Transcription of clpP is enhanced by a unique tandem repeat sequence in Streptococcus mutans

Discovery by metagenomics of a functional tandem repeat sequence that controls gene expression in bacteria

The ability to degrade exogenous compounds is acquired by adaptive processes of microorganisms when they are exposed to compounds that are foreign to their existing enzyme systems. Previously, we reported that simultaneous point mutations and mobile genetic elements cause the evolution and optimization of the degradation systems for aromatic compounds. In the present study, we propose another element with this role—tandem repeats. The novel metagenomic tandem repeat (MTR) sequence T(G/A)ACATG(A/C)T was identified in the 5′-untranslated regions of catechol 2,3-dioxygenase (C23O)-encoding genes by metagenomic analysis. Recombinant Escherichia coli carrying a C23O gene with various numbers of MTRs exhibited increased C23O protein expression and enzyme activity compared with cells expressing the C23O gene without MTRs. Real-time reverse transcription-PCR showed that changes in the numbers of MTRs affected the levels of detectable C23O mRNA in the E. coli host. Furthermore, the mRNAs transcribed from C23O genes containing various numbers of MTRs had longer half-lives than those transcribed from a C23O gene without MTRs. Thus, MTRs would affect the translation efficiency of the gene expression system. MTRs may change the expression levels of their downstream genes for adaptation to a fluctuating environment.

Involvement of ClpE ATPase in Physiology of Streptococcus mutans

Streptococcus mutans, a dental pathogen, harbors at least three Clp ATPases (ClpC, ClpE, and ClpX) that form complexes with ClpP protease and participate in regulated proteolysis. Among these, the function of ClpE ATPase is poorly understood. We have utilized an isogenic clpE-deficient strain derived from S. mutans UA159 and evaluated the role of ClpE in cellular physiology. We found that loss of ClpE leads to increased susceptibility against thiol stress but not to oxidative and thermal stress. Furthermore, we found that the mutant displays altered tolerance against some antibiotics and altered biofilm formation. We performed a label-free proteomic analysis by comparing the mutant with the wild-type UA159 strain under nonstressed conditions and found that ClpE modulates a relatively limited proteome in the cell compared to the proteomes modulated by ClpX and ClpP. Nevertheless, we found that ClpE deficiency leads to an overabundance of some cell wall synthesis enzymes, ribosomal proteins, and an unknown protease encoded by SMU.2153. Our proteomic data strongly support some of the stress-related phenotypes that we observed. Our study emphasizes the significance of ClpE in the physiology of S. mutans. IMPORTANCE When bacteria encounter environmental stresses, the expression of various proteins collectively known as heat shock proteins is induced. These heat shock proteins are necessary for cell survival specifically under conditions that induce protein denaturation. A subset of heat shock proteins known as the Clp proteolytic complex is required for the degradation of the misfolded proteins in the cell. The Clp proteolytic complex contains an ATPase and a protease. A specific Clp ATPase, ClpE, is uniquely present in Gram-positive bacteria, including streptococci. Here, we have studied the functional role of the ClpE protein in Streptococcus mutans, a dental pathogen. Our results suggest that ClpE is required for survival under certain antibiotic exposure and stress conditions but not others. Our results demonstrate that loss of ClpE leads to a significantly altered cellular proteome, and the analysis of those changes suggests that ClpE's functions in S. mutans are different from its functions in other Gram-positive bacteria.

Induction of clpP expression by cell-wall targeting antibiotics in Streptococcus mutans

Streptococcus mutans is one of the major bacteria of the human oral cavity that is associated with dental caries. The pathogenicity of this bacterium is attributed to its ability to rapidly respond and adapt to the ever-changing conditions of the oral cavity. The major player in this adaptive response is ClpP, an intracellular protease involved in degradation of misfolded proteins during stress responses. S. mutans encodes a single clpP gene with an upstream region uniquely containing multiple tandem repeat sequences (RSs). Here, we explored expression of clpP with respect to various stresses and report some new findings. First, we found that at sub-inhibitory concentration, certain cell-wall damaging antibiotics were able to induce clpP expression. Specifically, third- and fourth-generation cephalosporins that target penicillin-binding protein 3 (PBP3) strongly enhanced the clpP expression. However, induction of clpP was weak when the first-generation cephalosporins with lower affinity to PBP3 were used. Surprisingly, carbapenems, which primarily target PBP2, induced expression of clpP the least. Second, we found that a single RS element was capable of inducing clpP expression as efficiently as with the wild-type seven RS elements. Third, we found that the RS-element-mediated modulation of clpP expression was strain dependent, suggesting that specific host factors might be involved in the transcription. And finally, we observed that ClpP regulates its own expression, as the expression of clpP-gusA was higher in a clpP-deficient mutant. This suggests that ClpP is involved in the degradation of activator(s) involved in its own transcription.

Degradation of SsrA-tagged proteins in streptococci

In prokaryotes, a conserved small RNA molecule, called tmRNA, rescues ribosomes from proteins that are abnormally truncated due to the presence of rare codons or degraded mRNA. During the rescue process, a peptide tag (SsrA) encoded by tmRNA is cotranslationally added to the truncated polypeptides, thereby targeting these proteins for proteolytic degradation. In Escherichia coli, ClpXP and ClpAP proteases primarily degrade SsrA-tagged proteins. Other proteases such as Lon and FtsH also participate in the degradation in E. coli. However, in Bacillus subtilis, ClpXP is the major protease that degrades the SsrA-tagged proteins. Degradation of SsrA-tagged protein in streptococci is not well understood except that ClpXP is responsible for the majority of the degradation. Here we show that in Streptococcus mutans, in addition to ClpXP, two other Clp complexes, ClpCP and ClpEP, are also involved in the degradation. We also found that ClpCP- and ClpEP-mediated proteolysis of SsrA-tagged substrates is induced by heat stress. As ClpCP and ClpEP proteins are highly conserved in streptococci, we predicted that ClpEP- and ClpCP-mediated degradation of SsrA-tagged proteins might be operational in other streptococci.

Regulated proteolysis of the alternative sigma factor SigX in Streptococcus mutans: implication in the escape from competence

BACKGROUND

SigX (σX), the alternative sigma factor of Streptococcus mutans, is the key regulator for transcriptional activation of late competence genes essential for taking up exogenous DNA. Recent studies reveal that adaptor protein MecA and the protease ClpC act as negative regulators of competence by a mechanism that involves MecA-mediated proteolysis of SigX by the ClpC in S. mutans. However, the molecular detail how MecA and ClpC negatively regulate competence in this species remains to be determined. Here, we provide evidence that adaptor protein MecA targets SigX for degradation by the protease complex ClpC/ClpP when S. mutans is grown in a complex medium.

RESULTS

By analyzing the cellular levels of SigX, we demonstrate that the synthesis of SigX is transiently induced by competence-stimulating peptide (CSP), but the SigX is rapidly degraded during the escape from competence. A deletion of MecA, ClpC or ClpP results in the cellular accumulation of SigX and a prolonged competence state, while an overexpression of MecA enhances proteolysis of SigX and accelerates the escape from competence. In vitro protein-protein interaction assays confirm that MecA interacts with SigX via its N-terminal domain (NTD1-82) and with ClpC via its C-terminal domain (CTD123-240). Such an interaction mediates the formation of a ternary SigX-MecA-ClpC complex, triggering the ATP-dependent degradation of SigX in the presence of ClpP. A deletion of the N-terminal or C-terminal domain of MecA abolishes its binding to SigX or ClpC. We have also found that MecA-regulated proteolysis of SigX appears to be ineffective when S. mutans is grown in a chemically defined medium (CDM), suggesting the possibility that an unknown mechanism may be involved in negative regulation of MecA-mediated proteolysis of SigX under this condition.

CONCLUSION

Adaptor protein MecA in S. mutans plays a crucial role in recognizing and targeting SigX for degradation by the protease ClpC/ClpP. Thus, MecA actually acts as an anti-sigma factor to regulate the stability of SigX during competence development.

Contribution of ClpP to stress tolerance and virulence properties of Streptococcus mutans

Abilities to tolerate environmental stresses and to form biofilms on teeth surface are key virulence attributes of Streptococcus mutans, the primary causative agent of human dental caries. ClpP, the chief intracellular protease of S. mutans, along with ATPases degrades altered proteins that might be toxic for bacteria, and thus plays important roles in stress response. To further understand the roles of ClpP in stress response of S. mutans, a ClpP deficient strain was constructed and used for general stress tolerance, autolysis, mutacins production, and virulence assays. Here, we demonstrated that inactivation of ClpP in S. mutans resulted in a sensitive phenotype to several environmental stresses, including acid, cold, thermal, and oxidative stresses. The ClpP deficient strain displayed slow growth rates, poor growth yields, formation of long chains, increased clumping in broth, and reduced capacity to form biofilms in presence of glucose. Mutacins production and autolysis of S. mutans were also impaired by mutation of clpP. Animals study showed that clpP mutation increased virulence of S. mutans but not significant. However, enhanced abilities to survive lethal acid and to form biofilm in sucrose were observed in ClpP deficient strain. Our findings revealed a broad impact of ClpP on several virulence properties of S. mutans and highlighted the relevance of ClpP proteolysis with progression of diseases caused by S. mutans.

ClpL is required for folding of CtsR in Streptococcus mutans

ClpL, a member of the HSP100 family, is widely distributed in Gram-positive bacteria but is absent in Gram-negative bacteria. Although ClpL is involved in various cellular processes, such as the stress tolerance response, long-term survival, virulence, and antibiotic resistance, the detailed molecular mechanisms are largely unclear. Here we report that ClpL acts as a chaperone to properly fold CtsR, a stress response repressor, and prevents it from forming protein aggregates in Streptococcus mutans. In vitro, ClpL was able to successfully refold urea-denatured CtsR but not aggregated proteins. We suggest that ClpL recognizes primarily soluble but denatured substrates and prevents the formation of large protein aggregates. We also found that in vivo, the C-terminal D2-small domain of ClpL is essential for the observed chaperone activity. Since ClpL widely contributes to various cellular functions, we speculate that ClpL chaperone activity is necessary to maintain cellular homeostasis.

CtsR regulation in mcsAB-deficient Gram-positive bacteria

CtsR is an important repressor that modulates the transcription of class III stress genes in Gram-positive bacteria. In Bacillus subtilis, a model Gram-positive organism, the DNA binding activity of CtsR is regulated by McsAB-mediated phosphorylation of the protein where phosphorylated CtsR is a substrate for degradation by the ClpCP complex. Surprisingly, the mcsAB genes are absent from many Gram-positive bacteria, including streptococci; therefore, how CtsR activity is modulated in those bacteria remains unknown. Here we show that the posttranslational modulation of CtsR activity is different in Streptococcus mutans, a dental pathogen. We observed that of all of the Clp-related proteins, only ClpL is involved in the degradation of CtsR. Neither ClpP nor ClpC had any effect on the degradation of CtsR. We also found that phosphorylation of CtsR on a conserved arginine residue within the winged helix-turn-helix domain is necessary for modulation of the repressor activity of CtsR, as demonstrated by both in vitro and in vivo assays. We speculate that CtsR is regulated posttranslationally by a different mechanism in S. mutans and possibly in other streptococci.

Transcriptome analysis reveals that ClpXP proteolysis controls key virulence properties of Streptococcus mutans

The ClpXP proteolytic complex is critical for maintaining cellular homeostasis, as well as expression of virulence properties. However, with the exception of the Spx global regulator, the molecular mechanisms by which the ClpXP complex exerts its influence in Streptococcus mutans are not well understood. Here, microarray analysis was used to provide novel insights into the scope of ClpXP proteolysis in S. mutans. In a ΔclpP strain, 288 genes showed significant changes in relative transcript amounts (P≤0.001, twofold cut-off) as compared with the parent. Similarly, 242 genes were differentially expressed by a ΔclpX strain, 113 (47 %) of which also appeared in the ΔclpP microarrays. Several genes associated with cell growth were downregulated in both mutants, consistent with the slow-growth phenotype of the Δclp strains. Among the upregulated genes were those encoding enzymes required for the biosynthesis of intracellular polysaccharides (glg genes) and malolactic fermentation (mle genes). Enhanced expression of glg and mle genes in ΔclpP and ΔclpX strains correlated with increased storage of intracellular polysaccharide and enhanced malolactic fermentation activity, respectively. Expression of several genes known or predicted to be involved in competence and mutacin production was downregulated in the Δclp strains. Follow-up transformation efficiency and deferred antagonism assays validated the microarray data by showing that competence and mutacin production were dramatically impaired in the Δclp strains. Collectively, our results reveal the broad scope of ClpXP regulation in S. mutans homeostasis and identify several virulence-related traits that are influenced by ClpXP proteolysis.

ClpP of Streptococcus mutans differentially regulates expression of genomic islands, mutacin production, and antibiotic tolerance

Streptococcus mutans is the primary etiological agent of human dental caries and, at times, of infective endocarditis. Within the oral cavity, the pathogen is subjected to conditions of stress. A well-conserved protein complex named ClpP (caseinolytic protease) plays a vital role in adaptation under stress conditions. To gain a better understanding of the global role of the ClpP protease in cellular homeostasis, a transcriptome analysis was performed using a DeltaclpP mutant strain. The expression levels of more than 100 genes were up- or downregulated in the DeltaclpP mutant compared to the wild type. Notably, the expression of genes in several genomic islands, such as TnSmu1 and TnSmu2, was differentially modulated in the DeltaclpP mutant strain. ClpP deficiency also increased the expression of genes associated with a putative CRISPR locus. Furthermore, several stress-related genes and genes encoding bacteriocin-related peptides and many transcription factors were also found to be altered in the DeltaclpP mutant strain. A comparative analysis of the two-dimensional protein profile of the wild type and the DeltaclpP mutant strains showed altered protein profiles. Comparison of the transcriptome data with the proteomic data identified four common gene products, suggesting that the observed altered protein expression of these genes could be due to altered transcription. The results presented here indicate that ClpP-mediated proteolysis plays an important global role in the regulation of several important traits in this pathogen.