Patent application title: SIGNAL PEPTIDES, NUCLEIC ACID MOLECULES AND METHODS FOR TREATMENT OF CARIES
Yi-Chen Cathy Huang (Toronto, CA)
Celine Levesque (Toronto, CA)
Dennis G. Cvitkovitch (Oakville, CA)
The Governing Council of the University of Toronto
IPC8 Class: AA61K3816FI
Class name: Designated organic active ingredient containing (doai) peptide containing (e.g., protein, peptones, fibrinogen, etc.) doai 25 or more peptide repeating units in known peptide chain structure
Publication date: 2010-01-21
Patent application number: 20100016234
Patent application title: SIGNAL PEPTIDES, NUCLEIC ACID MOLECULES AND METHODS FOR TREATMENT OF CARIES
Yi-Chen Cathy Huang
Dennis G. Cvitkovitch
MERCHANT & GOULD PC
The Governing Council of the University of Toronto
Origin: MINNEAPOLIS, MN US
IPC8 Class: AA61K3816FI
Patent application number: 20100016234
Compounds that competitively inhibit binding of CSP to S. mutans histidine
kinase are provided. The compounds are preferably a peptide or an
antibody, and are preferably a derivative of [SEQ ID NO:2], a fragment of
[SEQ ID NO:2] or a derivative of a fragment of [SEQ ID NO:2]. Methods of
making these compounds and their use for inhibiting the growth of S.
mutans, for inhibiting dental caries, and for improving dental health are
21. A CSP analog comprising a polypeptide having 95% sequence identity to SEQ ID NO: 11, wherein the polypeptide inhibits genetic competence.
22. The CSP analog of claim 21, wherein the polypeptide comprises a single amino acid deletion of SEQ ID NO: 11.
23. The CSP analog of claim 21, wherein the polypeptide comprises a single amino acid substitution of SEQ ID NO: 11.
24. The CSP analog of claim 21, wherein the polypeptide comprises a single amino acid addition of SEQ ID NO: 11.
25. The CSP analog of claim 21, wherein the polypeptide is selected from the group consisting of SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 46, SEQ ID NO: 48, and SEQ ID NO: 51.
26. A pharmaceutical composition comprising a CSP analog of claim 21 and pharmaceutically acceptable carrier.
27. A method of inhibiting a biofilm comprising applying a pharmaceutical composition according to claim 25 to the biofilm.
28. A method of claim 27, further comprising administering an antibiotic.
29. A nucleic acid comprising an oligonucleotide encoding a CSP analog of claim 21.
30. An expression vector comprising the nucleic acid of claim 29.
31. A host cell comprising the expression vector of claim 30.
32. A method of expressing a CSP analog comprising culturing the host cell of claim 31 in culture medium.
33. A fusion protein comprising the CSP analog of claim 21 and a second peptide.
34. A fusion protein of claim 33, wherein the CSP analog is selected from the group consisting of SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 46, SEQ ID NO: 48, and SEQ ID NO: 51.
35. A nucleic acid molecule encoding the fusion protein of claim 33.
36. A pharmaceutical composition comprising the fusion protein of claim 33 and a pharmaceutically acceptable carrier.
37. A method of inhibiting a biofilm comprising administering the pharmaceutical composition of claim 36.
38. The method of claim 36 further comprising administering an antibiotic.
39. An expression vector comprising the nucleic acid of claim 35.
40. A host cell comprising the expression vector of claim 39.
41. A method of producing a fusion protein comprising culturing the host cell of claim 40 in culture medium
42. An antimicrobial composition comprising a) the CSP analog of claim 21, and b) a surfactant, a disinfectant, or both a surfactant and a disinfectant.
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a continuation application of U.S. patent application Ser. No. 11/005,636 filed Dec. 6, 2004, which is a continuation-in-part of U.S. patent application Ser. No. 09/833,017, now U.S. Pat. No. 6,923,962, filed Apr. 10, 2001, which application claims the benefit under 35 U.S.C. §119(e) of U.S. Provisional Patent Application No. 60/269,949 filed Feb. 20, 2001. The disclosures of said applications are hereby incorporated herein by reference.
BACKGROUND OF INVENTION
1. Field of the Invention
The invention generally relates to compounds and methods that inhibit or disrupt microbial biofilms involved in infections in man and animals and in biofouling of surfaces susceptible to microbial accumulation.
2. Description of the Related Art
Bacteria often attach and accumulate on surfaces, enabling them to resist removal and killing by mechanical and chemical means. This can result in persistent and chronic infections and fouling of devices that are in contact with liquids containing the colonizing bacteria. Bacteria respond to signals resulting from the proximity, density, and identity of microbial neighbors. Through the process of quorum sensing (QS), bacteria can indirectly determine population density by sensing concentration of a secreted signal molecule (Bassler, 2002). The ability of bacteria to communicate with one another by QS and behave collectively as a group confers significant advantages, including more efficient proliferation, better access to resources and niches, and a stronger defense against competitors (Jefferson, 2004). Many QS systems having various effects on bacterial cell physiology have been studied. Examples include biofilm differentiation in Pseudomonas aeruginosa (Davies et al., 1998), swarming motility in Serratia liquefaciens (Eberl et al., 1999), competence development in Streptococcus pneumoniae (Lee and Morrison, 1999) and Streptococcus mutans (Li et al., 2001), and induction of virulence factors in Staphylococcus aureus (Ji et al., 1995).
Controlling bacterial biofilms is desirable for almost every human enterprise in which solid surfaces are introduced into non-sterile aqueous environments. U.S. Pat. No. 6,024,958 describes peptides that attempt to control biofilm formation by preventing bacterial adherence to teeth. In addition to occurrence in dental caries, medical examples of biofilm growth include cases involving indwelling medical devices, joint implants, prostatitis, endocarditis, and respiratory infections. In fact, the Centers for Disease Control and Prevention (CDC; Atlanta, Ga.) estimate that 65% of human bacterial infections involve biofilms. Non-medical examples of biofilm colonization are water and beverage lines, cooling towers, radiators, aquaculture contamination, submerged pumps and impellers, hulls of commercial, fishing and military vessels and literally every situation where biofouling occurs. The potential benefits of basic research focused at biofilm physiology and genetics with the ultimate goal of controlling surface-mediated microbial growth are limitless.
Interest in the study of biofilm-grown cells has increased partly because biofilm growth provides a microenvironment for cells to exist in a physical and physiological state that can increase their resistance to antimicrobial compounds and mechanical forces (reviewed in Costerton and Lewandowski, Adv Dent Res, 11: 192-195). Growth in biofilms can also facilitate the transfer of genetic information between different species (Christensen et al. Appl Environ Microbiol, 64:2247-2255). Recent evidence suggests that biofilm-grown cells may display a dramatically different phenotype when compared with their siblings grown in liquid culture. In some, this altered physiological state has been shown to result from gene activation initiated by contact with surfaces (Finlay and Falkow. Microbiol Molec Rev, 61:136-169) or from signal molecules produced by the bacteria allowing them to sense the cell density (quorum sensing) (Davies et al. Appl Environ Microbiol, 61:860-867). Biofilms may also act as `genotypic reservoirs`, allowing persistence, transfer and selection of genetic elements conferring resistance to antimicrobial compounds.
Streptococcus mutans is the principal etiological agent of dental caries in humans. None of the known types of S. mutans antibiotics has satisfactorily controlled caries. There is a need to identify new ways to control S. mutans induced caries.
SUMMARY OF THE INVENTION
In accordance with certain embodiments of the present invention a compound is provided that competitively inhibits binding of CSP [SEQ ID NO:1] to S. mutans histidine kinase [SEQ ID NO:2]. In certain embodiments the compound is a peptide or an antibody. In some embodiments the compound is a derivative of SEQ ID NO:5, a fragment of SEQ ID NO:5 or a derivative of a fragment of SEQ ID NO:5.
In accordance with certain embodiments of the present invention methods of making an above-described compound are provided. In still other embodiments of the invention methods are provided in which an above-described compound is used for inhibiting the growth of S. mutans, for inhibiting dental caries, or for improving dental health. These and other embodiments, features and advantages of the invention will be apparent with reference to the following description and drawings.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the schematic layout of the arrangement of the genetic locus encoding the signal peptide precursor (ComC) [SEQ ID NO:4], the histidine kinase (ComD) [SEQ ID NO:2] and the response regulator (ComE) [SEQ ID NO:3]. Note that this arrangement is different from other loci in related streptococci for the following reasons: a). The comC gene [SEQ ID NO:4] is transcribed from its own unique promoter, unlike the genes thus far described in other streptococci that are arranged in an operon-like cluster with the comC/DE genes being transcribed from a single promoter, b) The comC gene [SEQ ID NO:4] is separated by 148 nucleotides from the comD gene [SEQ ID NO:6].
FIG. 2 shows the nucleic acid molecule that is SEQ ID NO:4. In a preferred embodiment, the figure shows a nucleic acid encoding CSP (competence signal peptide [SEQ ID NO:5]). FIG. 2 also shows histidine kinase [SEQ ID NO:6] sequences and response regulator [SEQ ID NO:7] sequences. FIG. 2A. S. mutans comC gene [SEQ ID NO:4]. Encodes a precursor to a signal peptide [SEQ ID NO:1]. FIG. 2B. S. mutans CSP encoding sequence [SEQ ID NO:5]. Encodes a Competence Signal Peptide [SEQ ID NO:11]. FIG. 2c. S. mutans comD gene [SEQ ID NO:6]. Encodes a response regulator that activates transcription of a number of genes. FIG. 2D. S. mutans comE gene [SEQ ID NO:7].
FIG. 3. Sequence of the deduced amino acid sequence of the signal peptide [SEQ ID NO:1], histidine kinase [SEQ ID NO:2], and response regulator [SEQ ID NO:3]. FIG. 3A. S. mutans ComC protein (CSP Precursor) [SEQ ID NO:1]. FIG. 3B. S. mutans ComD protein (Histidine Kindase) [SEQ ID NO:2]. FIG. 3c. S. mutans ComE protein (Response Regulator) [SEQ ID NO:3].
FIG. 4. The deduced amino acid sequence of the signal peptide precursor in various strains and its predicted cleavage site. The original peptide is expressed as a 46 amino acid peptide that is cleaved after the glycine-glycine residues to generate an active signal peptide.
FIG. 5 shows the peptide that is SEQ ID NO:11. The synthetic signal peptide is effective at inducing competence, biofilm formation and acid tolerance in Streptococcus mutans.
FIG. 6 shows the natural activity of the signal/receptor system functioning in vitro in model biofilms as determined by the ability of various strains of S. mutans to accept donor plasmid DNA conferring erythromycin resistance.
FIG. 7 is a table illustrating the effect of synthetic peptide on genetic competence in S. mutans cells. Induction of genetic transformation in Streptococcus mutans by synthetic competence stimulating peptide (SCSP).
FIG. 8 is a list of the primers used to amplify the genes or internal regions of the target genes by polymerase chain reaction (PCR) for subsequent sequencing or inactivation.
FIG. 9 shows the ComCDE local region [SEQ ID NO:18 and SEQ ID NO:19]. The ComC (first highlighted region; nucleotide 101 to 241), ComD (second highlighted region; nucleotides 383 to 1708) and ComE (third highlighted region; nucleotides 1705 to 2457) proteins are highlighted.
FIG. 10 shows the comX DNA sequence [SEQ ID NO:28], protein sequence [SEQ ID NO:29], and the comX gene local region [SEQ ID NO:30] with 100 bp included both upstream and downstream (promoter is upstream). FIG. 10A. S. mutans comX gene [SEQ ID NO:28]. FIG. 10B. S. mutans ComX protein [SEQ ID NO:29]. FIG. 10c. S. mutans comX gene local region [SEQ ID NO:30].
FIG. 11 shows the comA and comB nucleotide [SEQ ID NO:31] and [SEQ ID NO:33] and amino acid sequences [SEQ ID NO:32] and [SEQ ID NO:34]. ComA and ComB are the components of the CSP exporter. FIG. 11A. S. mutans comA gene [SEQ ID NO:31]. FIG. 11B. S. mutans ComA protein [SEQ ID NO:32]. FIG. 11c. S. mutans comB gene [SEQ ID NO:33] FIG. 11D. S. mutans ComB protein [SEQ ID NO:34].
FIG. 12 illustrates the effect of synthetic peptide on acid resistance tolerance in S. mutans comC deficient cells. Addition of synthetic signal peptide (CSP) [SEQ ID NO:11] into the culture of the comC mutant restored the ability of the mutant to survive a low pH challenge when compared to the parent strain NG8.
FIG. 13 is a schematic representation of quorum sensing circuit in S. mutans.
FIG. 14 shows the effect of different concentrations of H1 on genetic transformation of S. mutans wild-type UA159. Results are expressed as the mean±SE of three independent experiments.
FIG. 15 shows the effect of different concentrations of H1 on genetic transformation of S. mutans comD null mutant.
FIG. 16 shows the effect of different concentrations (μg/ml) of CSP and H1 on cell growth ofS. mutans wild-type UA159 in THYE at pH 5.5. Means OD600 values±SE, Results represent the average of three independent experiments.
FIG. 17 effect of different concentrations (μg/ml) of CSP and H1 on cell growth of S. mutans wild-type UA159 in THYE at pH 7.5. Means OD600 values±SE. Results represent the average of three independent experiments.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
In some Gram-positive bacteria (including Streptococcus mutans), when a specific histidine kinase receptor located in the cell membrane is disrupted, the cells become ineffective at developing a biofilm. The cells growing in this biofilm environment use a small peptide signal molecule to activate the receptor in surrounding cells, thereby communicating the message to form a biofilm. This same signal peptide and histidine kinase are also involved in the induction of genetic competence, the cell's ability to take up and incorporate DNA from its extracellular environment, as well as that of acid tolerance, the cell's ability to survive pH levels as low as pH 3.0. A mechanism that blocks the signal molecule from activating the histidine kinase receptor molecule provides a novel method for controlling microbial biofilms, either alone or in combination with chemical or physical means.
We have identified a genetic locus in S. mutans consisting of three genes that encode: 1) a peptide precursor [SEQ ID NO:1] that is processed during export into a secreted 21-amino acid peptide (CSP) [SEQ ID NO:11]; 2) a histidine kinase [SEQ ID NO:2] that acts as a cell surface receptor activated by the peptide; 3) a response regulator [SEQ ID NO:3] that activates a number of other genes involved in genetic competence, biofilm formation, and acid tolerance of S. mutans. These properties have been attributed to the bacterium's ability to cause dental caries. Inactivation of any of these three genes or impairment of interaction or activity of any of their encoded proteins will disrupt the bacterium's ability to take up foreign DNA, form biofilms, and tolerate acidic pH.
Streptococcus mutans is a resident of the biofilm environment of dental plaque, a matrix of bacteria and extracellular material that adheres to the tooth surface. Under appropriate environmental conditions populations of S. mutans and the pH of the surrounding plaque will drop. S. mutans, being among the most acid tolerant organisms residing in dental plaque, will increase its numbers in this acidic environment and eventually become a dominant member of the plaque community. This situation eventually leads to dissolution of the tooth enamel, resulting in the development of dental caries. We control the accumulation and acid tolerance of this bacterium to make it less able to cause caries. We accomplish this by using inhibitors of an extracellular signal peptide that promotes the expression of genes involved in S. mutans biofilm formation and acid tolerance. Compounds are disclosed that inhibit the action of the peptide. These inhibitors can include peptides, antibodies, or other agents that specifically inhibit the activation of the histidine kinase and the family of genes activated as a result of the histidine kinase activation by the signal molecule. Inhibitors include: modified structures of the peptide where amino acids are removed from the N-- and/or COOH terminal of the peptide and/or substitutions of internal amino acid residues. We delete, one, two to 5, 6 to 10 and 10 to 15 amino acids from the peptide (for example at either terminal) and measure competitive inhibition of signal peptide binding to histidine kinase (1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more amino acids are deleted and inhibition measured). Inhibitors also include antibodies raised against the 21-amino acid CSP [SEQ ID NO:11] alone or coupled to a larger molecule to increase immunogenicity. We also test inhibitors described in Barrett et al. Proc. Natl. Acad. Sci USA 95:5317-5322) and measure competitive inhibition of signal peptide binding to histidine kinase.
In addition to identifying the genes encoding this signaling/sensing system, we have identified and chemically synthesized a 21-amino acid peptide [SEQ ID NO:11] that promotes biofilm formation and acid tolerance of S. mutans. A survey of the literature and genome databases reveals that genes similar to this signal-receptor system are present in most Gram-positive bacteria, and therefore an inhibitor, or family of related inhibitors may be effective at inhibiting biofilm formation among a large group of bacteria.
Treatment or prevention of dental caries comprises addition of compounds that inhibit the stimulatory action of the 21-amino acid peptide [SEQ ID NO:11] on biofilm formation and acid tolerance of S. mutans. This is accomplished by delivery of these compounds to the biofilm and/or to incorporate these inhibitors into materials to control growth on surfaces. This includes delivery by topical application, alone or in combination with other compounds including toothpaste, mouthwash, food or food additives.
Streptococcus mutans is also implicated in causing infective endocarditis. Inhibitors of biofilm formation, and hence aggregation are useful in the treatment of these bacterial infections as well.
Identification and Characterization of Competence Signal Peptide (CSP), Histidine Kinase (UK) and Response Regulator (RR)
Competence Signal Peptide
An isolated CSP from S. mutans is provided in accordance with certain embodiments of the present invention. Also provided in accordance with certain embodiments of the present invention is a recombinant isolated CSP [SEQ ID SEQ 11] peptide produced by a cell including a nucleic acid molecule encoding CSP [SEQ ID NO:5] operably linked to a promoter. Further provided in accordance with certain embodiments of the present invention is an isolated nucleic acid molecule encoding a CSP [SEQ ID NO:5]. The peptide we work with is preferably chemically synthesized.
CSP-encoding nucleic acid molecules [SEQ ID NO:5] and molecules having sequence identity or which hybridize to the CSP-encoding sequence and which encode a peptide having CSP activity (preferred percentages for sequence identity are described below) as well as vectors including these molecules are provided in accordance with various embodiments of the present invention. In certain embodiments of the invention, CSP [SEQ ID NO:11] or peptides having sequence identity (preferred percentages described below) or which have CSP activity are provided. The nucleic acid molecules and peptides disclosed herein may be from S. mutans and they may be isolated from a native source, synthetic or recombinant. CSP [SEQ ID NO:11] or peptides having sequence identity, which have CSP activity, as prepared by the processes described in this application, are also provided in accordance with the present invention.
In accordance with certain embodiments of the present invention, an isolated HK [SEQ ID NO:2] from S. mutans is disclosed. Also disclosed is a recombinant isolated HK polypeptide produced by a cell including a nucleic acid molecule encoding HK [SEQ ID NO:6] operably linked to a promoter. In another embodiment of the invention an isolated nucleic acid molecule encoding a HK polypeptide [SEQ ID NO:2] is disclosed.
HK-encoding nucleic acid molecules and molecules having sequence identity or which hybridize to the HK-encoding sequence [SEQ ID NO:6] and which encode a protein having HK activity (preferred percentages for sequence identity are described below) as well as vectors including these molecules are disclosed as part of the present invention. In accordance with some embodiments of the present invention, HK [SEQ ID NO:2] or polypeptides having sequence identity (preferred percentages described below) or which have HK activity are disclosed. The nucleic acid molecules and polypeptides disclosed herein may be from S. mutans and they may be isolated from a native source, synthetic or recombinant. Also provided according to certain embodiments of the present invention is HK [SEQ ID NO:2] or polypeptides having sequence identity, which have HK activity, as prepared by the processes described in this application.
In accordance with certain embodiments of the present invention an isolated RR [SEQ ID NO:3] from S. mutans is disclosed. A recombinant isolated RR [SEQ ID NO:3] polypeptide produced by a cell including a nucleic acid molecule encoding RR [SEQ ID NO:7] operably linked to a promoter is provided according to certain other embodiments of the present invention. Still other embodiments of the invention include an isolated nucleic acid molecule encoding a RR polypeptide.
Certain embodiments of the invention include RR-encoding nucleic acid molecules and molecules having sequence identity or which hybridize to the RR-encoding sequence [SEQ ID NO:7] and which encode a polypeptide having RR activity (preferred percentages for sequence identity are described below) as well as vectors including these molecules. Some embodiments of the invention also include RR [SEQ ID NO:3] or polypeptides having sequence identity (preferred percentages described below) or which have RR activity. The nucleic acid molecules and polypeptides of the invention may be from S. mutans and they may be isolated from a native source, synthetic or recombinant. Certain embodiments of the invention include RR [SEQ ID NO:3] or polypeptides having sequence identity, which have RR activity, as prepared by the processes described in this application.
The comA and comB nucleotide [SEQ ID NO:31 and SEQ ID NO:33] and amino acid sequences [SEQ ID NO:32 and SEQ ID NO:34] are also aspects of certain embodiments of the invention. ComA and ComB are components of the CSP exporter. The discussion of variants, sequence identity etc. for CSP, HK, RR applies to both the full sequences shown in the figures as well as bracketed portions of sequences (coding regions). The peptides and polypeptides may be natural, recombinantly produced or synthetic.
Functionally Equivalent Nucleic Acid Molecules
Certain embodiments of the invention include nucleic acid molecules that are functional equivalents of all or part of the CSP sequence in SEQ ID NO:5. (A nucleic acid molecule may also be referred to as a DNA sequence or nucleotide sequence in this application. All these terms have the same meaning as nucleic acid molecule). Functionally equivalent nucleic acid molecules are DNA and RNA (such as genomic DNA, complementary DNA, synthetic DNA, and messenger RNA molecules) that encode peptides having the same or similar CSP activity as the CSP peptide shown in SEQ ID NO:11. Functionally equivalent nucleic acid molecules can encode peptides that contain a region having sequence identity to a region of a CSP peptide [SEQ ID NO:11] or more preferably to the entire CSP peptide. Identity is calculated according to methods known in the art. The ClustalW program (preferably using default parameters) [Thompson, J D et al., Nucleic Acid Res. 22:4673-4680.], described below, is most preferred. For example, if a nucleic acid molecule (called "Sequence A") has 90% identity to a portion of the nucleic acid molecule in SEQ ID NO:5, then Sequence A will preferably be identical to the referenced portion of the nucleic acid molecule in SEQ ID NO:5, except that Sequence A may include up to 10 point mutations, such as substitutions with other nucleotides, per each 100 nucleotides of the referenced portion of the nucleic acid molecule in SEQ ID NO:5. Mutations described in this application preferably do not disrupt the reading frame of the coding sequence. Nucleic acid molecules functionally equivalent to the CSP sequences can occur in a variety of forms as described below.
Nucleic acid molecules may encode conservative amino acid changes in CSP peptide [SEQ ID NO:11]. Certain embodiments of the invention include functionally equivalent nucleic acid molecules that encode conservative amino acid changes within a CSP amino acid sequence and produce silent amino acid changes in CSP.
Nucleic acid molecules may encode non-conservative amino acid substitutions, additions or deletions in CSP peptide. Some embodiments of the invention include functionally equivalent nucleic acid molecules that make non-conservative amino acid changes within the CSP amino acid sequence in SEQ ID NO:11. Functionally equivalent nucleic acid molecules include DNA and RNA that encode peptides, peptides and proteins having non-conservative amino acid substitutions (preferably substitution of a chemically similar amino acid), additions, or deletions but which also retain the same or similar CSP activity as the CSP peptide shown in SEQ ID NO:11. The DNA or RNA can encode fragments or variants of CSP. Fragments are useful as immunogens and in immunogenic compositions (U.S. Pat. No. 5,837,472). The CSP or CSP-like activity of such fragments and variants is identified by assays as described below. Fragments and variants of CSP encompassed by the present invention should preferably have at least about 40%, 60%, 80% or 95% sequence identity to the naturally occurring CSP nucleic acid molecule, or a region of the sequence, such as the coding sequence or one of the conserved domains of the nucleic acid molecule, without being identical to the sequence in SEQ ID NO:11. Sequence identity is preferably measured with the ClustalW program (preferably using default parameters) (Thompson, J D et al., Nucleic Acid Res. 22:4673-4680).
Nucleic acid molecules functionally equivalent to the CSP nucleic acid molecule in SEQ ID NO:5 will be apparent from the following description. For example, the sequence shown in SEQ ID NO:5 may have its length altered by natural or artificial mutations such as partial nucleotide insertion or deletion, so that when the entire length of the coding sequence within SEQ ID NO:5, is taken as 100%, the functional equivalent nucleic acid molecule preferably has a length of about 60-120% thereof, more preferably about 80-110% thereof. Fragments may be less than 60%.
Nucleic acid molecules containing partial (usually 80% or less, preferably 60% or less, more preferably 40% or less of the entire length) natural or artificial mutations so that some codons in these sequences code for different amino acids, but wherein the resulting peptide retains the same or similar CSP activity as that of a naturally occurring CSP peptide [SEQ ID NO:11]. The mutated DNAs created in this manner should preferably encode a peptide having at least about 40%, preferably at least about 60%, at least about 80%, and more preferably at least about 90% or 95% sequence identity to the amino acid sequence of the CSP peptide in SEQ ID NO:11. The ClustalW program preferably assesses sequence identity.
Since the genetic code is degenerate, the nucleic acid sequence in SEQ ID NO:5 is not the only sequence which may code for a peptide having CSP activity. This invention includes nucleic acid molecules that have the same essential genetic information as the nucleic acid molecule described in SEQ ID NO:5. Nucleic acid molecules (including RNA) having one or more nucleic acid changes compared to the sequences described in this application and which result in production of a peptide shown in SEQ ID NO:11 are within the scope of various embodiments of the invention.
Other functional equivalent forms of CSP-encoding nucleic acids can be isolated using conventional DNA-DNA or DNA-RNA hybridization techniques. Thus, certain embodiments of the present invention also include nucleic acid molecules that hybridize to one or more of the sequences in SEQ ID NO:5 or its complementary sequence, and that encode expression for peptides, peptides and proteins exhibiting the same or similar activity as that of the CSP peptide produced by the DNA in SEQ ID NO:5 or its variants. Such nucleic acid molecules preferably hybridize to the sequence in SEQ ID NO:5 under moderate to high stringency conditions (see Sambrook et al. Molecular Cloning: A Laboratory Manual, Most Recent Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). High stringency washes have low salt (preferably about 0.2% SSC), and low stringency washes have high salt (preferably about 2% SSC). A temperature of about 37° C. or about 42° C. is considered low stringency, and a temperature of about 50-65° C. is high stringency. Some embodiments of the invention also include a method of identifying nucleic acid molecules encoding a CSP activator peptide (preferably a mammalian peptide), including contacting a sample containing nucleic acid molecules including all or part of SEQ ID NO:5 (preferably at least about 15 or 20 nucleotides of SEQ ID NO:5) under moderate or high stringency hybridization conditions and identifying nucleic acid molecules which hybridize to the nucleic acid molecules including all or part of SEQ ID NO:5. Similar methods are described in U.S. Pat. No. 5,851,788, which is incorporated by reference in its entirety.
Certain embodiments of the present invention also include methods of using all or part of the nucleic acid molecules which hybridize to all or part of SEQ ID NO:5, for example as probes or in assays to identify antagonists or inhibitors of the peptides produced by the nucleic acid molecules (described below). Some embodiments of the present invention include methods of using nucleic acid molecules having sequence identity to the CSP nucleic acid molecule (as described below) in similar methods.
Certain embodiments of the invention also include a nucleic acid molecule detection kit including, preferably in a suitable container means or attached to a surface, a nucleic acid molecule as disclosed herein encoding CSP [SEQ ID NO:5] or a peptide having CSP activity and a detection reagent (such as a detectable label). Other variants of kits will be apparent from this description and teachings in patents such as U.S. Pat. Nos. 5,837,472 and 5,801,233, which are incorporated by reference in their entirety.
A nucleic acid molecule described above is considered to have a function substantially equivalent to the CSP nucleic acid molecules [SEQ ID NO:5] of the present invention if the peptide [SEQ ID NO:11] produced by the nucleic acid molecule has CSP activity. A peptide has CSP activity if it can stimulate genetic competence and acid tolerance in S. mutans. Activation of the HK [SEQ ID NO:2]/RR [SEQ ID NO:3] is shown where a peptide is capable of stimulating the uptake and incorporation of foreign DNA. We describe below how the activity of these peptide-mediated processes can be measured by determining the efficiency of plasmid uptake, which is a measure of genetic competence. Since the ability to transport and incorporate foreign DNA relies on activation of the HK [SEQ ID NO:2]/RR [SEQ ID NO:3] and subsequent genes activated by the signal cascade initiated by the signal peptide, measurement of the conferment of erythromycin resistance by cells exposed to the peptide and plasmid DNA conferring erythromycin resistance indicates its level of function. Conversely if an inhibitor is capable of interfering with the action of the peptide the competence assay will indicate this by a corresponding decrease in the number of cells that acquire erythromycin resistance as described in the assays below (assays of genetic competence and assay of transformation of biofilms). Activation of the HK [SEQ ID NO:2]/RR [SEQ ID NO:3] is also shown where a peptide is capable of stimulating an acid tolerance response. We describe below how the activity of these peptide-mediated processes can be measured by determining the survival rate of cells in acidic pH conditions. Since the ability to survive exposure to acidic pH depends on the activation of the HK/RR and subsequent genes activated by the signal peptide, measurement of the survival of S. mutans in low pH conditions indicates the level of function of the signal peptide. Conversely, if an inhibitor is capable of interfering with the signal peptide sensing system the assay for acid adaptation will indicate this by a corresponding decrease in the survival rate of cells grown in acidic pH conditions as described in the assay below (assay of acid adaptation).
Production of CSP in Eukaryotic and Prokaryotic Cells
The nucleic acid molecules disclosed herein may be obtained from a cDNA library. The nucleotide molecules can also be obtained from other sources known in the art such as expressed sequence tag analysis or in vitro synthesis. The DNA described in this application (including variants that are functional equivalents) can be introduced into and expressed in a variety of eukaryotic and prokaryotic host cells. A recombinant nucleic acid molecule for the CSP contains suitable operatively linked transcriptional or translational regulatory elements. Suitable regulatory elements are derived from a variety of sources, and they may be readily selected by one with ordinary skill in the art (Sambrook, J, Fritsch, E. E. & Maniatis, T. (Most Recent Edition). Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press. New York; Ausubel et al. (Most Recent Edition). Current Protocols in Molecular Biology, John Wiley & Sons, Inc.). For example, if one were to upregulate the expression of the nucleic acid molecule, one could insert a sense sequence and the appropriate promoter into the vector. Promoters can be inducible or constitutive, environmentally- or developmentally-regulated, or cell- or tissue-specific. Transcription is enhanced with promoters known in the art for expression. The CMV and SV40 promoters are commonly used to express desired peptide in cells. Other promoters known in the art may also be used (many suitable promoters and vectors are described in the applications and patents referenced in this application).
If one were to downregulate the expression of the nucleic acid molecule, one could insert the antisense sequence and the appropriate promoter into the vehicle. The nucleic acid molecule may be either isolated from a native source (in sense or antisense orientations), synthesized, or it may be a mutated native or synthetic sequence or a combination of these.
Examples of regulatory elements include a transcriptional promoter and enhancer or RNA polymerase binding sequence, a ribosomal binding sequence, including a translation initiation signal. Additionally, depending on the vector employed, other genetic elements, such as selectable markers, may be incorporated into the recombinant molecule. Other regulatory regions that may be used include an enhancer domain and a termination region. The regulatory elements may bacterial, fungal, viral or avian in origin. Likewise the regulatory elements may originate from animal, plant, yeast, insect or other sources, including synthetically produced elements and mutated elements.
In addition to using the expression vectors described above, the peptide may be expressed by inserting a recombinant nucleic acid molecule in a known expression system derived from bacteria, viruses, yeast, mammals, insects, fungi or birds. The recombinant molecule may be introduced into the cells by techniques such as Agrobacterium tumefaciens-mediated transformation, particle-bombardment-mediated transformation, direct uptake, microinjection, coprecipitation, transfection and electroporation depending on the cell type. Retroviral vectors, adenoviral vectors, Adeno Associated Virus (AAV) vectors, DNA virus vectors and liposomes may be used. Suitable constructs are inserted in an expression vector, which may also include markers for selection of transformed cells. The construct may be inserted at a site created by restriction enzymes.
In one embodiment of the invention, a cell is transfected with a nucleic acid molecule of the invention inserted in an expression vector to produce cells expressing a peptide encoded by the nucleic acid molecule.
Another embodiment of the invention relates to a method of transfecting a cell with a nucleic acid molecule disclosed herein, inserted in an expression vector to produce a cell expressing the CSP peptide [SEQ ID NO:11] or other peptide of the invention. In accordance with certain embodiments of the invention a method is provided for expressing the disclosed peptides in a cell. A preferred process would include culturing a cell including a recombinant DNA vector including a nucleic acid molecule encoding CSP [SEQ ID NO:5] (or another nucleic acid molecule of the invention) in a culture medium so that the peptide is expressed. The process preferably further includes recovering the peptide from the cells or culture medium.
Certain embodiments of the present invention include oligonucleotide probes made from the cloned CSP nucleic acid molecules described in this application or other nucleic acid molecules disclosed herein (see Materials and Methods section). The probes may be 15 to 20 nucleotides in length. A preferred probe is at least 15 nucleotides of SEQ ID NO:5. Certain embodiments of the invention also include at least 15 consecutive nucleotides of SEQ ID NO:5. The probes are useful to identify nucleic acids encoding CSP peptides as well as peptides functionally equivalent to CSP. The oligonucleotide probes are capable of hybridizing to the sequence shown in SEQ ID NO:5 under stringent hybridization conditions. A nucleic acid molecule encoding a peptide disclosed herein may be isolated from other organisms by screening a library under moderate to high stringency hybridization conditions with a labeled probe. The activity of the peptide encoded by the nucleic acid molecule is assessed by cloning and expression of the DNA. After the expression product is isolated, the peptide is assayed for CSP activity as described in this application.
Functionally equivalent CSP nucleic acid molecules from other cells, or equivalent CSP-encoding cDNAs or synthetic DNAs, can also be isolated by amplification using Polymerase Chain Reaction (PCR) methods. Oligonucleotide primers, such as degenerate primers, based on SEQ ID NO:5 can be prepared and used with PCR and reverse transcriptase (E. S. Kawasaki (1990), In Innis et al., Eds., PCR Protocols, Academic Press, San Diego, Chapter 3, p. 21) to amplify functional equivalent DNAs from genomic or cDNA libraries of other organisms. The oligonucleotides can also be used as probes to screen cDNA libraries.
Functionally Equivalent Peptides, Peptides and Proteins
The present invention includes not only the peptides encoded by the sequences disclosed herein, but also functionally equivalent peptides, peptides and proteins that exhibit the same or similar CSP peptide activity.
We designed and synthesized peptide analogs based on the native sequence of the S. mutans CSP and assayed their ability to interfere with competence development, acid tolerance response, and biofilm formation.
Peptide Analogs were Altered Based on the Amino Acid Sequence of Native CSP.
A panel of 17 peptide analogs with modification in length and hydrophobicity were designed and synthesized. The first set of peptide analogs were generated by deleting the 1st, 2nd, 3rd, 4th, or 5th residues from the N- and C-termini of the mature CSP sequence. The second set included peptide analogs with substitutions of charged internal residues with neutral (valine) or hydrophobic (alanine) residues. The peptide analogs synthesized and tested in this study are listed at Table 1.
Peptide Analog H1 is Capable of Inhibiting Genetic Competence.
All 17 peptide analogs designed and synthesized based on the sequence of the native S. mutans CSP were first screened for their ability to hinder transformation efficiency in the S. mutans wild-type UA159 strain. Among them, analog H1 caused a significant decrease (18-fold) in transformation efficiency compared to that of the natural transformation (without addition of exogenous CSP) of the S. mutans UA159 strain (Table 2 and FIG. 2). These results demonstrate that H1 inhibited the S. mutans natural genetic transformation. The competence regulon identified and characterized by our laboratory indicated that transformation in S. mutans is a comD-dependent process. To test the hypothesis that the peptide analog H1 is able to compete with the natural CSP produced by S. mutans for occupying the ComD histidine kinase receptor, we tested the ability of H1 to induce genetic competence in an S. mutans comD null mutant. As expected, the results showed that the effect of peptide analog H1 is indeed accomplished via the comD ComD receptor, and therefore is a ComD-dependent process (FIG. 3).
In contrast, the peptide analogs IH-1, IH-2, B1, and C1 showed no significant effect on transformation efficiency compared to the wild-type CSP (Table 2). These results suggested that these peptide analogs have retained the native CSP activity despite the sequence modifications. However, the transformation efficiency of S. mutans UA159 in the presence of the peptide analogs D1, E1, F1, G1, A2, B2, C2, D2, E2, F2, G2, or B3 is diminished compared to the wild-type CSP (5 μg CSP). This suggested that these peptide analogs behave similarly to CSP in terms of competence stimulation but may not have the same affinity for the comD receptor as the native wild-type CSP.
TABLE-US-00001 TABLE 1 Modified versions of the mature S. mutans CSP peptide Peptide Analog Amino acid sequence Modification CSP SGSLSTFFRLFNRSFTQALGK mature wild-type CSP sequence [SEQ ID NO: 11] IH-1 GSLSTFFRLFNRSFTQALGK 1st residue removed from N' [SEQ ID NO: 35] IH-2 SGSLSTFFRLFNRSFTQALG 1st residue removed from C' [SEQ ID NO: 36] B1 S SLSTFFRLFNRSFTQALGK 2nd residue removed from N' [SEQ ID NO: 37] C1 SG LSTFFRLFNRSFTQALGK 3rd residue removed from N' [SEQ ID NO: 38] D1 SGS STFFRLFNRSFTQALGK 4th residue removed from N' [SEQ ID NO: 39] E1 SGSL TFFRLFNRSFTQALGK 5th residue removed from N' [SEQ ID NO: 40] F1 SGSLSTFFRLFNRSFTQAL K 2nd residue removed from C' [SEQ ID NO: 41] G1 SGSLSTFFRLFNRSFTQA GK 3rd residue removed from C' [SEQ ID NO: 42] H1 SGSLSTFFRLFNRSFTQ LGK 4th residue removed from C' [SEQ ID NO: 43] A2 SGSLSTFFRLFNRSFT ALGK 5th residue removed from C' [SEQ ID NO: 44] B2 SGSLSTFFVLFNRSFTQALGK Substitution of 1st R residue with V [SEQ ID NO: 45] C2 SGSLSTFFALFNRSFTQALGK Substitution of 1st R residue with A [SEQ ID NO: 46] D2 SGSLSTFFRLFNVSFTQALGK Substitution of 2nd R residue with V [SEQ ID NO: 47] E2 SGSLSTFFRLFNASFTQALGK Substitution of 2nd R residue with A [SEQ ID NO: 48] F2 SGSLSTFFRLFNRSFTQALGV Substitution of K residue with V [SEQ ID NO: 49] G2 SGSLSTFFRLFNRSFTQALGA Substitution of K residue with A [SEQ ID NO: 50] B3 SGTLSTFFRLFNRSFTQA JH1005 CSP sequence [SEQ ID NO: 51]
TABLE-US-00002 TABLE 2 Effect of 5 μg/ml of peptide analogs on competence of S. mutans wild-type UA159 Peptide Transformation Transformation Analog efficiency (vs no CSP) efficiency (vs 5 μg CSP) CSP 1554-fold increase -- IH-1 no effecta no effect IH-2 no effect no effect B1 no effect no effect C1 no effect no effect D1 275-fold increase 6-fold decrease E1 791-fold increase 2-fold decrease F1 541-fold increase 3-fold decrease G1 848-fold increase 2-fold decrease H1 18-fold decrease 28,000-fold decrease A2 125-fold increase 7-fold decrease B2 4-fold increase 414-fold decrease C2 32-fold increase 48-fold decrease D2 99-fold increase 16-fold decrease E2 252-fold increase 6-fold decrease F2 543-fold increase 3-fold decrease G2 56-fold increase 28-fold decrease B3 195-fold increase 8-fold decrease aNo effect: no significant difference by comparison with CSP.
TABLE-US-00003 TABLE 3 Effect of 5 μg/ml of peptide analogs on growth at pH 7.5, acid resistance, and biofilm formation of S. mutans wild-type UA159 Peptide Growth Acid resistance Biofilm formation analog (pH 7.5) (pH 5.5) (SDM-glucose) CSP ↓ growth growth no effect IH-1 ↓ growth growth no effect IH-2 ↓ growth growth no effect B1 ↓ growth growth no effect C1 ↓ growth growth no effect D1 ↓ growth growth no effect E1 ↓ growth growth no effect F1 ↓ growth ↓ growth ↓ 36.7% biomass G1 ↓ growth growth ↓ 24.4% biomass H1 no effect ↓ growth no effect A2 no effect ↓ growth no effect B2 no effect ↓ growth no effect C2 no effect ↓ growth no effect D2 no effect ↓ growth no effect E2 no effect ↓ growth ↓ 38.9% biomass F2 ↓ growth ↓ growth ↓ 38.7% biomass G2 ↓ growth ↓ growth ↓ 35.6% biomass B3 no effect ↓ growth ↓ 34.4% biomass
Multiple Peptide Analogs Affect Cell Growth in an Acidic Medium.
In order to determine if the peptide analogs were capable of inhibiting the acid tolerance mechanisms of S. mutans, the cells' ability to withstand acid challenge typically encountered in dental plaque, the S. mutans UA159 cells were grown in THYE medium at pH 7.5 and pH 5.5 in the presence of various concentrations of peptide analogs. The results presented at Table 3 showed that the peptide analogs F1, F2, and G2 caused a diminution of cell growth at pH 7.5 and 5.5. The peptide analogs H1, A2, B2, C2, D2, E2, and B3 have no effect on S. mutans cell growth at pH 7.5. Moreover, when the same peptide analogs were tested at pH 5.5, the results showed that there was a significant decrease in cell growth. Interestingly, the peptide analog H1 involved in the inhibition of genetic competence is also able to inhibit the S. mutans cell growth in an acidic medium (FIG. 4), while the growth at neutral pH is unaffected (FIG. 5).
Peptide Analogs Inhibit of S, mutans Biofilm Formation.
It has been demonstrated that the S. mutans comC null mutant unable to produce the CSP signal peptide forms a biofilm lacking the wild-type architecture. Moreover, the exogenous addition of synthetic CSP restores the wild-type phenotype in the comC defective mutant (Li et al., 2002). Therefore, CSP seems to play an integral part in S. mutans biofilm formation. Consequently, the peptide analogs were tested for their ability to inhibit the formation of S. mutans biofilms. Results presented at Table 3 indicated that the peptide analogs F1, G1, E2, F2, G2 and B3 had a significantly reduced biomass ranging from 24.4% to 38.9% compared to the S. mutans biofilm grown in the presence of wild-type CSP suggesting that these peptide analogs are able to hinder the signal pathway regulating the formation of biofilm by S. mutans. Peptide analog E2 could be a potent S. mutans QS inhibitor as it elicited a significant decrease in biofilm formation as well as inhibited cell growth at pH 5.5 without affecting the cell growth at neutral pH.
A peptide is considered to possess a function substantially equivalent to that of the CSP peptide [SEQ ID NO:11] if it has CSP activity. CSP activity means that it is able to confer genetic competence to S. mutans, as measured by an increased ability to incorporate and express foreign genetic material, when added to cells as described in the assay of genetic competence below. CSP activity also means that the peptide is able to confer an acid tolerance response in S. mutans as measured by an increase in cell survival under acidic pH conditions when added to cells as described in the assay for acid adaptation below. Functionally equivalent peptides, peptides and proteins include peptides, peptides and proteins that have the same or similar protein activity as CSP when assayed, i.e. they are able to stimulate genetic competence and low pH tolerance (the ability to withstand acid challenges of pH 3.5-pH 3.0 for up to 3 hours) in S. mutans. A peptide has CSP activity if it is capable of increasing the frequency of uptake and expression of foreign DNA as described in the following assay for genetic competence and if the peptide can promote an acid tolerance response as described in the assay for acid adaptation.
Identity refers to the similarity of two peptides or proteins that are aligned so that the highest order match is obtained. Identity is calculated according to methods known in the art, such as the ClustalW program. For example, if a peptide (called "Sequence A") has 90% identity to a portion of the peptide in SEQ ID NO:3, then Sequence A will be identical to the referenced portion of the peptide in SEQ ID NO:3, except that Sequence A may include up to 1 point mutations, such as substitutions with other amino acids, per each 10 amino acids of the referenced portion of the peptide in SEQ ID NO:3. Peptides, peptides and proteins functional equivalent to the CSP peptides can occur in a variety of forms as described below.
Peptides biologically equivalent in function to CSP peptide include amino acid sequences containing amino acid changes in the CSP sequence [SEQ ID NO:11]. The functional equivalent peptides have at least about 40% sequence identity, preferably at least about 60%, at least about 75%, at least about 80%, at least about 90% or at least about 95% sequence identity, to the natural CSP peptide [SEQ ID NO:11] or a corresponding region. The ClustalW program preferably determines sequence identity. Most preferably, 1, 2, 3, 4, 5, 5-10, 10-15 amino acids are modified.
Variants of the CSP peptide may also be created by splicing. A combination of techniques known in the art may be used to substitute, delete or add amino acids. For example, a hydrophobic residue such as methionine can be substituted for another hydrophobic residue such as alanine. An alanine residue may be substituted with a more hydrophobic residue such as leucine, valine or isoleucine. An aromatic residue such as phenylalanine may be substituted for tyrosine. An acidic, negatively-charged amino acid such as aspartic acid may be substituted for glutamic acid. A positively-charged amino acid such as lysine may be substituted for another positively-charged amino acid such as arginine. Modifications of the peptides disclosed herein may also be made by treating such peptide with an agent that chemically alters a side group, for example, by converting a hydrogen group to another group such as a hydroxy or amino group.
Peptides having one or more D-amino acids are contemplated in certain embodiments of the present invention. Also contemplated are peptides where one or more amino acids are acetylated at the N-terminus. Those skilled in the art recognize that a variety of techniques are available for constructing peptide mimetics (i.e., a modified peptide or peptide or protein) with the same or similar desired biological activity as the corresponding disclosed peptide but with more favorable activity than the peptide with respect to characteristics such as solubility, stability, and/or susceptibility to hydrolysis and proteolysis. See for example, Morgan and Gainor, Ann. Rep. Med. Chem., 24:243-252(1989).
Certain embodiments of the invention also include hybrid nucleic acid molecules and peptides, for example where a nucleic acid molecule from the nucleic acid molecule disclosed herein is combined with another nucleic acid molecule to produce a nucleic acid molecule which expresses a fusion peptide. One or more of the other domains of CSP described in this application could also be used to make fusion peptides. For example, a nucleotide domain from a molecule of interest may be ligated to all or part of a nucleic acid molecule encoding CSP peptide (or a molecule having sequence identity) described in this application. Fusion nucleic acid molecules and peptides can also be chemically synthesized or produced using other known techniques. Certain embodiments of the invention include a nucleic acid molecule encoding a fusion peptide or a recombinant vector including the nucleic acid molecule.
The variants preferably retain the same or similar CSP activity as the naturally occurring CSP [SEQ ID NO:11]. The CSP activity of such variants can be assayed by techniques described in this application and known in the art.
Variants produced by combinations of the techniques described above but which retain the same or similar CSP activity as naturally occurring CSP [SEQ ID NO:11] are also included in certain embodiments of the invention (for example, combinations of amino acid additions, and substitutions).
Variants of CSP produced by techniques described above which competitively inhibit CSP activity are also included in certain embodiments of the invention (for example, combinations of amino acid additions, and substitutions).
Variants of CSP produced by techniques described above which decrease transformation efficiency of bacteria are also included in the invention (for example, combinations of amino acid additions, and substitutions).
Variants of CSP produced by techniques described above which decrease biofilm formation are also included in certain embodiments of the invention (for example, combinations of amino acid additions, and substitutions).
Variants of CSP encompassed by the present invention preferably have at least about 40% sequence identity, preferably at least about 60%, 75%, 80%, 90% or 95% sequence identity, to the naturally occurring peptide, or corresponding region or moiety of the peptide, or corresponding region. Sequence identity is preferably measured with the ClustalW.
Histidine Kinase & Response Regulator
Certain embodiments of the invention also include sequences having identity with the histidine kinase, response regulator of the invention and comA and comB. Preferred percentages of identity (nucleic acid molecule and polypeptide) are the same as those described for the CSP.
As well, probes and antibodies for a histidine kinase [SEQ ID NO:2 and SEQ ID NO:6], response regulator [SEQ ID NO:3 and SEQ ID NO:7] comA [SEQ ID NO:31 and SEQ ID NO:32] or comB [SEQ ID NO:33 and SEQ ID NO:34] may be prepared using the description in this application and techniques known in the art. The description for preparation of CSP variants and mutants is also applicable to the histidine kinase [SEQ ID NO:2 and SEQ ID NO:6], response regulator [SEQ ID NO:3 and SEQ ID NO:7] or comA [SEQ ID NO:31 and SEQ ID NO:32] and comB [SEQ ID NO:33 and SEQ ID NO:34] of the invention. Certain embodiments of the invention also include fragments of HK having HK activity, fragments of RR [SEQ ID NO:3 and SEQ ID NO:7] having RR activity and fragments of comA [SEQ ID NO:31 and SEQ ID NO:32] or comB [SEQ ID NO:33 and SEQ ID NO:34] having activity.
Design of CSP Peptide Competitive Inhibitors
The activity of the CSP peptide [SEQ ID NO:11] may be varied by carrying out selective site-directed mutagenesis. We characterize the binding domain and other critical amino acid residues in the peptide that are candidates for mutation, insertion and/or deletion. Sequence variants may be synthesized. A DNA plasmid or expression vector containing the CSP nucleic acid molecule [SEQ ID NO:5] or a nucleic acid molecule having sequence identity may be used for these studies using the U.S.E. (Unique site elimination) mutagenesis kit from Pharmacia Biotech or other mutagenesis kits that are commercially available, or using PCR. Once the mutation is created and confirmed by DNA sequence analysis, the mutant peptide is expressed using an expression system and its activity is monitored. This approach is useful to identify CSP inhibitors. All these modifications of the CSP DNA sequences presented in this application and the peptides produced by the modified sequences are encompassed by the present invention.
The CSP inhibitors are also useful when combined with a carrier in a pharmaceutical composition. The compositions are useful when administered in methods of medical treatment or prophylaxis of a disease, disorder or abnormal physical state caused by S. mutans. Certain embodiments of the invention also include methods of medical treatment of a disease, disorder or abnormal physical state characterized by excessive S. mutans or levels or activity of CSP peptide [SEQ ID NO:11], for example by administering a pharmaceutical composition including a carrier and a CSP inhibitor. Caries is one example of a disease, which can be treated or prevented by antagonizing CSP [SEQ ID NO:11].
The pharmaceutical compositions can be administered to humans or animals by methods such as food, food additives, gel, toothpaste, mouthwash, dental floss or chewing gum in methods of medical treatment. The peptides of the invention may be coupled to lipids or carbohydrates. This increases their ability to adhere to teeth, either by prolonging the duration of the adhesion or by increasing its affinity, or both. They may also be coupled to polymers, for example in dental work (eg. crowns, braces, fillings) or dental floss. The pharmaceutical compositions can be administered to humans or animals. Dosages to be administered depend on individual patient condition, indication of the drug, physical and chemical stability of the drug, toxicity of the desired effect and the chosen route of administration (Robert Rakel, ed., Conn's Current Therapy (1995, W.B. Saunders Company, USA)). The pharmaceutical compositions are used to treat diseases caused by streptococcal infections such as caries and endocarditis.
CSP activity could be blocked by antisense mRNA or by inhibiting the activity of the exporter that secretes it from the cell. We have the sequence of these exporters. There are two copies of the genes (comAB) [SEQ ID NO:31 and SEQ ID NO:33] that are involved in export.
Nucleic acid molecules (antisense inhibitors of CSP) and competitive inhibitors of CSP may be introduced into cells using in vivo delivery vehicles such as liposomes. They may also be introduced into these cells using physical techniques such as microinjection and electroporation or chemical methods such as coprecipitation or using liposomes.
The pharmaceutical compositions can be prepared by known methods for the preparation of pharmaceutically acceptable compositions which can be administered to patients, and such that an effective quantity of the nucleic acid molecule or peptide is combined in a mixture with a pharmaceutically acceptable vehicle. Suitable carriers are described, for example in Remington's Pharmaceutical Sciences (Remington's Pharmaceutical Sciences, Mack Publishing Company, Easton, Pa., USA). Carriers include saline and D5W (5% dextrose and water). Excipients include additives such as a buffer, solubilizer, suspending agent, emulsifying agent, viscosity controlling agent, flavor, lactose filler, antioxidant, preservative or dye. There are preferred excipients for stabilizing peptides for parenteral and other administration. The excipients include serum albumin, glutamic or aspartic acid, phospholipids and fatty acids.
On this basis, the pharmaceutical compositions could include an active compound or substance, such as a CSP inhibitor, in association with one or more pharmaceutically acceptable vehicles or diluents, and contained in buffered solutions with a suitable pH and isoosmotic with the physiological fluids. The methods of combining the active molecules with the vehicles or combining them with diluents is well known to those skilled in the art. The compositions may also contain additives such as antioxidants, buffers, bacteriostatis, bactericidal antibiotics and solutes which render the formulation isotonic in the intended recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents. The composition could include a targeting agent for the transport of the active compound to specified sites.
According to another aspect of the present invention, there is provided a process of producing cells genetically modified to produce a CSP derivative which inhibits transformation efficiency. Another aspect comprises administering to a patient S. mutans genetically modified to produce a CSP derivative which inhibits transformation efficiency. Methods of producing and administering genetically engineered cells are known in the art, see, for example, WO002/44230.
A further aspect of the present invention provides the use in the preparation of a medicament for administration to a mammalian patient to alleviate dental caries, of viable, transfected S. mutans genetically modified to produce a CSP derivative which inhibits transformation efficiency.
According to another aspect of the present invention, there is provided a process of producing cells genetically modified to produce a CSP derivative which inhibits biofilm formation. Another aspect comprises administering to a patient cells genetically modified to produce a CSP derivative which inhibits biofilm formation.
A further aspect of the present invention provides the use in the preparation of a medicament for administration to a mammalian patient to improve oral health or to alleviate dental caries, of viable, transfected cells genetically modified to produce a CSP derivative which inhibits biofilm formation.
Antibodies directed against CSP [SEQ ID NO:11] would provide protection against caries. Antibodies may be manufactured as described below. Alternatively, a disclosed peptide [SEQ ID NO:11] or a fragment thereof may be used with a carrier to make a vaccine. The peptide or fragment may also be conjugated to another molecule to increase its antigenicity. Antibodies can also be coupled to the peptide (Brady, L J. et al., "Monoclonal Antibody-Mediated Modulation of the Humoral Immune Response against Mucosally Applied Streptococcus mutans" (in press). In order to enhance the immune response the peptide can be coupled to KLH, ovalbumin, or thyroglobulin prior to immunization. The vaccine composition will trigger the mammal's immune system to produce antibodies. Certain embodiments of the invention include vaccine compositions and methods of vaccinating a mammal, preferably a human, against dental caries by administering to the mammal an effective amount of a vaccine composition. Techniques for preparing and using vaccines are known in the art. To prepare the vaccine, the peptide, or a fragment of the peptide, may be mixed with other antigens (of different immunogenicity), a vehicle or an excipient. Examples of peptide vaccines are found in U.S. Pat. Nos. 5,679,352, 5,194,254 and 4,950,480. Techniques for preparing vaccines involving site-directed mutagenesis are described in U.S. Pat. Nos. 5,714,372, 5,543,302, 5,433,945, 5,358,868, 5,332,583, 5,244,657, 5,221,618, 5,147,643, 5,085,862 and 5,073,494. Vaccines may be administered by known techniques, such as topical or parenteral administration. Vast changes are taking place in vaccinology consequent to the introduction of new technologies. Acellular purified fractions devoid of side effects, non-pathogenic but immunogenic mutants, recombinant technology, conjugated vaccines, combination vaccines (to limit the number of injections). Vaccine delivery systems can deliver multiple doses of the vaccine at a single contact point. A genetically engineered oral vaccine is useful to impart better and longer duration of immunity. Oral vaccines are useful. The nose as a route for immunization is also useful. DNA alone can constitute the vaccines, inducing both humoral and cell-mediated immune responses. Live recombinant vaccines are also useful. Potent adjuvants add to the efficacy of the vaccines. One can also `humanize` mouse monoclonals by genetic engineering and express these efficiently in plants. These recombinant antibodies are opening out an era of highly specific and safe therapeutic interventions. An advantage of preformed antibodies directed at a defined target and given in adequate amounts is the certainty of efficacy in every recipient, in contrast to vaccines, where the quality and quantum of immune response varies from individual to individual. For example, nasal immunization may be done as described in C. Jespersgaard et al. "Protective Immunity against Streptococcus mutans Infection in Mice after Intranasal Immunization with the Glucan-Binding Region of S. mutans Glucosyltransferase" Infection and Immunity, December 1999, p. 6543-6549, Vol. 67, No. 12. Vaccine compositions may comprise solid or liquid formulations such as gels, sprays, inhalants, tablets, toothpastes, mouthwashes or chewing gum.
For vaccine application, cholera toxin can be used by coupling the peptide to its B-subunit to stimulate production of secretory antibody i.e., Coupling to CTB. Screening for inhibitors of CSP.
Inhibitors are preferably directed towards CSP [SEQ ID NO:11] to block S. mutans competence, low pH tolerance and biofilm formation.
A method of identifying a compound which reduces the interaction of CSP [SEQ ID NO:11] with HK [SEQ ID NO:2], can include: contacting (i) CSP [SEQ ID NO:11] with (ii) HK [SEQ ID NO:2], a CSP-binding fragment of HK or a derivative of either of the foregoing in the presence of the compound; and b) determining whether the interaction between (i) and (ii) is reduced, thereby indicating that the compound reduces the interaction of CSP [SEQ ID NO:11] and HK [SEQ ID NO:2]. A CSP inhibitor (caries treating or preventing compound) inhibits the interaction between (i) and (ii). By way of example, one can screen a synthetic peptide library. One could also screen small non-peptide organic molecules.
In one embodiment, the invention includes an assay for evaluating whether test compounds are capable of acting as agonists or antagonists for CSP, or a peptide having CSP functional activity, including culturing cells containing DNA which expresses CSP [SEQ ID NO:5], or a peptide having CSP activity so that the culturing is carried out in the presence of at least one compound whose ability to modulate CSP activity is sought to be determined and thereafter monitoring the cells for either an increase or decrease in the level of CSP [SEQ ID NO:11] or CSP activity. Other assays (as well as variations of the above assay) will be apparent from the description of this invention and techniques such as those disclosed in U.S. Pat. Nos. 5,851,788, 5,736,337 and 5,767,075 which are incorporated by reference in their entirety. For example, the test compound levels may be either fixed or variable.
Preparation of Antibodies
The CSP peptide [SEQ ID NO:11] is also useful as an antigen for the preparation of antibodies that can be used to purify or detect other CSP-like peptides. Antibodies may also block CSP [SEQ ID NO:11] binding to HK [SEQ ID NO:2]. Antibodies are preferably targeted to the entire CSP [SEQ ID NO:11] sequence. The CSP peptide [SEQ ID NO:11 ] may be conjugated to other compounds, in order to increase immunogenicity.
We generate polyclonal antibodies against CSP [SEQ ID NO:11], which is a unique sequence. Monoclonal and polyclonal antibodies are prepared according to the description in this application and techniques known in the art. For examples of methods of preparation and uses of monoclonal antibodies, see U.S. Pat. Nos. 5,688,681, 5,688,657, 5,683,693, 5,667,781, 5,665,356, 5,591,628, 5,510,241, 5,503,987, 5,501,988, 5,500,345 and 5,496,705, which are incorporated by reference in their entirety. Examples of the preparation and uses of polyclonal antibodies are disclosed in U.S. Pat. Nos. 5,512,282, 4,828,985, 5,225,331 and 5,124,147 which are incorporated by reference in their entirety. Antibodies recognizing CSP can be employed to screen organisms or tissues containing CSP peptide [SEQ ID NO:11] or CSP-like peptides. The antibodies are also valuable for immuno-purification of CSP or CSP-like peptides from crude extracts.
An antibody (preferably the antibody described above) may be used to detect CSP [SEQ ID NO:11] or a similar peptide, for example, by contacting a biological sample with the antibody under conditions allowing the formation of an immunological complex between the antibody and a peptide recognized by the antibody and detecting the presence or absence of the immunological complex whereby the presence of CSP [SEQ ID NO:11] or a similar peptide is detected in the sample. Certain embodiments of the invention also include compositions preferably including the antibody, a medium suitable for the formation of an immunological complex between the antibody and a peptide recognized by the antibody and a reagent capable of detecting the immunological complex to ascertain the presence of CSP [SEQ ID NO:11] or a similar peptide. Certain embodiments of the invention also include a kit for the in vitro detection of the presence or absence of CSP [SEQ ID NO:11] or a similar peptide in a biological sample, wherein the kit preferably includes an antibody, a medium suitable for the formation of an immunological complex between the antibody and a peptide recognized by the antibody and a reagent capable of detecting the immunological complex to ascertain the presence of CSP [SEQ ID NO:11] or a similar peptide in a biological sample. Further background on the use of antibodies is provided, for example in U.S. Pat. Nos. 5,695,931 and 5,837,472, which are incorporated by reference in their entirety.
Assay of Genetic Competence
The ability of the peptide to activate the HK [SEQ ID NO:2] and RR [SEQ ID NO:3] and the subsequent genes involved in the conferral of the properties of genetic competence, acid tolerance and biofilm formation can be determined by measuring the efficiency of uptake and expression of DNA (preferably plasmid DNA) in S. mutans when exposed to signal peptide and/or inhibitor. Two methods modified based on the protocols described by Perry et al. Infect Immun, 41:722-727 and Lindler and Macrina J Bacteriol, 166:658-665 are used to assay genetic competence. The method involves adding DNA and CSP DNA [SEQ ID NO:5] (preferably plasmid DNA) to a S. mutans culture (or culture of a bacteria expressing CSP [SEQ ID NO:11] or a variant thereof). The rate of transformation is then determined. S. mutans is preferably grown in THYE plus 5% horse serum (THYE-HS). After 2-hr incubation, 1 μg/ml plasmid DNA or 10 μg/ml of chromosomal DNA is added to the culture. To assay induction of competence, competence signal peptide, (SCSP) [SEQ ID NO:11] is then added to the cultures, incubation continued for 30 minutes with a final concentration of 500 ng/ml of SCSP added to each sample. After the 30-minute incubation equal amounts of DNA is added to each well (1 μg/ml plasmid or 10 μg/ml of chromosomal DNA) and incubation continued for another 2 hrs. Cell dilutions were immediately spread on THYE agar plates plus appropriate antibiotics. Transformation frequency was expressed as the number of transformants (antibiotic resistant cells) per number of viable recipients. This is determined by comparing the number of cells able to grow in the presence of antibiotic (conferred by the applied plasmid or chromosomal DNA) relative to the total number of cells present (i.e., that grow in the absence of antibiotic). A higher value indicates a higher rate of transformation and thus is reflective of a stimulatory effect by the peptide. Consequently, addition of a molecule that successfully acts as an inhibitor results in a lower ratio of transformants/recipients, indicating that the inhibitor is effective at blocking activity of the CSP [SEQ ID NO:11]. CSP deficient cells may also be used in a variation of these assays. One can identify compounds that inhibit CSP or variants thereof by adding a test compound to the mixture to determine if the rate of transformation is decreased by the addition of the test compound.
The activity of the system can also be measured by an in vitro assay that relies on the measurement of marker protein expression (such as green fluorescent protein (GFP)) via expression from a fusion to a promoter controlled by the signal cascade initiated by CSP [SEQ ID NO:11]/HK [SEQ ID NO:2] /RR [SEQ ID NO:3]. One such promoter occurs immediately 5' proximal to the S. mutans comX gene. S. mutans cells grown in microtiter wells are exposed to the CSP [SEQ ID NO:11] and/or inhibitor and the level of fluorescence of the comX::GFP strain is measured to give a quantitative measure of CSP [SEQ ID NO:11] stimulation (and conversely inhibitor activity). One can identify compounds that inhibit CSP [SEQ ID NO:11] or variants thereof by adding a test compound to the mixture to determine if the quantitative, measure of CSP [SEQ ID NO:11] stimulation is decreased by the addition of the test compound.
Assay of Acid Resistance Tolerance
The ability of CSP [SEQ ID NO:11] to promote acid resistance tolerance is determined by measuring the cell survival rate of S. mutans when exposed to acidic pH. In one example, S. mutans are first grown in batch culture to assay acid tolerance response in `standard` log- and stationary-phase cells by using a modification of methods described previously by Svensater et al. Oral Microbiol. Immunol., 12:266-73. Mid-log-phase cells are obtained by transferring one volume of overnight culture into nine volumes (1:10) of fresh TYG medium (pH 7.5) and incubated at 37° C. with 5% CO2 for 2 hours. These cells are then collected by centrifugation at 8,000×g for 10 min and resuspended in 2 ml of fresh TYG (pH 5.5) at various cell densities as determined by O.D600. The cells are induced for acid adaptation by incubation at pH 5.5 for 2 h at 37° C. with 5% CO2. The adapted log-phase cells are then exposed to the killing pH. Killing pH is pre-determined by incubating unadapted, mid-log phase cells in TYG medium at pH values from 6.0 to 2.0. Stationary-phase cells are prepared by re-suspending late-log phase cells in TY medium (tryptone-yeast extract) without glucose. The culture is incubated at 37° C. for 2 h to allow the cells to fully enter into stationary phase. Induction of acid adaptation in stationary-phase cells follows a similar procedure to that for log-phase cells. Adaptation of both log- and stationary-phase cells to acidic pH is determined by measuring the ability of bacterial cells to survive a killing pH for 3 h. Acid killing is initiated by resuspending cells in the same volume of fresh TYG (pH 3.5) and an aliquot of cell suspension is taken immediately from each sample to determine total viable cell number at zero time. The cells are then incubated for 3 h at 37° C. with 5% CO2 and an aliquot of sample is taken to determine survival rate by viable cell counts. Addition of a molecule that successfully acts as an inhibitor results in a decrease in the acid resistance tolerance of S mutans resulting in a corresponding decrease in cell survival indicating that the inhibitor is effective at blocking activity of CSP. CSP deficient cells may also be used in a variation of these assays wherein addition of the signal peptide can complement the acid-adaptation-defective phenotype of a comC deficient cell. One can identify compounds that inhibit CSP or variants thereof by adding a test compound to the mixture to determine if the survival rate of cells is decreased by the addition of the test compound.
Cells transformed with a nucleic acid molecule disclosed herein (histidine kinase [SEQ ID NO:6], CSP [SEQ ID NO:5] or response regulator [SEQ ID NO:7]) are useful as research tools. For example, one may obtain a cell (or a cell line, such as an immortalized cell culture or a primary cell culture) that does not express histidine kinase [SEQ ID NO:2], CSP [SEQ ID NO:11] or response regulator [SEQ ID NO:3], insert a histidine kinase [SEQ ID NO:6], CSP [SEQ ID NO:5] or response regulator [SEQ ID NO:7] nucleic acid molecule in the cell, and assess the level of expression and activity. Alternatively, histidine kinase [SEQ ID NO:6], CSP [SEQ ID NO:5] or response regulator [SEQ ID NO:7] nucleic acid molecules may be over-expressed in a cell that expresses a histidine kinase [SEQ ID NO:2], CSP [SEQ ID NO:11] or response regulator [SEQ ID NO:3] nucleic acid molecule. In another example, experimental groups of cells may be transformed with vectors containing different types of histidine kinase, CSP or response regulator nucleic acid molecules to assess the levels of polypeptides and peptides produced, its functionality and the phenotype of the cells. The polypeptides and peptides are also useful for in vitro analysis of histidine kinase, CSP [SEQ ID NO:11] or response regulator [SEQ ID NO:3] activity or structure. For example, the polypeptides and peptides produced can be used for microscopy or X-ray crystallography studies.
The histidine kinase [SEQ ID NO:2 and SEQ ID NO:6], CSP [SEQ ID NO:5 and SEQ ID NO:11] or response regulator [SEQ ID NO:3 and SEQ ID NO:7] nucleic acid molecules and polypeptides are also useful in assays for the identification and development of compounds to inhibit and/or enhance polypeptide or peptide function directly. For example, they are useful in an assay for evaluating whether test compounds are capable of acting as antagonists for histidine kinase [SEQ ID NO:2], CSP [SEQ ID NO:11] or response regulator [SEQ ID NO:3] by: (a) culturing cells containing a nucleic acid molecule which expresses histidine kinase [SEQ ID NO:2], CSP [SEQ ID NO:11] or response regulator peptides [SEQ ID NO:3] (or fragments or variants thereof having histidine kinase [SEQ ID NO:2], CSP or response regulator activity) wherein the culturing is carried out in the presence of increasing concentrations of at least one test compound whose ability to inhibit histidine kinase [SEQ ID NO:2], CSP [SEQ ID NO:11] or response regulator [SEQ ID NO:3] is sought to be determined; and (b) monitoring in the cells the level of inhibition as a function of the concentration of the test compound, thereby indicating the ability of the test compound to inhibit histidine kinase [SEQ ID NO:2], CSP [SEQ ID NO:11] or response regulator [SEQ ID NO:3] activity.
Suitable assays may be adapted from, for example, U.S. Pat. No. 5,851,788.
Materials and Methods:
Growth Conditions of Cells
Cells are grown in Todd Hewitt yeast extract medium at various dilutions with and without 5% horse serum and 0.01% hog gastric mucin.
Protocol for Transformation of Biofilm-Grown Cells
Biofilms are developed on polystyrene microtiter plates to provide a rapid and simple method for assaying biofilm formation, and hence activity of the peptide [SEQ ID NO:11]/receptor [SEQ ID NO3]/kinase [SEQ ID NO:2] system. Formation of biofilms is initiated by inoculating 20 μl of cell suspension into each well containing 2 ml of biofilm medium (4× diluted Todd-Hewitt Yeast Extract supplemented with final concentration of 0.01% hog gastric mucin) for overnight incubation at 37° C. under an anaerobic condition. After 20-h incubation, fluid medium is removed and added with 2 ml of pre-warmed, fresh THYE plus 5% horse serum. The cultures are incubated for 30 minutes and each well is supplemented with a final concentration of 200 ng/ml of synthetic competence stimulating peptide (SCSP) and varying concentrations of the inhibitor and the incubation is continued. After 30 minutes, plasmid DNA (1 mg/ml) or chromosomal DNA (10 mg/ml) is added to each well and the cultures are incubated for an additional 2 hr. Planktonic cells are then removed and the wells are washed once with PBS buffer. Biofilm cells are collected into 2 ml fresh medium by a gentle sonication or washing the wells using a pipette. The samples are centrifuged at 12,000×g for 5 min. Both biofilm and planktonic cells are resuspended into 200 μl of fresh medium and are immediately spread on THYE agar plus appropriate antibiotics. Transformation frequency is determined after 48-h of incubation.
Genome Database Analysis
Homologues of the Streptococcus pneumoniae comD/comE genes encoding a histidine kinase/response regulator system were identified. This sequence was used to design primers to amplify the region from a number of S. mutans isolates. An open reading frame consisting of 138 nucleotides was located 148 nucleotides 5' proximal from the end of the comD homolog in the opposite orientation (FIG. 1). This ORF was found to encode a peptide of 46-amino acid [SEQ ID NO:1] in length, the precursor of the 21-amino acid CSP [SEQ ID NO:11].
PCR Amplification and Nucleotide Sequencing
The comCDE genes [SEQ ID NO:18 and SEQ ID NO:19] were amplified from the genomes of several S. mutans isolates by PCR using primers designed based on the genome database sequence and their nucleotide sequences determined. The deduced amino acid sequences are compared among the isolates by sequence alignment to confirm identity.
Genes are inactivated by integration of internal homologous fragments into the suicide vector pVA8912. Mutants defective in each of the individual genes (comC, comD, comE) are inactivated and their phenotypes are compared to the parent strain NG8 for their abilities to form biofilms, tolerate acidic pH (pH 2-4), and transport and incorporate DNA. The knockout mutants of com D and comE were constructed by insertion-duplication mutagenesis, whereas the knockout comC mutant was created by allelic exchange via insertion of an erythromycin resistance determinant into the comC locus (Li et al, 2001). All mutant strains were therefore resistant to erythromycin. The wild-type strain was subcultured routinely on Todd-Hewitt-Yeast Extract (THYE) agar plates (BBL; Becton Dickinson, Cockeysville, Md.), whereas the mutants were maintained on THYE agar plus 10 μg/ml of erythromycin. A minimal medium (DMM) was prepared to grow biofilms by a modification of the method described previously (Loo et al, 2000). The medium contained 58 mM K2HPO4, 15 mM KH2PO4, 10 mM (NH4)2SO4, 35 mM NaCl, 2 mM MgSO2 7H2O, 0.2% (wt/vol) Casamino Acids and was supplemented with filter-sterilized vitamins, (0.04 mM nicotinic acid, 0.1 mM pyridoxine HCl, 0.01 mM pantothenic acid, 1 μM riboflavin, 0.3 μM thiamin HCl, and 0.05 μM D-biotin), amino acids (4 mM L-glutamic acid, 1 mM L-arginine HCl, 1.3 mM L-cysteine HCl, and 0.1 mM L-tryptophan) and 20 mM glucose.
Creation of comD Deletion Mutant.
An S. mutans UA159 comD null mutant was constructed by a PCR-based deletion strategy involving restriction-ligation and allelic replacement as described previously (Lau et al., 2002). The primers used to construct and confirm the S. mutans comD deletion mutant are
TABLE-US-00004 [SEQ ID NO: 52] P1-HK13 (5'-CACAACAACTTATTGACGCTATCCC-3'), [SEQ ID NO: 53] P2-HK13 (5'-GGCGCGCCAACTGGCAACAGGCAGCAGACC-3'), [SEQ ID NO: 54] P3-HK13 (5'-GGCCGGCCTCAAAACGATGCTGTCAAGGG-3'), [SEQ ID NO: 55] P4-HK13 (5'-AGATTATCATTGGCGGAAGCG-3'), [SEQ ID NO: 56] Erm-19 (5'-GGCGCGCCCCGGGCCCAAAATTTGTTTGAT-3'), and [SEQ ID NO: 57] Erm-20 (5'-GGCCGGCCAGTCGGCAGCGACTCATAGAAT-3').
Synthesis of Synthetic Peptide
The sequence of the processed peptide was deduced by determining the cleavage site to be located beside the gly-gly amino acid residues (numbers 24 and 25) (FIG. 4). A peptide was synthesized corresponding to amino acid sequence of residues 26-46 inclusive.
Synthesis of Peptide Analogs;
The sequences of the peptide analogs used in this study are listed in Table 1. The peptides were synthesized by methods known in the art. The peptides were dissolved to 1 mg per ml in sterile distilled deionized water. To any insoluble peptides, 10% (vol/vol) acetic acid, 20% (vol/vol) acetonitrile or 100% (vol/vol) dimethylformamide (DMF) was subsequently added. Peptides were stored at -20° C. until used.
Restoration of Phenotypic Defects by Addition of CSP
To determine if the synthetic peptide could restore defective phenotypes of the comC mutants, a chemically synthesized 21-amino acid competence-stimulating peptide (CSP) [SEQ ID NO:11] (Li et al., 2001) was used in complementary experiments. The peptide was freshly dissolved in sterile distilled water to a concentration of 1 mg/ml. The CSP solution was then added to the cultures at a final concentration of 2 μg/ml 2 h after inoculation of bacterial cells.
The parent and mutant strains were grown in THYE medium for assaying their growth curves using a Bioscreen Microbiology Reader incorporating a multi-well disposable microtiter plate (Bioscreen C, Helsinki, Finland). The Bioscreen Reader was equipped with Biolink software program that allowed us to record and display the growth curves and growth rate calculations automatically. The growth of the strains was initiated by inoculating 5 μl of cell suspension into each well containing 200 μl of fresh THYE medium. The cell suspensions were pre-adjusted to the same optical density at O.D600 before inoculation. The plates were then placed in the Bioscreen system, which was set up to read optical density automatically every 15 minutes with shaking. The readings of optical density were automatically recorded and converted into growth curves. Each assay was performed in quadruplicate.
Bacterial Strains and Growth Conditions
Seven strains of S. mutans were used in this study (strains include: BM71, GB14, H7, JH1005, LT11, NG8, and UAB159. All the strains were cultured from freeze-dried ampoules and routinely maintained on Todd-Hewitt Yeast Extract (THYE) plates. For selection of antibiotic resistant colonies following transformation, the medium was supplemented with either erythromycin (Em) (10 μg/ml) or kanamycin (Km) (500 μg/ml).
S. mutans strain wild-type UA159 and its comD null mutant were routinely grown on Todd-Hewitt supplemented with 0.3% (wt/vol) yeast extract (THYE) agar plates and incubated at 37° C. in air with 5% CO2. For biofilm experiments, S. mutans strains were grown in a semidefined minimal medium (SDM) supplemented with 5 mM glucose as described previously (Li et al., 2002). The replicative plasmid pDL289 (Buckley et al., 1995) was used as donor DNA for genetic transformation experiments. Plasmid DNA was prepared from Escherichia coli cultures by using a commercial plasmid preparation kit (Qiagen). When needed, antibiotics were added as follows: 10 μg erythromycin per ml or 500 μg kanamycin per ml for S. mutans, and 50 μg kanamycin per ml for E. coli.
Assay for Biofilms Formed on Polystyrene Microtiter Plates (a)
Biofilms were developed on polystyrene microtiter plates to provide a rapid and simple method for assaying genetic transformation. A 4× diluted THYE medium supplemented with final concentration of 0.01% hog gastric mucin was used as biofilm medium (BM). Formation of biofilms was initiated by inoculating 20 μl of cell suspension into each well containing 2 ml of BM and four wells were set up: two for assaying transformation and two for quantification of biofilms. After cultures were incubated at 37° C. for 20 h under an anaerobic condition, fluid medium was removed for viable cell counts. The wells were rinsed once with 10 mM PBS buffer (pH 7.2) and biofilm cells were collected in 2 ml PBS by a gentle sonication for 15 seconds. Both biofilm and the planktonic cells were immediately spread on THYE plates using a spiral system (Spriral Plater, Model D, Cincinnati, Ohio) and incubated at 37° C. under an anaerobic condition. Formation of biofilms was quantified by viable cell counts after 48 h of incubation.
Biofilm Assay. (b)
Biofilms were developed in 96-well polystyrene microtiter plates. The growth of the biofilm was initiated by inoculating 10 μl of an overnight S. mutans UA159 culture into 300 μl of SDM-glucose containing different concentrations (0, 0.1, 0.5, 2, and 5 μg per ml) of peptide analogs in the individual wells of a 96-well microtiter plate. Wells without cells were used as blank controls. The microtiter plates were then incubated at 37° C. in air with 5% CO2 for 16 h without agitation. After the incubation, the planktonic cells were carefully removed and the plates were air dried overnight. The plates were then stained with 0.01% (wt/vol) safranin for 10 min, rinsed with sterile distilled water and air dried. Biofilms were quantified by measuring the absorbance of stained biofilms at 490 nm with a microplate reader (model 3550; Bio-Rad Laboratories, Richmond, Calif.).
To determine if the peptide analogs had any impact on the development of genetic competence, S. mutans UA159 wild-type cells were assayed for genetic transformation. Overnight cultures of S. mutans UA159 were diluted (1:20) with prewarmed THYE broth and incubated at 37° C. in air with 5% CO2 until an optical density (OD) of approximately 0.1 at 600 nm was reached. The culture was then divided into six aliquots containing 1 μg/ml of plasmid pDL289 and different concentrations (0, 0.1, 0.5, 2, and 5 μg per ml) of peptide analogs. The cultures were incubated at 37° C. in air with 5% CO2 for 2.5 h, gently sonicated for 10 s to disperse the streptococcal chains, and spread on THYE plates containing kanamycin. Plates were incubated at 37° C. in air with 5% CO2 for 48 h. Total recipient cells were counted by spreading serial dilutions on THYE agar plates without antibiotic. Transformation efficiency was expressed as the percentage of kanamycin resistant transformants over the total number of recipient cells.
Acid resistance Assay.
The effect of peptides on acid tolerance was evaluated by assessment of growth in THYE at pH 7.5 and pH 5.5. Overnight S. mutans wild-type UA159 cells were diluted (1:20) with prewarmed THYE broth and incubated at 37° C. in air with 5% CO2 until an OD600 of approximately 0.4 was reached. A 20-fold dilution was made into 400 μl of either THYE pH 7.5 or THYE pH 5.5 broth containing different concentrations (0, 0.1, 0.5, 2, and 5 μg per ml) of peptide analogs and added in the individual wells of a 100-well Bioscreen C plate in triplicate. Wells without cells were used as blank controls. A Bioscreen microbiology reader (Labsystems, Helsinki, Finland) was employed to continuously grow cells and measure cell growth for 16 h at 37° C. Measurements were taken every 20 min with shaking to prevent cell aggregation.
Assay for "Steady-State" Biofilms
Biofilms were also grown in a chemostat-based biofilm fermentor to define and optimize the conditions for genetic competence of biofilm-grown cells. The biofilm fermentor was modified in the Mechanical Engineering and Glass Blowing Shops, University of Toronto, based on a similar system described previously (Li and Bowden, 1994). The vessel was made of glass with a working volume of 400 ml. The vessel lip was constructed of stainless steel with 10 sampling ports, which allowed sterile insertion and retrieval of glass rods (0.5 cm in diameter, approximately 4.0 cm2 area immersed in fluid medium), providing abiotic surfaces for accumulation of biofilms. Temperature in the chemostat vessel was maintained at 37° C.±0.1 by a temperature controller (Model R-600F, Cole Farmer Instrument Cop., Vernon Hill, Ill.). The culture pH was controlled by a pH control unit (Digital pH Meter/Controller, Model 501-3400, Barnant Corp. Barrington, Ill.) through the addition of 1M KOH or 1M HCl. The vessel was placed on a magnetic stirrer (Fisher Scientific) and the culture was stirred at 200 rpm by a polypropylene coated magnetic stirrer bar (3 cm in length). Continuous cultures were obtained by pumping fresh 4× diluted THYE medium supplemented with a final concentration of 0.01% hog gastric mucin (Type III, Sigma) into the vessel (400 ml) at the desired dilution rates. Daily maintenance of the chemostat included optical density reading, viable cell counts and pH measurement in fluid cultures. When the cultures reached "steady-state" (at least 10 mean generation times), glass rods were aseptically inserted into the chemostat for the initiation of biofilm formation. Then, biofilms of different ages were removed from the cultures for both genetic transformation and quantification of biofilms using viable cell counts.
Scanning Electron Microscopy (SEM)
To examine spatial distribution and biofilm thickness by scanning electron microscopy, biofilms of different ages were removed by slicing off the bottom of the microtiter wells that were then washed once with 10 mM KPO4 and fixed with 2 ml of 3.7% formaldehyde in 10 mM KPO4 buffer overnight. The samples were then dehydrated with a series of alcohol baths (30%, 50%, 70%, 95% and 100%), critical point dried with liquid CO2, mounted and sputter coated with gold. The samples were then examined using a scanning electron microscope (Model S-2500, Hitachi Instruments, San Jose, Calif.).
Two methods modified based on the protocols described by Perry et al (Infect Immun, 41:722-727) and Lindler and Macrina (J Bacteriol, 166:658-665) were used to assay natural transformation of biofilm cells. Biofilms formed on polystyrene microtiter plates were added with 2 ml of pre-warmed, fresh THYE plus 5% horse serum (THYE-HS) immediately following removal of the BM medium, and the incubation continued at 37° C. After 2 h incubation, a final concentration of 1 μg/ml plasmid DNA or 10 μg/ml of chromosomal DNA was added to each well. The cultures were incubated for an additional 2 h before collection of the cells for plating. To assay induction of competence by synthetic competence stimulating peptide (SCSP) [SEQ ID NO:11], the cultures were incubated for 30 min and a final concentration of 500 ng/ml of SCSP [SEQ ID NO:11] was added to each well. After a 30 min incubation, equal amounts of DNA was added to each well (1 μg/ml plasmid or 10 μg/ml of chromosomal DNA) and incubation continued for another 2 h. Fluid medium was then removed from individual wells and the wells were washed once with PBS buffer. Biofilm cells were collected into 2 ml PBS buffer by gentle sonication or by washing the wells using a pipette. The samples were centrifuged at 12,000×g for 5 min. Both biofilm and planktonic cells were resuspended into 200 μl of fresh medium and were immediately spread on THYE agar plates plus appropriate antibiotics. For the biofilms developed in the chemostat, rods with biofilm cells were removed and placed into 2 ml of pre-warmed, fresh THYE-HS medium for 30 min incubation. Transformation was then initiated by using the same methods as described above. The planktonic cells were also removed to compare the transformation frequency. After completion of the transformation procedures, both biofilm and planktonic cells were spread on THYE agar plus appropriate antibiotic. Transformation frequency was assessed after 48-h incubation. Transformation frequency was expressed as the number of transformants per μg DNA per viable recipient at the time of DNA added.
Both plasmid and chromosomal DNA were used as donor DNA to assay genetic transformation in this study. Plasmid DNA included an integrative plasmid, pVAGTFA carrying an erythromycin resistance (Emr) determinant and a fragment of the S. mutans gtfA gene. The replicative plasmid, pDL289 carrying a kanamycin resistance gene (Kmr) was also used. Chromosomal DNA harboring an Emr gene was prepared from a recombinant S. mutans strain harboring a chromosomally integrated copy of pVAGTFA.
The present invention has been described in detail and with particular reference to the preferred embodiments; however, it will be understood by one having ordinary skill in the art that changes can be made without departing from the spirit and scope thereof. For example, where the application refers to peptides, it is clear that polypeptides may often be used. Likewise, where a gene is described in the application, it is clear that nucleic acid molecules or gene fragments may often be used.
All publications (including GenBank entries), patents and patent applications are incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety.
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57146PRTStreptococcus mutans 1Met Lys Lys Thr Leu Ser Leu Lys Asn Asp Phe Lys Glu Ile Lys Thr1 5 10 15Asp Glu Leu Glu Ile Ile Ile Gly Gly Ser Gly Ser Leu Ser Thr Phe 20 25 30Phe Arg Leu Phe Asn Arg Ser Phe Thr Gln Ala Leu Gly Lys 35 40 452441PRTStaphylococcus mutans 2Met Asn Glu Ala Leu Met Ile Leu Ser Asn Gly Leu Leu Thr Tyr Leu1 5 10 15Thr Val Leu Phe Leu Leu Phe Leu Phe Ser Lys Val Ser Asn Val Thr 20 25 30Leu Ser Lys Lys Glu Leu Thr Leu Phe Ser Ile Ser Asn Phe Leu Ile 35 40 45Met Ile Ala Val Thr Met Val Asn Val Asn Leu Phe Tyr Pro Ala Glu 50 55 60Pro Leu Tyr Phe Ile Ala Leu Ser Ile Tyr Leu Asn Arg Gln Asn Ser65 70 75 80Leu Ser Leu Asn Ile Phe Tyr Gly Leu Leu Pro Val Ala Ser Ser Asp 85 90 95Leu Phe Arg Arg Ala Ile Ile Phe Phe Ile Leu Asp Gly Thr Gln Gly 100 105 110Ile Val Met Gly Ser Ser Ile Ile Thr Thr Tyr Met Ile Glu Phe Ala 115 120 125Gly Ile Ala Leu Ser Tyr Leu Phe Leu Ser Val Phe Asn Val Asp Ile 130 135 140Gly Arg Leu Lys Asp Ser Leu Thr Lys Met Lys Val Lys Lys Arg Leu145 150 155 160Ile Pro Met Asn Ile Thr Met Leu Leu Tyr Tyr Leu Leu Ile Gln Val 165 170 175Leu Tyr Val Ile Glu Ser Tyr Asn Val Ile Pro Thr Leu Lys Phe Arg 180 185 190Lys Phe Val Val Ile Val Tyr Leu Ile Leu Phe Leu Ile Leu Ile Ser 195 200 205Phe Leu Ser Gln Tyr Thr Lys Gln Lys Val Gln Asn Glu Ile Met Ala 210 215 220Gln Lys Glu Ala Gln Ile Arg Asn Ile Thr Gln Tyr Ser Gln Gln Ile225 230 235 240Glu Ser Leu Tyr Lys Asp Ile Arg Ser Phe Arg His Asp Tyr Leu Asn 245 250 255Ile Leu Thr Ser Leu Arg Leu Gly Ile Glu Asn Lys Asp Leu Ala Ser 260 265 270Ile Glu Lys Ile Tyr His Gln Ile Leu Glu Lys Thr Gly His Gln Leu 275 280 285Gln Asp Thr Arg Tyr Asn Ile Gly His Leu Ala Asn Ile Gln Asn Asp 290 295 300Ala Val Lys Gly Ile Leu Ser Ala Lys Ile Leu Glu Ala Gly Asn Lys305 310 315 320Lys Ile Ala Val Asn Val Glu Val Ser Ser Lys Ile Gln Leu Pro Glu 325 330 335 Met Glu Leu Leu Asp Phe Ile Thr Ile Leu Ser Ile Leu Cys Asp Asn 340 345 350Ala Ile Glu Ala Ala Phe Glu Ser Leu Asn Pro Glu Ile Gln Leu Ala 355 360 365Phe Phe Lys Lys Asn Gly Ser Ile Val Phe Ile Ile Gln Asn Ser Thr 370 375 380Lys Glu Lys Gln Ile Asp Val Ser Lys Ile Phe Lys Glu Asn Tyr Ser385 390 395 400Thr Lys Gly Ser Asn Arg Gly Ile Gly Leu Ala Lys Val Asn His Ile 405 410 415Leu Glu His Tyr Pro Lys Thr Ser Leu Gln Thr Ser Asn His His His 420 425 430Leu Phe Lys Gln Leu Leu Ile Ile Lys 435 4403250PRTStaphylococcus mutans 3Met Ile Ser Ile Phe Val Leu Glu Asp Asp Phe Leu Gln Gln Gly Arg1 5 10 15Leu Glu Thr Thr Ile Ala Ala Ile Met Lys Glu Lys Asn Trp Ser Tyr 20 25 30Lys Glu Leu Thr Ile Phe Gly Lys Pro Gln Gln Leu Ile Asp Ala Ile 35 40 45Pro Glu Lys Gly Asn His Gln Ile Phe Phe Leu Asp Ile Glu Ile Lys 50 55 60Lys Glu Glu Lys Lys Gly Leu Glu Val Ala Asn Gln Ile Arg Gln His65 70 75 80Asn Pro Ser Ala Val Ile Val Phe Val Thr Thr His Ser Glu Phe Met 85 90 95Pro Leu Thr Phe Gln Tyr Gln Val Ser Ala Leu Asp Phe Ile Asp Lys 100 105 110Ser Leu Asn Pro Glu Glu Phe Ser His Arg Ile Glu Ser Ala Leu Tyr 115 120 125Tyr Ala Met Glu Asn Ser Gln Lys Asn Gly Gln Ser Glu Glu Leu Phe 130 135 140Ile Phe His Ser Ser Glu Thr Gln Phe Gln Val Pro Phe Ala Glu Ile145 150 155 160Leu Tyr Phe Glu Thr Ser Ser Thr Ala His Lys Leu Cys Leu Tyr Thr 165 170 175Tyr Asp Glu Arg Ile Glu Phe Tyr Gly Ser Met Thr Asp Ile Val Lys 180 185 190Met Asp Lys Arg Leu Phe Gln Cys His Arg Ser Phe Ile Val Asn Pro 195 200 205Ala Asn Ile Thr Arg Ile Asp Arg Lys Lys Arg Leu Ala Tyr Phe Arg 210 215 220Asn Asn Lys Ser Cys Leu Ile Ser Arg Thr Lys Leu Thr Lys Leu Arg225 230 235 240Ala Val Ile Ala Asp Gln Arg Arg Ala Lys 245 2504141DNAStaphylococcus mutans 4atgaaaaaaa cactatcatt aaaaaatgac tttaaagaaa ttaagactga tgaattagag 60attatcattg gcggaagcgg aagcctatca acatttttcc ggctgtttaa cagaagtttt 120acacaagctt tgggaaaata a 141563DNAStaphylococcus mutans 5agcggaagcc tatcaacatt tttccggctg tttaacagaa gttttacaca agctttggga 60aaa 6361326DNAStaphylococcus mutans 6atgaatgaag ccttaatgat actttcaaat ggtttattaa cttatctaac cgttctattt 60ctcttgtttc tattttctaa ggtaagtaat gtcactttat cgaaaaagga attaactctt 120ttttcgataa gcaattttct gataatgatt gctgttacga tggtgaacgt aaacctgttt 180tatcctgcag agcctcttta ttttatagct ttatcaattt atcttaatag acagaatagt 240ctttctctaa atatatttta tggtctgctg cctgttgcca gttctgactt gtttaggcgg 300gcaatcatat tctttatctt ggatggaact caaggaattg taatgggcag tagcattata 360accacctata tgatcgagtt tgcaggaata gcgctaagtt acctctttct cagtgtgttc 420aatgttgata ttggtcgact taaagatagt ttgaccaaga tgaaggtcaa aaaacgcttg 480attccaatga atattactat gcttctatac taccttttaa tacaggtatt gtatgttata 540gagagttata atgtgatacc gactttaaaa tttcgtaaat ttgtcgttat tgtctatctt 600attttatttt tgattctgat ctcattttta agccaatata ccaaacaaaa ggttcaaaat 660gagataatgg cacaaaagga agctcagatt cgaaatatca cccagtatag tcagcaaata 720gaatctcttt acaaggatat tcgaagtttc cgccatgatt atctgaatat tttaactagc 780ctcagattag gcattgaaaa taaagattta gctagtattg aaaagattta ccatcaaatc 840ttagaaaaaa caggacatca attgcaggat acccgttata atatcggcca tctagctaat 900attcaaaacg atgctgtcaa gggtatcttg tcagcaaaaa tcttagaagc tcagaataaa 960aagattgctg tcaatgtaga agtctcaagt aaaatacaac tgcctgagat ggagttgctt 1020gatttcatta ccatactttc tatcttgtgt gataatgcca ttgaggctgc tttcgaatca 1080ttaaatcctg aaattcagtt agcctttttt aagaaaaatg gcagtatagt ctttatcatt 1140cagaattcca ccaaagaaaa acaaatagat gtgagtaaaa tttttaaaga aaactattcc 1200actaaaggct ccaatcgcgg tattggttta gcaaaggtga atcatattct tgaacattat 1260cccaaaacca gtttacaaac aagcaatcat catcatttat tcaagcaact cctaataata 1320aaatag 13267753DNAStaphylococcus mutans 7atgatttcta tttttgtatt ggaagatgat tttttacaac aaggacgtct tgaaaccacc 60attgcagcta tcatgaaaga aaaaaattgg tcttataaag aattgactat ttttggaaaa 120ccacaacaac ttattgacgc tatccctgaa aagggcaatc accagatttt ctttttggat 180attgaaatca aaaaagagga aaagaaagga ctggaagtag ccaatcagat tagacagcat 240aatcctagtg cagttattgt ctttgtcacg acacattctg agtttatgcc cctcactttt 300cagtatcagg tatctgcttt ggattttatt gataaatctt tgaatcctga ggagttctcc 360caccgcattg aatcagcgct gtattatgct atggaaaaca gccagaagaa tggtcaatca 420gaggaacttt ttattttcca ttcatctgaa actcagtttc aggtcccttt tgctgagatt 480ctgtattttg aaacatcttc aacagcccat aagctctgcc tttatactta tgatgaacgg 540attgaattct acggcagtat gactgacatt gttaaaatgg ataagagact ttttcagtgc 600catcgctctt ttattgtcaa tcctgccaat attacccgta ttgatcggaa aaaacgcttg 660gcctattttc gaaataataa gtcttgtctt atttcacgaa ctaagttaac aaaactgaga 720gctgtgattg ctgatcaaag gagagcaaaa tga 753846PRTStaphylococcus mutans 8Met Lys Lys Thr Pro Ser Leu Lys Asn Asp Phe Lys Glu Ile Lys Thr1 5 10 15Asp Glu Leu Glu Ile Ile Ile Gly Gly Ser Gly Ser Leu Ser Thr Phe 20 25 30Phe Arg Leu Phe Asn Arg Ser Phe Thr Gln Ala Leu Gly Lys 35 40 45946PRTStaphylococcus mutans 9Met Lys Lys Thr Leu Ser Leu Lys Asn Asp Phe Lys Glu Ile Lys Thr1 5 10 15Asp Glu Leu Glu Ile Ile Ile Gly Gly Ser Gly Ser Leu Ser Thr Phe 20 25 30Phe Arg Leu Phe Asn Arg Ser Phe Thr Gln Ala Leu Gly Lys 35 40 451043PRTStaphylococcus mutans 10Met Lys Lys Thr Leu Ser Leu Lys Asn Asp Phe Lys Glu Ile Lys Thr1 5 10 15Asp Glu Leu Glu Ile Ile Ile Gly Gly Ser Gly Thr Leu Ser Thr Phe 20 25 30Phe Arg Leu Phe Asn Arg Ser Phe Thr Gln Ala 35 401121PRTArtificialSynthetic signal peptide 11Ser Gly Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr1 5 10 15Gln Ala Leu Gly Lys 201219DNAArtificialSynthetic ComC Forward Primer 12agttttttgt ctggctgcg 191320DNAArtificialSynthetic ComC Backward Primer 13tccactaaag gctccaatcg 201424DNAArtificialSynthetic ComD Forward Primer 14cgctaagtta cctctttctc agtg 241521DNAArtificialSynthetic ComD Backward Primer 15gcttcctttt gtgccattat c 211621DNAArtificialSynthetic ComE Forward Primer 16cctgaaaagg gcaatcacca g 211722DNAArtificialSynthetic ComE Backward Primer 17gcgatggcac tgaaaaagtc tc 22182557DNAStaphylococcus mutans 18acattatgtg tcctaaggaa aatattactt tttcaagaaa atccatgatt ttttcataaa 60aaatagtata ctaattataa tcaaaaaaag gagatataaa atgaaaaaaa cactatcatt 120aaaaaatgac tttaaagaaa ttaagactga tgaattagag attatcattg gcggaagcgg 180aagcctatca acatttttcc ggctgtttaa cagaagtttt acacaagctt tgggaaaata 240agataggcta acattggaat aaaacaaggc tggatttatt attccagcct ttttaaatgt 300aaaataaaaa tacagggtta aataatcaag tgtgctgtcg tggatgagaa gataaaacta 360tctcttagag aataggcctc ctctatttta ttattaggag ttgcttgaat aaatgatgat 420gattgcttgt ttgtaaactg gttttgggat aatgttcaag aatatgattc acctttgcta 480aaccaatacc gcgattggag cctttagtgg aatagttttc tttaaaaatt ttactcacat 540ctatttgttt ttctttggtg gaattctgaa tgataaagac tatactgcca tttttcttaa 600aaaaggctaa ctgaatttca ggatttaatg attcgaaagc agcctcaatg gcattatcac 660acaagataga aagtatggta atgaaatcaa gcaactccat ctcaggcagt tgtattttac 720ttgagacttc tacattgaca gcaatctttt tattctgagc ttctaagatt tttgctgaca 780agataccctt gacagcatcg ttttgaatat tagctagatg gccgatatta taacgggtat 840cctgcaattg atgtcctgtt ttttctaaga tttgatggta aatcttttca atactagcta 900aatctttatt ttcaatgcct aatctgaggc tagttaaaat attcagataa tcatggcgga 960aacttcgaat atccttgtaa agagattcta tttgctgact atactgggtg atatttcgaa 1020tctgagcttc cttttgtgcc attatctcat tttgaacctt ttgtttggta tattggctta 1080aaaatgagat cagaatcaaa aataaaataa gatagacaat aacgacaaat ttacgaaatt 1140ttaaagtcgg tatcacatta taactctcta taacatacaa tacctgtatt aaaaggtagt 1200atagaagcat agtaatattc attggaatca agcgtttttt gaccttcatc ttggtcaaac 1260tatctttaag tcgaccaata tcaacattga acacactgag aaagaggtaa cttagcgcta 1320ttcctgcaaa ctcgatcata taggtggtta taatgctact gcccattaca attccttgag 1380ttccatccaa gataaagaat atgattgccc gcctaaacaa gtcagaactg gcaacaggca 1440gcagaccata aaatatattt agagaaagac tattctgtct attaagataa attgataaag 1500ctataaaata aagaggctct gcaggataaa acaggtttac gttcaccatc gtaacagcaa 1560tcattatcag aaaattgctt atcgaaaaaa gagttaattc ctttttcgat aaagtgacat 1620tacttacctt agaaaataga aacaagagaa atagaacggt tagataagtt aataaaccat 1680ttgaaagtat cattaaggct tcattcattt tgctctcctt tgatcagcaa tcacagctct 1740cagttttgtt aacttagttc gtgaaataag acaagactta ttatttcgaa aataggccaa 1800gcgttttttc cgatcaatac gggtaatatt ggcaggattg acaataaaag agcgatggca 1860ctgaaaaagt ctcttatcca ttttaacaat gtcagtcata ctgccgtaga attcaatccg 1920ttcatcataa gtataaaggc agagcttatg ggctgttgaa gatgtttcaa aatacagaat 1980ctcagcaaaa gggacctgaa actgagtttc agatgaatgg aaaataaaaa gttcctctga 2040ttgaccattc ttctggctgt tttccatagc ataatacagc gctgattcaa tgcggtggga 2100gaactcctca ggattcaaag atttatcaat aaaatccaaa gcagatacct gatactgaaa 2160agtgaggggc ataaactcag aatgtgtcgt gacaaagaca ataactgcac taggattatg 2220ctgtctaatc tgattggcta cttccagtcc tttcttttcc tcttttttga tttcaatatc 2280caaaaagaaa atctggtgat tgcccttttc agggatagcg tcaataagtt gttgtggttt 2340tccaaaaata gtcaattctt tataagacca atttttttct ttcatgatag ctgcaatggt 2400ggtttcaaga cgtccttgtt gtaaaaaatc atcttccaat acaaaaatag aaatcattat 2460ttctccttta atcttctatt taggttagct gattaacact atacacagaa aaggtataaa 2520acgatatcac tcaataaaat ctactaactt aataacc 2557192557DNAStaphylococcus mutans 19ggttattaag ttagtagatt ttattgagtg atatcgtttt ataccttttc tgtgtatagt 60gttaatcagc taacctaaat agaagattaa aggagaaata atgatttcta tttttgtatt 120ggaagatgat tttttacaac aaggacgtct tgaaaccacc attgcagcta tcatgaaaga 180aaaaaattgg tcttataaag aattgactat ttttggaaaa ccacaacaac ttattgacgc 240tatccctgaa aagggcaatc accagatttt ctttttggat attgaaatca aaaaagagga 300aaagaaagga ctggaagtag ccaatcagat tagacagcat aatcctagtg cagttattgt 360ctttgtcacg acacattctg agtttatgcc cctcactttt cagtatcagg tatctgcttt 420ggattttatt gataaatctt tgaatcctga ggagttctcc caccgcattg aatcagcgct 480gtattatgct atggaaaaca gccagaagaa tggtcaatca gaggaacttt ttattttcca 540ttcatctgaa actcagtttc aggtcccttt tgctgagatt ctgtattttg aaacatcttc 600aacagcccat aagctctgcc tttatactta tgatgaacgg attgaattct acggcagtat 660gactgacatt gttaaaatgg ataagagact ttttcagtgc catcgctctt ttattgtcaa 720tcctgccaat attacccgta ttgatcggaa aaaacgcttg gcctattttc gaaataataa 780gtcttgtctt atttcacgaa ctaagttaac aaaactgaga gctgtgattg ctgatcaaag 840gagagcaaaa tgaatgaagc cttaatgata ctttcaaatg gtttattaac ttatctaacc 900gttctatttc tcttgtttct attttctaag gtaagtaatg tcactttatc gaaaaaggaa 960ttaactcttt tttcgataag caattttctg ataatgattg ctgttacgat ggtgaacgta 1020aacctgtttt atcctgcaga gcctctttat tttatagctt tatcaattta tcttaataga 1080cagaatagtc tttctctaaa tatattttat ggtctgctgc ctgttgccag ttctgacttg 1140tttaggcggg caatcatatt ctttatcttg gatggaactc aaggaattgt aatgggcagt 1200agcattataa ccacctatat gatcgagttt gcaggaatag cgctaagtta cctctttctc 1260agtgtgttca atgttgatat tggtcgactt aaagatagtt tgaccaagat gaaggtcaaa 1320aaacgcttga ttccaatgaa tattactatg cttctatact accttttaat acaggtattg 1380tatgttatag agagttataa tgtgataccg actttaaaat ttcgtaaatt tgtcgttatt 1440gtctatctta ttttattttt gattctgatc tcatttttaa gccaatatac caaacaaaag 1500gttcaaaatg agataatggc acaaaaggaa gctcagattc gaaatatcac ccagtatagt 1560cagcaaatag aatctcttta caaggatatt cgaagtttcc gccatgatta tctgaatatt 1620ttaactagcc tcagattagg cattgaaaat aaagatttag ctagtattga aaagatttac 1680catcaaatct tagaaaaaac aggacatcaa ttgcaggata cccgttataa tatcggccat 1740ctagctaata ttcaaaacga tgctgtcaag ggtatcttgt cagcaaaaat cttagaagct 1800cagaataaaa agattgctgt caatgtagaa gtctcaagta aaatacaact gcctgagatg 1860gagttgcttg atttcattac catactttct atcttgtgtg ataatgccat tgaggctgct 1920ttcgaatcat taaatcctga aattcagtta gcctttttta agaaaaatgg cagtatagtc 1980tttatcattc agaattccac caaagaaaaa caaatagatg tgagtaaaat ttttaaagaa 2040aactattcca ctaaaggctc caatcgcggt attggtttag caaaggtgaa tcatattctt 2100gaacattatc ccaaaaccag tttacaaaca agcaatcatc atcatttatt caagcaactc 2160ctaataataa aatagaggag gcctattctc taagagatag ttttatcttc tcatccacga 2220cagcacactt gattatttaa ccctgtattt ttattttaca tttaaaaagg ctggaataat 2280aaatccagcc ttgttttatt ccaatgttag cctatcttat tttcccaaag cttgtgtaaa 2340acttctgtta aacagccgga aaaatgttga taggcttccg cttccgccaa tgataatctc 2400taattcatca gtcttaattt ctttaaagtc attttttaat gatagtgttt ttttcatttt 2460atatctcctt tttttgatta taattagtat actatttttt atgaaaaaat catggatttt 2520cttgaaaaag taatattttc cttaggacac ataatgt 25572047PRTStaphylococcus mutans 20Met Ile Ile Ser Asn Ser Ser Val Leu Ile Ser Leu Lys Ser Phe Phe1 5 10 15Asn Asp Ser Val Phe Phe Ile Leu Tyr Leu Leu Phe Leu Ile Ile Ile 20 25 30Ser Ile Leu Phe Phe Met Lys Lys Ser Trp Ile Phe Leu Lys Lys 35 40 452136PRTStaphylococcus mutans 21Met Ala Leu Ser His Lys Ile Glu Ser Met Val Met Lys Ser Ser Asn1 5 10 15Ser Ile Ser Gly Ser Cys Ile Leu Leu Glu Thr Ser Thr Leu Thr Ala 20 25 30Ile Phe Leu Phe 352242PRTStaphylococcus mutans 22Met Ala Glu Thr Ser Asn Ile Leu Val Lys Arg Phe Tyr Leu Leu Thr1 5 10 15Ile Leu Gly Asp Ile Ser Asn Leu Ser Phe Leu Leu Cys His Tyr Leu 20 25 30Ile Leu Asn Leu Leu Phe Gly Ile Leu Ala 35 402327PRTStreptococcus mutans 23Met Val Cys Cys Leu Leu Pro Val Leu Thr Cys Leu Gly Gly Gln Ser1
5 10 15Tyr Ser Leu Ser Trp Met Glu Leu Lys Glu Leu 20 252434PRTStaphylococcus mutans 24Met Ala Leu Lys Lys Ser Leu Ile His Phe Asn Asn Val Ser His Thr1 5 10 15Ala Val Glu Phe Asn Pro Phe Ile Ile Ser Ile Lys Ala Glu Leu Met 20 25 30Gly Cys2557PRTStaphylococcus mutans 25Met Leu Trp Lys Thr Ala Arg Arg Met Val Asn Gln Arg Asn Phe Leu1 5 10 15Phe Ser Ile His Leu Lys Leu Ser Phe Arg Ser Leu Leu Leu Arg Phe 20 25 30Cys Ile Leu Lys His Leu Gln Gln Pro Ile Ser Ser Ala Phe Ile Leu 35 40 45Met Met Asn Gly Leu Asn Ser Thr Ala 50 552680PRTStaphylococcus mutans 26Met Cys Arg Asp Lys Asp Asn Asn Cys Thr Arg Ile Met Leu Ser Asn1 5 10 15Leu Ile Gly Tyr Phe Gln Ser Phe Leu Phe Leu Phe Phe Asp Phe Asn 20 25 30Ile Gln Lys Glu Asn Leu Val Ile Ala Leu Phe Arg Asp Ser Val Asn 35 40 45Lys Leu Leu Trp Phe Ser Lys Asn Ser Gln Phe Phe Ile Arg Pro Ile 50 55 60Phe Phe Phe His Asp Ser Cys Asn Gly Gly Phe Lys Thr Ser Leu Leu65 70 75 802734PRTStaphylococcus mutans 27Met Ile Ala Ala Met Val Val Ser Arg Arg Pro Cys Cys Lys Lys Ser1 5 10 15Ser Ser Asn Thr Lys Ile Glu Ile Ile Ile Ser Pro Leu Ile Phe Tyr 20 25 30Leu Gly28480DNAStaphylococcus mutans 28atggaagaag attttgaaat tgtttttaat aaggttaagc caattgtatg gaaattaagc 60cgttattact ttattaaaat gtggactcgt gaagattggc aacaagaggg aatgttgatt 120ttgcaccaat tattaaggga acatccagaa ttagaagagg atgatacaaa attgtatatc 180tattttaaga cacgtttttc taattacatt aaagatgttt tgcgtcagca agaaagtcag 240aaacgtcgtt ttaatagaat gtcttatgaa gaagtcggtg agattgaaca ctgtttgtca 300agtggcggta tgcaattgga tgaatatatt ttatttcgtg atagtttgct tgcatataaa 360caaggtctga gtactgaaaa gcaagagctg tttgagcgct tggtagcagg agagcacttt 420ttgggaaggc aaagtatgct gaaagattta cgtaaaaaat taagtgattt taaggaaaaa 48029160PRTStaphylococcus mutans 29Met Glu Glu Asp Phe Glu Ile Val Phe Asn Lys Val Lys Pro Ile Val1 5 10 15Trp Lys Leu Ser Arg Tyr Tyr Phe Ile Lys Met Trp Thr Arg Glu Asp 20 25 30Trp Gln Gln Glu Gly Met Leu Ile Leu His Gln Leu Leu Arg Glu His 35 40 45Pro Glu Leu Glu Glu Asp Asp Thr Lys Leu Tyr Ile Tyr Phe Lys Thr 50 55 60Arg Phe Ser Asn Tyr Ile Lys Asp Val Leu Arg Gln Gln Glu Ser Gln65 70 75 80Lys Arg Arg Phe Asn Arg Met Ser Tyr Glu Glu Val Gly Glu Ile Glu 85 90 95His Cys Leu Ser Ser Gly Gly Met Gln Leu Asp Glu Tyr Ile Leu Phe 100 105 110Arg Asp Ser Leu Leu Ala Tyr Lys Gln Gly Leu Ser Thr Glu Lys Gln 115 120 125Glu Leu Phe Glu Arg Leu Val Ala Gly Glu His Phe Leu Gly Arg Gln 130 135 140Ser Met Leu Lys Asp Leu Arg Lys Lys Leu Ser Asp Phe Lys Glu Lys145 150 155 16030680DNAStaphylococcus mutans 30gtaaataaaa cagccagtta agatgggaca tttatgtcct gttcttaaag tctttttcgt 60tttataataa ttttattata aaaggaggtc atcgtaatag atggaagaag attttgaaat 120tgtttttaat aaggttaagc caattgtatg gaaattaagc cgttattact ttattaaaat 180gtggactcgt gaagattggc aacaagaggg aatgttgatt ttgcaccaat tattaaggga 240acatccagaa ttagaagagg atgatacaaa attgtatatc tattttaaga cacgtttttc 300taattacatt aaagatgttt tgcgtcagca agaaagtcag aaacgtcgtt ttaatagaat 360gtcttatgaa gaagtcggtg agattgaaca ctgtttgtca agtggcggta tgcaattgga 420tgaatatatt ttatttcgtg atagtttgct tgcatataaa caaggtctga gtactgaaaa 480gcaagagctg tttgagcgct tggtagcagg agagcacttt ttgggaaggc aaagtatgct 540gaaagattta cgtaaaaaat taagtgattt taaggaaaaa tagttaaaaa gggaaagaat 600ggaacatgtg attgtaccat tctttttggt tgaaaattaa gaaaagttat tataaattat 660tggtttaaca tgccatatta 680312280DNAStaphylococcus mutans 31atgaaacaag ttatttatgt tgttttaatc gtcatagccg ttaacattct cttagagatt 60atcaaaagag taacaaaaag gggagggaca gtttcgtcat ctaatccttt accagatggg 120cagtctaagt tgttttggcg cagacattat aagctagtac ctcagattga taccagagac 180tgtgggccgg cagtgctggc atctgttgca aagcattacg gatctaatta ctctatcgct 240tatctgcggg aactctcaaa gactaacaag cagggaacaa cagctcttgg cattgttgaa 300gctgctaaaa agttaggctt tgaaacacgc tctatcaagg cggatatgac gctttttgat 360tataatgatt tgacctatcc ttttatcgtc catgtgatta aaggaaaacg tctgcagcat 420tattatgtcg tctatggcag ccagaataat cagctgatta ttggagatcc tgatccttca 480gttaaggtga ctaggatgag taaggaacgc tttcaatcag agtggacagg ccttgcaatt 540ttcctagctc ctcagcctaa ctataagcct cataaaggtg aaaaaaatgg tttgtctaat 600ttcttcccgt tgatctttaa gcagaaagct ttgatgactt atattatcat agctagcttg 660attgtgacgc tcattgatat tgtcggatca tactatctcc aaggaatatt ggacgagtac 720attcctgatc agctgatttc aactttagga atgattacga ttggtctgat aataacctat 780attatccagc aggtcatggc ttttgcaaaa gaatacctct tggccgtact cagtttgcgt 840ttagtcattg atgttatcct gtcttatatc aaacatattt ttacgcttcc tatgtctttc 900tttgcgacaa ggcgaacagg agaaatcacg tctcgtttta cagatgccaa tcagattatt 960gatgctgtag cgtcaaccat cttttcaatc tttttagata tgactatggt aattttggtt 1020ggtggggttt tgttggcgca aaacaataac cttttctttc taaccttgct ctccattccg 1080atttatgcca tcattatttt tgctttcttg aaaccctttg agaaaatgaa tcacgaagtg 1140atggaaagca atgctgtggt aagttcttct atcattgaag atatcaatgg gatggaaacc 1200attaaatcac tcacaagtga gtccgctcgt tatcaaaaca ttgatagtga atttgttgat 1260tatttggaga aaaactttaa gctacacaag tatagtgcca ttcaaaccgc attaaaaagc 1320ggtgctaagc ttatcctcaa tgttgtcatt ctctggtatg gctctcgtct agttatggat 1380aataaaatct cagttggtca gcttatcacc tttaatgctt tgctgtctta tttctcaaat 1440ccaattgaaa atattatcaa tctgcaatcc aaactgcagt cagctcgcgt tgccaataca 1500cgtcttaatg aggtctatct tgtcgaatct gaatttgaaa aagacggcga tttatcagaa 1560aatagctttt tagatggtga tatttcgttt gaaaatcttt cttataaata tggatttggg 1620cgagatacct tatcagatat taatttatca atcaaaaaag gctccaaggt cagtctagtt 1680ggagccagtg gttctggtaa aacaactttg gctaaactga ttgtcaattt ctacgagcct 1740aacaagggga ttgttcgaat caatggcaat gatttaaaag ttattgataa gacagctttg 1800cggcggcata ttagctattt gccgcaacag gcctatgttt ttagtggctc tattatggat 1860aatctcgttt taggagctaa agaaggaacg agtcaggaag acattattcg tgcttgtgaa 1920attgctgaaa tccgctcgga cattgaacaa atgcctcagg gctatcagac agagttatca 1980gatggtgccg gtatttctgg cggtcaaaaa cagcggattg ctttagctag ggccttatta 2040acacaggcac cggttttgat tctggatgaa gccaccagca gtcttgatat tttgacagaa 2100aagaaaatta tcagcaatct cttacagatg acggagaaaa caataatttt tgttgcccac 2160cgcttaagca tttcacagcg tactgacgaa gtcattgtca tggatcaggg aaaaattgtt 2220gaacaaggca ctcataagga acttttagct aagcaaggtt tctattataa cctgtttaat 228032760PRTStaphylococcus mutans 32Met Lys Gln Val Ile Tyr Val Val Leu Ile Val Ile Ala Val Asn Ile1 5 10 15Leu Leu Glu Ile Ile Lys Arg Val Thr Lys Arg Gly Gly Thr Val Ser 20 25 30Ser Ser Asn Pro Leu Pro Asp Gly Gln Ser Lys Leu Phe Trp Arg Arg 35 40 45His Tyr Lys Leu Val Pro Gln Ile Asp Thr Arg Asp Cys Gly Pro Ala 50 55 60Val Leu Ala Ser Val Ala Lys His Tyr Gly Ser Asn Tyr Ser Ile Ala65 70 75 80Tyr Leu Arg Glu Leu Ser Lys Thr Asn Lys Gln Gly Thr Thr Ala Leu 85 90 95Gly Ile Val Glu Ala Ala Lys Lys Leu Gly Phe Glu Thr Arg Ser Ile 100 105 110Lys Ala Asp Met Thr Leu Phe Asp Tyr Asn Asp Leu Thr Tyr Pro Phe 115 120 125Ile Val His Val Ile Lys Gly Lys Arg Leu Gln His Tyr Tyr Val Val 130 135 140Tyr Gly Ser Gln Asn Asn Gln Leu Ile Ile Gly Asp Pro Asp Pro Ser145 150 155 160Val Lys Val Thr Arg Met Ser Lys Glu Arg Phe Gln Ser Glu Trp Thr 165 170 175Gly Leu Ala Ile Phe Leu Ala Pro Gln Pro Asn Tyr Lys Pro His Lys 180 185 190Gly Glu Lys Asn Gly Leu Ser Asn Phe Phe Pro Leu Ile Phe Lys Gln 195 200 205Lys Ala Leu Met Thr Tyr Ile Ile Ile Ala Ser Leu Ile Val Thr Leu 210 215 220Ile Asp Ile Val Gly Ser Tyr Tyr Leu Gln Gly Ile Leu Asp Glu Tyr225 230 235 240Ile Pro Asp Gln Leu Ile Ser Thr Leu Gly Met Ile Thr Ile Gly Leu 245 250 255Ile Ile Thr Tyr Ile Ile Gln Gln Val Met Ala Phe Ala Lys Glu Tyr 260 265 270Leu Leu Ala Val Leu Ser Leu Arg Leu Val Ile Asp Val Ile Leu Ser 275 280 285Tyr Ile Lys His Ile Phe Thr Leu Pro Met Ser Phe Phe Ala Thr Arg 290 295 300Arg Thr Gly Glu Ile Thr Ser Arg Phe Thr Asp Ala Asn Gln Ile Ile305 310 315 320Asp Ala Val Ala Ser Thr Ile Phe Ser Ile Phe Leu Asp Met Thr Met 325 330 335Val Ile Leu Val Gly Gly Val Leu Leu Ala Gln Asn Asn Asn Leu Phe 340 345 350Phe Leu Thr Leu Leu Ser Ile Pro Ile Tyr Ala Ile Ile Ile Phe Ala 355 360 365Phe Leu Lys Pro Phe Glu Lys Met Asn His Glu Val Met Glu Ser Asn 370 375 380Ala Val Val Ser Ser Ser Ile Ile Glu Asp Ile Asn Gly Met Glu Thr385 390 395 400Ile Lys Ser Leu Thr Ser Glu Ser Ala Arg Tyr Gln Asn Ile Asp Ser 405 410 415Glu Phe Val Asp Tyr Leu Glu Lys Asn Phe Lys Leu His Lys Tyr Ser 420 425 430Ala Ile Gln Thr Ala Leu Lys Ser Gly Ala Lys Leu Ile Leu Asn Val 435 440 445Val Ile Leu Trp Tyr Gly Ser Arg Leu Val Met Asp Asn Lys Ile Ser 450 455 460Val Gly Gln Leu Ile Thr Phe Asn Ala Leu Leu Ser Tyr Phe Ser Asn465 470 475 480Pro Ile Glu Asn Ile Ile Asn Leu Gln Ser Lys Leu Gln Ser Ala Arg 485 490 495Val Ala Asn Thr Arg Leu Asn Glu Val Tyr Leu Val Glu Ser Glu Phe 500 505 510Glu Lys Asp Gly Asp Leu Ser Glu Asn Ser Phe Leu Asp Gly Asp Ile 515 520 525Ser Phe Glu Asn Leu Ser Tyr Lys Tyr Gly Phe Gly Arg Asp Thr Leu 530 535 540Ser Asp Ile Asn Leu Ser Ile Lys Lys Gly Ser Lys Val Ser Leu Val545 550 555 560Gly Ala Ser Gly Ser Gly Lys Thr Thr Leu Ala Lys Leu Ile Val Asn 565 570 575Phe Tyr Glu Pro Asn Lys Gly Ile Val Arg Ile Asn Gly Asn Asp Leu 580 585 590Lys Val Ile Asp Lys Thr Ala Leu Arg Arg His Ile Ser Tyr Leu Pro 595 600 605Gln Gln Ala Tyr Val Phe Ser Gly Ser Ile Met Asp Asn Leu Val Leu 610 615 620Gly Ala Lys Glu Gly Thr Ser Gln Glu Asp Ile Ile Arg Ala Cys Glu625 630 635 640Ile Ala Glu Ile Arg Ser Asp Ile Glu Gln Met Pro Gln Gly Tyr Gln 645 650 655Thr Glu Leu Ser Asp Gly Ala Gly Ile Ser Gly Gly Gln Lys Gln Arg 660 665 670Ile Ala Leu Ala Arg Ala Leu Leu Thr Gln Ala Pro Val Leu Ile Leu 675 680 685Asp Glu Ala Thr Ser Ser Leu Asp Ile Leu Thr Glu Lys Lys Ile Ile 690 695 700Ser Asn Leu Leu Gln Met Thr Glu Lys Thr Ile Ile Phe Val Ala His705 710 715 720Arg Leu Ser Ile Ser Gln Arg Thr Asp Glu Val Ile Val Met Asp Gln 725 730 735Gly Lys Ile Val Glu Gln Gly Thr His Lys Glu Leu Leu Ala Lys Gln 740 745 750Gly Phe Tyr Tyr Asn Leu Phe Asn 755 76033900DNAStaphylococcus mutans 33atggatccta aatttttaca aagtgcagaa ttttatagga gacgctatca taattttgcg 60acactattaa ttgttccttt ggtctgcttg attatcttct tggtcatatt cctttgtttt 120gctaaaaaag aaattacagt gatttctact ggtgaagttg caccaacaaa ggttgtagat 180gttatccaat cttacagtga cagttcaatc attaaaaata atttagataa taatgcagct 240gttgagaagg gagacgtttt aattgaatat tcagaaaatg ccagtccaaa ccgtcagact 300gaacaaaaga atattataaa agaaagacaa aaacgagaag agaaggaaaa gaaaaaacac 360caaaagagca agaaaaagaa gaagtctaag agcaagaaag cttccaaaga taagaaaaag 420aaatcgaaag acaaggaaag cagctctgac gatgaaaatg agacaaaaaa ggtttcgatt 480tttgcttcag aagatggtat tattcatacc aatcccaaat atgatggtgc caatattatt 540ccgaagcaaa ccgagattgc tcaaatctat cctgatattc aaaaaacaag aaaagtgtta 600atcacctatt atgcttcttc tgatgatgtt gtttctatga aaaaggggca aaccgctcgt 660ctttccttgg aaaaaaaggg aaatgacaag gttgttattg aaggaaaaat taacaatgtc 720gcttcatcag caactactac taaaaaagga aatctcttta aggttactgc caaagtaaag 780gtttctaaga aaaatagcaa actcatcaag tatggtatga caggcaagac agtcactgtc 840attgataaaa agacttattt tgattatttc aaagataaat tactgcataa aatggataat 90034300PRTStaphylococcus mutans 34Met Asp Pro Lys Phe Leu Gln Ser Ala Glu Phe Tyr Arg Arg Arg Tyr1 5 10 15His Asn Phe Ala Thr Leu Leu Ile Val Pro Leu Val Cys Leu Ile Ile 20 25 30Phe Leu Val Ile Phe Leu Cys Phe Ala Lys Lys Glu Ile Thr Val Ile 35 40 45Ser Thr Gly Glu Val Ala Pro Thr Lys Val Val Asp Val Ile Gln Ser 50 55 60Tyr Ser Asp Ser Ser Ile Ile Lys Asn Asn Leu Asp Asn Asn Ala Ala65 70 75 80Val Glu Lys Gly Asp Val Leu Ile Glu Tyr Ser Glu Asn Ala Ser Pro 85 90 95Asn Arg Gln Thr Glu Gln Lys Asn Ile Ile Lys Glu Arg Gln Lys Arg 100 105 110Glu Glu Lys Glu Lys Lys Lys His Gln Lys Ser Lys Lys Lys Lys Lys 115 120 125Ser Lys Ser Lys Lys Ala Ser Lys Asp Lys Lys Lys Lys Ser Lys Asp 130 135 140Lys Glu Ser Ser Ser Asp Asp Glu Asn Glu Thr Lys Lys Val Ser Ile145 150 155 160Phe Ala Ser Glu Asp Gly Ile Ile His Thr Asn Pro Lys Tyr Asp Gly 165 170 175Ala Asn Ile Ile Pro Lys Gln Thr Glu Ile Ala Gln Ile Tyr Pro Asp 180 185 190Ile Gln Lys Thr Arg Lys Val Leu Ile Thr Tyr Tyr Ala Ser Ser Asp 195 200 205Asp Val Val Ser Met Lys Lys Gly Gln Thr Ala Arg Leu Ser Leu Glu 210 215 220Lys Lys Gly Asn Asp Lys Val Val Ile Glu Gly Lys Ile Asn Asn Val225 230 235 240Ala Ser Ser Ala Thr Thr Thr Lys Lys Gly Asn Leu Phe Lys Val Thr 245 250 255Ala Lys Val Lys Val Ser Lys Lys Asn Ser Lys Leu Ile Lys Tyr Gly 260 265 270Met Thr Gly Lys Thr Val Thr Val Ile Asp Lys Lys Thr Tyr Phe Asp 275 280 285Tyr Phe Lys Asp Lys Leu Leu His Lys Met Asp Asn 290 295 3003520PRTArtificialSynthetic peptide IH-1 35Gly Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr Gln1 5 10 15Ala Leu Gly Lys 203620PRTArtificialSynthetic peptide IH-2 36Ser Gly Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr1 5 10 15Gln Ala Leu Gly 20 3720PRTArtificialSynthetic peptide B1 37Ser Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr Gln1 5 10 15Ala Leu Gly Lys 203820PRTArtificialSynthetic peptide C1 38Ser Gly Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr Gln1 5 10 15Ala Leu Gly Lys 203920PRTArtificialSynthetic peptide D1 39Ser Gly Ser Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr Gln1 5 10 15Ala Leu Gly Lys 204020PRTArtificialSynthetic peptide E1 40Ser Gly Ser Leu Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr Gln1 5 10 15Ala Leu Gly Lys 204120PRTArtificialSynthetic peptide F1 41Ser Gly Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr1 5 10 15Gln Ala Leu Lys 204220PRTArtificialSynthetic peptide G1 42Ser Gly Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr1 5 10 15Gln Ala Gly Lys 204320PRTArtificialSynthetic peptide H1 43Ser Gly Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr1 5 10 15Gln Leu Gly Lys 204420PRTArtificialSynthetic peptide A2 44Ser Gly Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr1 5 10 15Ala Leu Gly
Lys 204521PRTArtificialSynthetic peptide B2 45Ser Gly Ser Leu Ser Thr Phe Phe Val Leu Phe Asn Arg Ser Phe Thr1 5 10 15Gln Ala Leu Gly Lys 204621PRTArtificialSynthetic peptide C2 46Ser Gly Ser Leu Ser Thr Phe Phe Ala Leu Phe Asn Arg Ser Phe Thr1 5 10 15Gln Ala Leu Gly Lys 204721PRTArtificialSynthetic peptide D2 47Ser Gly Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Val Ser Phe Thr1 5 10 15Gln Ala Leu Gly Lys 204821PRTArtificialSynthetic peptide E2 48Ser Gly Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Ala Ser Phe Thr1 5 10 15Gln Ala Leu Gly Lys 204921PRTArtificialSynthetic peptide F2 49Ser Gly Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr1 5 10 15Gln Ala Leu Gly Val 205021PRTArtificialSynthetic peptide G2 50Ser Gly Ser Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr1 5 10 15Gln Ala Leu Gly Ala 205118PRTArtificialSynthetic peptide B3 51Ser Gly Thr Leu Ser Thr Phe Phe Arg Leu Phe Asn Arg Ser Phe Thr1 5 10 15Gln Ala5225DNAArtificialSynthetic P1-HK13 primer 52cacaacaact tattgacgct atccc 255330DNAArtificialSynthetic P2-HK13 primer 53ggcgcgccaa ctggcaacag gcagcagacc 305429DNAArtificialSynthetic P3-HK13 primer 54ggccggcctc aaaacgatgc tgtcaaggg 295521DNAArtificialSynthetic P4-HK13 primer 55agattatcat tggcggaagc g 215630DNAArtificialSynthetic Erm-19 primer 56ggcgcgcccc gggcccaaaa tttgtttgat 305730DNAArtificialSynthetic Erm-20 primer 57ggccggccag tcggcagcga ctcatagaat 30
Patent applications by Celine Levesque, Toronto CA
Patent applications by Dennis G. Cvitkovitch, Oakville CA
Patent applications by Yi-Chen Cathy Huang, Toronto CA
Patent applications by The Governing Council of the University of Toronto
Patent applications in class 25 or more peptide repeating units in known peptide chain structure
Patent applications in all subclasses 25 or more peptide repeating units in known peptide chain structure