ABSTRACT: Transcriptional profiling of the Δ835np mutant vs the wild-type strain grown in BHI to OD600=0.5. An intimate linkage between the regulation of biofilm formation, stress tolerance and genetic competence exists in the dental caries pathogen Streptococcus mutans. We previously reported that the rcrRPQ genes, which encode ABC exporters (RcrPQ) and a MarR-family transcriptional regulator (RcrR) that represses the expression of the rcr operon, play a dominant role in regulation of development of genetic competence and connect competence with stress tolerance and (p)ppGpp production in S. mutans. Here we identify the region required for efficient RcrR binding to the rcr promoter region using purified recombinant RcrR (rRcrR) protein in electrophoretic mobility shift and fluorescence polarization assays. DNA fragments carrying mutations in the binding region resulted in decreased binding of rRcrR. Direct binding of RcrR to the comX gene promoter in vitro revealed that RcrR has the potential to directly regulate competence development. Likewise, direct interactions of rRcrR with the promoter region of relP, encoding a (p)ppGpp synthase, show the potential for RcrR-dependent modulation of (p)ppGpp pools. Introduction of mutations into the RcrR binding sites in the rcrR promoter region in vivo demonstrated that optimal RcrR binding is essential for proper expression of competence genes and optimal transformation efficiency. Transcription profiling by RNA-seq and mircroarrays of strains with mutations in rcrR showed that genes in the competence pathway were those most differentially expressed. Thus, here and in a accompanying paper, we establish mechanisms by which the products of the rcrRPQ operon integrate com gene expression, genetic transformation, ppGpp metabolism and stress tolerance in S. mutans Two-condition experiment, Δ835np mutant vs the wild-type strain. Biological replicates: 4 per strain, independently grown and harvested. One replicate per array
Project description:Transcriptional Profiling of Streptococcus mutans UA159 Grown in Continuous Culture using TV Media Supplemented With 10 mM vs 100 mM Glucose. The genetic and phenotypic responses of Streptococcus mutans, an organism known to be strongly associated with the development of dental caries, to changes in carbohydrate availability were investigated. S. mutans UA159 or a derivative of UA159 lacking ManL, which is the EIIAB component (EIIABMan) of a mannose/glucose permease of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) and a dominant effector of catabolite repression, were grown in continuous culture to steady-state in conditions of excess (100 mM) or limiting (10 mM) glucose. Microarrays using RNA from S. mutans UA159 revealed that 174 genes were differentially expressed in response to changes in carbohydrate availability (P < 0.001). Glucose-limited cells possessed higher PTS activity, could acidify the environment more rapidly and to a greater extent, and produced more ManL protein than cultures grown with excess glucose. Loss of ManL adversely affected carbohydrate transport and acid tolerance. Comp arison of the HPr protein in S. mutans UA159 and the manL deletion strain indicated that the differences in behaviors of the strains were not due to major differences in HPr pools or HPr phosphorylation status. Therefore, carbohydrate availability alone can dramatically influence the expression of physiologic and biochemical pathways that contribute directly to the virulence of S. mutans, and ManL has a profound influence on this behavior. Two-condition experiment, growth in 10 mM vs 100 mM glucose. Biological replicates: 3 per condition, independently grown and harvested. One replicate per array
Project description:The glucose/mannose-PTS permease EIIMan encoded by manLMN in the dental caries pathogen Streptococcus mutans has a dominant influence on sugar-specific, CcpA-independent catabolite repression (CR). Mutations in manL affect energy metabolism and virulence-associated traits, including biofilm formation, acid tolerance and competence. Using promoter:reporter fusions, expression of the manLMN and the fruRKI operons, encoding a transcriptional regulator, a fructose-1-P kinase and a fructose-PTS permease EIIFru, respectively, was monitored in response to carbohydrate source and in mutants lacking CcpA, FruR, and components of EIIMan. Expression of genes for EIIMan and EIIFru was directly regulated by CcpA and CR, as evinced by in vivo and in vitro methods. Unexpectedly, not only was the fruRKI operon negatively regulated by FruR, but so was manLMN. Carbohydrate transport by EIIMan had a negative influence on expression of manLMN, but not fruRKI. In agreement with the proposed role of FruR in regulating these PTS operons, loss of fruR or fruK substantially altered growth on a number of carbohydrates, including fructose. RNA deep sequencing revealed profound changes in gene regulation caused by deletion of fruK or fruR. Collectively, these findings demonstrate intimate interconnection of the regulation of two major PTS permeases in S. mutans and reveal novel and important contributions of fructose metabolism to global regulation of gene expression. Overall design: mRNA profiling of the wild type UA159 and two mutants fruK-13 and fruR, each grown to exponential phase in batch on a rich medium BHI.
Project description:Streptococcus mutans, the organism most frequently associated with the development of dental caries, is able to utilize a diverse array of carbohydrates for energy metabolism. One such molecule is trehalose, a disaccharide common in human foods, which has recently been implicated in enhancing the virulence of epidemic strains of the pathogen, Clostridium difficile. In this study, deletion mutants of all three genes in the putative S. mutans trehalose utilization operon were characterized and shown to be required for wild-type levels of growth when trehalose was the only carbohydrate source provided. Interestingly, the TreR transcriptional regulator appeared to be critical for responding to oxidative stress, and for mounting a protective stress tolerance response following growth at moderately acidic pH. RNAseq of a treR deletion mutant suggested that in S. mutans, TreR acts as a trehalose-sensing activator of transcription of the tre operon, rather than a repressor, as described in other species. In addition, deletion of treR caused the down-regulation of a number of genes involved in genetic competence and bacteriocin production, supporting results of a recent study linking trehalose and the S. mutans competence pathways. Finally, deletion of treR compromised the ability of S. mutans to inhibit the growth of the competing species, Streptococcus gordonii and Lactococcus lactis. Taken together, this study solidifies the role of the S. mutans tre operon in trehalose utilization and suggests novel functions for the TreR regulator, including roles in stress response and competitive fitness. Overall design: Transcriptional profiling was performed using RNA extracted from cultures of S. mutans parent strain UA159 and the ∆treR derivative grown in tryptone-yeast extract medium supplemented with either glucose, galactose or trehalose.
Project description:BACKGROUND: Streptococcus mutans, the etiological agent of human dental caries, displays complex regulation of natural genetic competence. Competence development in S. mutans is controlled by a peptide derived from ComS (comX inducing peptide, XIP); which along with the cytosolic regulator ComR controls the expression of the alternative sigma factor comX, the master regulator of competence development. ComR-XIP controls the expression of both PcomX and PcomS, with the latter creating a positive feedback loop. Recently, a gene embedded within the coding region of comX was discovered and designated xrpA (comX regulatory peptide A). XrpA was found to be an antagonist of ComX, but the mechanism was not established. In this study, we began to dissect how XrpA exerts control over competence development in S. mutans. METHODS: RNA-Seq was utilized to compare the transcriptomes of S. mutans wild-type strain UA159 (3 replicates), UA159 with addition of 2 uM sXIP (3 replicates) and with a mutant of xrpA (comX::T162C; 3 replicates). Strains were grown to OD600 nm = 0.5 in FMC medium before harvest. sXIP was added at OD600 nm = 0.2. Deep sequencing was performed at the University of Florida ICBR facilities (Gainesville, FL). Approximately 20 million short-reads were obtained for each sample. After removing adapter sequences from each short-read and trimming of the 3’-ends by quality scores (59), the resulting sequences were mapped onto the reference genome of strain UA159 (GenBank accession no. AE014133) using the short-read aligner. Mapped short-read alignments were then converted into readable formats using SAMTOOLS. RESULTS: Using an optimzed data analysis workflow, we mapped 14-19 million reads per sample to the genome of UA159. For viewing of the mapped reads aligned to the genome, .bam files were uploaded into the Integrative Genomics Viewer (IGV – version 2.3.55) (61). A .csv file containing raw read counts for each replicate (3) was then uploaded to Degust (http://degust.erc.monash.edu/) and edgeR analysis performed to determine Log2 fold change and a false discovery rate (FDR). Comparison of the transcriptome by RNA-Seq of the wild-type with the mutant lacking XrpA revealed 56 differentially expressed genes, with 34 upregulated in xrpA and 22 downregulated. Many of the upregulated genes were competence-related genes, including comX and genes that are a part of the ComX regulon of S. mutans . Since loss of xrpA caused upregulation of competence genes, we also analyzed the transcriptome of UA159 treated with 2 uM sXIP to induce competence, with UA159 treated with vehicle (DMSO) as a control. Cells treated with sXIP had 137 genes differentially expressed compared to the DMSO control. CONCLUSIONS: Collectively, these data reveal that the novel regulator XrpA exerts its influence over competence development by impacting ComRS functions, resulting in decreased expression of comX and late com gene expression that negatively impact transformability. These results highlight XrpA as a new negative regulator of competence signaling as well as broaden our understanding of the complex regulatory mechanisms that modulate competence and virulence in S. mutans. Overall design: Streptococcus mutans mRNA profiles were generated for UA159, UA159 + 2 uM sXIP, and an xrpA mutant strain (comX::T162C) in FMC medium at OD600 nm = 0.5 by deep sequencing, in triplicate
Project description:Polymicrobial biofilms are of large medical importance, but little is known about their physiology and the underlying interspecies interactions. Here we studied two human pathogens, the opportunistic fungus Candida albicans and the caries promoting bacterium Streptococcus mutans. Both species formed biofilms in monoculture, with C. albicans growing mainly in the virulence-associated hyphae form, and S. mutans forming a thick layer of extracellular polymeric substances (EPS). Biofilm growth was enhanced in dual-species biofilms, which reached twice the biomass of monospecies biofilms and higher cell numbers of both S. mutans and C. albicans. EPS production by S. mutans was strongly suppressed in dual-species biofilms. Virulence traits of S. mutans, e.g. genetic competence, biofilm formation and bacteriocin synthesis are controlled by quorum sensing through activation of the alternative sigma factor SigX. SigX is induced by the pheromones CSP (competence stimulating factor) or XIP (sigX inducing peptide). Strong induction of sigX was observed in dual species biofilms indicated by fluorescence of a reporter strain for the sigX promoter, S. mutans PcomX-gfp, as well as by qRT-PCR of comX. The peak of sigX expression occurred after 10 h of biofilm growth. Conditioned media from mixed biofilms but not from C. albicans or S. mutans cultivated alone activated sigX in the reporter strain. Deletion mutants for the comC and comS genes encoding the precursors of CSP and XIP, respectively, were constructed. Conditioned media from mixed biofilms with S. mutans DcomS were unable to induce sigX in the reporter strain, while deletion of comC had no effect. These data show that synthesis of XIP was induced in S. mutans by coculture with C. albicans. Transcriptome analysis of S. mutans in single and mixed biofilms confirmed strong induction of comS, sigX, and the downstream late competence genes in dual-species biofilms. Among the late competence genes, fratricins were discovered for the first time. The comCDE operon and bacteriocin related genes were also induced, but much weaker. Genes related to oxidative stress, chaperones and glycosyltransferase genes required for EPS synthesis from sucrose were down-regulated, while glycogen synthesis genes were up-regulated, indicating that S. mutans was protected from oxidative stress and provided with excess sugar for storage polymer synthesis in mixed biofilms. The data show that in dual-species biofilms, C. albicans improves growth of S. mutans, suppresses its EPS formation and induces the complete quorum sensing signalling system, thus fundamentally changing the virulence properties of the caries pathogen, including its potential interactions with other members of the polymicrobial dental plaque community. Dual-species biofilms of S. mutans and C. albicans and single-species biofilms of S. mutans were cultivated in 24-well microtitre plates in YNBB medium. Transcriptional profiles of S. mutans in single- and dual-species biofilms were analysed at early (6 h) and late (10 h) logarithmic phase of the biofilm growth, as well as after 24 h when biofilms entered stationary phase. Transcriptional profiles of S. mutans grown in the dual-species biofilms were compared to profiles obtained for single-species biofilm from the same time point. Three biological and one to two technical replicas were used in the microarray study. RNA samples were labeled with Cy3 or Cy5 using the ULS fluorescent labeling kit (Kreatech, Germany). Seven hundred nanograms of Cy3 or Cy5 labeled RNA after fragmentation were hybridized to the microarray at 65°C for 17 h using the Agilent hybridization chamber according to the manufacturer's instructions. The arrays were scanned using the Agilent DNA microarray scanner and the raw data were extracted using Agilent Feature Extraction software (v. 10.7).
Project description:In this report, codY mutant strains were constructed and used to demonstrate the relationship of (p)ppGpp synthesized by RelP and RelQ with the activation of CodY. In addition, because CodY has not been studied in S. mutans, we used microarrays to demonstrate that this protein function as a global regulator of gene expression in S. mutans. Keywords: stress response, gene knockout analysis For microarray analysis, cells were grown in complete FMC to an optical density at 600 nm (OD600) of 0.3 collected by centrifugation, quick frozen in a dry-ice/ethanol bath, and stored at - 80∞C for RNA isolation. RNA was isolated from exponential phase (OD600 0.3), as described previously. All samples were digested with DNase I (Ambion, Austin, TX) and purified using the RNeasy mini kit column (Qiagen, Inc., Chatsworth, CA). RNA concentrations were determined spectrophotometrically in triplicate and one µg of RNA was run in a formaldehyde gel to verify RNA quality. Reverse transcription (RT) reaction was performed with 10 mg of RNA following the protocol provided by TIGR with minor modifications. Transcriptome analysis was performed using the S. mutans UA159 microarrays provided by The Institute for Genomic Research (TIGR). The microarrays consisted of 1,948 70-mer oligonucleotides representing 1,960 open reading frames printed four times on the surface of each microarray slide. Additional details regarding the arrays are available at http://pfgrc.tigr.org/descriptions/S_mutans.shtml. A reference RNA prepared from a large-scale culture of S. mutans UA159 cells that had been grown in BHI broth to an OD600 = 0.5 was used in every experiment. cDNA labeling was performed according to TIGR protocols with minor modifications as described elsewhere. Four cDNA samples originating from four independent cultures of UA159 and JLcodY strains were hybridized to the arrays along with the reference cDNA, generating a total of 16 slides. Hybridizations were performed in a Maui hybridization chamber (BioMicro Systems, Salt Lake City, UT). Additional details regarding array protocols are available at http://pfgrc.tigr.org/protocols/protocols.shtml. Data from all individual experiments were analyzed using Spotfinder software and normalized using Midas according to TIGR specifications (http://www.tigr.org/software/). Statistical analysis was carried out using BRB Arrays Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a P-value of 0.001.
Project description:The induction of genetic competence is a strategy used by bacteria to increase their genetic repertoire under stressful environmental conditions. Recently, Streptococcus pneumoniae has been shown to co-ordinate the uptake of transforming DNA with fratricide via increased expression of the peptide pheromone responsible for competence induction. Here, we document that environmental stress-induced expression of the peptide pheromone competence-stimulating peptide (CSP) in the oral pathogen Streptococcus mutans. We showed that CSP is involved in the stress response and determined the CSP-induced regulon in S. mutans by microarray analysis. Contrary to pneumococcus, S. mutans responds to increased concentrations of CSP by cell lysis in only a fraction of the population. We have focused on the mechanism of cell lysis and have identified a novel bacteriocin as the ‘death effector’. Most importantly, we showed that this bacteriocin causes cell death via a novel mechanism of action: intracellular action against self. We have also identified the cognate bacteriocin immunity protein, which resides in a separate unlinked genetic locus to allow its differential regulation. The role of the lytic response in S. mutans competence is also discussed. Together, these findings reveal a novel autolytic pathway in S. mutans which may be involved in the dissemination of fitness-enhancing genes in the oral biofilm. Streptococcus mutans UA159 were grown with 2 uM CSP or without (uninduced control) to mid-log phase. Total RNA was extracted as described above. The cDNAs were prepared for hybridization using the PFGRC protocol. Microarray chips were scanned using a Gene Pix 4000B (Axon) and analyzed using the TM4 Microarray Software Suite (http://www.tm4.org/). Transcript levels were measured by cDNA hybridized to a fourfold redundant S. mutans microarray and averaged for three replicated hybridizations. Differential gene expression was based on a post-normalization cut-off of ±> twofold.
Project description:The induction of genetic competence is a strategy used by bacteria to increase their genetic repertoire under stressful environmental conditions. Recently, Streptococcus pneumoniae has been shown to co-ordinate the uptake of transforming DNA with fratricide via increased expression of the peptide pheromone responsible for competence induction. Here, we document that environmental stress-induced expression of the peptide pheromone competence-stimulating peptide (CSP) in the oral pathogen Streptococcus mutans. We showed that CSP is involved in the stress response and determined the CSP-induced regulon in S. mutans by microarray analysis. Contrary to pneumococcus, S. mutans responds to increased concentrations of CSP by cell lysis in only a fraction of the population. We have focused on the mechanism of cell lysis and have identified a novel bacteriocin as the ‘death effector’. Most importantly, we showed that this bacteriocin causes cell death via a novel mechanism of action: intracellular action against self. We have also identified the cognate bacteriocin immunity protein, which resides in a separate unlinked genetic locus to allow its differential regulation. The role of the lytic response in S. mutans competence is also discussed. Together, these findings reveal a novel autolytic pathway in S. mutans which may be involved in the dissemination of fitness-enhancing genes in the oral biofilm. Overall design: Streptococcus mutans UA159 were grown with 2 uM CSP or without (uninduced control) to mid-log phase. Total RNA was extracted as described above. The cDNAs were prepared for hybridization using the PFGRC protocol. Microarray chips were scanned using a Gene Pix 4000B (Axon) and analyzed using the TM4 Microarray Software Suite (http://www.tm4.org/). Transcript levels were measured by cDNA hybridized to a fourfold redundant S. mutans microarray and averaged for three replicated hybridizations. Differential gene expression was based on a post-normalization cut-off of ±> twofold.
Project description:The production of (p)ppGpp by Streptococcus mutans UA159 is catalyzed by three gene products, RelA, RelP and RelQ. Here, we investigate the role of the RelA (Rel) homologue of S. mutans in the stringent response and in global control of gene expression. RelA of S. mutans was shown to synthesize pppGpp in vitro from GTP and ATP in the absence of added ribosomes, as well as in vivo in an E. coli relA-spoT mutant. Mupirocin (MUP) was shown to induce high levels of (p)ppGpp production in S. mutans in a relA-dependent manner, with a concommitant reduction in GTP pools. Keywords: (p)ppGpp, nutrient starvation, biofilm, virulence, stress Overall design: For microarray analysis, cells were grown in the chemically-defined medium FMC to an optical density at 600 nm (OD600) of 0.3 and the cultures were divided into two aliquots. To one aliquot, 500 ng ml-1 of MUP was added and the cells were incubated at 37oC for 20 minutes (MUP-treated cells), while the other aliquot was collected by centrifugation and immediately frozen (MUP-control cells). Since MUP treatment resulted in rapid growth arrest, the final OD600 of experimental and control samples were essentially identical. Four individual Cy3-labeled cDNA samples originating from four different cultures of UA159 and JLrelA strains grown under control (FMC) and experimental conditions (FMC containing MUP) were hybridized to the arrays along with Cy5-labeled reference cDNA, generating a total of 16 slides. The ratios of the signals of the test RNAs with that of the uniform reference RNA were analyzed within and between slides.