[0001] 1. Field of the Invention
[0002] This invention relates to bacteriophage-encoded enzymes useful in preventing dental caries and periodontal diseases. More specifically, this invention relates to lysozyme-like enzymes isolated from bacteriophages which are capable of killing cariogenic bacteria and other periodontal disease-causing organisms. The invention also relates to dextranase-like enzymes suitable for dental treatments (i.e., loosening plaque) and other applications where it is desired to remove dextran and other bacterial polysaccharides (i.e., mutan) synthesized from sucrose.
[0003] 2. Description of the Related Art
[0004] Phages have been known to be present in the human mouth for many years (Meyers, C. E. et al (1958)
[0005] With regard to their function in dental plaque, phages are likely to influence the plaque flora in several potentially significant ways. Prophages, for example, provide immunity to super-infection by homoimmune phages and would presumably assist lysogens which carry them in competing with other bacteria in plaque by killing phage-sensitive competitors in a manner analogous to bacteriocinogenic cells. The semi-solid nature of dental plaque provides an especially favorable environment for this type of competition. Alternatively, lytic phage would be expected to select for phage-resistant mutants of sensitive strains and for mucoid mutants (phenotypically phage-resistant), which could well have altered colonizing and pathogenic properties. Actinophage-resistant mutants have in fact already been used to study cell surface structures that appear to be involved in specific, intergeneric oral bacterial coagreggation reactions (Delisle, A. L. et al (1988)
[0006] The literature on
[0007] Feary was the next to report isolating phages for
[0008] Klein and Frank also reported the presence of phages in cariogenic streptococci (and Actinomyces) (Klein et al (1973)
[0009] Higuchi et al ((1977)
[0010] Upon reviewing the literature on
[0011] Prior art methods for combatting the oral bacteria which lead to dental caries have relied on physical or chemical treatments to remove plaque or kill microorganisms, in a non-specific manner. Desirable organisms were therefore removed along with the target organisms. In the case of antibiotic treatments, resistant mutants often developed, rendering further treatment ineffective.
[0012] Current treatments which claim to reduce the numbers of organisms in dental plaque include a number of mouthwashes (rinses) that contain a variety of bacteriostatic and bacteriocidal organic chemicals. These chemicals include phenols, alcohols, peroxides, detergents/surfactants, quaternary ammonium compounds, root extracts (sanguinarine) and fluorides. A mouthrinse containing the bis-biguanide antibiotic chlorhexidine is now available, by prescription only, in the U.S. With the exception of fluorides and chlorhexidine, none of the currently available oral health care products have been demonstrated to be highly therapeutically effective in reducing plaque or preventing caries.
[0013] Therefore, in view of the aforementioned deficiencies attendant with prior art methods of treating and preventing dental caries and periodontal diseases, it should be apparent that there still exists a need in the art for a method of effectively combatting the oral bacteria which lead to these conditions.
[0014] In contrast to prior art methods of treating and preventing dental caries and periodontal diseases, the phage-encoded enzymes of the present invention do not lead to development of resistant bacterial mutants, because their development in response to the present compositions would require too drastic an alteration in the basic structure of the bacterial cell wall.
[0015] Accordingly, a major object of the present invention is to provide a method for the treatment and prevention of dental caries and periodontal diseases using phage-encoded anti-bacterial enzymes to kill the organisms causing these diseases in the oral cavity.
[0016] Another object of the present invention is to provide a method for studying the cell wall of an oral bacterium by treating the bacterium with a phage-encoded enzyme which degrades the cell wall.
[0017] A further object of the present invention is to provide a method for preventing spoilage of fresh, refrigerated or pasteurized perishable items by treating these items with a phage-encoded anti-bacterial enzyme which inhibits growth of a gram-positive spoilage bacterium on the items.
[0018] Another object is to provide a method for the removal of insoluble dextran polysaccharides by treating with a phage-encoded enzyme.
[0019] A still further object of the present invention is to provide a method for the removal of dental plaque by treating the oral cavity with a phage-encoded enzyme.
[0020] A still further object of the present invention is to provide an isolated and purified phage-encoded anti-bacterial enzyme which inhibits the establishment of an oral bacterium.
[0021] Another object of the present invention is to provide an isolated and purified phage-encoded enzyme which can be used to remove insoluble dextran polysaccharides.
[0022] Yet another object of the present invention is to provide an isolated and purified phage-encoded enzyme which can be used to remove dental plaque.
[0023] Another object of the present invention is to provide DNA fragments isolated from bacteriophage which encode the enzymes of the present invention.
[0024] A further object of the present invention is to provide an expression vector containing the DNA fragments encoding the enzymes of the present invention.
[0025] A still further object of the present invention is to provide a host cell containing an expression vector including DNA fragments encoding the enzymes of the present invention.
[0026] Another object of the present invention is to provide antibodies to the enzymes of the present invention.
[0027] A still further object of the present invention is to provide vehicles for supplying and treating with the enzymes of the present invention.
[0028] Yet another object of the present invention is to provide a genetically engineered non-cariogenic organism which produces phage-encoded enzymes that inhibit the establishment of a cariogenic organism.
[0029] With the foregoing and other objects, advantages and features of the invention that will become hereinafter apparent, the nature of the invention may be more clearly understood by reference to the following detailed description of the preferred embodiments of the invention and to the appended claims.
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[0039]
[0040] More particularly, the present invention relates to the discovery and use of a family of bacteriolytic enzymes encoded on the genome(s) of bacterial viruses (bacteriophages) which infect the oral bacteria that are thought to be the etiological agents of dental caries and periodontal diseases. Specifically, this invention covers the source, production and use of phage-encoded, lysozyme-like enzymes in topical treatment preparations to kill (a) cariogenic bacteria on tooth surfaces, and (b) periodontal disease organisms in periodontal pockets, in order to halt their destructive effects. Such enzymes can thus be used to both treat and prevent dental diseases.
[0041] Other applications of these lysozyme-like enzymes include cleaning or disinfecting of dental appliances, including fixed and removable bridges, partial and full dentures, caps and crowns; veterinary applications; orthodontic and surgical appliances; implant materials; temporary crowns, caps and bridges; endodontic uses (root canals); periodontal treatments (root scaling, cleaning); preparation of enamel, dentinal and cemental surfaces for restorations.
[0042] The invention also relates to phage-encoded dextranase enzymes which can be used for dental application such as removing plaque. In addition, these enzymes may be utilized in non-dental applications, such as in industrial sugar processing and refining operations in which sugar is stored, transported or pumped as liquid solutions. Bacterial contamination of such solutions is common, which results in increased viscosity of the solutions, clogged pipes, valves, etc., due to the insoluble dextran polysaccharides synthesized by the bacteria. Removal of these dextran polysaccharides can be accomplished by addition of dextranase enzymes. Similar treatments might be useful in many other types of food processing operations involving liquid sucrose (i.e., sugar solutions).
[0043] In order to colonize, survive and grow in dental plaque, cariogenic streptococci apparently evolved their unique combination of phenotypic properties, namely the ability to produce special adherent extracellular polysaccharides (EPS) from sucrose, to be resistant to salivary lysozyme, and to tolerate the high acid conditions in this econiche. Phages which infect these organisms also had to evolve in order to grow in this environment, and in so doing acquired new, possibly unique, mechanisms to efficiently adsorb to and lyse their host cells, even at low pH.
[0044] That the phages produce lysozyme-like enzymes is suggested by the finding that growth of a phage in a bacterial broth culture results in complete lysis; after 1-2 hr. there is no visible evidence of cellular debris, indicating nearly complete dissolution of host cell walls. Further, phage-resistant mutants and non-homologous strains of
[0045] Considerable difficulty has in fact been experienced in isolating phage-resistant mutants, due to the presence of lytic enzyme(s) in phage lysates. Unless lysates are diluted 10
[0046] Furthermore, non-growing, stationary-phase cells of
[0047] Since the phage can grow normally in high acid conditions (low pH), their lysozymes are unique in this property, animal lysozymes being virtually inactive at low pH. The lytic enzymes of the present invention are active at low pH, and thus are effective under the conditions which exist in vivo in dental plaque. This is significant since bacteria which inhabit dental plaque are quite resistant to animal lysozymes under these conditions.
[0048] Also, because of their high activity under conditions of low pH, another use of the antibacterial, lytic enzymes described in this invention is their inclusion in food products and other perishable commodities to prevent bacterial spoilage. These enzymes are more active, and therefore more effective, in acid foods such as cheeses than chicken lysozyme, which has been used for this purpose. Thus, the use of the present enzymes in acid foods to prevent spoilage should, therefore, function much better than presently available commercial lysozyme preparations.
[0049] The present invention also includes phage-encoded dextranase enzymes. This enzymatic activity has been found to be present in phage lysates by spotting onto Blue dextran agar plates (0.1%, w/v). This method is relatively sensitive and in fact has been used to detect the expression of
[0050] The phage glucan-degrading enzymes of the present invention degrade dextran and the caries-related EPSs of the cariogenic streptococci that constitute the major components of dental plaque. The phage enzymes enable the phage to infect host bacteria even when the bacteria are grown in the presence of sucrose, which results in their synthesis of large amounts of soluble and insoluble extracellular polysaccharides (EPSs). Thus, EPS-depolymerizing enzymes could be effectively used to remove this material from teeth.
[0051] The present invention includes anti-caries products incorporating either whole, infectious phages or the appropriate, purified phage-encoded enzymes. Treatments involving whole, infectious phage have the advantage of providing a highly specific, long term biological mechanism for controlling cariogenic bacteria. Once intact phage colonize the plaque, they should survive for considerable periods of time, attacking sensitive cells as they arise, and maintaining their number at low, non-cariogenic levels.
[0052] In addition, the enzymes of the present invention, being proteins, adhere to dental plaque well, and so act over considerable periods of time. Continued, intermittent applications of these enzymes can then be used to prevent the re-establishment of these bacteria in the oral cavity.
[0053] Vehicles for the enzymes can include mouthwashes/rinses, topical gels/ointments, toothpastes/powders, slow release implants/coatings, chewing gums and the like. Application of phage-encoded enzymes facilitates plaque removal both in the home and in the dentist's office. Physical removal of dental plaque can be carried out using any known topical means, including dental floss, toothpaste (including abrasive toothpastes), plaque-loosening mouthwashes and professional cleaning by a dentist or dental hygienist. Other preventive measures include pit and fissure sealants (for children) and various fluoride-containing toothpastes and gels (to reduce the acid-solubility of enamel).
[0054] Phage lysates (preparations obtained by growing phage on a susceptible host in broth culture), which contain unpurified lytic enzymes in relatively dilute concentrations, degrade the cell walls of (and thus kill) certain gram-positive bacteria found in dental plaque. This is observed with phages of Actinomyces and of
[0055] The enzymes (or infectious phage) on which this invention is based are “natural” products, having been isolated from human mouths initially and therefore do not have any harmful effect on oral tissues. Chicken lysozyme is presently given GRAS status (generally recognized as safe) by the FDA for use in food products. Ingestion of phage lysozymes would therefore be harmless. Being proteins, they should be readily degraded by normal digestive enzymes, and thus should not harm tissues or beneficial microorganisms in the gastrointestinal tract.
[0056] Since phage-encoded enzymes are not normally synthesized in large amounts during phage growth, cloning their genes into appropriate vectors allows these enzymes to be produced in large quantities for purification. This invention therefore includes the construction and use of such recombinant DNA vectors and their appropriate hosts.
[0057] Additional embodiments of this invention include genetically engineered, non-cariogenic organisms (such as
[0058] This approach, described by Hillman & Socransky (Replacement therapy for the prevention of dental disease,
[0059] Target cariogenic or periodonto-pathogenic bacteria may be from the genera Actinobacillus, Actinomyces, Bacteroides, Capnocytophaga, Eikenella, Eubacterium, Fusobacterium, Haemophilus, Lactobacillus, Peptostreptococcus, Porphyromonas, Prevotella, Rothia, Selenomonas, Streptococcus, Treponema, Wolinella.
[0060] At the present time antibacterial phage lysozymes can be demonstrated to be produced by bacteriophages which infect the following gram-positive, caries-related species:
[0061] Phages have also been isolated for
[0062] Furthermore, the sources of the enzymes which form the basis of this invention are not limited to the oral bacteriophages isolated to date, but should include any additional bacterial viruses, including those of other bacterial species, which may be discovered in the future.
[0063] Host strains are grown in nutrient broth appropriate for the particular species and strain utilized. A preferable broth for
[0064] Phage are isolated from the host strain by any manner known in the art, including isolation from nutrient broth, or from lysed cells on agar plates. Most preferably, phage are isolated from the host bacteria from overnight confluent lysis top agarose plates. Phage suspensions are treated with nucleases and precipitated by any known means, preferably using polyethylene glycol (PEG). Phage are isolated by centrifugation of the phage-precipitant solutions, followed by density gradient centrifugation or by sedimentation.
[0065] The resulting isolated phages are tested to determine host susceptibility, usually by production of clear plaques on top agarose. Phage titers are determined by counting the number of plaques formed at a particular dilution of phage. The phage can be examined using electron microscopy to study their size and morphology.
[0066] To confirm the identity and composition of the phage isolated by the above procedures, phage structural proteins are examined by disrupting the phage by boiling in SDS+β-ME and electrophoresing lysate proteins on an acrylamide gel. Western blots may be used to identify particular proteins, and the presence or absence of certain proteins may be determined using immunological assays such as enzyme-linked immunosorbant assays (ELISA), radioimmune assays, and the like.
[0067] Once purified solutions of the enzymes are obtained, one can also examine the DNA structures of and genetic relationships among
[0068] Phage DNA can be isolated by methods well known in the art, including methods described by Delisle et al (
[0069] The isolated DNA is analyzed by any means known in the art, including electron microscopy, Southern blots, restriction enzyme analysis and electrophoresis to determine relative mobilities, and the like. Particular DNA fragments, i.e., those which contain the genes of interest, or fragments thereof, can be isolated by restriction digestion, and elution from agarose gels, or by chromatographic methods.
[0070] By digesting the ends of the DNA fragment with the same enzyme or a similarly cutting enzyme as that used to digest a particular cloning vector, the DNA fragment of interest can be inserted into an appropriate cloning vector. Alternatively, DNA fragments and vectors may be blunt-ended with Klenow fragment or with mung bean nuclease. DNA sequences from each phage can be cloned into the appropriate plasmid and phage vectors, using standard recombinant DNA techniques, in order to isolate phage genes which code for the following proteins of interest: (a) lysozymes; (b) other cell wall lysins; (c) dextranases; (d) depolymerases active against other extracellular polysaccharides synthesized by their hosts from sucrose (mutan); and (e) the receptor site adsorption proteins which determine serotype-specificity. Cloning vectors of interest include any known in the art, such as pBS, pUC and M13-based plasmids for sequencing, pBR322-based plasmids and phage (such as λgt10) and expression vectors, such as λgt11 and the like.
[0071] The presence of phage-encoded genes in recombinant clones of
[0072] The cloned fragments can then be sequenced, and phage-specific oligonucleotide probes designed for other purposes, including PCR amplification, site-directed mutagenesis, and isolation of related sequences. In this regard, the invention also relates to phage-encoded enzymes which contain mutations which call on the proteins to substantially retain their enzymatic activity. In addition, the phage-encoded enzymes may be specifically engineered to contain mutations which increase or alter their activity or characteristics in a desired manner.
[0073] The cloned fragments can then be inserted into replicable expression vectors which comprise a nucleic acid encoding the subject gene, i.e., the coding sequence is operably linked to a nucleotide sequence element capable of effecting expression of the phage-encoded enzyme. In particular, the nucleotide sequence elements can be a promoter, a transcription enhancer element, a termination signal, a translation signal, or a combination of two or more of these elements, generally including at least a promoter element.
[0074] Replicable expression vectors are generally DNA molecules engineered for controlled expression of a desired gene, especially where it is desirable to produce large quantities of a particular gene product, or polypeptide. The vectors comprise one or more nucleotide sequences operably linked to a gene to control expression of that gene, the gene being expressed, and an origin of replication which is operable in the contemplated host. Preferably the vector encodes a selectable marker, for example, antibiotic resistance. Replicable expression vectors can be plasmids, bacteriophages, cosmids and viruses. Any expression vector comprising RNA is also contemplated.
[0075] The replicable expression vectors of this invention can express phage-encoded enzyme at high levels. These vectors are preferably derived from a prokaryote.
[0076] Prokaryotic vectors include bacterial plasmids and bacteriophage vectors that can transform or infect such hosts as
[0077] Another aspect of this invention provides a homogenous protein encoded by the subject phage-encoded genes. Moreover, peptides and fragments as well as chemically modified derivatives of this protein are also contemplated.
[0078] Purification of the subject phage-encoded proteins from natural or recombinant sources can be accomplished by conventional purification means such as ammonium sulfate precipitation, gel filtration chromatography, ion exchange chromatography, adsorption chromatography, affinity chromatography, chromatafocusing, HPLC, FPLC, and the like. Where appropriate, purification steps can be done in batch or in columns. Fractions containing the phage-encoded enzyme are identified by enzymatic activity.
[0079] Peptide fragments can be prepared by proteolysis or by chemical degradation. Typical proteolytic enzymes are trypsin, chymotrypsin, V8 protease, subtilisin and the like; the enzymes are commercially available, and protocols for performing proteolytic digests are well known. Peptide fragments are purified by conventional means, as described above. Peptide fragments can often be identified by amino acid composition or sequence. Peptide fragments are useful as immunogens to obtain antibodies against the subject phage-encoded enzyme.
[0080] The present invention also relates to antibodies to the subject phage-encoded enzymes. Such antibodies may be monoclonal or polyclonal and are contemplated to be useful in developing detection assays (immunoassays) for proteins, monitoring the activity of the phage-encoded enzyme and in purifying the phage-encoded enzyme. Thus, in accordance with this invention, an antibody to a phage-encoded enzyme encompasses monoclonal or polyclonal antibodies or to antigenic parts thereof.
[0081] Both polyclonal and monoclonal antibodies are obtainable by immunization of an animal with purified enzyme, purified recombinant enzyme, fragments of these proteins, or purified fusion proteins of the enzyme with another protein. In the case of monoclonal antibodies, partially purified proteins or fragments may serve as immunogens. The methods of obtaining both types of antibodies are well known in the art with excellent protocols for antibody production being found in Harlow et al. (1988)
[0082] Polyclonal sera are relatively easily prepared by injection of a suitable laboratory animal with an effective amount of the purified enzyme, or parts thereof, collecting serum from the animal, and isolating specific sera by any of the known immunoadsorbent techniques. Antibodies produced by this method are useful in virtually any type of immunoassay.
[0083] Monoclonal antibodies are particularly useful because they can be produced in large quantities and with a high degree of homogeneity. Hybridoma cell lines which produce monoclonal antibodies are prepared by fusing an immortal cell line with lymphocytes sensitized against the immunogenic preparation and is done by techniques which are well known to those who are skilled in the art. (See, for example, Douillard, I. Y. and Hoffman, T., “Basic Facts About Hybridomas”, in
[0084] The genes coding for the enzymes of the present invention can also be cloned into other organisms to facilitate and improve the production and purity of their respective enzymes by a variety of genetic engineering techniques. Protein engineering techniques are then employed to modify the properties of these enzymes, for example to improve their stability, i.e. at low pH.
[0085] The following examples are presented in order to more fully illustrate the preferred embodiments of the invention. They should in no way be construed, however, as limiting the broad scope of the invention.
[0086] Bacteriophages and host strains.
[0087] The following 3
[0088] Growth and Purification of Phages.
[0089] Each of the above host strains were grown in TYNP broth, which is composed of 30 g/l Trypticase Soy Broth (BBL Labs), 5 g/l yeast extract, 5 g/l neopeptone (Difco) and 5 g/l K
[0090] The results in Table 1 were obtained with phages M102, e10 and f1, which infect certain strains of serotype c, e and f of TABLE 1 Isolation Host Phage Host Serotype Other Sensitive Strains M102 P42 c UA174 e10 LM7 e P4, B14 f1 OMZ 175 f JH 34
[0091] Preliminary studies with the 3 viruses can be summarized as follows. Each phage produced clear plaques, which vary in size from 2-4 mm (
[0092] Phage adsorption and growth was not prevented in sucrose-containing media (
[0093] Each phage produced plaques only on some strains of a single serotype. In the case of M102, 6 of 19 fresh clinical
[0094] Electron microscopy of the phages revealed that each was the same type and size virion. They belong to Bradley's morphotype B, having a polyhedral head and long, non-contractile tails (TABLE 2 Size of phage virions Phage Head Tail Length Tail Width M102 67 nm ± 0.4 283 nm ± 4 8.3 nm ± 0.1 f1 68 nm ± 0.4 286 nm ± 6 8.3 nm ± 0.1 e10 68 nm ± 0.4 287 nm ± 10 8.3 nm ± 0.1
[0095] Lysates of each phage, obtained by infecting a growing broth culture of sensitive cells, diluted even to 10
[0096] The size and number of structural proteins of each phage is determined by SDS-PAGE of SDS-β-meOH-boiled whole phage, using standard 10% Laemmli gels. Western blots are used with the antisera produced below to determine which proteins are antibody-detectable. Gel-separated proteins are transferred to nitrocellulose membranes, using a Bio-Rad Trans-Blot apparatus, reacted with antiphage serum and then detected with commercially obtained horseradish peroxidase-conjugated anti-rabbit IgG antibodies.
[0097] 5-10 major proteins are detected in each phage, with the most abundant in each case being tail subunits (due to the very large size of the phage tails). If it becomes necessary to determine the location of certain proteins in the intact phage, chemical treatments can be used to separate various phage components, e.g., heads and tails, and these can be identified by electron microscopy.
[0098] In some electron micrographs, a thin fiber extending from the tip of each phage tail can be observed. These are thought to be protein and not DNA since they have been observed in DNase-treated lysates. By analogy to phage lambda, it seems likely that this fiber is the adsorption apparatus of the phage.
[0099] Phage DNAs were isolated from purified phage by treatment with Proteinase K in the presence of EDTA and SDS, extracting with phenol and CHCl
[0100] Many of the methods utilized protocols given in Sambrook et al (J. Sambrook, E.F. Fritsch and T. Maniatis (1989) TABLE 3 Size and composition of phage DNAs Phage Tm (° C.) % G + C Length (kb) M102 84.2 ± 1 38.0 32.1 ± 2 e10 83.3 ± 1 37.3 33.5 ± 5 f1 83.7 ± 1 37.0 30.9 ± 2
[0101] Characterization of Phase DNAs.
[0102] Each phage DNA is examined by electron microscopy (e.m.; E. Spiess and R. Lurz (1988)
[0103] All phage DNAs are restricted with a battery of restriction enzymes, preferably EcoRI, BamHI and HindIII, and the resulting patterns (and fragment sizes) compared. They are mapped, insofar as possible by the classical techniques of mixed, partial and sequential digests. To locate sites which occur with high frequency or which cannot be unambiguously mapped, fragments are end-labeled using the standard partial digest approach, by biotinylating known end fragments and using them as probes to order the sites by hybridization with Southern blots of partial digests. This method confirms whether the phage genomes have permuted or unique sequences and terminal redundancy (or terminal repeats, if their genomes are not circularly permuted).
[0104] The SfiI linker mapping system (Promega) is one way to map the phage DNAs in more detail. This method involves subcloning into λGEM-11, 12 (EMBL3, 4 derivatives), excising the fragment with SfiI, partially digesting with test enzymes and then hybridizing Southern blots of agarose gels with oligo probes specific for each uniquely constructed SfiI terminus (Promega).
[0105] Phage DNA Relationships.
[0106] Each DNA is restricted with an appropriate enzyme(s) to cut each phage DNA into small fragments, and is electrophoresed in agarose gels, depurinated with 0.25 N HCl, denatured with alkali, neutralized and transferred to filters by the Southern blot procedure. The blots are hybridized with in vitro labeled, heat denatured whole phage DNAs to determine which fragments of each phage carry sequences in common with the labeled phages. Probes for specific genes (or regions of each genome) can also be used on similar blots to reveal more detailed relationships than can be obtained using whole phage DNA probes. In general, these probe sequences are isolated from recombinant phages/plasmids by using the appropriate restriction enzymes. The desired sequences are separated by excising bands from preparative-scale low melting point agarose gels, purified with GENECLEAN (Bio 101) or QIAGEN and, after heat-denaturing, labeled in vitro with biotin. The latter is accomplished by the photobiotin technique (BRL) or by incorporating biotin-7-dATP in a standard nick translation system (BRL). Hybridized probes are detected by the streptavidin-alkaline phosphatase BluGENE® system (BRL).
[0107] Heteroduplex mapping (by electron microscopy) is also conducted by the method of (A. Romero, R. Lopez, R. Lurz and P. Garcia (1990)
[0108] These methods are used to detect deletions, gene rearrangements and other DNA sequence differences among the phages, and the existence of unique sequences, which may be correlated with host range specificity.
[0109] The results obtained by hybridizing each phage DNA with the two biotinylated whole phage DNA probes are listed in Table 4. Both probe DNAs hybridized with all three phages, indicating that they shared some common sequences. Neither probe hybridized to any host strain tested nor to media, saliva, or unrelated phage DNAs, providing the membranes were treated with proteinase K, which was necessary to eliminate background reactions.
TABLE 4 Hybridization of phage DNAs Labeled Probe DNA Test Phage M102 e10 N3 0 0 A1 0 0 M102 + + e10 + + f1 + +
[0110] Restricting each phage DNA with EcoRI, BamHI and HindIII produced fragment patterns unique to each phage (
[0111] Lysoplate detection of lysozyme-like activity against
[0112] The high diffusibility of the active agent in each well (see
[0113]
[0114] The protocol for growing and washing cells of TABLE 5 Size of lysis zones, in mm, caused by 3 phage lysate pH M102 e10 f1 4.0 7 7 11 5.0 6 5 9 6.0 6 5 9 7.0 4 4 7 8.0 — — 6 9.0 — — 6
[0115] In some experiments pH optima of 5-6 were obtained, but clearly these enzymes are capable of working well at very low pH values. When similar plates were made with 0.1% w/v lyophilized cells of
[0116] The
[0117] The Actinomyces phage lysozymes are only effective against strains of TABLE 6 Host range of Bacteriophage Species Strain Serotype Plasmid M102 e10 f1 AHT a − − − − BHT b − − − − P42-SM c − + − − 10449 c − − − − UA174 c + + − − V318 c + − − − UA101 c + − − − LM7 e + − + − LM7-SM e − − + − P4 e − − + − B14 e − − + − OMZ175-SM f − − − + 6715 g − − − − OMZ176 d − − − −
[0118]
TABLE 7 List of oral and non-oral gram-positive species which have been tested and found to be resistant to lysis and plaque formation by all 3 Species Strains H 10556, C104 10588, 488, DL1 (Challis) J22, 10557, H1 Group H Channon, FW227, 8684, E91/46 Streptococcus SM PK509 4646 MG-1, T14V 4698 W23 25923 19615
[0119] Actinomyces Phages.
[0120] Studies on Actinomyces phages have yielded some data and general information which are relevant and can be applied to the present invention. First, the small, Group I phages (A. L. Delisle, J. A. Donkersloot, P. E. Kolenbrander and C. A. Tylenda (1986)
[0121] Bacillus Phages.
[0122] It turns out that the phage-encoded lysozymes of the small Bacillus phages (M. S. Saedi, K. J. Garvey and J. Ito (1987)
[0123] By comparing the DNA sequences of the above phage lysozymes, and taking into account the codon bias observed in the known sequences of 2 cloned C 5′ ACT AT GGT TGG GGT CAT TAT GG 3′ T
[0124] By making appropriate base changes and varying hybridization stringency conditions, such probes can be used to identify even more distantly related sequences. It should also be noted that several restriction sites occur within the phage lysozyme sequences examined above (including EcoRI); this information is used in selecting enzymes for cloning these genes intact.
[0125] Since introns do not occur in any known dsDNA phages (with the sole exception of T4), determining the nucleotide sequence of a phage gene reveals the true amino acid sequence of its corresponding protein. The DNA sequence upstream of the first codon also provides information on how the expression of the gene may be regulated since this region codes for the ribosomal binding sites, operators and promoters that are used for expression.
[0126] Small, random fragments of phage DNAs are cloned into the plasmid vectors pUC19 and pBluescript, by standard procedures (J. Sambrook, E. F. Fritsch and T. Maniatis (1989) A Laboratory Manual, 2nd ed. Cold Spring Harbor Lab. Press, N.Y. 3 vols.). Since phage vectors do not rely on host viability (and because they also cause release of intracellular constituents, thereby facilitating detection of foreign proteins) fragments are also cloned in λgt10.
[0127] If the phage lysozymes prove to be lethal when expressed in
[0128] Preparation of DNA Fragments.
[0129] Partial digests of each phage DNA are made with HaeIII, a frequent 4-base cutter that generates blunt end fragments or Sau3AI which generates BamHI-compatible ends. Conditions are varied (time, enzyme concentration) to maximize production of appropriate-size fragments (5-10 kb) which are then fractionated by sucrose density gradient centrifugation (J. Sambrook, E. F. Fritsch and T. Maniatis (1989) A Laboratory Manual, 2nd ed. Cold Spring Harbor Lab. Press, N.Y. 3 vols.). These are purified by phenol extraction and ethanol precipitation and, with-out further treatment, used to clone in both types of vectors.
[0130] Plasmid Cloning.
[0131] Plasmids are cut with BamHI (or with EcoRI and then blunt-ended) and dephosphorylated with calf intestinal alkaline phosphatase (CIAP; J. Sambrook, E. F. Fritsch and T. Maniatis (1989) A Laboratory Manual, 2nd ed. Cold Spring Harbor Lab. Press, N.Y. 3 vols.). After removing the CIAP, the vector and fragments are mixed in various ratios, ligated with the appropriate amount of T4 ligase and then transformed (or electroporated) into
[0132] Phage Cloning.
[0133] λgt10 is purchased as purified cos-ligated, coRI-cut, dephosphorylated molecules (BRL). The 4 basepair 5′ overhangs are filled in, to produce blunt ends, by treatment with the Klenow-fragment of DNA polymerase and dATP and dTTP (J. Sambrook, E. F. Fritsch and T. Maniatis (1989) A Laboratory Manual, 2nd ed. Cold Spring Harbor Lab. Press, N.Y. 3 vols.). After phenol extracting and precipitating, the vector and fragment DNAs are mixed in the appropriate ratios and blunt-end ligated. The resulting concatamers are packaged in vitro (BRL Packagene system) and plated on
[0134] Detection of Recombinants.
[0135] Plasmid transformants are plated on LB agar containing ampicillin, to select for cells which acquire a plasmid, and IPTG+X-gal. The latter two substances will result in blue colonies if a complementation occurs between the lacZΔ 15 peptide of the host and the ΔlacZ peptide fragment of the vector, whereas inserts in the vector result in colorless colonies. The latter are picked and screened for the desired genes.
[0136] In the λgt10 cloning system, the hf1 host is so efficiently lysogenized by the wild type phage that most of the resulting plaques are due to interruptions in the cI gene, which give rise to clear plaques, and are therefore mainly recombinant phages. These are screened for the presence of the desired genes or gene products.
[0137] Screening Recombinants.
[0138] Colony and plaque blots are made to detect the presence of probe-related sequences by standard hybridization methods, using the phage lysozyme probe described above.
[0139] To detect enzymatically active proteins, several methods are employed. For phage lysozymes, colonies/plaques are overlaid with 3-5 ml of top agarose seeded with 10% (v/v) of a 50-fold concentrated suspension of washed cells of the appropriate
[0140] A third method to detect expression of phage lysozyme in
[0141] If the lysozyme detection methods do not work satisfactorily, colony/plaque blots are probed with phage lysozyme-specific oligonucleotides. These probes are synthesized on a DNA synthesizer. An amide linker is added to the last 5′ base and after purifying on an ABS oligo purification cartridge, alkaline phosphatase is directly attached to the linker (GIBCO/BRL ACES system). Hybridized probe is detected by the ACES chemiluminescent system (BRL). Specificity and optimum hybridization conditions are determined with the appropriate phage DNAs to ensure that the sequence is in fact present in the phage genome. Other alternative screening procedures include simply assaying recombinant cell extracts for lysozyme-like activity or purifying the enzyme from a broth lysate, preparing antiserum to it and then using this antiserum to detect antibody-reactive proteins in colony/plaque blots.
[0142] To detect EPS depolymerases, agar overlays containing Blue dextran (Sigma) are made on top of recombinant colonies and observed for halos (J. F. Barrett, T. A. Barrett and R. Curtiss III (1987)
[0143] It should be pointed out that, if the cell wall-lytic enzymes encoded by these phages do not turn out to be true lysozymes (i.e., muramidases) and are therefore unrelated to other known phage lysozymes, their genes can still be isolated since the above screening methods will detect such enzymes as long as they cause visible lysis or growth inhibition of host cells.
[0144] Sequencing.
[0145] The isolated phage genes (cloned as above) are sequenced by the dideoxy technique, utilizing fluorescent ddNTPs, in an Applied Biosystems automated sequencer. If the genes prove to be of manageable size they are sequenced by subcloning into an M13 sequencing vector or by using the pBluescript vector itself. The later is used to generate ss DNA phage for sequencing since it contains the fl origin of replication and ssDNA phage progeny are produced from it by infecting the host with the appropriate helper phage. This allows standard M13 sequencing methods to be used. If the cloned sequences are too long to use this approach, shorter fragments are subcloned by using appropriate restriction enzymes or by preparing a series of deletion fragments covering the region of interest (J. Sambrook, E. F. Fritsch and T. Maniatis (1989) A Laboratory Manual, 2nd ed. Cold Spring Harbor Lab. Press, N.Y. 3 vols.). Alternatively, primers are synthesized, as sequencing data is obtained, to extend into more distant regions. Sequencing systems include the Sequenase system (U.S. Biochem. Corp.) and Taq polymerase sequencing PCR techniques. These techniques obviate the need to subclone fragments of interest.
[0146] A. Detection of dextranase in phage lysates.
[0147] The Blue dextran (Sigma)-containing medium dex 10 was found to be the most sensitive dextranase detection medium (Ref: Donkersloot, J. A. and R. J. Harr. 1979. More sensitive test agar for detection of dextranase-producing oral streptococci and identification of two glucan synthesis-defective dextranase mutants of Streptococcus mutans 6715.
[0148] pH Optimum of Lysate Dextranases.
[0149] To determine the approximate pH optima of the dextranase in phage lysates, 10 ml of autoclaved 0.85% NaCl containing 0.25% blue dextran and 0.6% agarose (buffered to various pHs with 0.010 M phosphate) were pipetted into 5 cm petri dishes, allowed to solidify and then wells were cut from the agar with a 5 mm diameter cork borer. The wells were filled with 100-125 μl of sterile filtered phage lysate and the plates were incubated overnight at 37° C. The size of the resulting clear (dextranase) zones, in mm, are given in Table 8.
TABLE 8 Dextranase activity in phage lysates pH Phage Lysate 4.4 5.0 6.0 6.8 M102 8 8 7.5 7.5 (weak) e10 8.5 10 9.5 9.0 f1 10 11 10 8.5
[0150] The data suggest pH optima of 5-6, with significant activity at 4.4 (the lowest tested), indicating these enzymes would be active in highly acidic, caries-active dental plaque.
[0151] Association of Dextranase with Phase Virions.
[0152] The three phages were sedimented by centrifuging sterile filtered lysates for 2 hours at 48,000×g. The phage pellets, but not the supernatant fluids, contained dextranase activity when tested by the above described agarose plate method (at pH 5.0 and 6.0). As this technique does not rule out the possibility of contamination with small amounts of host dextranase, the phage were purified by equilibrium CsCl density gradient centrifugation. Seven grams of CsCl were added to each 10 ml of filtered lysate and the resulting mixtures were centrifuged at 30,000 rpm for 65 hours in a Beckman SW 41 rotor. Three-drop fractions were collected from the bottom of each tube and tested for dextranase activity by placing 100 Ml into separate wells of pH 5.0 agarose-blue dextran plates (as above). In each case the two fractions containing the purified, whole phage band (density=1.40 g/cc) had dextranase activity. Proteins (enzymes) have a much lower buoyant density than whole phage virions (which contain DNA) so contamination of this band with host dextranase is extremely unlikely. The data therefore suggest that the phages have a dextranase-like enzyme as part of their tail structure.
[0153] While the invention has been described and illustrated herein by references to various specific material, procedures and examples, it is understood that the invention is not restricted to the particular material combinations of material, and procedures selected for that purpose. Numerous variations of such details can be implied as will be appreciated by those skilled in the art.