, K141, and L148 exhibited self-association defects and were required for maximal activation by ExsA. Disruption of self-association resulted in decreased binding to T3SS promoters, particularly loss of binding by the second ExsA monomer. Removing the NTD or increasing the space between the ExsA-binding sites restored the ability of the second ExsA monomer to bind the PexsC promoter. This finding indicated that, in the absence of self-association, the NTD prevents binding by a second monomer. Similar findings were seen with the PexoT promoter; however, binding of the second ExsA monomer in the absence of self-association also required the presence of a high-affinity site 2. Based on these data, ExsA self-association is necessary to overcome inhibition by the NTD and to compensate for low-affinity binding sites, thereby allowing for full occupation and activation of ExsA-dependent promoters. Therefore, ExsA self-association is indispensable and provides an attractive target for antivirulence therapies.

RcsB positively regulates the Yersinia Ysc-Yop type III secretion system by activating expression of the master transcriptional regulator LcrF

The Rcs phosphorelay is a complex signaling pathway used by the family Enterobacteriaceae to sense, respond and adapt to environmental changes during free-living or host-associated lifestyles. In this study, we show that the Rcs phosphorelay pathway positively regulates the virulence plasmid encoded Ysc-Yop type III secretion system (T3SS) in the enteropathogen Yesinia pseudotuberculosis. Both the overexpression of the wild-type Rcs regulator RcsB or the constitutive active RscB(D56E) variant triggered more abundant Ysc-Yop synthesis and secretion, whereas the non-phosphorylatable mutant RcsB(D56Q) negated this. Congruently, enhanced Yops expression and secretion occurred in an in cis rscB(D56E) mutant but not in an isogenic rscB(D56Q) mutant. Screening for regulatory targets of RcsB identified the virG-lcrF operon that encodes for LcrF, the Ysc-Yop T3SS master regulator. Protein-DNA binding assays confirmed that RcsB directly bound to this operon promoter, which subsequently caused stimulated lcrF transcription. Moreover, active RcsB enhanced the ability of bacteria to deliver Yop effectors into immune cells during cell contact, and this promoted an increase in bacterial viability. Taken together, our study demonstrates the role of the Rcs system in regulating the Ysc-Yop T3SS in Yersinia and reports on RcsB being the first transcriptional activator known to directly control lcrF transcription.