HmsB enhances biofilm formation in Yersinia pestis

Small RNA SmsR1 modulates acidogenicity and cariogenic virulence by affecting protein acetylation in Streptococcus mutans

Post-transcriptional regulation by small RNAs and post-translational modifications (PTM) such as lysine acetylation play fundamental roles in physiological circuits, offering rapid responses to environmental signals with low energy consumption. Yet, the interplay between these regulatory systems remains underexplored. Here, we unveil the cross-talk between sRNAs and lysine acetylation in Streptococcus mutans, a primary cariogenic pathogen known for its potent acidogenic virulence. Through systematic overexpression of sRNAs in S. mutans, we identified sRNA SmsR1 as a critical player in modulating acidogenicity, a key cariogenic virulence feature in S. mutans. Furthermore, combined with the analysis of predicted target mRNA and transcriptome results, potential target genes were identified and experimentally verified. A direct interaction between SmsR1 and 5'-UTR region of pdhC gene was determined by in vitro binding assays. Importantly, we found that overexpression of SmsR1 reduced the expression of pdhC mRNA and increased the intracellular concentration of acetyl-CoA, resulting in global changes in protein acetylation levels. This was verified by acetyl-proteomics in S. mutans, along with an increase in acetylation level and decreased activity of LDH. Our study unravels a novel regulatory paradigm where sRNA bridges post-transcriptional regulation with post-translational modification, underscoring bacterial adeptness in fine-tuning responses to environmental stress.

Reciprocal regulation of NagC and quorum sensing systems and their roles in hmsHFRS expression and biofilm formation in Yersinia pseudotuberculosis

Biofilm formation by Yersinia pseudotuberculosis is regulated by quorum sensing (QS) and dependent on the haemin storage locus hms , required for the extracellular polysaccharide poly-N -acetylglucosamine (poly-GlcNAc) production. In Escherichia coli NagC regulates both GlcNAc biosynthesis and metabolism with GlcNAc acting as a signal that co-ordinates these and other activities. However, the contribution of NagC and GlcNAc to biofilm development in Y. pseudotuberculosis is not known. Here we show that a Y. pseudotuberculosis nagC mutant is impaired for biofilm production on abiotic (glass) and biotic (Caenorhabitis elegans ) surfaces. Genetic complementation restored poly-GlcNAc production and biofilm formation on C. elegans . Using lux -based promoter fusions, hmsHFRS expression was found to be nagC dependent. Given that NagC and QS both regulate aggregation and biofilm formation, we investigated their regulatory relationship using lux -based promoter fusions. These revealed that (i) nagC is negatively autoregulated, but expression can be partially restored in the nagC mutant by exogenous GlcNAc, (ii) NagC negatively regulates the ytbI and ypsI QS genes and (iii) nagC expression is reduced in the ytbI , ypsI and ypsR mutants but not the ytbR mutant. These data establish the existence of a reciprocal regulatory relationship between NagC and QS, which in the case of the luxRI pair ytbRI , is also GlcNAc-dependent. NagC and GlcNAc are therefore components of a regulatory system involving QS that modulates biofilm formation and aggregation.

The role of RNA regulators, quorum sensing and c-di-GMP in bacterial biofilm formation

Biofilms provide an ecological advantage against many environmental stressors, such as pH and temperature, making it the most common life-cycle stage for many bacteria. These protective characteristics make eradication of bacterial biofilms challenging. This is especially true in the health sector where biofilm formation on hospital or patient equipment, such as respirators, or catheters, can quickly become a source of anti-microbial resistant strains. Biofilms are complex structures encased in a self-produced polymeric matrix containing numerous components such as polysaccharides, proteins, signalling molecules, extracellular DNA and extracellular RNA. Biofilm formation is tightly controlled by several regulators, including quorum sensing (QS), cyclic diguanylate (c-di-GMP) and small non-coding RNAs (sRNAs). These three regulators in particular are fundamental in all stages of biofilm formation; in addition, their pathways overlap, and the significance of their role is strain-dependent. Currently, ribonucleases are also of interest for their potential role as biofilm regulators, and their relationships with QS, c-di-GMP and sRNAs have been investigated. This review article will focus on these four biofilm regulators (ribonucleases, QS, c-di-GMP and sRNAs) and the relationships between them.

Transcriptional Regulation of hmsB, A Temperature-Dependent Small RNA, by RovM in Yersinia pestis Biovar Microtus

HmsB, a temperature-dependent sRNA, promotes biofilm formation by Yersinia pestis, but whether its own expression is regulated by other regulators is still poorly understood. RovM is a global regulator that activates biofilm formation but represses the virulence of Y. pestis. In this work, the results of primer extension, quantitative real-time PCR (qRT-PCR), and LacZ fusion demonstrated that RovM was able to activate hmsB expression. However, the results of electrophoretic mobility shift assay (EMSA) showed that His-RovM did not bind to the upstream DNA region of hmsB. Thus, RovM may exert its regulatory action on hmsB expression in an indirect manner. The data presented here enriched the content of the regulatory circuits that control gene expression in Y. pestis.

Quorum sensing and QsvR tightly control the transcription of vpa0607 encoding an active RNase II-type protein in Vibrio parahaemolyticus

Vibrio parahaemolyticus, a Gram-negative, halophilic bacterium, is a leading cause of acute gastroenteritis in humans. AphA and OpaR are the master quorum sensing (QS) regulators operating at low cell density (LCD) and high cell density (HCD), respectively. QsvR is an AraC-type protein that integrates into the QS system to control gene expression by directly controlling the transcription of aphA and opaR. However, the regulation of QsvR itself remains unclear to date. In this study, we show that vpa0607 and qsvR are transcribed as an operon, vpa0607-qsvR. AphA indirectly activates the transcription of vpa0607 at LCD, whereas OpaR and QsvR directly repress vpa0607 transcription at HCD, leading to the highest expression levels of vpa0607 occurs at LCD. Moreover, VPA0607 acts as an active RNase II-type protein in V. parahaemolyticus and feedback inhibits the expression of QsvR at the post-transcriptional level. Taken together, this work deepens our understanding of the regulation of QsvR and enriches the integration mechanisms of QsvR with the QS system in V. parahaemolyticus.

Nlp enhances biofilm formation by Yersinia pestis biovar microtus

Biofilms formed by Yersinia pestis are able to attach to and block flea's proventriculus, which stimulates the transmission of this pathogen from fleas to mammals. In this study, we found that Nlp (YP1143) enhanced biofilm formation by Y. pestis and had regulatory effects on biofilm-associated genes at the transcriptional level. Phenotypic assays, including colony morphology assay, crystal violet staining, and Caenorhabditis elegans biofilm assay, disclosed that Nlp strongly promoted biofilm formation by Y. pestis. Further gene regulation assays showed that Nlp stimulated the expression of hmsHFRS, hmsCDE and hmsB, while had no regulatory effect on the expression of hmsT and hmsP at the transcriptional level. These findings promoted us to gain more understanding of the complex regulatory circuits controlling biofilm formation by Y. pestis.

Molecular and Genetic Mechanisms That Mediate Transmission of Yersinia pestis by Fleas

The ability to cause plague in mammals represents only half of the life history of Yersinia pestis. It is also able to colonize and produce a transmissible infection in the digestive tract of the flea, its insect host. Parallel to studies of the molecular mechanisms by which Y. pestis is able to overcome the immune response of its mammalian hosts, disseminate, and produce septicemia, studies of Y. pestis-flea interactions have led to the identification and characterization of important factors that lead to transmission by flea bite. Y. pestis adapts to the unique conditions in the flea gut by altering its metabolic physiology in ways that promote biofilm development, a common strategy by which bacteria cope with a nutrient-limited environment. Biofilm localization to the flea foregut disrupts normal fluid dynamics of blood feeding, resulting in regurgitative transmission. Many of the important genes, regulatory pathways, and molecules required for this process have been identified and are reviewed here.

Transcriptional regulation of Yersinia pestis biofilm formation

Yersinia pestis, the causative agent of plague, is transmitted primarily by infected fleas in nature. Y. pestis can produce biofilms that block flea's proventriculus and promote flea-borne transmission. Transcriptional regulation of Y. pestis biofilm formation plays an important role in the response to complex changes in environments, including temperature, pH, oxidative stress, and restrictive nutrition conditions, and contributes to Y. pestis growth, reproduction, transmission, and pathogenesis. A set of transcriptional regulators involved in Y. pestis biofilm production simultaneously controls a variety of biological functions and physiological pathways. Interactions between these regulators contribute to the development of Y. pestis gene regulatory networks, which are helpful for a quick response to complex environmental changes and better survival. The roles of crucial factors and regulators involved in response to complex environmental signals and Y. pestis biofilm formation as well as the precise gene regulatory networks are discussed in this review, which will give a better understanding of the complicated mechanisms of transcriptional regulation in Y. pestis biofilm formation.

QsvR integrates into quorum sensing circuit to control Vibrio parahaemolyticus virulence

Vibrio parahaemolyticus, the leading cause of seafood-associated gastroenteritis worldwide, requires the two type-III secretion systems (T3SS1 and T3SS2) and a thermostable direct hemolysin (encoded by tdh1 and tdh2) for full virulence. The tdh genes and the T3SS2 gene cluster constitute an 80 kb pathogenicity island known as Vp-PAI located on the chromosome II. Expression of T3SS1 and Vp-PAI is regulated in a quorum sensing (QS)-dependent manner but its detailed mechanisms remain unknown. Herein, we show that three factors (QS regulators AphA and OpaR and an AraC-type transcriptional regulator QsvR) form a complex regulatory network to control the expression of T3SS1 and Vp-PAI genes. At low cell density (LCD), whereas Vp-PAI expression is repressed, T3SS1 genes are induced by AphA, which directly binds (an operator region of) the exsBAD-vscBCD operon. At high cell density (HCD), the bacterium turns off T3SS1 expression by replacing AphA with OpaR, triggering the induction of Vp-PAI. Furthermore, QsvR binds to the regulatory regions of all the tested T3SS1 and Vp-PAI genes to activate their transcription at HCD. Taken together, our data highlight how multiple QS regulators contribute to the pathogenicity of V. parahaemolyticus by precisely controlling the expression of major virulence determinants during different stages of growth.

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.

Transcriptional Regulation Between the Two Global Regulators RovA and CRP in Yersinia pestis biovar Microtus

Yersinia pestis is a dangerous bacterial pathogen that can cause plague. Both RovA and cyclic AMP receptor protein (cAMP-CRP) are required for regulating biofilm- and virulence-related genes in Y. pestis. In this study, the transcriptional regulation between RovA and cAMP-CRP were analyzed by using primer extension, quantitative RT-PCR, LacZ fusion, and electrophoretic mobility shift assay. The results indicated that RovA repressed crp transcription in an indirect manner, while that RovA had no regulatory action on cyaA at the transcriptional level. In addition, cAMP-CRP did not regulate the transcription of rovA. Taken together with our previous results, complex regulatory interactions of RovA, cAMP-CRP, and PhoP/PhoQ in Y. pestis were revealed, which would promote us gain deeper understanding about coordinative modulation of biofilm- and virulence-related regulator genes.

bifA Regulates Biofilm Development of Pseudomonas putida MnB1 as a Primary Response to H2O2 and Mn2

Pseudomonas putida (P. putida) MnB1 is a widely used model strain in environment science and technology for determining microbial manganese oxidation. Numerous studies have demonstrated that the growth and metabolism of P. putida MnB1 are influenced by various environmental factors. In this study, we investigated the effects of hydrogen peroxide (H₂O₂) and manganese (Mn²⁺) on proliferation, Mn²⁺ acquisition, anti-oxidative system, and biofilm formation of P. putida MnB1. The related orthologs of 4 genes, mco, mntABC, sod, and bifA, were amplified from P. putida GB1 and their involvement were assayed, respectively. We found that P. putida MnB1 degraded H₂O₂, and quickly recovered for proliferation, but its intracellular oxidative stress state was maintained, with rapid biofilm formation after H₂O₂ depletion. The data from mco, mntABC, sod and bifA expression levels by qRT-PCR, elucidated a sensitivity toward bifA-mediated biofilm formation, in contrary to intracellular anti-oxidative system under H₂O₂ exposure. Meanwhile, Mn²⁺ ion supply inhibited biofilm formation of P. putida MnB1. The expression pattern of these genes showed that Mn²⁺ ion supply likely functioned to modulate biofilm formation rather than only acting as nutrient substrate for P. putida MnB1. Furthermore, blockade of BifA activity by GTP increased the formation and development of biofilms during H₂O₂ exposure, while converse response to Mn²⁺ ion supply was evident. These distinct cellular responses to H₂O₂ and Mn²⁺ provide insights on the common mechanism by which environmental microorganisms may be protected from exogenous factors. We postulate that BifA-mediated biofilm formation but not intracellular anti-oxidative system may be a primary protective strategy adopted by P. putida MnB1. These findings will highlight the understanding of microbial adaptation mechanisms to distinct environmental stresses.

"Fleaing" the Plague: Adaptations of Yersinia pestis to Its Insect Vector That Lead to Transmission

Interest in arthropod-borne pathogens focuses primarily on how they cause disease in humans. How they produce a transmissible infection in their arthropod host is just as critical to their life cycle, however. Yersinia pestis adopts a unique life stage in the digestive tract of its flea vector, characterized by rapid formation of a bacterial biofilm that is enveloped in a complex extracellular polymeric substance. Localization and adherence of the biofilm to the flea foregut is essential for transmission. Here, we review the molecular and genetic mechanisms of these processes and present a comparative evaluation and updated model of two related transmission mechanisms.

Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages

Non-coding small RNAs (sRNAs) are found in practically all bacterial genomes and play important roles in regulating gene expression to impact bacterial metabolism, growth, and virulence. We performed transcriptomics analysis to identify sRNAs that are differentially expressed in Yersinia pestis that invaded the human macrophage cell line THP-1, compared to pathogens that remained extracellular in the presence of host. Using ultra high-throughput sequencing, we identified 37 novel and 143 previously known sRNAs in Y. pestis. In particular, the sRNA Ysr170 was highly expressed in intracellular Yersinia and exhibited a log2 fold change ~3.6 higher levels compared to extracellular bacteria. We found that knock-down of Ysr170 expression attenuated infection efficiency in cell culture and growth rate in response to different stressors. In addition, we applied selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to determine the secondary structure of Ysr170 and observed structural changes resulting from interactions with the aminoglycoside antibiotic gentamycin and the RNA chaperone Hfq. Interestingly, gentamicin stabilized helix 4 of Ysr170, which structurally resembles the native gentamicin 16S ribosomal binding site. Finally, we modeled the tertiary structure of Ysr170 binding to gentamycin using RNA motif modeling. Integration of these experimental and structural methods can provide further insight into the design of small molecules that can inhibit function of sRNAs required for pathogen virulence.

RNA Regulators: Formidable Modulators of Yersinia Virulence

A large repertoire of RNA-based regulatory mechanisms, including a plethora of cis- and trans-acting noncoding RNAs (ncRNAs), sensory RNA elements, regulatory RNA-binding proteins, and RNA-degrading enzymes have been uncovered lately as key players in the regulation of metabolism, stress responses, and virulence of the genus Yersinia. Many of them are strictly controlled in response to fluctuating environmental conditions sensed during the course of the infection, and certain riboregulators have already been shown to be crucial for virulence. Some of them are highly conserved among the family Enterobacteriaceae, while others are genus-, species-, or strain-specific and could contribute to the difference in Yersinia pathogenicity. Importantly, the analysis of Yersinia riboregulators has not only uncovered crucial elements and regulatory mechanisms governing host-pathogen interactions, it also revealed exciting new venues for the design of novel anti-infectives.

New insights into Legionella pneumophila biofilm regulation by c-di-GMP signaling

The waterborne pathogen Legionella pneumophila grows as a biofilm, freely or inside amoebae. Cyclic-di-GMP (c-di-GMP), a bacterial second messenger frequently implicated in biofilm formation, is synthesized and degraded by diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), respectively. To characterize the c-di-GMP-metabolizing enzymes involved in L. pneumophila biofilm regulation, the consequences on biofilm formation and the c-di-GMP concentration of each corresponding gene inactivation were assessed in the Lens strain. The results showed that one DGC and two PDEs enhance different aspects of biofilm formation, while two proteins with dual activity (DGC/PDE) inhibit biofilm growth. Surprisingly, only two mutants exhibited a change in global c-di-GMP concentration. This study highlights that specific c-di-GMP pathways control L. pneumophila biofilm formation, most likely via temporary and/or local modulation of c-di-GMP concentration. Furthermore, Lpl1054 DGC is required to enable the formation a dense biofilm in response to nitric oxide, a signal for biofilm dispersion in many other species.

Plasmid pPCP1-derived sRNA HmsA promotes biofilm formation of Yersinia pestis

Background

The ability of Yersinia pestis to form a biofilm is an important characteristic in flea transmission of this pathogen. Y. pestis laterally acquired two plasmids (pPCP1and pMT1) and the ability to form biofilms when it evolved from Yersinia pseudotuberculosis. Small regulatory RNAs (sRNAs) are thought to play a crucial role in the processes of biofilm formation and pathogenesis.

Results

A pPCP1-derived sRNA HmsA (also known as sR084) was found to contribute to the enhanced biofilm formation phenotype of Y. pestis. The concentration of c-di-GMP was significantly reduced upon deletion of the hmsA gene in Y. pestis. The abundance of mRNA transcripts determining exopolysaccharide production, crucial for biofilm formation, was measured by primer extension, RT-PCR and lacZ transcriptional fusion assays in the wild-type and hmsA mutant strains. HmsA positively regulated biofilm synthesis-associated genes (hmsHFRS, hmsT and hmsCDE), but had no regulatory effect on the biofilm degradation-associated gene hmsP. Interestingly, the recently identified biofilm activator sRNA, HmsB, was rapidly degraded in the hmsA deletion mutant. Two genes (rovM and rovA) functioning as biofilm regulators were also found to be regulated by HmsA, whose regulatory effects were consistent with the HmsA-mediated biofilm phenotype.

Conclusion

HmsA potentially functions as an activator of biofilm formation in Y. pestis, implying that sRNAs encoded on the laterally acquired plasmids might be involved in the chromosome-based regulatory networks implicated in Y. pestis-specific physiological processes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0793-5) contains supplementary material, which is available to authorized users.

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.

The hmsT 3' untranslated region mediates c-di-GMP metabolism and biofilm formation in Yersinia pestis

Yersinia pestis, the cause of plague, forms a biofilm in the proventriculus of its flea vector to enhance transmission. Biofilm formation in Y. pestis is regulated by the intracellular levels of cyclic diguanylate (c-di-GMP). In this study, we investigated the role of the 3' untranslated region (3'UTR) in hmsT mRNA, a transcript that encodes a diguanylate cyclase that stimulates biofilm formation in Y. pestis by synthesizing the second messenger c-di-GMP. Deletion of the 3'UTR increased the half-life of hmsT mRNA, thereby upregulating c-di-GMP levels and biofilm formation. Our findings indicate that multiple regulatory sequences might be present in the hmsT 3'UTR that function together to mediate mRNA turnover. We also found that polynucleotide phosphorylase is partially responsible for hmsT 3'UTR-mediated mRNA decay. In addition, the hmsT 3'UTR strongly repressed gene expression at 37°C and 26°C, but affected gene expression only slightly at 21°C. Our findings suggest that the 3'UTR might be involved in precise and rapid regulation of hmsT expression, allowing Y. pestis to fine-tune c-di-GMP synthesis and consequently regulate biofilm production to adapt to the changing host environment.

Genetic Regulation of Yersinia pestis

Y. pestis exhibits dramatically different traits of pathogenicity and transmission, albeit their close genetic relationship with its ancestor-Y. pseudotuberculosis, a self-limiting gastroenteric pathogen. Y. pestis is evolved into a deadly pathogen and transmitted to mammals and/or human beings by infected flea biting or directly contacting with the infected animals. Various kinds of environmental changes are implicated into its complex life cycle and pathogenesis. Dynamic regulation of gene expression is critical for environmental adaptation or survival, primarily reflected by genetic regulation mediated by transcriptional factors and small regulatory RNAs at the transcriptional and posttranscriptional level, respectively. The effects of genetic regulation have been shown to profoundly influence Y. pestis physiology and pathogenesis such as stress resistance, biofilm formation, intracellular survival, and replication. In this chapter, we mainly summarize the progresses on popular methods of genetic regulation and on regulatory patterns and consequences of many key transcriptional and posttranscriptional regulators, with a particular emphasis on how genetic regulation influences the biofilm and virulence of Y. pestis.

Yersinia pestis and Yersinia pseudotuberculosis infection: a regulatory RNA perspective

Yersinia pestis, responsible for causing fulminant plague, has evolved clonally from the enteric pathogen, Y. pseudotuberculosis, which in contrast, causes a relatively benign enteric illness. An ~97% nucleotide identity over 75% of their shared protein coding genes is maintained between these two pathogens, leaving much conjecture regarding the molecular determinants responsible for producing these vastly different disease etiologies, host preferences and transmission routes. One idea is that coordinated production of distinct factors required for host adaptation and virulence in response to specific environmental cues could contribute to the distinct pathogenicity distinguishing these two species. Small non-coding RNAs that direct posttranscriptional regulation have recently been identified as key molecules that may provide such timeous expression of appropriate disease enabling factors. Here the burgeoning field of small non-coding regulatory RNAs in Yersinia pathogenesis is reviewed from the viewpoint of adaptive colonization, virulence and divergent evolution of these pathogens.