CA2290653A1

CA2290653A1 - Streptococcus sag-a, a structural protein associated with sls activity

Info

Publication number: CA2290653A1
Application number: CA002290653A
Authority: CA
Inventors: Joyce De Azavedo; Darrin Bast; Sergio Borgia; Stephen Betschel; Donald Low
Original assignee: Individual
Current assignee: Mount Sinai Hospital Corp
Priority date: 1998-03-20
Filing date: 1999-03-18
Publication date: 1999-09-30
Also published as: WO1999049049A1; AU2823299A

Abstract

The invention relates to nucleic acid molecules encoding sagA and homologous nucleic acid molecules as well as peptides encoded by the nucleic acid molecules.

Description

S7REPTOCOCCUS SAG-A, A STRUCTURAL PROTEIN ASSOCIATED WITH SLS ACTIVITY
BACKGROUND TO THE INVENTION
The Streptococci are a medically important genera of microbes known to cause several types of disease in humans. Most strains of streptococci causing human infection belong to group A
streptococci (GAS). GAS are the cause of strep throat, scarlet fever, impetigo, cellulitis-erysipelas, rheumatic fever, acute glomerular nephritis, endocarditis, necrotizing fasciitis, brain abscesses, meningitis, osteomyelitis, pharyngitis, pneumonia, rheumatic carditis, and toxic shock. The prototype organism is Streptococcus pyogenes.
Streptolysin S (SLS) is produced by virtually all strains of GAS and it has a direct cytopathic effect on a broad range of cell types (Bernheimer A.W., 1954; Freer, J.H. and J.P. Arbuthriott, 1976; Ginsburg, I. 1970). SLS is an oxygen-stable, nonimmunogenic cytotoxin which causes a zone of beta-hemolysis observed on the surface of blood agar. This property, used routinely in the clinical laboratory to identify GAS, distinguishes SLS activity from streptolysin O (SLO). SLO is an oxygen-labile, immunogenic hemolysin which does not cause beta-hemolysis on the surface of blood agar plates (Ginsburg, I. 1970).
The cytolytic spectrum of SLS is broad, including not only erythrocytes of all tested eukaryotes but also lymphocytes, polymorphonuclear leukocytes, platelets, several tissue culture cell lines, tumor cells, bacterial protoplasts, and L forms of bacteria as well as intracellular organelles such as mitochondria and lysozomes (Ginsburg, I. 1970). By weight, it is one of the most toxic agents known (Alouf, J.E. 1980; Koyama, J. and F.
Egami, 1963; and Lai, C.Y. et al, 1978).
sUI~ARY OF THS INVBNTION
The present inventors generated two SLS deficient mutants using transposon (Tn) 9I6 mutagenesis from two clinical Streptococcus pyogenes isolates of M1 and M18 serotypes. They demonstrated that the non-hemolytic transconjugants were significantly reduced in virulence in a dermonecrotic mouse model of subcutaneous infection, despite exhibiting identical phenotypic characteristics as their isogenic parents, including growth rates, protease, streptolysin O, and DNAase activities and exoprotein and M protein profiles. Further characterization of these non-hemolytic transconjugants revealed that each contained a single Tn916 insertion located in the promoter region of an open reading frame (ORF). A 390-by region of genomic DNA corresponding to the chromosomal point of insertion of Tn916 was sequenced (see SEQ ID
NO. 12) and a novel structural gene associated with SLS activity was identified. The gene Was designated sagA. The polypeptides encoded by the gene are herein referred to as " SAG-A
Polypeptides" , " SAG-A" or " SAG-A Peptides" .
Studies have shown that inactivation of the sagA gene reduces virulence of S. pyogeaes in mice, and that SAG-A plays a direct role in tissue necrosis.
Broadly stated the present invention relates to isolated nucleic acid molecules encoding SAG-A Polypeptides.
A further aspect of the invention provides isolated nucleic acid molecules encoding a SAG-A Polypeptide, particularly Streptococcus pyogenes SAG-A polypeptides, including mRNAs, DNAS, cDNAs, genomic DNAs, PNAs, as well as antisense analogs and biologically, diagnostically, prophylactically, clinically or therapeutically useful variants or fragments thereof, and compositions comprising same.
In an embodiment, the invention relates to an isolated gene encoding SAG-A. The gene allows the production of purified SAG-A
by subcloning the gene into expression vectors under the control of strong constitutive or inducible promoters. Since the genetic code is degenerate, those skilled in the art will recognize that the nucleic acid sequence in Figure 2 (SEQ ID NO: 1) is not the only sequence which may be used to code for a peptide having the functions of the SAG-A peptide. Changes in the nucleotide sequence which result in production of a chemically equivalent or chemically similar amino acid, are included within the scope of the invention. Variants of the proteins of the invention may be made, for example, with protein engineering techniques such as site-directed mutagenesis which are well known in the art for substitution of amino acids. A combination of techniques known in the art may be used to substitute, delete, or add amino acids.
In a particular embodiment, the invention provides an isolated nucleic acid molecule consisting of the nucleotide sequence of SEQ ID NO: 1, 3, or 5 or a nucleotide sequence selected from the group having at least: 40% homology, 65%

homology, 75% homology, 85% homology, 95% homology and 98%
homology to the nucleotide sequence of SEQ ID N0: 1, 3, or 5. The invention also includes an isolated nucleic acid molecule which hybridizes to the above nucleic acid molecules under stringent hybridization conditions. The nucleic acid molecule may be DNA or RNA. The nucleic acid molecule may encode a lantibiotic or lantibiotic fragment i.e. a polypeptide with the characteristics of a lantibiotic. In a preferred embodiment, the nucleic acid molecule encodes a peptide consisting of the amino acid sequence of SEQ ID NO: 2, 4, or 6. The nucleic acid molecule may be isolated from a group A streptococci cell.
The invention also contemplates an isolated SAG-A
polypeptide encoded by a nucleic acid molecule of the invention.
The invention also contemplates biologically, diagnostically, prophylactically, clinically or therapeutically useful variants thereof, including truncations, analogs, allelic or species variations thereof, or a homolog of a polypeptide of the invention or a truncation thereof. (Variants including truncations, analogs, allelic or species variations, and homologs are collectively referred to herein as " SAG-A Related Polypeptides" ). Among the preferred embodiments of the invention are variants of SAG-A
polypeptide encoded by naturally occurring alleles of the sagA
gene.
The nucleic acid molecules of the invention may be inserted into an appropriate vector, and the vector may contain the necessary elements for the transcription and translation of an inserted coding sequence. Accordingly, vectors may be constructed which comprise a nucleic acid molecule of the invention, and where appropriate one or more transcription and translation elements linked to the nucleic acid molecule. Therefore, vectors are contemplated within the scope of the invention which comprise regulatory sequences of the invention, as well as chimeric gene constructs wherein a regulatory sequence of the invention is operably linked to a heterologous nucleic acid, and a transcription termination signal.
A vector can be used to transform host cells to express a SAG-A Polypeptide or SAG-A Related Polypeptide. Therefore, the invention further provides host cells containing a vector of the invention. The invention also includes a cell consisting of the nucleic acid molecules. In another embodiment, the invention is a cell into which the expression vector is inserted.
The protein 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 transformation, transfection and electroporation.
Retroviral vectors, adenoviral 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. Gene expression levels may be controlled with a transcription initiation region that regulates transcription of the gene or gene fragment of interest in a cell such as a prokaryotic cell or a eukaryotic cell. The transcription initiation region may be part of the construct or the expression vector. The transcription initiation domain or promoter may include an RNA polymerase binding site and an mRNA
initiation site. Other regulatory regions that may be used include an enhancer domain and a termination region. The regulatory elements described above may be from animal, plant, yeast, bacterial, fungal, viral, avian, insect or other sources, including synthetically produced elements and mutated elements.
Transcription is enhanced with promoters known in the art. The promoters may be inducible promoters and/or tissue-specific promoters. These promoters may be selected by one skilled in the art depending on the desired transcription initiation rate and/or efficiency.
In one embodiment of the invention, a cell is transformed with the gene of the invention or a fragment of the gene and inserted in an expression vector to produce cells expressing the SAG-A peptide. The gene or gene fragment may be either isolated from a native source (in sense or antisense orientations), synthesized, a mutated native or synthetic sequence, or a combination of these.
Another embodiment of the invention relates to a method of transforming a cell with the gene of the invention or a fragment of the gene, inserted in an expression vector to produce a cell expressing the SAG-A peptide. The invention also relates to a method of expressing the SAG-A peptides of the invention in the cells.
Levels of gene expression may be controlled with genes that code for anti-sense RNA inserted in the expression cassettes or vectors described above.
The invention further broadly contemplates a recombinant SAG-A Polypeptide, or SAG-A Related Polypeptide obtained using a method of the invention.
The invention also includes hybrid genes and peptides, for example where a nucleotide sequence from the gene of the invention is combined with another nucleotide sequence to produce a fusion polypeptide or peptide. Fusion genes and polypeptides or peptides can also be chemically synthesized or produced using other known techniques.
The invention further contemplates antibodies having specificity against an epitope of a SAG-A Polypeptide, or a SAG-A
Related Polypeptide of the invention. Antibodies may be labeled with a detectable substance and used to detect polypeptides of the invention in biological samples, tissues, and cells.
The invention also permits the construction of nucleotide probes that are unique to nucleic acid molecules of the invention.
Therefore, the invention also relates to a probe comprising a sequence encoding a polypeptide of the invention, or a portion (i.e. fragment) thereof.
DNA probes made from the sagA gene or other nucleic acid molecules of the invention may be used to identify genes similar to sagA. These genes could be identified using standard genetic techniques which are well known in the art. The probes will usually be 15 or more nucleotides in length and preferably at Least 30 or more nucleotides. The gene fragments are capable of hybridizing to SEQ ID NO: 1, 3, or 5 or the other sequences of the invention under stringent hybridization conditions. A nucleic acid molecule encoding a peptide of the invention may be isolated from other organisms by screening a library under stringent hybridization conditions with a labeled probe.
The nucleic acid molecules of the invention may be used for therapeutic or prophylactic purposes, in particular genetic immunization. Among the particularly preferred embodiments of the invention are naturally occurring allelic variants of SAG-A and polypeptides encoded thereby.
The invention also provides inhibitors of SAG-A polypeptides or SAG-A Related Polypeptides of the invention, useful as antibacterial agents including for example antibodies of the invention.
Still further the invention provides a method for evaluating a test substance or compound for its ability to modulate the activity of a SAG-A Polypeptide, or a SAG-A Related Polypeptide of the invention. For example, a substance or compound which inhibits or enhances the cytolytic activity of a SAG-A Polypeptide, or a SAG-A Related Polypeptide may be evaluated.
Compounds which modulate the activity of a polypeptide of the invention may also be identified using the methods of the invention by comparing the pattern and level of expression of a nucleic acid molecule or polypeptide of the invention in host cells, in the presence, and in the absence of the compounds.
In accordance with one aspect of the invention, a polypeptide or peptide of the invention (or the fragments of the peptide) may be used in an assay to identify compounds that bind the polypeptide or peptide. Methods known in the art may be used to identify agonists and antagonists of the polypeptides or peptides.
Methods are also contemplated that identify compounds or substances (e. g. polypeptides) which interact with sagA regulatory sequences (e. g. promoter sequences, enhancer sequences, negative modulator sequences).
The substances and compounds identified using the methods of the invention may be SagA agonists or antagonists, preferably bacteriostatic or bactericidal agonists and antagonists.
In accordance with certain embodiments of the invention, there are provided products, compositions, and methods for assessing sagA expression, treating disease caused by organisms producing streptolysin S (e. g. GAS), for example, strep throat, scarlet fever, impetigo, cellulitis-erysipelas, rheumatic fever, acute glomerular nephritis, endocarditis, and necrotizing fasciitis, assaying genetic variation, and administering a SAG-A
Poiypeptide or SAG-A Related Polypeptide to an organism to raise an immunological response against a bacteria especially a GAS.
In accordance with a further aspect of the invention, there are provided processes for utilizing polypeptides or nucleic acid molecules, for in vitro purposes related to scientific research, synthesis of DNA and manufacture of vectors.
These and other aspects, features, and advantages of the present invention should be apparent to those skilled in the art from the following drawings and detailed description.

Preferred embodiments of the invention will be described in relation to the drawings in Which:
Figure 1A is a blot of a Southern hybridization analysis of HindIII restriction digests of genomic DNA from hemolytic wildtype isolates and non-hemolytic transconjugants all possessing at least one copy of Tn916, probed with tetM;
Figure 1B is a blot of a Southern hybridization analysis of HindIII restriction digests of genomic DNA from hemolytic wildtype isolates and non-hemolytic transconjugants all possessing at least one copy of Tn916, probed with tetM;
Figure 2 shows the nucleotide sequence and protein translation of sagA
Figure 3 is a blot of total RNA extracted from mutant SBNHS
(lanes 2-7) and wildtype MGAS166s (lanes 7-13) quantified, standardized, blotted and probed using a PCR amplicon of sagA
labeled with a'~P;
Figure 4 is a graph showing comparisons of mean weight changes of mice after infection with wild type (MGAS166s; TlBPs) and the respective isogenic non-hemolytic mutants (SBNHS; SB30-2);
Figure 5A is a photograph of a hairless SKH1 mice 24 hours after infection with 106 cfu of the SLS producing wildtype MGAS166s (A);
Figure 5B is a photograph of a hairless SKH1 mice 24 hours after infection with 106 cfu of the SLS-deficient Tn916 mutant SBNHS;
Figure 6A is a photograph of a tissue biopsy from euthanized mice which were infected with 106 efu of the SLS-producing wildtype MGAS166s or the SLS-deficient Tn916 mutant SBNH5;
Figure 6B is a photograph of a tissue biopsy from euthanized mice which were infected with 106 cfu of the SLS-deficient Tn916 mutant SBNH5; and _g_ Figure 7 shows the amino acid sequence of a polypeptide of the invention with a proposed cleavage site for polypeptides of the invention having features consistent with a lantibiotic.
DETAILBD D88CRIPTION OF TH$ INVBNTION
In accordance with the present invention there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See for example, Sambrook, Fritsch, & Maniatis, Molecular Cloning: A Laboratory Manual, Second Edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y); DNA Cloning: A Practical Approach, Volumes I and II (D. N. Glover ed. 1985); Oligonucleotide Synthesis (M..J. Gait ed. 1984); Nucleic Acid Hybridization B.D. Hames &
S.J. Higgins eds. (1985); Transcription and Translation B.D. Hames & S.J. Higgins eds (/984); Animal Cell Culture R.I. Freshney, ed.
(1986); Immobilized Cells and enzymes IRL Press, (1986); and B.
Perbal, A Practical Guide to Molecular Cloning (1984).
Nucleic Acid Molecules of the Inveatioa As hereinbefore mentioned, the invention provides isolated sagA nucleic acid molecules. The term "isolated" refers to a nucleic acid (or polypeptide) removed from its natural environment, purified or separated, or substantially free of cellular material or culture medium when produced by recombinant DNA techniques, or chemical reactants, or other chemicals when chemically synthesized. Preferably, an isolated nucleic acid is at least 60% free, more preferably at least 75% free, and most preferably at least 90% free from other components with which they are naturally associated. The term "nucleic acid" is intended to include modified or unmodified DNA, RNA, including mRNAs, DNAs, cDNAs, and genomic DNAs, or a mixed polymer, and can be either single-stranded, double-stranded or triple-stranded. For example, a nucleic acid sequence may be a single-stranded or double-stranded DNA, DNA that is a mixture of single-and double-stranded regions, or single-, double- and triple-stranded regions, single-and double-stranded RNA, RNA that may be single-stranded, or more typically, double-stranded, or triple-stranded, or a mixture of regions comprising RNA or DNA, or both RNA and DNA. The strands in such regions may be from the same molecule or from different molecules. The DNAs or RNAs may contain one or more modified bases. For example, the DNAs or RNAs may have backbones modified for stability or for other reasons. A nucleic acid sequence includes an oligonucleotide, nucleotide, or polynucleotide.
Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name a few examples, are nucleic acid molecules, as the term is used herein.
It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful functions known to those skilled in the art. The term 'nucleic acid molecule"
embraces such chemically, enzymatically or metabolically modified forms of nucleic acids, as well the chemical forms of DNA and RNA
characteristic of viruses and cells, including simple and complex cells. The term " nucleic acid molecule" and in particular DNA or RNA, refers only to the primary and secondary structure and it does not limit it to any particular tertiary forms.
The nucleic acid molecules Which encode for a SAG-A
polypeptide (may include only the coding sequence for the polypeptide; the coding sequence for the polypeptide and additional coding sequences (e. g. processing protease sequences, transporter sequences such as sequences of translocators of the ATP-binding cassette transporter family, immunity gene sequences, leader or transporter sequences, propolypeptide sequences, a pre-or pro- or prepro- protein sequences (e.g. SEQ ID NO. 4 and 6), marker sequences]; the coding sequence for the polypeptide (and optionally additional coding sequence) and non-coding sequences (e. g. non-coding 5' and 3' sequences, such as transcribed, non-translated sequences, termination signals, ribosome binding sites, sequences that stabilize mRNA, polyadenyiation signals) of the polypeptide. A nucleic acid molecule of the invention may comprise a structural gene and its naturally associated sequences that control gene expression.
Therefore, the term " nucleic acid molecule encoding a polypeptide" encompasses a nucleic acid molecule which includes only coding sequence for the polypeptide as well as a nucleic acid molecule which includes additional coding and/or non-coding sequences.
In an embodiment of the invention an isolated nucleic acid molecule is contemplated which comprises:
(i) a nucleic acid sequence encoding a polypeptide having substantial sequence identity to the amino acid sequence of SEQ. ID. NO. 2, 4 or 6;
(ii) a nucleic acid sequence having at least 95% identity to a nucleic acid molecule encoding a polypeptide comprising the amino acid sequence of SEQ. ID. NO. 2, 4 or 6;
(iii) a nucleic acid molecule encoding a polypeptide comprising the amino acid sequence of SEQ. ID. N0. 2, 4 or 6;
(iv) a nucleic acid sequence complementary to (i), iii), or (iii);
(v} a nucleic acid sequence differing from any of (i),(ii), or (iii), in codon sequences due to the degeneracy of the genetic code;
(vi) a nucleic acid sequence comprising at least 5 nucleotides capable of hybridizing to a nucleic acid sequence in SEQ. ID. NO. 1, 3, or 5 or to a degenerate form thereof;
(vii) a nucleic acid sequence encoding a truncation, an analog, an allelic or species variation of a polypeptide comprising the amino acid sequence shown in SEQ. ID. NO.
2, 4, or 6; or (viii) a fragment, or allelic or species variation of (i) , (ii) or (iii) .
In a specific embodiment, the isolated nucleic acid molecule comprises:
(i) a nucleic acid sequence having substantial sequence identity or sequence similarity with a nucleic acid sequence shown in SEQ. ID. NO. l, 3 or 5;
(ii) nucleic acid sequences complementary to (i), preferably complementary to the full nucleic acid sequence shown in SEQ. ID. NO. l, 3, or 5;
(iii) nucleic acid sequences differing from any of the nucleic acid sequences of (i) or (ii) in codon sequences due to the degeneracy of the genetic code; or (iv) a fragment, or allelic or species variation of (i), (ii) or (iii) .
The invention relates to a nucleic acid molecule encoding the complementary nucleotide sequence of any of the nucleic acid molecules described above.The term " complementary" refers to the natural binding of nucleic acid molecules under permissive salt and temperature conditions by base-pairing. For example, the sequence "A-G-T" binds to the complementary sequence " T-C-A".
Complementarity between two single-stranded molecules may be " partial" , in which only some of the nucleic acids bind, or it may be complete when total complementarity exists between the single stranded molecules.
In a preferred embodiment the isolated nucleic acid comprises a nucleic acid sequence encoding the amino acid sequence of Streptococcus pyogenes SAG-A shown in SEQ. ID. N0. 2 or 6, or comprises the nucleic acid sequence of Streptococcus pyogenes sagA
shown in SEQ. ID. NO. 1 or S wherein T can also be U.
The terms " sequence similarity" or " sequence identity"
refer to the relationship between two or more amino acid or nucleic acid sequences, determined by comparing the sequences, which relationship is generally known as " homology" . Identity in the art also means the degree of sequence relatedness between amino acid or nucleic acid sequences, as the case may be, as determined by the match between strings of such sequences. Both identity and similarity can be readily calculated (Computational Molecular Biology, Lesk, A.M., ed., Oxford University Press New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D.W, ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A.M., and Griffin, H.G. eds.
Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, New York, 1987; and Sequence Analysis Primer, Gribskov, M, and Devereux, J., eds. M.
Stockton Press, New York, 1991). While there are a number of existing methods to measure identity and similarity between two amino acid sequences or two nucleic acid sequences, both terms are well known to the skilled artisan (Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, New York, 1987; Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds. M. Stockton Press, New York, 1991; and Carillo, H., and Lipman, D. SIAM J.
Applied Math., 48:1073, 1988). Preferred methods for determining identity are designed to give the largest match between the sequences tested. Methods to determine identity are codified in computer programs. Preferred computer program methods for determining identity and similarity between two sequences include but are not limited to the GCG program package (Devereux, J. et al, Nucleic Acids Research 12(1): 387, 1984), BLASTP, BLASTN, and FASTA (Atschul, S.F, et al., J. Molec. Biol. 215:403, 1990).
Identity or similarity may also be determined using the alignment algorithm of Dayhoff et al [Methods in Enzymology 91: 524-545 (1983) ] .
By way of example, a nucleic acid molecule having a nucleic acid sequence having at least, for example 95% identity to a reference nucleic acid sequence of SEQ ID NO: 1, 3 or 5 indicates that the nucleic acid sequence is identical to the reference sequence except that it may include up to five point mutations per each 100 nucleotides of the reference sequence. Therefore, to obtain a nucleic acid molecule having at least 95% identity to a reference sequence, up to 5% of the nucleotides in the reference sequence must be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. Mutations of the reference sequence may occur at the 5' or 3' terminal positions of the reference sequence, or anywhere between those terminal positions, interspersed either individually among nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence.
Preferably, the nucleic acids of the present invention have substantial sequence identity using the preferred computer programs cited herein, for example greater than 40% nucleic acid identity; preferably greater than 50% nucleic acid identity; more preferably greater than 65-80% sequence identity, and most preferably at least 90% to 99% sequence identity to the sequence shown in SEQ. ID. NO. l, 3, or 5.
Isolated nucleic acids comprising a sequence that differs from the nucleic acid sequence shown in SEQ. ID. NO. 1, 3, or 5 due to degeneracy in the genetic code are also within the scope of the invention. Such nucleic acids encode equivalent polypeptides but differ in sequence from the sequence of SEQ. ID. NO. 1, 3, or 5 due to degeneracy in the genetic code. As one example, DNA
sequence mutations within sagA may result in silent mutations that do not affect the amino acid sequence. Variations in one or more nucleotides may exist among strains within a population due to natural variation. Any and all such nucleic acid variations are within the scope of the invention. DNA sequence mutations may also occur which lead to changes in the amino acid sequence of SAG-A
Polypeptide. These amino acid variations are also within the scope of the present invention. In addition, strain or species variations i.e. variations in nucleotide sequence naturally occurring among different strains or species, are within the scope of the invention.
Another aspect of the invention provides a nucleic acid molecule which hybridizes under selective conditions, (e. g. high stringency conditions), to a nucleic acid which comprises a sequence which encodes a SAG-A Polypeptide of the invention.
Preferably the sequence encodes the amino acid sequence shown in SEQ. ID. N0. 2 and comprises at least 5, preferably at least 10, more preferably at least 15, and most preferably at least 20 nucleotides. In an embodiment, the nucleic acid molecule may also consist of a sequence selected from the group consisting of 8 to 10 nucleotides of the nucleic acid molecules described above, 11 to 25 nucleotides of the nucleic acid described above and 26 to 50 nucleotides of the nucleic acid molecules described above which hybridize to the nucleic acid molecules described above under stringent hybridization conditions.
Selectivity of hybridization occurs with a certain degree of specificity rather than being random. Appropriate stringency conditions which promote DNA hybridization are known to those skilled in the art, or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.
For example, 5.0 to 6.0 x sodium chloride/sodium citrate (SSC) or 0.5% SDS at about 45°C, followed by a wash of 2.0 x SSC at 50°C
may be employed. The stringency may be selected based on the conditions used in the wash step. By way of example, the salt concentration in the wash step can be selected from a high stringency of about 0.2 x SSC at 50°C. In addition, the temperature in the wash step can be at high stringency conditions, at about 65°C.
It will be appreciated that the invention includes nucleic acid molecules encoding a SAG-A Polypeptide, or a SAG-A Related Polypeptide, including truncations of the polypeptides, allelic and species variants, and analogs of the polypeptides as described herein. In particular, fragments of a nucleic acid of the invention are contemplated that are a stretch of at least about 5, preferably at least 10, more preferably at least 15, and most preferably at least 20 nucleotides, more typically at least 50 to S 200 nucleotides but less than 2 kb. It will further be appreciated that variant forms of the nucleic acid molecules of the invention which arise by alternative splicing of an mRNA corresponding to a cDNA of the invention are encompassed by the invention.
In an embodiment of the invention, peptide fragments of the proteins of the invention are provided which retain activity similar to SAG-A and the other peptides of the invention. The invention also includes peptide fragments of the proteins of the invention which can be used as a research tool to characterize the protein or its activity. Such peptides preferably consist of at least 5 amino acids. In preferred embodiments, they may consist of 6 to 10, 11 to 15, 16 to 25 or 26 to 50 amino acids of the proteins of the invention.
An isolated nucleic acid molecule of the invention which comprises DNA can be isolated by preparing a labeled nucleic acid probe based on all or part of the nucleic acid sequence shown in SEQ. ID. NO. 1, 3, or 5. The labeled nucleic acid probe is used to screen an appropriate DNA library (e.g. a cDNA or genomic DNA
library). For example, a cDNA library can be used to isolate a cDNA encoding a SAG-A Polypeptide, or a SAG-A Related Polypeptide, by screening the library with the labeled probe using standard techniques. Alternatively, a genomic DNA library can be similarly screened to isolate a genomic clone encompassing a sagA gene.
Nucleic acids isolated by screening of a cDNA or genomic DNA
library can be sequenced by standard techniques.
An isolated nucleic acid molecule of the invention that is DNA can also be isolated by selectively amplifying a nucleic acid of the invention. N Amplifying" or ~~ amplification " refers to the production of additional copies of a nucleic acid sequence and is generally carried out using polymerase chain reaction (PCR) technologies well known in the art (Dieffenbach, C. W. and G. S.
Dveksler (1995) PCR Primer, a Laboratory Manual, Cold Spring Harbor Press, Plainview, N.Y.). In particular, it is possible to design synthetic oligonucleotide primers from the nucleotide sequence shown in SEQ. ID. NO. 1, 3, or 5 (e.g. SEQ. ID. Nos. 5-14) for use in PCR. A nucleic acid can be amplified from cDNA or genomic DNA using these oligonucleotide primers and standard PCR
amplification techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA
sequence analysis. cDNA may be prepared from mRNA, by isolating total cellular mRNA by a variety of techniques, for example, by using the guanidinium-thiocyanate extraction procedure of Chirgwin et al., Biochemistry, 18, 5294-5299 (1979). cDNA is then synthesized from the mRNA using reverse transcriptase (for example, Moloney MLV reverse transcriptase available from Gibco/BRL, Bethesda, MD, or AMV reverse transcriptase available from Seikagaku America, Inc., St. Petersburg, FL).
An isolated nucleic acid molecule of the invention which is RNA can be isolated by cloning a cDNA encoding a SAG-A
Polypeptide, or a SAG-A Related Polypeptide into an appropriate vector which allows for transcription of the cDNA to produce an RNA molecule which encodes a SAG-A Polypeptide, or a SAG-A Related Polypeptide. For example, a cDNA can be cloned downstream of a bacteriophage promoter, (e.g. a T7 promoter) in a vector, eDNA can be transcribed in vitro with T7 polymerise, and the resultant RNA
can be isolated by conventional techniques.
Nucleic acid molecules of the invention may be chemically synthesized using standard techniques. Methods of chemically synthesizing polydeoxynucleotides are known, including but not limited to solid-phase synthesis which, like peptide synthesis, has been fully automated in commercially available DNA
synthesizers (See e.g., Itakura et al. U.S. Patent No. 4,598,049;
Caruthers et al. U.S. Patent No. 4,458,066; and Itakura U.S.
Patent Nos. 4,401,796 and 4,373,071).
Determination of whether a particular nucleic acid molecule is a sagA gene or encodes a SAG-A Polypeptide, or a SAG-A Related Polypeptide can be accomplished by expressing the cDNA in an appropriate host cell by standard techniques, and testing the expressed polypeptide in the methods described herein. A sagA
cDNA or cDNA encoding a SAG-A Polypeptide, or a SAG-A Related Polypeptide can be sequenced by standard techniques, such as dideoxynucleotide chain termination or Maxim-Gilbert chemical sequencing, to determine the nucleic acid sequence and the predicted amino acid sequence of the encoded polypeptide.

The initiation codon and untranslated sequences of a nucleic acid molecule of the invention may be determined using computer software designed for the purpose, such as PC/Gene (IntelliGenetics Inc., Calif.). The transcription regulatory sequences of a nucleic acid molecule of the invention and/or encoding a SAG-A Polypeptide, or a SAG-A Related Polypeptide may be identified by using a nucleic acid molecule of the invention to probe a genomic DNA clone library. Regulatory elements can be identified using standard techniques. The function of the elements can be confirmed by using these elements to express a reporter gene such as the lacZ gene which is operatively linked to the elements. These constructs may be introduced into cultured cells using conventional procedures.
In an embodiment of the invention a nucleic acid molecule is provided comprising a regulatory sequence of sagA as shown in SEQ.
ID. N0. 7.
The invention contemplates nucleic acid molecules comprising all or a portion of a nucleic acid molecule of the invention comprising a regulatory sequence of a sagA contained in appropriate vectors. The vectors may contain heterologous nucleic acid sequences. ~~ Heterologous nucleic acid" refers to a nucleic acid not naturally located in the cell. Preferably, the heterologous nucleic acid includes a nucleic acid foreign to the cell.
In accordance with another aspect of the invention, the nucleic acid molecules isolated using the methods described herein are mutant sagA genes. For example, the mutant genes may be isolated from strains either known or proposed to have altered cytolytic activity. Mutant genes and mutant gene products may be used in therapeutic and diagnostic methods described herein. For example, a cDNA of a mutant sagA gene may be isolated using PCR as described herein, and the DNA sequence of the mutant gene may be compared to the normal gene to ascertain the mutations) responsible for the loss or alteration of function of the mutant gene product. A genomic library can also be constructed using DNA
from a strain known to carry a mutant gene, or a cDNA library can be constructed using RNA from strains suspected of expressing the mutant allele. A nucleic acid encoding a normal sagA gene or any suitable fragment thereof, may then be labeled and used as a probe to identify the corresponding mutant genes in such libraries.

Clones containing mutant sequences can be purified and subjected to sequence analysis. In addition, an expression library can be constructed using cDNA from RNA isolated from a strain known or suspected to express a mutant sagA gene. Gene products from putatively mutant strains may be expressed and screened, for example using antibodies specific for a SAG-A Polypeptide, or a SAG-A Related Polypeptide as described herein. Library clones identified using the antibodies can be purified and subjected to sequence analysis.
Antisense molecules and ribozymes are contemplated within the scope of the invention. They may be prepared by any method known in the art for the synthesis of nucleic acid molecules. These include techniques for chemically synthesizing oligonucleotides such as solid phase phosphoramidite chemical synthesis. Alternatively, RNA
molecules may be generated by in vitro and in vivo transcription of DNA sequences encoding SAG-A Polypeptide. Such DNA sequences may be incorporated into a wide variety of vectors with suitable RNA
polymerase promoters such as T7 or SP6. Alternatively, these cDNA
constructs that synthesize antisense RNA constitutively or inducibly can be introduced into cell lines, and cells. RNA
molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5~ and/or 3~ ends of the molecule or the use of phosphorothioate or 2' 0-methyl rather than phosphodiesterase linkages within the backbone of the molecule.
This concept is inherent in the production of PNAs and can be extended in all of these molecules by the inclusion of nontraditional bases such as inosine, queosine, and wybutosine, as well as acetyl-, methyl-, thio-, and similarly modified forms of adenine, cytidine, guanine, thymine, and uridine which are not as easily recognized by endogenous endonucleases.
Polvpe~tides of the Invention The term " polypeptide" used herein generally refers to any protein or peptide comprising two or more amino acids joined to each other by peptide bonds or modified peptide bonds. The term refers to both short chains (i.e. peptides, oligopeptides and oligomers) and to longer chains (i.e. proteins). Polypeptides may contain amino acids other than the 20 gene encoded amino acids.
Polypeptides include those modified by natural processes (e. g.

_18_ processing and other post-translational modifications) and by chemical modification techniques. The same type of modification may be present in the same or varying degree at several sites in a given polypeptide and a polypeptide may contain many modifications. Modifications may occur in the peptide backbone, the amino acid side-chains, and the amino or carboxyl termini.
Examples of modifications include acetylation; acylation; ADP-ribosylation; amidation; covalent attachment of flavin, a heme moiety, a nucleotide or nucleotide derivative, a lipid or lipid derivative, or phosphotidylinositol; cross-linking; cyclization;
disulfide bond formation; demethylation, formation of covalent cross-links; glycosylation; hydroxylation; iodination;
methylation; myristoylation; oxidation; proteoytic processing;
phosphorylation;, racemization; lipid attachment; sulfation, gamma-carboxylation of glutamic acid residues; and hydroxylation.
fBy way of example see Proteins-Structure and Molecular Properties 2"° Ed., T.E. Creighton, W.H. Freeman and Company, New York (1993), and Wold, F., Posttranslational Protein Modifications:
Perspectives and Prospects, pages 1-12 in Posttranslational Covalent Modification Of Proteins, B.C. Johnson, Ed. Academic Press, New (1983); Seifer et al., Meth. Enzymol 182:626 (1990);
and Rattan et al., Protein Synthesis: Posttranslational Modificatios and Aging, Ann. N.Y. Acad. Sci. 663:48 (1992)]. The polypeptides may be branched or cyclic, with or without branching.
The polypeptides of the invention include the polypeptide comprising the sequence of SEQ. ID. NO. 2, 4, or 6. In addition to the amino acid sequences of SEQ. ID. N0.2, 4, or 6 the polypeptides of the present invention include truncations of the polypeptides of the invention, and analogs, and homologs of the polypeptides and truncations thereof as described herein.
Truncated polypeptides may comprise peptides having an amino acid sequence of at least five consecutive amino acids in SEQ.ID.
NO. 2, 4, or 6 where no amino acid sequence of five or more, six or more, seven or more, or eight or more, consecutive amino acids present in the fragment is present in a polypeptide other than a SAG-A Polypeptide. In an embodiment of the invention the fragment is a stretch of amino acid residues of at least 12 to 30 contiguous amino acids from particular sequences such as the sequences shown in SEQ.ID. NO. 2, 4 or 6.

The truncated polypeptides may have an amino group (-NH2), a hydrophobic group (for example, carbobenzoxyl, dansyl, or T-butyloxycarbonyl), an acetyl group, a 9-fluorenylmethoxy-carbonyl (PMOC) group, or a macromolecule including but not limited to lipid-fatty acid conjugates, polyethylene glycol, or carbohydrates at the amino terminal end. The truncated polypeptides may have a carboxyl group, an amido group, a T-butyloxycarbonyl group, or a macromolecule including but not limited to lipid-fatty acid conjugates, polyethylene glycol, or carbohydrates at the carboxy terminal end.
A truncated polypeptide or fragment may be free-standing or comprised within a larger polypeptide of which they form a part or region, most preferably as a single continuous region, of a single larger polypeptide.
In a preferred embodiment, the truncated polypeptides or fragments are biologically active and mediate activities of SAG-A.
The fragments may have similar activity or an improved activity, or a decreased undesirable activity. The fragments may be immunogenic in an animal and preferably are not immunoreactive with antibodies that are immunoreactive to polypeptides other than SAG-A. Particularly preferred fragments are those that confer a function essential for viability of GAS, or for initiation, maintaining or causing disease in an individual, particularly a human.
Cyclic polypeptides of the invention are also part of the present invention. Cyclization may allow the polypeptide to assume a more favorable conformation. Cyclization may be achieved using techniques known in the art. For example, disulfide bonds may be formed between two appropriately spaced components having free sulfhydryl groups, or an amide bond may be formed between an amino group of one component and a carboxyl group of another component.
Cyclization may also be achieved using an azobenzene-containing amino acid as described by Ulysse, L., et al., J. Am. Chem. Soc.
1995, 117, 8466-8467. The side chains of Tyr and Asn may be linked to form cyclic peptides. The components that form the bonds may be side chains of amino acids, non-amino acid components or a combination of the two.
It may be desirable to produce a cyclic polypeptide that is more flexible. A more flexible peptide may be prepared by introducing cysteines at the right and left position of the peptide and forming a disulphide bridge between the two cysteines.
The two cysteines are arranged so as not to deform the beta-sheet and turn. The peptide is more flexible as a result of the length of the disulfide linkage and the smaller number of hydrogen bonds in the beta-sheet portion. The relative flexibility of a cyclic peptide can be determined by molecular dynamics simulations.
Mimetics of polypeptides of the invention are also contemplated. Mimetics may be designed based on information i0 obtained by systematic replacement of L-amino acids by D-amino acids, replacement of side chains with groups having different electronic properties, and by systematic replacement of peptide bonds with amide bond replacements. Local conformational constraints can also be introduced to determine conformational requirements for activity of a candidate peptide mimetic. The mimetics may include isosteric amide bonds, or D-amino acids to stabilize or promote reverse turn conformations and to help stabilize the molecule. Cyclic amino acid analogues may be used to constrain amino acid residues to particular conformational states.
Peptoids may also be used which are oligomers of N-substituted amino acids and can be used as motifs for the generation of chemically diverse libraries of novel molecules.
Peptides having one or more D-amino acids are contemplated within the 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 with the same or similar desired biological activity as the corresponding peptide compound of the invention but with more favorable activity than the peptide with respect to solubility, stability, and/or susceptibility to hydrolysis and proteolysis. See for example, Morgan and Gainor, Ann. Rep. Med. Chem., 24:243-252 (1989?. Mimetics of a lantibivtic, nisin A, prepared by substitution, deletion and insertion of amino acids in the lantibiotic are taught in U.S.
Patent No. 5,594,103 (De Vos et aI.). Examples of other peptide mimetics are described in U.S. Patent No. 5,643,873. Mimetics of the proteins of the invention may also be made according to other techniques known in the art. For example, by treating a protein of the invention with an agent that chemically alters a side group by converting a hydrogen group to another group such as a hydroxy or amino group.
The polypeptides of the invention may also include analogs, and/or truncations thereof as described herein, which may include, but are not limited to the polypeptides, containing one or more amino acid substitutions, insertions, and/or deletions. Amino acid substitutions may be of a conserved or non-conserved nature.
Conserved amino acid substitutions involve replacing one or more amino acids with amino acids of similar charge, size, and/or hydrophobicity characteristics. When only conserved substitutions are made the resulting analog should be functionally equivalent to the native polypeptide. Non-conserved substitutions involve replacing one or more amino acids with one or more amino acids which possess dissimilar charge, size, and/or hydrophobicity characteristics. 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.
One or more amino acid insertions may be introduced into a polypeptide of the invention. Amino acid insertions may consist of single amino acid residues or sequential amino acids ranging from about 2 to 15 amino acids in length.
Deletions may consist of the removal of one or more amino acids, or discrete portions from the polypeptide sequence. The deleted amino acids may or may not be contiguous. The lower limit length of the resulting analog with a deletion mutation is about 10 amino acids, preferably 20 amino acids.
An allelic variant at the polypeptide level differs from another polypeptide by only one, or at most, a few amino acid substitutions. A species variation of a polypeptide of the invention is an allelic variation which is naturally occurring among different species. The polypeptides of the invention also include homologs and/or truncations thereof as described herein.
Such homologs include polypeptides whose amino acid sequences are WO 99!49049 PCT/CA99100240 comprised of the amino acid sequences of regions from other species that hybridize under selective hybridization conditions (see discussion of selective and in particular stringent hybridization conditions herein) with a probe used to obtain a polypeptide of the invention. These homologs will generally have the same regions which are characteristic of a polypeptide of the invention. It is anticipated that a polypeptide comprising an amino acid sequence which is at least 20% identical, preferably at least 40% identical, more preferably at least 60% identical, and most preferably at least 80%-95% identical with an amino acid sequence of SEQ. ID. N0.2, 4, or 6 will be a homolog. A percent amino acid sequence similarity or identity is calculated using the methods described herein, preferably the computer programs described herein.
The invention also contemplates isoforms of the polypeptides of the invention. An isoform contains the same number and kinds of amino acids as the polypeptide of the invention, but the isoform has a different molecular structure. The isoforms contemplated by the present invention are those having the same properties as a polypeptide of the invention as described herein.
The present invention also includes polypeptides of the invention conjugated with a selected polypeptide (see description of targeting agents below), or a marker polypeptide (see below) to produce fusion polypeptides. Additionally, immunogenic portions of a polypeptide of the invention are within the scope of the invention.
Antigenically, epitopically, or immunologically equivalent variants of a SAG-A polypeptide form a particular aspect of this invention. Antigenically equivalent variants encompass a polypeptide or its equivalent which will be recognized by certain antibodies which when raised to the polypeptide of the invention, interfere with the activity of a polypeptide of the invention. An immunologically equivalent derivative encompasses a peptide or equivalent which when used in a suitable formulation to raise antibodies in a vertebrate, produces antibodies which interfere with the activity of a polypeptide of the invention.
A polypeptide of the invention may be prepared using recombinant DNA methods. Accordingly, the nucleic acid molecules of the present invention having a sequence which encodes a polypeptide of the invention may be incorporated in a known manner into an appropriate expression vector which ensures good expression of the polypeptide. Possible expression vectors include but are not limited to chromosomal, episomal, and virus-derived vectors. For example, the vectors may be derived from bacterial plasmids, from bacteriophage, from transposons, from yeast episomes, from insertions elements, from yeast chromosomal elements, from viruses such as baculoviruses, papova virus, such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses; and vectors derived from combinations thereof, such as those derived from plasmid, and bacteriophage genetic elements, such as cosmids and phagemids.
Generally, any system or vector suitable to maintain, produce or express a nucleic acid of the invention and/or to express a polypeptide of the invention in a selected host cell may be used.
The invention therefore contemplates a vector of the invention containing a nucleic acid molecule of the invention, and optionally the necessary regulatory sequences for the transcription and translation of the inserted polypeptide-sequence. Suitable regulatory sequences may be derived from a variety of sources, including bacterial, fungal, plant, viral, avian, mammalian, or insect genes, or other sources (For example, see the regulatory sequences described in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Selection of appropriate regulatory sequences is dependent on the host cell chosen as discussed below, and may be readily accomplished by one of ordinary skill in the art. The necessary regulatory sequences may be supplied by a native polypeptide and/or its flanking regions.
~ In an embodiment of the invention, a recombinant nucleic acid molecule for a SAG-A peptide is provided that contains suitable 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. For example, if one were to upregulate the expression of the gene, one could insert the sense sequence and the appropriate promoter into the vehicle. If one Were to downregulate the expression of the gene, one could insert the antisense sequence and the appropriate promoter into the vehicle.

These techniques are known to those skilled in the art.
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.
The invention further provides a vector comprising a DNA
nucleic acid molecule of the invention cloned into the vector in an antisense orientation. That is, the DNA molecule is linked to a regulatory seguence in a manner which allows for expression, by transcription of the DNA molecule, of an RNA molecule which is antisense to a nucleic acid sequence of a nucleic acid molecule of the invention. Regulatory sequences linked to the antisense nucleic acid can be chosen which direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance a viral promoter and/or enhancer, or regulatory sequences can be chosen which direct tissue or cell type specific expression of antisense RNA.
The expression vector of the invention may also contain a marker gene which facilitates the selection of host cells transformed or transfected with a vector of the invention.
Examples of marker genes are genes encoding a polypeptide such as 6418 and hygromycin which confer resistance to certain drugs, ~i-galactosidase, chloramphenicol acetyltransferase, firefly luciferase, or an immunoglobulin or portion thereof such as the Fc portion of an immunoglobulin preferably IgG. The markers can be introduced on a separate vector from the nucleic acid of interest.
The vectors may also contain genes which encode a fusion moiety which provides increased expression of the recombinant polypeptide; increased solubility of the recombinant polypeptide;
and aid in the purification of the target recombinant polypeptide by acting as a ligand in affinity purification. For example, a proteolytic cleavage site may be added to the target recombinant polypeptide to allow separation of the recombinant polypeptide from the fusion moiety subsequent to purification of the fusion polypeptide. Typical fusion expression vectors include pGEX
(Amrad Corp., Melbourne, Australia), pMAL (New England Biolabs, Beverly, MA) and pRITS (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase (GST), maltose E binding polypeptide, or polypeptide A, respectively, to the recombinant polypeptide.
Appropriate secretion signals may also be incorporated into the expressed polypeptide to facilitate secretion of the translated polypeptide.
The vectors may be introduced into host cells to produce a transformed or transfected host cell. The terms "transfected" and "transfection" encompass the introduction of nucleic acid (e.g. a vector) into a cell by one of many standard techniques. A cell is ~~ transformed" by a nucleic acid when the transfected nucleic acid effects a phenotypic change. Prokaryotic cells can be transformed with nucleic acid by, for example, electroporation or calcium-chloride mediated transformation. Nucleic acid can be introduced into mammalian cells via conventional techniques such as calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofectin, transvection, cationic lipid-mediated transfection, scrape loading, transduction, ballistic introduction, infection. electroporation or microinjection. Suitable methods for transforming and transfecting host cells can be found in Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory press (1989)), and other laboratory textbooks.
Suitable host cells include a wide variety of prokaryotic and eukaryotic host cells. For example, the polypeptides of the invention may be expressed in bacterial cells such as streptococci, staphylococci, enterococci, E. coli, streptomyces, lactic acid bacteria, and Bacillus swbstilis, fungal cells such as yeast cells and Aspergillus cells, insect cells such as Drosophila S2 and Spodoptera Sf9; animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, 293, and plant cells. Other suitable host cells can be found in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (199 1).
A host cell may also be chosen which modulates the expression of an inserted nucleic acid sequence, or modifies (e. g.
glycosylation or phosphorylation) and processes (e.g. cleaves) the polypeptide in a desired fashion. Host systems or cell lines may be selected which have specific and characteristic mechanisms for post-translational processing and modification of polypeptides.
For long-term high-yield stable expression of the polypeptide, cell lines and host systems which stably express the gene product may. be engineered.
Polypeptides of the invention can be recovered and purified from recombinant host cells by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography, lectin chromatography, and in particular high performance liquid chromatography. If a polypeptide is denatured during isolation and purification well known refolding techniques may be used to regenerate the active conformation.
In accordance with one aspect of the invention a method is provided for preparing a SAG-A Polypeptide, or SAG-A Related Polypeptide utilizing the purified and isolated nucleic acid molecules of the invention. In particular, a method for preparing a SAG-A Polypeptide, or a SAG-A Related Polypeptide is provided comprising:
(a) transferring a vector of the invention comprising a nucleic acid sequence encoding a SAG-A Polypeptide, or a SAG-A
Related Polypeptide, into a host cell;
(b) selecting transformed host cells from untransformed host cells;
(c) culturing a selected transformed host cell under conditions which allow expression of the SAG-A Polypeptide, or a SAG-A Related Polypeptide; and (d) isolating the SAG-A Polypeptide, or SAG-A Related Polypeptide.
Host cells may also comprise genes encoding accessory proteins including but not limited to processing proteases (e. g.
see SEQ ID NO. 8 and 9), translocators of the ATP-binding cassette transporter family (e. g. see SEQ. ID. NO. 10 and 11), regulatory proteins, and dedicated producer self-protection mechanisms. These genes may be those naturally associated with SAG-A or associated with other proteins including nisin, Pep5, subtilin, epilancin, epidermin, gallidermin, lacticin, streptoccin, salivaricin A, mutacin, lactocin S, carnocin, or cytolysin L1 or L2 (see Sahl et al Eur. J. Biochem. 230:827, 1995). The genes encoding the accessory proteins may be introduced into the host cell as part of the vector comprising a nucleic acid molecule of the invention or they may be on a separate vector.
Host cells and in particular cell lines produced using the methods described herein may be particularly useful in screening and evaluating substances or compounds that modulate the activity of a polypeptide of the invention.
The polypeptides of the invention may also be prepared by chemical synthesis using techniques well known in the chemistry of polypeptides such as solid phase synthesis or synthesis in homogenous solution ( See for example, Merrifield, 1964, J. Am.
Chem. Assoc. 85:2149-2154, Houbenweyl, 1987, Methods of Organic Chemistry, ed. E. Wansch, Vol. 15 I and II, Thieme, Stuttgartsee, J. M. Stewart, and J.D. Young, Solid Phase Peptide Synthesis, 2"d Ed., Pierce Chemical Co., Rockford III. (1984) and G. Barany and R.B. Merrifield, The Peptides: Analysis Synthesis, Biology editors E. Gross and J. Meienhofer Vol. 2 Academic Press, New York, 1980, pp. 3-254 for solid phase synthesis techniques;
and M Bodansky, Principles of Peptide Synthesis, Springer-Verlag, Berlin 1984, and E. Gross and J. Meienhofer, Eds., The Peptides:
Analysis, Synthesis, Biologu, supra, Vol 1, for classical solution synthesis.) N-terminal or C-terminal fusion or chimeric polypeptides comprising a polypeptide of the invention conjugated with other molecules, such as polypeptides (e. g. markers or targeting agents) may be prepared by fusing, through recombinant techniques, the N-terminal or C-terminal of a polypeptide of the invention, and the sequence of a selected polypeptide or marker polypeptide with a desired biological function. The resultant fusion polypeptides contain a polypeptide of the invention fused to the selected polypeptide or marker polypeptide as described herein.
Polv~efltidas With Lantibiotic Characteristics The amino acid sequence of the SAG-A polypeptide shown in SEQ. ID. NO. 1 exhibits close similarities with the class of bacterial peptides known as lantibiotics (Borgia 1997). Sequence characterization information for sagA is described in Example 1.
Several features characteristic of this class of molecules are described in Example 1 and known in the art. The similarity of many of these features with SAG-A shows that it is related to the lantibiotic class of molecules.

Lantibiotics constitute a unique class of ribosomally-synthesized, antimicrobial peptides produced by gram positive bacteria. Their unique structural properties result from the presence of intra-molecular rings formed by thioether bonds of the post-translationally modified amino acids lanthionine (Lan) and 3-methyllanthionine (MeLan) (Nes and Tagg 1996).
Lantibiotics are synthesized on the ribosome as a prepeptide or precursor which undergoes several post-translational modifications and removal of leader sequences. The modifications may include dehydration of specific hydroxyl amino acids to form dehydroamino acids, addition of neighbouring sulfhydryl groups to form thioethers and in specific cases other modifications such as introduction of D-alanine residues from L-serine, formation of lysino-alanine bridges, formation of novel N-terminal blocking groups and oxidative decarboxylation of a C-terminal cysteine.
The first identified lantibiotic, nisin, produced by certain strains of Lactococcus lactis subsp. lactis, is the most widely used lantibiotic in the industrial sector (Delves-Broughton et al.
1996). Following its first successful application as a preservative in processed cheese products, it has since been used in numerous other foods and beverages, including beer, wine and low pH foods such as salad dressings. It is used in natural cheese production and as an adjunct in food processing (Delves-Broughton et al. 1996). It is also used in the treatment and prophylaxis of Helicobacter pylori associated peptic ulcer disease in humans (Blackburn and Projan 1994). Since nisin has also been demonstrated to be particularly bactericidal towards both Staphylococcus and Streptococcus species, it is used as an effective therapeutic agent in the treatment of bovine mastitis (Delves-Broughton et al. 1996).
Other lantibiotics also have numerous commercial applications. For example, the lantibiotic, mersacidin, produced by Bacillus subtilis HIL Y-85,54728 may be an alternative therapeutic agent for the treatment of staphylococcal infections since it is active in vivo against methicillin-resistant Staphylococcus aureus (MRSA) strains (Chatterjee et al. 1992).
U.S. Patent No. 5,667,991 (Koller et aI.) teaches a recombinant gene encoding mersacidin. U.S. Patent No. 5,112,806 (De Vos et al.) discloses pharmaceutical compositions containing mersacidin.

Several patents have been filed on the use of lantibiotics in other therapeutic combinations. U.S. Patent No. 5,458,876 (Monticello) discloses a composition for lysing Listeria monocytogenes containing lysozyme and either of the lantibiotics nisin and subtilin. U.S. Patent Nos. 5,512,269 and 5,683,675 (Molina y Vedia, et a~.) teach a method of facilitating the clearance of retained pulmonary secretions in a subject by administering lantibiotics topically to the lungs. U.S. Patent No.
5,043,176 discloses a synergistic antimicrobial composition consisting of an antimicrobial polypeptide, a buffering component and a hypothiocyanate component. U.S. Patent No. 5,670,138 discloses a lantibiotic mouth care product. A more comprehensive review of additional lantibiotics and their applications is found in Ray and Daeschel 1992, Klaenhammer 1993 and De Vuyst and Vandamme 1994.
Despite the widespread potential applications of lantibiotics, they are individually distinct in their bactericidal activity. This limitation creates a need for novel lantibiotics which can be used in the food and pharmaceutical industries.
The invention provides a novel peptide with features consistent with or characteristic of a lantibiotic, encoded by a gene of the invention. The invention also includes an isolated peptide produced from nucleic acid molecules described herein, including an isolated peptide produced from an expression vector.
In a preferred embodiment, the isolated peptide consists of the amino acid sequence in SEQ ID NO: 2 or an isolated peptide having at least 40% homology, 65% homology, 75% homology, 85% homology, 95% homology and 98% homology to the peptide of SEQ ID NO: 2. The peptide is preferably a lantibiotic. The peptide can be isolated from a group A streptococci cell. The invention also includes an isolated peptide consisting of at least 5 amino acids, 6 to 15 amino acids or 15 to 30 amino acids of the peptides described above.
The invention also contemplates a precursor of a polypeptide of the invention which when expressed in bacteria is converted after translation to the protein streptolysin A. In particular, the invention contemplates a prepeptide or precursor protein (SEQ
ID NO 2) having a propeptide part of the polypeptide (e.g. SEQ ID
NO. 6) fused to one or more leader sequences (e. g. SEQ~ID No.4).

Some or all of the leader sequences may be removed (e.g. SEQ ID
NO. 4) to provide a propeptide which is modified during biosynthesis to form a polypeptide having features consistent with a mature lantibiotic. See Figure 7 showing the proposed Gly-Gly cleavage site.
The invention provides a gene leader fragment encoding a peptide leader sequence which induces post-translational modification of amino acids selected from the group consisting of Cys, Ser, Thr, and mixtures thereof, the fragment comprising the sequence of SEQ ID NO. 3. A polypeptide sequence is also provided which when attached as a leader to a protein precursor which undergoes post-translational modification, assists in inducing the modification, comprising a polypeptide having the biological function of the amino acid sequence of SEQ ID NO. 4.
The invention also contemplates modifications of the prepeptides produced by coupling leader sequences from other lantibiotics including nisin, Pep5, subtilin, epilancin, epidermis, gallidermin, lacticin, streptoccin, salivaricin A, mutacin, lactocin S, carnocin, or cytolysis L1 or L2, to a propeptide part of the protein (e. g. SEQ ID N0. 6). In addition, leader sequences of a polypeptide of the invention having a structure consistent with a lantibiotic can be coupled to propeptides of other lantibiotics including nisin, Peps, subtilin, epilancin, epidermis, gallidermin, lacticin, streptoccin, salivaricin A, mutacin, lactocin S, carnocin, or cytolysis L1 or L2 (See Sahl et al Eur. J. Biochem. 230:827, 1995).
Polypeptides of the invention with features characteristic of a lantibiotic may be produced by inserting an expression vector containing a nucleic acid of the invention in a cell and expressing the peptide.
Still further the invention relates to methods for identifying substances that affect a polypeptide having characteristics of a lantibiotic. Such substances may be identified by determining if a test substance affects the conversion of a precursor of a polypeptide of the invention to the mature protein. The precursor or mature protein may be assayed using 3snown methods to determine the affect of the substance.
The invention also relates to food products, pharmaceutical compositions or vaccines containing these peptides, and to a method for producing a lantibiotic by inserting an expression vector in a cell and expressing the peptide.
Antibodies A polypeptide of the invention (e.g. SEQ ID NO 2, 4, or 6) S can be used to prepare antibodies specific for the polypeptides.
Antibodies can be prepared which bind a distinct epitope in an unconserved region of the polypeptide. An unconserved region of the polypeptide is one that does not have substantial sequence homology to other polypeptides. A region from a conserved region such as a well-characterized sequence can also be used to prepare an antibody to a conserved region of a polypeptide of the invention. Antibodies having specificity for a polypeptide of the invention may also be raised from fusion polypeptides created by expressing fusion polypeptides in host cells as described herein.
IS The invention can employ intact monoclonal or polycional antibodies; chimeric, single chain antibodies (see U.S. Pat No.
4,946,778), simianized antibodies, humanized antibodies (Jones, P.
et al., Nature 321:522, 1986 or Tempest et al., Biotechnology 9:266, 1991), immunologically active fragments (e.g. a Fab or (Fab)2 fragment), an antibody heavy chain, and antibody light chain, a genetically engineered single chain Fv molecule (Ladner et al, U.S. Pat. No. 4,946,778), or a chimeric antibody, for example, an antibody which contains the binding specificity of a marine antibody, but in which the remaining portions are of human 2S origin. Antibodies including monoclonal and polyclonal antibodies, fragments and chimeras, etc. may be prepared using methods known to those skilled in the art.
The antibodies of the invention may be used to isolate or to identify clones expressing a polypeptide of the invention or to purify the polypeptides using affinity chromatography. The antibodies of the invention may also be used in diagnostic and therapeutic applications as described herein.
Ac~lications of the Nuclaic Acid Molecules, Polvoectida , and Antibodies of the Invention 3S It would be apparent to one skilled in the art that the nucleic acid molecules and polypeptides of the invention may be employed as research reagents and materials for the discovery of treatments of, and diagnostics for disease, particularly human disease, as further discussed herein.

The nucleic acid molecules, SAG-A Polypeptide, or SAG-A
Related Polypeptide, and antibodies of the invention may be used in the diagnosis of disease. For example, they may have utility in the diagnosis of the stage of infection and the type of infection.
Eukaryotes (herein also " individuals" ), particularly mammals, and especially humans infected with an organism comprising a nucleic acid or polypeptide of the invention may be monitored or diagnosed by detecting and/or localizing the nucleic acids and polypeptides of the invention.
The applications of the present invention also include methods for the identification of substances or compounds that modulate the biological activity of a polypeptide of the invention (See below). The substances and compounds, as well as polypeptides, nucleic acids, and antibodies of the invention, etc.
may be used for the treatment of diseases. (See below).
Diaanoetic Methods A variety of methods can be employed for the diagnostic and prognostic evaluation of diseases. Such methods may, for example, utilize nucleic acid molecules of the invention, and fragments thereof, and antibodies directed against polypeptides of the invention, including peptide fragments.
The methods described herein for detecting nucleic acid molecules and polypeptides can be used in the diagnosis of infectious diseases especially caused by GAS by detecting polypeptides and nucleic acid molecules of the invention.
The nucleic acid molecules and polypeptides of the invention are markers for group A streptococci and accordingly the antibodies and probes described herein may also be used to characterize a species or strain of GAS.
The methods described herein may be performed by utilizing pre-packaged diagnostic kits comprising at least one specific nucleic acid or antibody described herein, which may be conveniently used, e.g., in clinical settings, to screen and diagnose patients and to screen and identify those individuals having a particular type or stage of infection.
Nucleic acid-based detection techniques and peptide detection techniques are described below. The samples that may be analyzed using the methods of the invention include those which are known or suspected to contain sagA or a polypeptide of the invention. The methods may be performed on biological samples including but not limited to cells, lysates of cells which have been incubated in cell culture, DNA (in solutions or bound to a solid support such as for Southern analysis), RNA (in solution or bound to a solid support such as for northern analysis), an extract from cells or a tissue, and biological fluids such as serum, urine, blood, and CSF. The samples may be derived from a patient or a culture.
Methods for Detectinc Nucleic Acid Molecules of th~ Invention The nucleic acid molecules of the invention allow those skilled in the art to construct nucleotide probes for use in the detection of nucleic acid sequences of the invention in biological materials. Suitable probes include nucleic acid molecules based on nucleic acid sequences encoding at least 5 sequential amino acids from regions of the SAG-A Polypeptide, or a SAG-A Related Polypeptide (see SEQ. ID. No. 1 or 3), preferably they comprise 15 to 30 nucleotides.
A nucleotide probe may be labeled with a detectable substance such as a radioactive label that provides for an adequate signal and has sufficient half-life such as 32p, 3g~ 14C
or the like. Other detectable substances that may be used include antigens that are recognized by a specific labeled antibody, fluorescent compounds, enzymes, antibodies specific for a labeled antigen, and luminescent compounds. An appropriate label may be selected having regard to the rate of hybridization and binding of the probe to the nucleotide to be detected and the amount of nucleotide available for hybridization. Labeled probes may be hybridized to nucleic acids on solid supports such as nitrocellulose filters or nylon membranes as generally described in Sambrook et al, 1989, Molecular Cloning, A Laboratory Manual (2nd ed.). The nucleic acid probes may be used to detect sagA
genes, preferably in human biological samples. The nucleotide probes may also be useful for example in the diagnosis or prognosis of infections particularly those caused by GAS, and in monitoring the progression of these conditions, or monitoring a therapeutic treatment.
The probe may be used in hybridization techniques to detect a sagA gene. The technique generally involves contacting and incubating nucleic acids (e. g. recombinant DNA molecules, cloned genes) obtained from a sample from a patient or other cellular source with a probe of the present invention under conditions favourable for the specific annealing of the probes to complementary sequences in the nucleic acids. After incubation, the non-annealed nucleic acids are removed, and the presence of nucleic acids that have hybridized to the probe if any are detected.
The detection of nucleic acid molecules of the invention may involve the amplification of specific gene sequences using an amplification method such as PCR, followed by the analysis of the amplified molecules using techniques known to those skilled in the art. Suitable primers can be routinely designed by one skilled in the art.
Genomic DNA may be used in hybridization or amplification i5 assays of biological samples to detect abnormalities involving sagA structure, including point mutations, insertions, deletions, and chromosomal rearrangements. For example, direct sequencing, single stranded conformational polymorphism analyses, heteroduplex analysis, denaturing gradient gel electrophoresis, chemical mismatch cleavage, and oligonucleotide hybridization may be utilized.
Deletions and insertions can be detected by a change in size of the amplified product in comparison to the genotype of a reference sequence. Point mutations can be identified by hybridizing amplified DNA to labeled sagA nucleic acid sequences.
Matched sequences can be distinguished from mismatched duplexes by RNase digestion or by differences in melting temperatures. DNA
sequence differences may also be detected by alterations in the electrophoretic mobility of the DNA fragments in gels, with or without denaturing agents, or by direct DNA sequencing. Nuclease protection assays (e. g. RNase and S1 protection or a chemical cleavage method) may be used to detect sequence changes at specific locations.
Mutations or polymorphisms in a nucleic acid molecule of the invention may be detected by a variety of known techniques to allow for example, for serotyping. RT-PCR preferably in conjunction with automated detection systems (e.g. GeneScan) can be used. For example, primers derived from SEQ ID NO: 1 or 5 may be used to amplify nucleic acids isolated from an infected individual and the amplified nucleic acids may be subjected to various techniques for elucidation of the DNA sequence. Using this method, mutations may be detected and used to diagnose infection and to serotype and/or classify the infectious agent.
In an embodiment of the invention a method is provided for diagnosing disease, preferably bacterial infections, more preferably infections caused by GAS, comprising determining from a sample derived from an individual an increased level of expression of a nucleic acid molecule of the invention, in particular a nucleic acid molecule of SEQ ID NO:1 or 5. Increased or decreased expression of sagA nucleic acids may be measured using any of the methods well known in the art for the quantification of nucleic acids such as for example, amplification, PCR, RT-PCR, RNase production, Northern blotting, and other hydridization methods.
t5 Methods for Detectinc Polvceptides Antibodies specifically reactive with a SAG-A Polypeptide, a SAG-A Related Polypeptide, or derivatives, such as enzyme conjugates or labeled derivatives, may be used to detect SAG-A
Polypeptides or SAG-A Related Polypeptides in various biological materials. They may be used as diagnostic or prognostic reagents and they may be used to detect increased or decreased levels of SAG-A Polypeptides or SAG-A Related Polypeptides, expression, or abnormalities in the structure of the polypeptides. A diagnostic assay may be used to detect the presence of an infection by detecting increased levels of SAG-A polypeptide to a control.
Immunoassays as well as other techniques such as Western Blot analysis can be used to determine levels of a polypeptide of the invention.
In vitro immunoassays may also be used to assess or monitor the efficacy of particular therapies. The antibodies of the invention may also be used in vitro to determine the level of SAG-A Polypeptide or SAG-A Related Polypeptide expression in cells genetically engineered to produce a SAG-A Polypeptide, or SAG-A
Related Polypeptide.
Antibodies of. the invention may be used in any known immunoassays that rely on the binding interaction between an antigenic determinant of a polypeptide of the invention, and the antibodies. Examples of such assays are radioimmunoassays, enzyme immunoassays te.g. ELISA), immunofluorescence, competitive binding *rB

assays, immunoprecipitation, latex agglutination, hemagglutination, and histochemical tests. The antibodies may also be used in Western Blot analysis. The antibodies may be used to detect and quantify polypeptides of the invention in a sample in order to determine their role in particular cellular events or pathological states, and to diagnose and treat such pathological states.
Cytochemical techniques known in the art for localizing antigens using light and electron microscopy may be used to detect a polypeptide of the invention. Generally, an antibody of the invention may be labeled with a detectable substance and a polypeptide may be detected based upon the presence of the detectable substance. Various methods of labeling antibodies are known in the art and may be used. Examples of detectable IS substances include, but are not limited to, the following:
radioisotopes (e.g. , 3 Fi, 1'C, 'sS, msl, 1'lI) , fluorescent labels (e. g., FITC, rhodamine, lanthanide phosphors), luminescent labels such as luminol; enzymatic labels (e. g., horseradish peroxidase, ~i-galactosidase, luciferase, alkaline phosphatase, acetylcholinesterase), biotinyl groups (which can be detected by marked avidin e.g., streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or calorimetric methods), predetermined polypeptide epitopes recognized by a secondary reporter (e. g., leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags). In some embodiments, labels are attached via spacer arms of various lengths to reduce potential steric hindrance. Antibodies may also be coupled to electron dense substances, such as ferritin or colloidal gold, which are readily visualised by electron microscopy.
The antibody or sample may be immobilized on a carrier or solid support which is capable of immobilizing cells, antibodies, etc. For example, the carrier or support may be nitrocellulose, or glass, polyacrylamides, gabbros, and magnetite. The support material may have any possible configuration including spherical (e.g. bead), cylindrical (e.g. inside surface of a test tube or well, or the external surface of a rod), or flat (e. g. sheet, test strip). Indirect methods may also be employed in which the primary antigen-antibody reaction is amplified by the introduction of a second antibody, having specificity for the antibody reactive against a polypeptide of the invention. By way of example, if the antibody having specificity against a polypeptide of the invention is a rabbit IgG antibody, the second antibody may be goat anti-rabbit gamma-globulin labeled with a detectable substance as described herein.
Where a radioactive label is used as a detectable substance, a polypeptide of the invention may be localized by radioautography. The results of radioautography may be quantitated by determining the density of particles in the radioautographs by various optical methods, or by counting the grains.
Methods for Identifvina or 8valuatina Substanoea/Comaounds The methods described herein are designed to identify substances or compounds that modulate the activity of a SAG-A
Polypeptide or SAG-A Related Polypeptide. " Modulate" refers to a change or an alteration in the biological activity of a polypeptide of the invention. Modulation may be an increase or a decrease in activity, a change in characteristics, or any other change in the biological, functional, or immunological properties of the polypeptide.
Substances and compounds identified using the methods of the invention include but are not limited to peptides such as soluble peptides including Ig-tailed fusion peptides, members of random peptide libraries and combinatorial chemistry-derived molecular libraries made of D- and/or L-configuration amino acids, phosphopeptides (including members of random or partially degenerate, directed phosphopeptide libraries), antibodies [e. g.
polyclonal, monoclonal, humanized, anti-idiotypic, chimeric, single chain antibodies, fragments, (e.g. Fab, F(ab)2, and Fab expression library fragments, and epitope-binding fragments thereof)], and small organic or inorganic molecules. A substance or compound may be an endogenous physiological compound or it may be a natural or synthetic compound.
Substances which modulate a SAG-A Polypeptide or SAG-A
Related Polypeptide can be identified based on their ability to interact with a SAG-A Polypeptide or SAG-A Related Polypeptide.
Therefore, the invention also provides methods for identifying substances which interact with a SAG-A Polypeptide or SAG-A

Related Polypeptide. Substances identified using the methods of the invention may be isolated, cloned and sequenced using conventional techniques. A substance that interacts with a polypeptide of the invention may be an agonist or antagonist of the biological or immunological activity of a polypeptide of the invention.
The term "agonist", refers to a molecule that increases the amount of, or prolongs the duration of, the activity of the polypeptide. The term °antagonist" refers to a molecule which decreases the biological or immunological activity of the polypeptide. Agonists and antagonists may include proteins, nucleic acids, carbohydrates, or any other molecules that interact with a polypeptide of the invention.
Substances which can interact with a polypeptide of the 1S invention may be identified by reacting the polypeptide with a test substance which potentially interacts with the polypeptide, under conditions Which permit the interaction, and removing and/or detecting complexes of the polypeptides and substance. Substance-polypeptide complexes, free substance, non-complexed polypeptide, or activated golypeptide may be assayed. Conditions which permit the formation of complexes may be selected having regard to factors such as the nature and amounts of the substance and the polypeptide.
Substance-polypeptide complexes, free substances or 2S non-complexed poiypeptides may be isolated by conventional isolation techniques, for example, salting out, chromatography, electrophoresis, gel filtration, fractionation, absorption, polyacrylamide gel electrophoresis, agglutination, or combinations thereof. To facilitate the assay of the components, antibody against the polypeptide or the substance, or labelled polypeptide, or a labelled substance may be utilized. The antibodies, polypeptides, or substances may be labelled with a detectable substance as described above. A polypeptide, or the substance used in the method of the invention may be insolubilized.
In an embodiment of the invention, there are provided methods for identifying compounds which bind to or otherwise interact With and inhibit or activate an activity of a polypeptide or nucleic acid molecule of the invention. The method may comprise contacting a polypeptide of nucleic acid molecule of the invention with a compound to be screened under conditions to permit binding to or other interaction between the compound and the polypeptide or nucleic acid molecule to assess the binding to or other interaction with the compound, such binding or interaction being associated with a second component capable of providing a detectable signal in response to the binding or interaction of the polypeptide or nucleic acid molecule with the compound, and determining whether the compound binds to or otherwise interacts with and activates or inhibits an activity of the polypeptide or nucleic acid molecule by detecting the presence or absence of a signal generated from the binding or interaction of the compound with the polypeptide or nucleic acid molecule.
The invention also contemplates a method for evaluating a compound for its ability to modulate the activity of a polypeptide of the invention, by assaying for an agonist or antagonist (i.e.
enhancer or inhibitor3 of the interaction of the polypeptide with a substance that binds or otherwise interacts with the polypeptide. The basic method for evaluating if a compound is an agonist or antagonist of the interaction of a polypeptide of the invention and a substance that interacts with the polypeptide, is to prepare a reaction mixture containing the polypeptide and the substance under conditions which permit the formation of substance- polypeptide complexes, in the presence of a test compound. The test compound may be initially added to the mixture, or may be added subsequent to the addition of the polypeptide and substance. Control reaction mixtures without the test compound or with a placebo are also prepared. The formation of complexes is detected and the formation of complexes in the control reaction but not in the reaction mixture indicates that the test compound interferes with the interaction of the polypeptide and substance.
The reactions may be carried out in the liquid phase or the polypeptide, substance, or test compound may be immobilized as described herein.
The reagents suitable for applying the methods of the invention to evaluate compounds that modulate a polypeptide of the invention may be packaged into convenient kits providing the necessary materials packaged into suitable containers. The kits may also include suitable supports useful in performing the methods of the invention.
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The nucleic acid sequences provided herein may be used in the discovery and development of antibacterial compounds. The encoded protein, upon expression, can be used as a target for the screening of antibacterial drugs. Additionally, the nucleic acid sequences encoding the amino terminal regions of the encoded protein or the translation facilitating sequences of the respective mRNA can be used to construct antisense sequences to control the expression of the coding sequence of interest.
Polypeptides of the invention that have characteristics of a lantibiotic may be used to design drugs. Since lantibiotics are gene-encoded peptides as opposed to peptide antibiotics synthesized by multi-enzyme complexes, site-directed mutagenesis can be used in the construction of modified SAG-A peptides. One skilled in the art is familiar with techniques to substitute amino acids for certain residues of SAG-A to optimize chemical and physical properties such as enhanced bactericidal action and stability. Techniques for the genetic engineering of ~~ new drugs"
are used to engineer SAG-A as has been done with the lantibiotic subtilin (Liu and Hansen 1992).
Vaccines The marked impairment in the virulence of two clinically relevant S. pyogenes strains by transposon insertion in the sag~1 promoter region shows that SAG-A plays an important role in GAS
pathogenesis. Therefore, antibodies directed against the SAG-A
peptide may provide protection against streptococcal infections and the peptide may be used in a human vaccine. The invention includes the antibodies, fragments of the antibodies and the hybridoma, which secretes the monoclonal antibodies.
Accordingly broadly stated, the invention contemplates a vaccine comprising an immunogenic polypeptide of the invention.
The polypeptides provided by the invention can be used to vaccinate a subject for protection from a particular disease, infection, or condition caused by an organism producing a SAG-A
polypeptide, particularly a GAS infection. A SAG-A Polypeptide or SAG-A Related Polypeptide (e.g, a fragment or variant), can be used to inoculate a host organism such that the host produces an active immune response (e. g. an antibody and/or T cell immune response) to the presence of the polypeptide which can later protect the host from infection by an organism producing the polypeptide. One skilled in the art will appreciate that an immune response especially a cell-mediated immune response to a polypeptide of the invention can provide later protection from reinfection or from infection from a closely related strain.
Immunization can be achieved through artificial vaccination (Kuby, J. Immunology W.H. Freeman and Co. New York, 1992). This immunization may be achieved by administering to individuals the polypeptide either alone or with a pharmaceutically acceptable carrier.
Immunogenic amounts of a polypeptide of the invention can be determined using standard procedures. Briefly, various concentrations of the polypeptide are prepared, administered to individuals, and the immunogenic response (e.g. production of antibodies or cell mediated immunity) to each concentration is determined. Procedures for monitoring the immunogenic response of individuals after inoculation with the polypeptide are well known.
For example, samples can be assayed using ELISA to detect the presence of specific antibodies, or lymphocytes, or cytokine production can be monitored. The specificity of a putative immunogenic antigen of a polypeptide can be determined by testing sera, other fluids or lymphocytes from the inoculated individual for cross-reactivity with any closely related poiypeptides.
The amount of the polypeptide administered will depend on the individual, the condition of the individual, the size of the individual etc. but will be at least an immunogenic amount. The polypeptide can be formulated with adjuvants and with additional compounds including cytokines, with a pharmaceutically acceptable carrier.
Techniques for preparing or 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, a vehicle or an excipient. Examples of peptide vaccines are found in U.S. Patent Nos. 5,679,352, 5,194,254 and 4,950,480. Techniques for preparing vaccines involving site directed mutagenesis are described in U.S.
Patent Nos. 5,714,372, 5,543,302, 5,433,945, 5,358,868, 5,332,583, 5,244,657, 5,221,618, 5,14?,643, 5,085,862 and 5,073,494. It will be appreciated that a SAG-A Polypeptide or SAG-A Related Polypeptide may be chemically treated (e. g. glutaraldehyde) before it is used as a vaccine. Chemical treatment may substantially *rB

decrease or destroy the biological activity of the polypeptide.
The pharmaceutically acceptable carrier or adjuvant employed in a vaccine of the present invention can be selected by standard criteria (Arnon, R. (ed.) " Synthetic Vaccines" I:83-92, CRC
Press, Inc. Boca Raton, Fla., 1987). By ~ pharmaceutically acceptable" is meant material that is not biologically or otherwise undesirable that is, the material may be administered to an individual along with the selected compound without causing any undesirable biological effects or interacting in an undesirable manner with any of the other components of the pharmaceutical compositions in which it is contained. The carrier or adjuvant may depend on the method of administration and the particular individual.
Methods of administration can be oral, sublingual, mucosal, inhaled, absorbed, or by injection. Actual methods of preparing appropriate dosage forms are known or will be apparent to those skilled in the art. (See for example, Remington's Pharmaceutical Sciences (Martin E.W. (ed) latest edition Mack Publishing Co.
Easton, Pa}.
Parenteral administration if used is generally characterized by injection. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection or as emulsions. A more recently revised approach for parenteral administration involves use of a slow release or sustained release system, such that a constant level of dosage is maintained (see for example U.S. Pat. No. 3,710,795}.
It is also contemplated that immunization can be achieved by a genetic immunization approach. A nucleic acid molecule of the invention may be used in genetic immunization employing a suitable delivery system. Examples of such systems include direct injection of plasmid DNA into muscles (Wolff et al., Hum Mol Genet 1992, 1:363; Manthorpe et al Hum Gene Ther 1963, 4:419); delivery of DNA
complexed with specific protein carriers (Wu et al., J. Biol.
Chem, 1989: 264, 16985}; coprecipitation of DNA with calcium phosphate (Benvenisty & Reshef, PNAS 1986, 83: 9551), encapsulation of DNA in various forms of liposomes (Kaneda et al., Science 243:375, 1989); particle bombardment (Tang et al. Nature, 1992, 356:152, Eisenbraun et al, DNA Cell Biol 1993, 12:791); and in vivo infection using cloned retroviral vectors (Seeger et al, PNAS 81:5849, 1984).
In an embodiment of the invention, a peptide of the invention is used as a human vaccine for preventing streptococcal disease, such as necrotizing fasciitis (NF) and streptococcal toxic-shock syndrome (STSS).
Comvositions and Treatmeats The polypeptides, nucleic acid molecules, substances or compounds identified by the methods described herein, antibodies, and antisense nucleic acid molecules of the invention may be used for modulating the activity of a polypeptide or nucleic acid molecule of the invention. The polypeptides etc. may have particular application in the treatment of diseases. Inhibitors or antagonists of a polypeptide of the invention having cytolytic IS activity may be used to treat disorders including diseases caused by streptococcal infections such as endocarditis, cellulitis, brain abscesses, glomerulonephritis, pneumonia, meningitis, osteomyelitis, pharyngitis, rheumatic fever, pneumonia, strep throat, scarlet fever, impetigo, necrotizing fasciitis, rheumatic carditis, and toxic shock.
Inhibitors and antagonists of a polypeptide of the invention are particularly useful in reducing tissue necrosis caused by an organism producing a polypeptide of the invention. Therefore, in a preferred embodiment the inhibitors or antagonists are used to treat necrotizing fasciitis.
A polypeptide of the invention which has characteristics of a lantibiotic (e.g. a SAG-A peptide) may be useful in both the pharmaceutical and food industries. It may exhibit antibacterial activity against a wide variety of gram-negative and gram-positive bacteria and it may be used as a food preservative, an antibacterial agent for medical use, a preservative for construction materials and/or paints, an antibacterial agent for horticultural use, a preservative for livestock feed, a preservative for fish feed, and the like, and it may be used as an antibacterial agent in a wide variety of fields.
The methods of preparing food preservative agents, including lantibiotics, and their use are well known in the art. For examples, see U.S. Patent Nos. 5,646,014, 5,453,420, 5,397,499, 5,260,271, 5,213,833, 5,026,856, 4,961,945, 4,728,376, 4,670,288, 4,538,002, 4,410,547, and 3,936,359. The applications for such polypeptides (e.g. SAG-A peptide) include some of the same uses of other lantibiotics known in the art. Some of the preferred advantages of the SAG-A peptide are due to its unique stability and solubility as compared with other lantibiotics when exposed to different food environments, features which are important when using SAG-A as a biopreservative. SAG-A may be used with a variety of solid, semi-solid and liquid food products. Also, the distinct antimicrobial activity of SAG-A against multidrug-resistant bacteria may be tested and characterized using techniques well known in the art.
Polypeptides of the invention having cytolytic activity may be used to lyse microbial and eukaryotic cells. Accordingly, the invention provides a method for lysing microbial and eukaryotic cells comprising contacting the cells with a polypeptide of the invention having cytolytic activity in an amount effective to lyse the cells. The cells include gram positive and gram negative procaryotic microorganisms (e.g. bacteria, fungi, viruses, or protozoans), neoplastic cells including lymphomas, leukemias, or carcinomas, or eukaryotic cells infected With an intracellular pathogenic microorganism. Cytolytic polypeptides of the invention may therefore be used to treat plants and animals against microbial infections, including bacterial, yeast, fungal, viral and protozoan infections and they may be used in the treatment of cancer. They may function synergistically with conventional therapeutic agents such as antibiotics and anti-cancer treatments, and they may be used as adjuvants.
Cytolytic polypeptides of the invention may be used to selectively lyse cells. Cells may be selectively lysed using a chimeric toxin comprising a cytolytic polypeptide of the invention operatively linked to a targeting agent. The polypeptide may be linked to the targeting agent via peptide linkages. The chimeric toxins allow therapeutic targeting of the toxic action of a cytolytic polypeptide of the invention to target cells such as tumor cells.
The targeting agent may be an any immunologic binding agent such as IgG, IgM, IgA, IgE, F(ab~)2, a univalent fragment such as Fab~, Fab, Dab, as well as engineered antibodies such as recombinant antibodies, humanized antibodies, bispecific antibodies, and the like. Monoclonal antibodies that bind specifically to carcinoma-associated antigens including glycoproteins, glycolipids, and mucins may be employed in the chimeric toxins of the invention (See Fink et al. Prog. Clin.
Pathol. 9:121-33, 1984; U.S. Pat. No. 4,737,579 describing monoclonal antibodies to non-small cell lung carcinomas; U.S. Pat.
No. 4,753,894 describing monoclonal antibodies to human breast cancer; U.S. Pat. No. 4,579,827 describing monoclonal antibodies to human gastrointestinal cancer; U.S. Pat. No. 4,713,352 describing monoclonal antibodies to human renal carcinoma; U.S.
Pat. No. 4, 612,282 describing monoclonal antibody B72.3 recognizing a tumor-associated mucin antigen; U.S. Pat. No.
4,708,930 describing monoclonal antibody KC-4; Young et al J. Exp Med 150:1008, 1979, Kneip et aI J. Immunol 131(3):1591, 1983, Rosen et al Cancer Research 44:2052, 1984, Varki et al Cancer Research 44:681, 1984, and U.S. Pat. Nos. 4, 507,391 and 4,579,827 describes monoclonal antibodies specific for glycolipid antigens associated with tumor cells).
Alternatively, growth factors, rather than antibodies, may be utilized as the reagents to target therapeutic agents to target cells. Any growth factor may be used for such a targeting purpose, so long as it binds to a target cell, generally by binding to a growth factor receptor present on the surface of such a cell. Suitable growth factors for targeting include, but are not limited to, VEGF/VPF (vascular endothelial growth factor/vascular permeability factor), FGF (which, as used herein, refers to the fibroblast growth factor family of proteins), TFG(3 (transforming growth factor beta), and pleitotropin. Preferably, the growth factor receptor to which the targeting growth factor binds should be present at a higher concentration on the surface of target cells (i.e. disease cells such as tumor cells) than on non-target cells (i.e. normal cells). Most preferably, the growth factor receptor to which the targeting growth factor binds should, further, be present at a higher concentration on the surface of target cells than on non-target cells.
A chimeric toxin of the invention may be produced using either standard recombinant DNA techniques or standard synthetic chemistry techniques, both of which are well known to those skilled in the art.

The polypeptides, substances, antibodies, and compounds of the invention may be formulated into pharmaceutical compositions for administration to subjects in a biologically compatible form suitable for administration in vivo. By ~~biologically compatible form suitable for administration in vivo" is meant a form of the substance to be administered in which any toxic effects are outweighed by the therapeutic effects. The substances may be administered to living organisms including humans, and animals.
Administration of a therapeutically active amount of the pharmaceutical compositions of the present invention is defined as an amount effective, at dosages and for periods of time necessary to achieve the desired result. For example, a therapeutically active amount of a substance may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of antibody to elicit a desired response in the individual. Dosage regima may be adjusted to provide the optimum therapeutic response. For example, several divided doses may be administered daily or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation. Dosages to be administered depend on individual patient condition, indication of the drug, physical and chemical stability of the drug, toxicity, the desired effect and on the chosen route of administration (Robert Rakel, ed., Conn's Current Therapy (1995, W.B. Saunders Company, USA)).
The compositions described herein can be prepared by per se known methods for the preparation of pharmaceutically acceptable compositions which can be administered to subjects, such that an effective quantity of the active substance is combined in a mixture with a pharmaceutically acceptable vehicle. Suitable vehicles are described, for example, in Remington~s Pharmaceutical Sciences (Remington's Pharmaceutical Sciences 18'h ed, (1990, Mack Publishing Company) and subsequent editions). On this basis, the compositions include, albeit not exclusively, solutions of the substances or compounds in association With one or more pharmaceutically acceptable vehicles or diluents, and contained in buffered solutions with a suitable pH and iso-osmotic with the physiological fluids.
Pharmaceutical compositions used to treat patients having diseases, disorders or abnormal physical states could include SAG-A or another peptide of the invention and an acceptable vehicle or excipient. Examples of vehicles 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. The protein may be formulated in solid or semisolid form, for example pills, tablets, dreams, ointments, powders, emulsions, gelatin capsules, capsules, suppositories, gels or membranes.
Routes of administration include oral, topical, rental, parenteral (injectable), local, inhalant and epidural IS administration. The compositions of the invention may also be conjugated to transgort molecules to facilitate transport of the molecules. The methods for the preparation of pharmaceutically acceptable compositions which can be administered to patients are known in the art.
The polypeptides etc. and compositions of the invention may be used alone, or in combination with another pharmaceutically active agent.
The invention also contemplates an antibody that specifically binds the therapeutically active ingredient used in a treatment or composition of the invention. The antibody may be used to measure the amount of the therapeutic molecule in a sample taken from a patient for purposes of monitoring the course of therapy.
The nucleic acid molecules encoding a polypeptide of the invention or any fragment thereof. or antisense sequences may be used for therapeutic purposes. Antisense to a nucleic acid molecule encoding a polypeptide of the invention may be used in situations to block the synthesis of the polypeptide. In particular, cells may be transformed with sequences complementary to nucleic avid molecules encoding a SAG-A Polypegtide or SAG-A
Related Polypeptide. Thus, antisense sequences may be used to modulate activity or to achieve regulation of gene function. This technology is well known in the art, and sense or antisense oligomers or larger fragments, can be designed from various locations along the coding or regulatory regions of sequences encoding a polypeptide of the invention.
Expression vectors may be derived from retroviruses, adenoviruses, herpes or vaccinia viruses or from various bacterial S plasmids for delivery of nucleic acid sequences to the target cells. Vectors that express antisense nucleic acid sequences of SAG-A Polypeptides can be constructed using techniques well known to those skilled in the art (see for example, Sambrook et al.).
Genes encoding a SAG-A Polypeptide can be turned off by transforming cells with expression vectors that express high levels of a nucleic acid molecule or fragment thereof which encodes a polypeptide of the invention. Such constructs may be used to introduce untranslatable sense or antisense sequences into a cell. Even if they do not integrate into the DNA, the vectors may continue to transcribe RNA molecules until all copies are disabled by endogenous nucleases. Transient expression may last for extended periods of time (e.g a month or more) with a non-replicating vector, or if appropriate replication elements are part of the vector system.
Modification of gene expression may be achieved by designing antisense molecules, DNA, RNA, or PNA, to the control regions of a sagA gene i.e. the promoters, and enhancers. Preferably the antisense molecules are oligonucleotides derived from the transcription initiation site (e.g. between positions -10 and +1o from the start site). Inhibition can also be achieved by using triple-helix base-pairing techniques. Triple helix pairing causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules (see Gee J.E. et al (1994) In: Huber, B.E.
and B.I. Carr, Molecular and Immunologic Approaches, Futura Publishing Co., Mt. Kisco, N.Y.). An antisense molecule may also be designed to block translation of mRNA by inhibiting binding of the transcript to the ribosomes.
Ribozymes, enzymatic RNA molecules, may be used to catalyze the specific cleavage of RNA. Ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage. For example, hammerhead motif ribozyme molecules may be engineered that can specifically and efficiently catalyze endonucleolytic cleavage of sequences encoding a polypeptide of the invention.
Specific ribosome cleavage sites within any RNA target may be initially identified by scanning the target molecule for ribozyme cleavage sites which include the following sequences:
GUA, GW, and GUC. Short RNA sequences of between 15 and 20 ribonucleotides corresponding to the region of the cleavage site of the target gene may be evaluated for secondary structural features which may render the oligonucleotide inoperable. The suitability of candidate targets may be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuciease protection assays.
The activity of the substances, compounds, antibodies, polypeptides, nucleic acid molecules, and compositions of the invention may be confirmed in in vitro cell systems or in animal experimental model systems (e. g. the dermonecretic mouse model described herein).
The following non-limiting examples are illustrative of the present invention:
BXAMPLBS
Facample 1. Characterization of sagA.
The sagA gene has features that are fundamental for encoding a functional transcript, specifically, consensus promoter elements upstream of an ATG start codon (Fig. 2). Also, Northern blot analyses have revealed that while sagA is transcriptionally active in the wild-type parent strains, mRNA transcripts are not produced in the non-hemolytic transconjugants. Based on sequence analysis, sagA encodes a 53 amino acid peptide containing a long string of cysteine residues spanning seven out of nine consecutive residues.
Its estimated translational size is consistent with the findings of Lai and colleagues (1978) that suggest SLS is a low molecular weight protein. Therefore, sagA is the proposed structural gene for SLS. The absence of features characteristic of a DNA binding regulator or processing enzyme shows that the gene is not encoding for a regulatory element of SLS. The sagA sequence is unique as it lacks homology with all known regulatory or structural determinants.
The amino acid sequence analysis of the sagA translational product revealed that a characteristic lantibiotic double glycine motif cleavage site (GG) is present 22 and 23 residues from the amino terminus, with a corresponding proline residue at position 21 also common to many lantibiotics (Sahl et al. 1995). As peptide cleavage has been shown to play a fundamental role in the biosynthesis of all lantibiotics, the presence of such a site in the SAG-A peptide shows a significant similarity between SAG-A and other lantibiotics. Moreover, if the SAG-A peptide were cleaved at this site, the two fragments generated would be of similar size and amino acid composition as those generated by the proteolytic cleavage of other lantibiotics. In particular, the unusually high percentage composition of cysteine, serine and threonine residues in the C-terminal fragment of SAG-A is characteristic of the lantibiotic pro-peptide or active fragment and shows that this domain of the SAG-A peptide represents the active lantibiotic/hemolysin. A distinct separation of the cysteine residues in the amino half of the 5AG-A pro-peptide and the serine residues in its carboxy terminus is characteristic of the type-A
group of lantibiotics (Jung 1991). In addition, the post-translational modification of cysteine residues may account for the lack of cysteine content in previously reported amino acid compositions of SLS (Alouf and Geoffroy 1988; Koyama 1963), as free cysteines are never found in lantibiotics. Also, the presence of intra-molecular rings formed by the thioether amino acids, lanthionine and 3-methyllanthionine, derived from the N-terminal cysteine residues in the putative pro-peptide of SAG-A may account for the previous unsuccessful attempts by Alouf (1988) to sequence SLS by Edman degradation. Finally, in terms of function, the association of SAG-A with hemolysis parallels the membrane and pore-forming ability of several lantibiotics of the type-A
category. In particular, Brock and Davie (1963) showed that the hemolytic activity of the lantibiotic cytolysin LL/LS, produced by Enterococcus faecalis, correlates with its bacteriocin action.
Interestingly, studies of the enterococcal cytolysin were first initiated because of its potential role as a virulence factor in infectious disease.
8RP$RI>IO;NTS LBADINO TO THB IDENTIFICATION OF T8B sagA Q8N8 Examples 2-12 describe in detail the studies leading to the identification of the sagA gene and its role in virulence.
8xamole 2 - Generation of non-hamolvtic tranaconiuQanta.
In this investigation, SLS-deficient Tn916 mutants were generated from two strains of GAS. Each of the wild-types were associated with severe streptococcal disease in humans (Musser et al. 1993; Schlievert et al. 1977). The mutants were compared to wild- type using a murine model of subcutaneous streptococcal infection, and a gene associated with SLS production designated sagA, for streptolysin S-associated gene, was identified. Non-hemolytic, tetracycline resistant transconjugants resulted from mating GAS strains MGAS166s and TlBPs with the Tn916 donor strain E. faecalis CG110 at a frequency of 10-' fox both recipients.
Transconjugants maintained the non-hemolytic phenotype after subculture on selective media. When Tn916 excision assays were conducted on non-hemolytic transconjugants derived from TlBPs and MGAS166s, the wildtype, beta-hemolytic phenotype was restored and detected as a zone of beta-hemolysis within a confluent mat of non-hemolytic bacteria. The frequency of excision of Tn916 was in the order of 10-° and 10-' for SBNfiS and SH30-2, respectively.
Because of the low frequency of Tn916 excision, it was necessary to screen fox hemolytic revertants on a confluent mat of bacteria.
Bxam~le 3 - aeaetic characterizatioa of the aoa-hamolvtic transconiuaaats and hemolvtic revertaate.
The Tn916 probe used spanned the only HindIII restriction site within Ta916. Cleavage at this site divides the transposon into two fragments of approximately 6 kb and 12 kb (Clewell et al. 1993). After HindIII digestion, each copy of Tn916 which has integrated into the chromosome of the recipient strains yields two bands that hybridize with the probe. Two HindIII fragments, approximately 14 and 7.8 kb, from each of the non-hemolytic mutants derived from MGAS166s hybridized with the tetM probe. For each non-hemolytic mutant derived from TlBPs, HindIII fragments of 14 and 6.5 kb hybridized with the tetM probe. This pattern was seen even in those non-hemolytic transconjugants which possessed more than a single insertion (Fig. 1). Two non-hemolytic transconjugants derived from Tl8Ps, designated SB30-2 and one from MGAS166s, designated SBNHS, were chosen for further study.
Excision of Tn916 from SB30-2 and SBNHS was permitted by growth in the absence of tetracycline and confirmed by detecting tetracycline susceptible, hemolytic revertants. Restoration of the wild phenotype is consistent with previous reports that Tn916 is capable of precise excision (Gawron-Burke and Clewell 1984). Two revertants were selected for further analysis, NHSrev and 30-2rev, derived from SBNH5 and SB30-2 respectively. Neither revertant hybridized with the tetM specific probe and excision of Tn916 was precise as it resulted in restoration of the hemolytic phenotype.
Bxam~la 4 - Analysis of Tn9I6 insertion site.
In order to identify the wild-type region into which Tn916 inserted, a genomic library of MGAS166s was generated using the low copy number plasmid, pACYCl84. Clones containing the wild-type region corresponding to the insertion site of Tn916 were identified using a 2.2 kb PI-PCR product which was generated using Tn916 derived outward reading primers. Three clones were identified containing a 3.8 kb fragment which hybridized with the Tn916 flanking region probe. A single clone, SL-1, was chosen for further analysis. Confirmation that the 3.8 kb insert in pSL-1 corresponded to the region interrupted by Tn916 insertion in the wildtype was done by probing HindIII digested genomic DNA from both MGAS166s and SBNHS with the 3.8 kb insert. A single band at 3.8 kb was detected in MGAS166s while two bands, at approximately 14 and 7.8 kb were detected in SBNHS.
The entire 3.8 kb insert in pSL-1 was sequenced in both directions yielding a fragment of exactly 3,732 bp. Analysis of the sequence using the Wisconsin GCG computer program identified several putative ORF~s. However, only a single ORF, designated sagA, demonstrated nearly all of the conserved elements of a functional transcript (Fig. 2). A consensus Shine-Dalgarno (AGGAGG) sequence is located exactly 10 by upstream of the ATG
start codon. Approximately 150 by upstream of this site is the -l0 promoter (TATAAT), and 167 by upstream of this lies the -35 promoter region sequence of TTTACA. The sagA ORF appears to code for a peptide of 53 amino acids which is devoid of a signal sequence. It is also interesting to note the unusual presence of several cysteine residues near the amino terminal; seven cysteines, five consecutive, followed by two tyrosines, followed by two more cysteine residues. Analysis of the sequence of sagA
using FASTA and BLAST searches failed to detect significant homology with other known sequences. Furthermore, the sequence of sagA was not found in the Oklahoma GAS genomic sequence data base.
To determine the exact insertion site of Tn916, PCR products were generated using primers based on the known 3.8 kb sequence coupled with outward reading primers from Tn916. PCR products were sequenced and allowed precise determination of the Tn916 insertion point Which was midway within the putative promoter region of sagA, 11 by downstream of the -35 element and 6 by upstream of the -10 TATA box.
Sequence analysis of PCR products of the genomic DNA
flanking Tn916 derived from SB30-2 confirmed that Tn9I6 insertion was in exactly the same locus. Furthermore, Tn916 was oriented in the same direction as it was in SBNHS.
Sxaamle 5 - Transcription of aavA.
To show that sagA was transcribed, RNA was isolated from MGAS166s and SBNH5 and probed with DNA corresponding only to sagA
(Fig. 3). A transcript was detected in RNA isolated from MGAS166s which gave a maximal signal at 4-6 hours post mid-log phase. The transcription product corresponded to a size of approximately 400 by which was in keeping with the expected size of an mRNA product from sagA. No detectable transcript was observed from RNA
isolated from SBNHS at any time point. Probing the same membranes with the 16s rRNA probe did not yield any differences between RNA
from MGAS166s and SBNHS.
Example 6 - M-tvninc of mutants.
M-typing of non-hemolytic transconjugants confirmed that M-protein was produced and both SB30-2 and SBNH5 had the same M-protein phenotype as their M18 and M1 parent strains respectively.
No difference in M-protein quantity was seen between MGAS166s and SBNHS by Western blotting using a monoclonal antibody to the constant region of M1 protein.
Example 7 - Hemolytic activity.
The non-hemolytic mutants SBNH5 and SB30-2 showed no beta-hemolysis on blood agar indicating that SLS activity had been ablated. Hemolysis profiles were identical to ATCC27762 which does not produce SLS but does produce SLO (Bernheimer 1954). An assay specific for SLO conducted under reducing conditions showed continued SLO production in all strains of GAS tested. Hemolysis was detected in the presence of the SLS inhibitor trypan blue but not in the presence of both trypan blue and the SLO inhibitor cholesterol (Table 2). SLS production peaked at late log phase for MGAS166s whereas there Was no detectable SLS activity for SBNHS at all points measured. These results confirm that SLO was not affected by the insertion of Tn9I6 and the absence of beta-hemolysis was attributable to the loss of SLS activity, a profile similar to the SLS-deficient Tn9I6 insertion mutants of Nida and Cleary (1983).
BxamDle 8 - Growth rate comaarisoas.
To determine if the mutation conferred by Tn9~6 insertion had affected growth in addition to ablating SLS activity, the growth rates of the mutants were compared to their parent strains.
There was no difference between the growth rate of either SB30-2 or SBNHS when each strain was compared to its respective parent strain.
8xampla 9 - Protein and hvaluronic acid capsule vroduction.
There was no difference in production of cell-associated and extracellular proteins, resolved by SDS-PAGE, between the non-hemolytic mutants and their parent strains suggesting that the Tn916 had no gross pleiotropic effect. In addition, hyaluronic acid production was measured and strains were tested for DNase and caseinase activity. Both non-hemolytic insertion mutants retained their respective wild types in all three assays (Table 3).
8xxsamla 10 - Reduced virulence of SLS deficient transconiuaants.
Reproducible, non-lethal lesions were generated following injection of 106 CFU MGAS166s and 10' CFU TlBPs subcutaneously into mice. The difference in inoculum size, needed to produce the same virulence profile, is likely due to inherent differences in virulence between M1 and Mle serotypes of GAS.
The non-hemolytic transconjugants, SB30-2 and SBNAS, showed markedly reduced virulence compared to their wild-type counterparts. Mice infected with 106 CFU of the wildtype strain MGAS166s exhibited a mean weight loss, -1.16 ~ 0.42 g, compared to mice Which received either SBNH5 or sterile cytodex alone (p<0.05, Fisher's PSLD). Mice which received 106 CFU of SBNH5 demonstrated a mean weight gain of +1.15 t 0.2 g in the first 24 hours after injection. This change in weight was not significantly different from the mean weight gain of +1.44 t 0.29 g seen in the uninfected controls (Fig. 4). Similarly, mice injected with lob CFU of the wildtype hemolytic TlBPs exhibited a significant mean weight loss, -0.66 t 0.28 g, in the first 24 hours after infection when compared to the weight gain observed in mice which received the i same infective dose of the non-hemolytic SB30-2, +0.54 ~ 0.13 g (p<0.05 Fisher's PS7~D) .
None of the nine mice which received the non-hemolytic transconjugant SBNHS developed a necrotic lesion, while 7 of the 9 mice (78%) which received the wildtype MGAS166s developed necrotic lesions (p=0.0007, Fisher s Exact test). Similarly, of the nine mice which received SB30-2, only one mouse (11%) developed a necrotic lesion compared to a of the 9 mice (89%) which developed necrotic lesion when injected with the wildtype Tl8Ps (p=0.001, Fisher s Exact test). Data for the M1 and M18 strain were similar to each other in two separate experiments.
Two phenotypic revertants, 30-2rev and NHSrev, from which Ta916 had excised, derived from SB30-2 and SBNH5 respectively were compared to the wild types, TlBPs and MGAS166s. The number of necrotic lesions and weight changes were not significantly different from that produced by the wild type in each case.
Sxamole 11 - Gross and histoloaical characterization of infected tissue.
In mice which were infected with MGAS166s, initial examination of the lesions revealed indurated zones surrounded by edema. The indurated zones subsequently progressed, yielding centralized ulceration and necrosis which did not penetrate the underlying musculature (Fig. 5). MGAS166s produced a maximum mean necrotic lesion size of 90.4 mmz. No necrotic lesions were observed in animals infected with SBNHS, though some animals did develop slight localized edema within 24 hours of infection similar to the mice which received sterile cytodex. Animals infected with the M18 strains, TlBPs and SB30-2, showed a similar pattern when comparing the wild-type with the non-hemolytic mutant. The maximum mean necrotic lesion area was 31 mm~ in animals infected with T18P. For the single animals which were infected with SB30-2 and developed lesions in two separate experiments, the maximum area was 10 mmz.
Twenty four hours post infection, biopsies of tissue from animals which had been infected with MGA5166s, differed histologically from SBNFiS or sterile cytodex inoculated animals.
Sections of tissue from mice which received MGAS166s demonstrated evidence of profuse acute inflammation with dense infiltration of neutrophils and tissue necrosis. Biopsies obtained from mice which received SBNHS did not show evidence of acute inflammation and no tissue damage was evident (Fig. 6). Gram staining of the sections revealed Gram positive cocci distributed throughout the tissue obtained from mice infected with MGAS166s, while tissue from mice which received SBNH5 failed to demonstrate any bacteria in all fields scanned. Examination of hematoxylin and eosin stained or Gram stained tissue sections from mice which received SBNFi5, did not show an appreciable difference compared with tissue from mice which received a sterile cytodex injection.
Example 12 - Culturing of lesions.
To determine if the phenotype of the infecting strains had remained the same as the injected organisms, lesions were cultured from animals which had received either MGAS166s or SBNH5 after 1 and 5 days. As there were no necrotic lesions on mice infected with SBNH5, the erythematous injection site, comparable in size to the lesion on the mice which received sterile cytodex, was excised for culturing. All lesions from animals which received MGAS166s grew tetracycline susceptible, hemolytic GAS. However, no organisms grew from tissue cultured at either 1 or 5 days from mice which had received SBNH5. In two separate experiments, one out of 9 mice infected with SB30-2 developed necrotic lesions from which hemolytic, tetracycline susceptible, GAS were cultured.
Animals infected with SB30-2 received an inoculum of 10~ CFU, probably sufficient to permit the emergence of revertants from which Tn9I6 had excised. Growth of the revertants may explain the production of the small necrotic lesion in animals infected with the non-hemolytic SB30-2 in two separate experiments.
Sxamnle 13. - Expression of the Sag-A Peptide A translational fusion between the C-terminal portion of the Escherichia coli produced maltose-binding protein (MBP) gene and the sagA sequence is constructed to allow the expression and subsequent purification of large quantities of the SAG-A peptide.
Expression systems that have all the components required for the correct post-translational modifications of the precursors and are known in the art are examined for the expression of the SAG-A
peptide. Expression systems have been described for nisin, subtilin, epidermis and Peps (Saris et al. 1996).
Example 14. - Antibodies directed to SACi-A
Subsequent to its purification, the MBP-SAG-A fusion protein is used to raise antibodies in rabbits. Monoclonal and polyclonal antibodies are prepared according to established techniques (Harlow E & Lane D (1988). Antibodies: a laboratory manual. Cold Spring Harbor Laboratory Press. New York). The protective role of anti-SAG-A antibodies was also identified in an animal model of infection. In addition, in vitro hemolysis inhibition studies are performed to characterize SAG-A specific antibodies that abrogate BLS activity.
Monoclonal and polyclonal antibodies are prepared according to other techniques known in the art. For examples of methods of the preparation and uses of monoclonal antibodies, see U.S. Patent 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. Examples of the preparation and uses of polyclonal antibodies are disclosed in U.S. Patent Nos. 5,512,282, 4,828,985, IS 5,225,331 and 5,124,147.
MATERIALS AND MSTFFODS USED 80R SXAMPhBS 1-12 Bacterial strains and culture conditions. Strains used in this investigation are listed in Table 1. Gram positive bacteria were grown in Todd-Hewitt broth (Oxoid, Basingstoke, England) or on Columbia agar (Oxoid) plates containing 5% defibrinated sheep blood (WOOdlyn Laboratories, Guelph, ON). When antibiotic selection was required, 2000 ug/ml streptomycin (Sigma Laboratories, St. Louis, MO) and 5 ~g/ml tetracycline (Sigma) were added to the appropriate media. Escherichia coli were propagated using Luria Bertani (LB) broth (Difco). When appropriate, 25 ~g/ml tetracycline and/or 50 ug/ml chloramphenicol were added to the media. Strains T18P, MGAS166, and CG110 were kindly provided by Drs. Patrick Schlievert, (University of Minnesota, Minneapolis, MN), James Musser (Baylor College of Medicine, Houston, TX) and Don Clewell (University of Michigan, Ann Arbor, MI) respectively.
Escherichia coli strain RN6851 (pRN6680) contains a 2.2 kb tetM
gene from Tn551 cloned into pBS-bluescript and was provided by Dr.
Barry Krieswirth (New York Public Health Research Institute, New York, NY).
M-typing and quantatation. Serotyping of recipient and non-hemolytic transconjugants was conducted by the National Reference Center for Streptococci (Edmonton, AB) in a blinded fashion according to standard techniques (Griffith 1934). M protein was quantitated by Western blot using monoclonal antibody to the constant region of the M1 protein (kindly performed by Vincent Fischetti, Rockefeller University) using published methods (Fischetti et aI. 1985).
Generation of transconjugants. Strains MGAS166 and T18P were made resistant to streptomycin by plating each strain on Columbia blood agar containing streptomycin and selecting a colony which became spontaneously resistant to streptomycin. Tn9I6 was mobilized from Enterococcus faecalis CG110 to MGAS166s and TlBPs by a variation of a method described by Nida et al. (1983). Cells of recipient and donor were added to a non-selective Columbia blood agar plate in a ratio of 1:1, which corresponded to 107 CFU of each strain, and the entire plate was cross-streaked using a sterile loop.
After overnight incubation at 37°C in 5% C02 the bacterial mat was replica-plated using Acutran sterile replicators (Schleicher and Schuell, Keene, NH) to selective media containing tetracycline and streptomycin. Non-hemolytic transconjugants were chosen which were devoid of a beta-hemolytic phenotype and were passaged at least l0 times on selective media to ensure stability of the mutant phenotype. Lancefield grouping was conducted on the non-hemolytic transconjugants (Prolab, Richmondhill, ON) as outlined by the manufacturer.
Southern hybridization aaalysis. A probe specific for the tetM
gene of Tn9I6 was used to identify the transposon insertion in the transconjugants. The tetM determinant was amplified from pRN6680 by the polymerase chain reaction (PCR) using T3/T7 universal primers (Stratagene Cloning Systems, LaJolla, CA) and parameters recommended by the manufacturer. The PCR product was confirmed by its size on a 0.7% agarose gel and was purified from the gel using the Qiaex II Gel Extraction Kit (Qiagen, Chatsworth, CA). The purified product was labeled using the enhanced chemiluminescence (ECL) direct labeling system (Amersham, oakville, ON) as outlined by the manufacturer. Genomic DNA was isolated from GAS as previously described (O'Connor and Cleary 1983). DNA was digested with HindIII (Boehringer-Mannheim, Laval, PQ), subjected to 0.7%
agarose gel electrophoresis, transferred to Hybond N+ nylon membranes (Amersham) and probed with the enhanced chemiluminescence labeled tetM specific probe as indicated by the manufacturer.
Cloning and sequencing. Genomic DNA from MGAS166s was digested i with HindIII, ligated into the HindIII site of pACYC184 (New England Biolabs, Mississauga, ON) and transformed into E. coli DHSaMCR high efficiency competent cells (Gibco BRL, Burlington, ON} using standard techniques (Gilman 1997). Plasmid DNA from transformants was isolated by alkaline lysis (Maniatis et al.
1989) and dot blotted by vacuum suction onto Hybond N+ membranes.
In order to identify transformants harboring the sequence disrupted by Tn916 in SBNHS, a probe based on the sequence flanking the transposon in SBNH5 was generated by partial-inverse PCR (PI-PCR) as follows (Pang and Knedt 1997). Genomic DNA from SBNHS was digested with HindIII, self-ligated and used as a template with outward reading primers based on the ends of Tn916.
The resulting amplicon consequently consisted of the sequence flanking Tn916 and was used as a probe for identifying transformants from MGAS166s harbouring the sequence associated with SLS production. Sequencing was done commercially (Mobix, Inc., Hamilton, ON) using an automated sequencer (Applied Biosystems, Oakville, ON) according to manufacturer s guidelines.
Analysis of sequence data was done using the Wisconsin GCG
sequence analysis software as well as the FASTA algorithm and BLAST search engines of the National Biotechnology Institute.
Northern Analysis. Total RNA was extracted using Trizol (Gibco BRL) according to manufacturers directions. RNA was isolated from bacteria at mid-log phase (O.D.sso=0.6 - 0.8) and then every two hours thereafter for a maximum of ten hours. Total RNA was standardized spectrophotometrically and resolved using 1.9%
formaldehyde/agarose gels. RNA electrophoresis and Northern blot transfer were performed using standard techniques (Gilman 1997).
DNA probes were labeled with a"PdCTP using Ready-to-Go DNA
labeling beads (Pharmacia Biotech, PQ) according to the manufacturer's instructions. Integrity of the RNA was checked simultaneously by probing all samples with a conserved 16S rRNA
sequence.
Bxcieion of Tn916. Phenotypic revertants were produced in a manner similar to that described by Nida and Cleary (1983).
Briefly, 106 CFU, determined by an optical density at 550 nm (O.D.55p) of 1.0-1.2, of a late log phase culture of non-hemolytic transconjugants were inoculated into 50 ml of non-selective Todd-Hewitt broth. After overnight incubation, 108 CFU were plated onto a single non-selective blood agar plate. Following overnight incubation, zones of hemolysis were identified within the bacterial mat, and colonies within the hemolytic zones were S subcultured on non-selective media to isolate the hemolytic revertants. Tetracycline resistance was determined by growth on Columbia blood agar plates containing tetracycline (5 Ng/ml}.
Growth rate analysis. To determine the growth rate of wildtype and mutant GAS, lOml of THB was inoculated with a single colony.
Mutants were grown in the presence of tetracycline. After overnight growth 106 CFU were used to inoculate 50 ml of Todd-Hewitt broth. O.D.55o readings using a Beckman spectrophotometer (Beckman Instruments Inc., Fullerton, CA) were taken at the time of inoculation and every hour subsequently for a period of 12 hours. Actual CFU at each time point were confirmed by serial dilutions and plating on Columbia blood agar.
Hemolysis assays. To confirm that SLO was still being produced by the non-hemolytic mutants, assays similar to those previously described by Smyth and Duncan were employed (Smyth and Duncan 1978). Late-log phase cultures (O.D.550 = 1.0-1.2) of GAS were centrifuged to pellet bacteria. Culture supernatants (750 ~1) were reduced by adding L-cysteine to a final concentration of 20 mM and incubating at ambient temperature for 10 min. An equal volume of a 5% solution of sheep erythrocytes, washed three times in 0.15 M
sodium phosphate buffer, pH 6.8 (PBS), and resuspended in the same buffer, was added to culture supernatants and samples were incubated at 37°C for 60 min. After centrifugation, the optical density of the supernatant Was read at 540 nm to determine the release of hemoglobin. An equivalent amount of lysed erythrocytes suspended in sterile Todd-Hewitt broth was used as a control to represent 100% hemolysis and sample values were recorded as a fraction of this value. Trypan blue (Sigma), at a final concentration of 13 ~g/ml, and cholesterol (Sigma), at a final concentration of 0.5 mg/ml were used as inhibitors of SLS and SLO
respectively. ATCC 21547 (SLO+, SLS+) and 27762 (SLO+, SLS-) were used as control strains (Table 1).
SLS activity Was also measured during early, mid and late log phase using the above method, overnight broth cultures of MGAS166s and SBNHS were subcultured in Todd-Hewitt broth and samples withdrawn hourly for a hours and immediately frozen at -70°C. Samples were thawed and bacteria pelleted by centrifugation. Serial dilutions of culture supernatant were added to PBS-washed 5% rabbit erythrocytes and incubated at 37°C for 60 min. Cells were removed by centrifugation and the O.D. determined as above.
Preparation of ~xtracellular and call associated proteins.
Bacteria were grown in 200 ml of Todd-Hewitt broth and samples were collected at either mid-log phase (O.D.SSO=0~6) or late-log phase (O.D.SSO=1.0-1.2). Bacteria were pelleted by centrifugation at 10,000 g for 15 min at 4°C. Ammonium sulfate was added to the culture supernatants gradually with constant shaking at 4°C until solution reached e0% saturation. After mixing gently overnight at 4°C, tubes were centrifuged at 10,000 rpm and supernatant was discarded. Ammonium sulfate precipitate was dissolved in 2 ml of 0.01 M ammonium bicarbonate (pH 7.0) and dialyzed against the same solution using Slide-A-Lyzer dialysis cassettes (Pierce Chemical Co., IL) overnight at 4°C. Dialysate samples were boiled for 5 min in SDS-PAGE loading buffer (Lamemelli 1970), resolved using a l0% SDS-polyacrylamide gel and stained with Coomassie brilliant blue R.
For analysis of cellular proteins, bacteria were grown in 10 ml of Todd-Hewitt broth and bacteria were pelleted when they reached mid-log or late-log phase. Supernatants were discarded and the pellets Were resuspended in 15 ~tl of 0.1% Triton X
(Sigma) and 25 mM PBS (pH 7.2), and vortexed briefly. After incubating cells at 37°C for 30 min, 15 ~1 of SDS-PAGE loading buffer was added and samples were resolved as described above.
Production of caseinas~ and DNaea. Caseinase activity was determined by the method of Wheeler et al. (Wheeler et al. 1991).
DNase production was determined using commercial media (Difco, Detroit, MI). In both assays, an equivalent inoculum of late-log phase organisms was spotted onto assay plates. Plates were incubated anaerobically overnight and zones of opacity or clearing were measured to determine caseinase or DNase activity respectively. SBNH5 and SB30-2 were tested with and without 5 ug/ml of tetracycline in the media.
Quantitatioa of hyaluronic acid. Bacteria were grown in 150 ml of Todd-Hewitt broth to an O.D.sso of 0.6 - 0.8. Mutants were grown in the presence of tetracycline. Aliquots of the cultures were removed, serially diluted and subcultured to confirm the exact number of CFU. The bacterial pellet was harvested by centrifugation and washed once with sterile distilled water. The pellet was resuspended in 1.5 ml of water and an equal volume of chloroform was added, mixed vigorously and incubated at room temperature for 1 hour. The mixture was centrifuged to separate the aqueous phase from the chloroform. The aqueous phase was used in the carbazole method of uronic acid quantitation as described by Knutson et aI (Knutson and Jeanes 1969). Human umbilical hyaluronic acid (Sigma) was used as a standard.
Dermoaecrotic mouse modal. Virulence of GAS strains was determined using a dermonecrotic mouse model as previously described (Bunce et al. 1992). Organisms were grown to mid-log phase (O.D,55p = 0.6 - 0.8) in Todd-Hewitt broth with appropriate antibiotic selection. A 100 ~1 volume of mid-log phase organisms was mixed with an equal volume of sterilized cytodex beads (Sigma) suspended in PBS at a concentration of 20 ~g/mL. The 200 gel cytodex/bacterial suspension was injected subcutaneously in the right flank of hairless, 4 week-old, male, crl:SKH1(hrhr)Br mice (Charles River, Wilmington, MA) weighing 15-20 g using a 1 ml tuberculin syringe. Nine animals were injected for each strain examined. Viable counts were performed on all cultures to confirm the exact number of CFU injected. Animals were weighed immediately prior to inoculation and every 24 hours subsequently fox a total of 5 days. The length and width of the lesions were measured daily by an observer blinded to the identity of the infecting strain. The wound area (A) was determined by A=(LxW)/2 where L is the longest axis and W is the shortest axis.
Culturing of necrotic laeioas and histopathology. To determine the phenotypes of the organisms in the lesions, a single animal was randomly chosen from each group 24 and 120 hours after infection and euthanized. The wounds were excised from euthanized animals and divided equally. One half of each lesion was cultured and the remainder was used for the preparation of histological specimens. Tissue for culture was suspended in 1 ml of sterile PBS and then ground in a sterile tissue homogenizer. Aliquots of the PBS/tissue homogenate were serially diluted and inoculated on either selective or non-selective Columbia blood agar plates and scored for beta-hemolysis. Histologic sections were prepared by immersion in 10% buffered formalin and embedded in paraffin.
Sections were stained with hematoxylin and eosin or tissue. Gram stain (Brown-Benn stain) and examined by light microscopy by a pathologist blinded to the source of the biopsies.
Statistics. Statistical analysis was conducted as described previously (Bunce et al. 1992). Group means for weight loss and lesion size were compared among groups by using analysis of variance (ANOVA). Post hoc tests were done using Fisher's protected least significant difference (Fisher s PSLD). P values reported, refer to the ANOVA tests. Significant differences between pairs of groups were reported if P < 0.05. Fisher's Exact test was used to compare counts of abscesses and dermonecrotic lesions.
Example 15 Using Tn917 mutagenesis followed by chromosome walking steps, eight genes located immediately downstream of sagA have been shown to be important for SLS production. Furthermore, the inactivation of each of these genes with the vector pVE6007 has lead to the generation of non-hemolytic mutants. The virulence of six of these mutants was examined by using a dermonecrotic mouse model as previously described (see above). The results are shown in Table 4. In contrast to mice infected with the wild-type strain, NZ131, those infected with sagA,E and F produced no necrotic lesion. However, due to the excision of the plasmid from the chromosome and hence reversion to their hemolytic phenotype, those mice infected with sagB,D and G produced lesions similar to NZ131. Mutants for sagX and sagl have not been tested. From these data, it can be concluded that sagA, E and F play an important role in the virulence of N2131.
The present invention has been described in terms of particular embodiments found or proposed by the present inventors to comprise preferred modes for the practice of the invention. It will be appreciated by those of skill in the art that, in light of the present disclosure, numerous modifications and changes can be made in the particular embodiments exemplified without departing from the intended scope of the invention. All such modifications are intended to be included within the scope of the appended claims.
All articles, patents and other documents described in this application are incorporated by reference in their entirety to the same extent as if each individual publication, patent or document was specifically and individually indicated to be incorporated by reference in its entirety. They are also incorporated to the extent that they supplement, explain, provide a background for, or teach methodology, techniques and/or compositions employed herein.

i TABLg 1. and relevantproperties Bacterial strains Strain Relevant Reference Comments Phenotype S.pyogenes T18P MlB,St',Tc',SLS"Schilvert Isolate associated with 1977 rheumatic fever MGAS166 Ml,St',Tc',SLS"Musser Invasive clinical isolate TlBPS MlB,Str, Tcs,SLS+See text Spontaneous Strr derivative of T18P

MGAS166s Ml,Str,Tcs, See text Spontaneous Str derivative SLS+

of MGAS166 SB30-2 MlB,Str,Tcr, See text Nonhemolytic derivative SLS of TlBPs 30-2rev MlB,Str,Tcs,SLS+See text Hemolytic derivative of SBNHSs Ml,Str, Tcr, See text non-hemolytic derivative SLS of MGAS166s NHSrev Ml,Str, Tcs, See text Hemolytic derivative SLS+ of SBNHS

SLS+, SLO+ ~ Hemolytic control strain SLS , SLO+ Ginsburg non-hemolytic control strain E. faecalis CG110 Sts, Tcr Gawron Tn9Z6 donor strain E.coli RN6851 Tc' NR Contains pRN6680 DHSaMCR mcrA,~80dlacAZMlSGibcoBRL Library efficiency competent cells SL-1 Tc, Cmr See Text Contains pACYC184 with 3.8kb insert Str, streptomycin Sts, streptomycin resistant; sensitive;
Tcs, tetracyclinesensitive; tetracycline Tcr, resistant;
Cmr, chloramphenicol resistant;
SLS, streptolysin S; NR, no reference.

i TABLB 2. Streptolysin O activity of wildtype and mutant streptococci r;ssay Fraction of complete lysisa exhibited by bacterial Contents strains Tl8Ps SB30-2 MGAS166s SBNHS ATCC2772 ATCC2154 Supernatant 0.57 0.48 0.56 0.45 0.62 0.78 Supernatant 0.64 0.50 0.48 0.39 0.58 0.69 with Trypan blush Supernatant 0.05 0.09 0.10 0.07 0.11 0.04 with trypan blue and cholesterolc a Complete lysis was determined by lysing 750 ~tL of 5% washed sheep erythrocytes in hypotonic saline and adding to an equal volume of sterile THB.
b Concentration of trypan blue was 13 ~g/mL
c Concentration of cholesterol was 0.5 mg/mL

TABLS 3. Phenotypic comparisons between hemolytic and non-hemolytic GAS
Strain Assay Caseinasea Dnasea Hyaluronic acid MGAS166s 12.8 +/- 1.3 mm 15.1 +/- 0.9 mm 2 fg / cfu SBNHS 12.2 +/- l.lmm 16.3 +/- 1.3 mm 3.1 fg / cfu TlBPs 0 mm 16.1 +/- 1.6 mm 68 fg / cfu SB30-2 0 mm 17.4 +/- 2.0 mm 54 fg / cfu aResults are zone diameters surrounding inoculum after overnight anaerobic incubation of assay plates at 37°C. Measurements are mean +/- standard deviation of three experiments.

N
N

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Z Z ~ f~

aZE moo! 0 NON

NJ

t N
O ~ i tlt ~ O
C

0 ~ O J ~ ~
p p c~ o J~ r C 0 N
D. 7, O C

J ~ C r- Z v C C

V

r p O . . . . 1 . , N .

J
V V

N

O O O ~ O

O + M ~ N ~
W

t t O (f CG st n ~ c~ 0~

O O ~ ~ O O ~ m m O O ~ ~ O O ~

C

'~

m ~. . E
~ ~ O O ~ ~ O O ~
~'9 er N

O ~ ", O

(~ Q ~ O O O ~ O O
~ N

o E

Z

0.-~ 0 0 0 0 0 0 0 ~N

+ + + ~. ~ +

v v v ~. ~. v 'r e~ t_ tp ~ N " v ~ W N
Z~i C C C O ~ O C C
O O

O~

O CV C N ~ '~ N O
C

C O m ii o; n ~ a; ~! ~E

.- c~ c~ r. .-W +.. v W v v v w C

C~ N M ~ O ~ ~- Gf 7. ~ ~,j~~O ,.,u~N~j ,~ tl NO
~ '1'1* ~ * * II * tf~

~ ~ 0f ~O O v ~ O
C C C C C

N N N ~ N N N m O

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a DETAILED DESCRIPTION OF THE DRAPTINGS
Figure 1. Southern hybridization analysis of HindIII restriction digests of genomic DNA probed tetM. (A) Hemolytic wildtype T18P
(Lane 1) does not hybridize with the tetM probe. Non-hemolytic transconjugants SB1-4, SB2-9, SB30-2, SB1-9, SB5-9, SB6-9, SB7-9, SBl-1, and SB8-2 (Lanes 2-20) all contain at least one copy of Tn916 and hybridize with the tetM probe. Isolates in lanes 2, 7 and 9 possess more than one insertion of Tn916. All lanes possess two bands hybridizing with the tetM probe corresponding to approximately 6.5 kb and l4kb. The Tn916 donor strain CG110 (Lane 11) contains several copies of Tn916. (B) Hemolytic wildtype MGAS166s (Lane 1) does not hybridize with the tetM probe. The non-hemolytic transconjugants SBNH1, SBNH3, SBNH4, SBNH5, SBNH6, SBNH7, and SBNHB (Lanes 2-7) all possess at least one copy of Tn916.
Isolates in lanes 3, 4, 7, and 8 possess more than a single insertion of Tn916. Isolates in all lanes possess two bands of a similar size of approximately 14 kb and 7.5 kb. The migration of molecular size standards (1 kb ladder) is indicated (in kilobases) on the left for both (A) and (H).
Figure 2. The nucleotide sequence and protein translation of sagA. A 390 by region of genomic DNA from MGAS166s is represented corresponding to the chromosomal point of insertion of Tn916 (D).
The conserved elements of the sagA ORF are indicated and the putative 53 amino acid translation product is represented. S.D.
indicates the Shine-Dalgarno consensus sequence. (The highest degree of homology was observed with epidermin and peps (from Staphylococcus epidermidis) matching 44% and 40% similarity respectively, and 22~ and 20% identity respectively. Calculations of homology are done using the FASTA (Pearson W.R. and Lipman D.J., 1988, PNAS 85: 2444-2448) and BLAST (Altschul S.F. and Lipman D.J., 1990 PNAS 87: 5509-5513) algorithms.) Figure 3. Total RNA extracted from mutant SBNHS (lanes 2-7) and wildtype MGAS166s (lanes 7-13) was quantified, standardized, blotted and probed using a PCR amplicon of sagA labeled with a'~P.
Lane 1 is a 0.16-1.77 kb RNA standard, lane 2 is SBNH5 RNA
harvested at mid-log phase, lanes 3-7 are SBNHS RNA at 2, 4, 6, 8 and 10 hours post mid-log phase respectively. Lane 8 is MGAS166s RNA harvested at mid log phase, lanes 9-13 are MGAS166s RNA at 2, 4, 6, 8 and 10 hours post mid-log phase respectively. The mutant strain is devoid of any transcripts from sagA while the wildtype contains sagA transcripts at all time points.
Figure 4. Comparisons of mean weight change are shown 24 hours after infection with wild type (MGAS166s; Tl8Ps) and the respective S isogenic non hemolytic mutants (SBNH5; SB30-2). Animals infected with non hemolytic mutants of each wild type gained weight in contrast to the marked weight loss caused by infection with the parent strains.
Figure 5. Photographs of hairless SKH1 mice 24 hours after infection with 106 cfu of either the SLS producing wildtype MGAS166s (A) or the SLS-deficient Tn916 mutant SBNHS (B). A well demarcated zone in induration with centralized necrosis is depicted on the right flank of a mouse infected with MGAS166s. No necrosis was seen in mice infected with SBNHS.
Figure 6. Tissue biopsies from euthanized mice which were infected with 106 cfu of either the SLS-producing wildtype MGAS166s (A) or the SLS-deficient Tn9I6 mutant SBNHS (B). The tissue section in (A) demonstrates acute inflammation with edema and tissue necrosis. The tissue depicted in (B) does not show evidence of necrosis and the inflammation is markedly reduced when compared with (A). Tissue samples were stained With hemotoxylin and eosin and final magnification is approximately x25.

RBFgRSNCEB
Alouf, J.E. and Geoffroy, C. (1988). Meth. In Enzym. 165:59-64.
Alouf, J.E. 1980, Pharmacol. Ther. 11:661-717.
Berraheimer, A. W. 1954. Streptococcal Infections, p. 19. Columbia University Press, New York. N.Y.
Blackburn, P. and Projan, S.J. (1994). United States Patent No:
5,304,540. Applied Microbiology Inc., New York, USA.
Borgia, S.M., Betschel, S.D., Low, D.E. and de Azavedo, J.C.S.
(1997). Advances in Experimental Medicine and Biology. 418:733-748.
Brock, T.D. and Davie, J.M. (1963). J. Bact. 86:708-712.
Bunce, C., Wheeler, L., Reed, G., Musser, J., and Barg, N. (1992) Infect. Immun. 60:2636-2640.
Chatterjee, S., Chatterjee, D.K., Jani, R.H., Blumbach, J., IS Ganguli, B.N., Klesel, N., Limbert, M. and Seibert, G. (1992).
J. Antibiot. 45:839-845.
Clewell, D. B. and Flannagan, S.E. (1993) The conjugative transposons of gram-positive bacteria. p. 369-393. Plenum Press, New York, N.Y.
Da Vuyst, L. and Vandamme, E.J. (eds) (1994}. Bacteriocins of lactic acid bacteria, Chapman and Hall, London.
Delves-Broughton, J., Blackburn, P., Evans, R.J. and Hugenholtz, J. (1996). Antonie van Leeuwenhoek 69:193-202.
Fischetti, V. A., Jones, K.F. and Scott, J.R. (1985) J. Exp. Med.
161:1384-1401.
freer, J.H. and J.P. Arbuthnott, 1976. Biochemical and Morphological alterations of membranes by bacterial toxins, p.
170-193. In A.W. Bernheimer (ed.) Mechanisms in bacterial toxicology. John Wiley and Sons, New York, N.Y.
Gawron-BUrke, C. and Clewell, D.B. (1982) Nature (London).
300:281-284.
Gaarron-Burke, C. and Clewell, D.B. (1984) J. Bacteriol. 159:214-221.
Gilmaa, M. (1997) Current protocols in molecular biology, p.
4.1.1-4.1.23. In F. M. Ausubell, R. Brent, R. E. Kingston, R.
D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.), John Wiley and Sons, New York, N.Y.
Ginsburg, I. (1970) Streptolysin S. p. 99-171. In T. C. Montie, S. Kadis, and S. J. Ajl (ed.), Microbial Toxins, Academic WO 99/49049 PCTlCA99100240 Press, New York, N. Y.
Jung, G. (1991). Agnew. Chem. Int. Ea. Eng. 30:1051-1192.
Klasnhammsr, T.R. (1993). FEMS Microbiol. Rev. 12:39-86.
Rnutson, C. A. and Jeanes, A. (1968) Ann. Biochem. 24:470-481.
Koyama, J. (1963). J. Biochem. 54:146-151.
Laemelli, U. K. (1970) Nature x27:680-685.
Lai, C.Y., Wang, M.-T., DeFaria and Akao, T. (1978). Arch.
Biochem. Biophys. 191:804-812.
Liu, W, and Hansen, J.N. (1992). J. Biol. Chem. 267:25078-25085.
Maniatis, T., Fritsch, E. and Sambrook, J. (1989) Small scale plasmid extraction, p. 1.21-1.31. In T. Maniatis, E. Fritsch, and J. Sambrook (ed.), Experiments in Molecular Genetics, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
Mussar, J., Kanjilal, S., Musher, D. et al. (1993) J. Infect. Dis.
167:337-346.
Nes, I.F. and Tagg, J.R. (1996) Antonie Van Leeuwenhoek 69:89-97 Nida, K. and Cleary, P.P. (1983) J. Bacteriol. 155:1156-1161.
O~Connor, S. P. and Cleary, P.P. (1987) J. Infect. Dis. 156:495-504.
Pang, K. M. and Knecht, D.A. (1997) BioTechniques 22:1046-1048.
Ray. B. and Daeschel, M. (eds) (1992). Food preservatives of microbial origin, CRC Press, Boca Raton FL.
Sahl, H.-G., Jack, R.W. and Bierman, G. (1995). FEES. 230:827-853.
Saris, P.E.J. Immonen, T,., Reis, M., and Sahl, H.-G. (1996) Arttonie van Leewenhoek 69:151-159.
Schliavert, P. M., Bettin, K.M. and Watson, D.W. (1977) Infect.
Immun. 16:673-679.
Smyth, C. J. and Duncan, J.L. (1978) Thiol-activated (oxygen-labile) cytolysins, p. 129-183. In: J. S. Jelijaszewicz and T.
Wadstrom (ed.), Bacterial Toxins and Cell Membranes. Academic Press, New York, N. Y.
9~haeler, M. C., Roe, M.H., Kaplan, E.L., Schlievert, P.M. and Todd, J.K. (1991)JAMAa66:533-537.

SEQUENCE LISTING
1) GENERAL INFORMATION:
(i) APPLICANTS: DE AZAVEDO, Joyce BAST, Darrin BORGIA, Sergio BETSCHEL, Stephen LOW, Donald (ii) TITLE OF INVENTION: Streptococcus Streptolysin S Nucleic Acid Molecule (iii) NUMBER OF SEQUENCES: 2 (2) INFORMATION FOR SEQ ID NO: l:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 390 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ix) FEATURE: DNA sequence for sagA gene (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:

ATAAGAACTA

GTCCTTGTTG

TCGCGTTCTT

AATTTACTTC

GCTCCTGGAG

TACTGGAAGT

AATAATCTAT

SUBSTITUTE SHEET (RULE 26) (2) INFORMATION FOR SEQ ID N0:2:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 53 amino acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ix) FEATURE: Protein sequence for SAG-A

(xi) SEQUENCE DESCRIPTION: SEQ ID
N0:2:

M L K F T S N I L A

T S V A E T T Q V A

P G G C C C C C T T

C C F S I A T G S G

N S Q G G S G S y T

P G K

SEQUENCE DESCRIPTION: SEQ ID N0:3 Leader na sequence CTTATGTTAA AATTTACTTC AAATATTTTA TAGCTGAAAC
GCTACTAGTG AACTCAAGTT

GCTCCTG GAG

SEQUENCE DESCRIPTION: SEQ ID N0:4 Leader amino acid sequence M L K F T S N I L A T

S V A E T T Q V A P G G

SUBSTITUTE SHEET (RULE 26) SEQUENCE DESCRIPTION: SEQ ID N0:5 propeptide na sequence GCTGCTGTTG CTGCTGTACT ACTTGTTGCT TCTCAATTGC TACTGGAAGT
GGTAATTCTC AAGGTGGTAG CGGAAGTTAT ACGCCAGGTA AATAATCTAT TTAGCATCTC
TATGTGGTAG TGATATTAAG GTAATGAGTT
SEQUENCE DESCRIPTION: SEQ ID N0:6 propeptide amino acid sequence C C C C C T T C C F S
I A T G S G N S Q G G
S G S Y T P G K
SEQUENCE DESCRIPTION: SEQ ID N0:7 regulatory na sequence ATCAGTTACT TATTAGATAA GGAGGTAAAC CTT
SEQUENCE DESCRIPTION: SEQ ID N0:8 processing protein na tgt cattttttac aaaggaacaa caacctaaag 721 agaattgtcc gccaataact gttgaaaaag caaggcaatt gtttgaattt aatacaaacc 781 acttgtcctt atcggattac catcatcaaa cggtgctaaa aacgtcaaag cagctagttg 841 ctcaacattt aatgcctaat gcaaccgata atcttagtca acattttttg atgaactata 901 aagctaataa taattattta ggcttccaag ctagtattgt cgactttttt acagattctg 961 ccgttgctaa tttttcaagt agttacgttt atgaaagtca ggaaaagata attcgtttac SUBSTITUTE SHEET (RULE 28) 1021 caaaacctac caagatatca actgctctgt cgacatgtat tataaaacga agaagtcatc 1081 gtcaattttc agatagacaa atgcctcttc aagatttatc aaacattctt tattatgcat 1141 gtggtgttag ttcacaagca tcaattagag atggagcatc agataagatt acactcagaa 1201 actgtgcttc aggtggaggt ttatacccta ttcatttagt tttttatgct agaaacatca 1261 gtaaattaat agatggtttc tatgaatatc taccctatca gcatgcacta aggtgttatc 1321 ggcatagctc tgaggaaaac gttagagatt ttgcggaata cggtgctatt aatgctgaaa 1381 attgtaatat tattattatt tatgtctacc attacatgaa aaatacacgt aaatatggga 1441 atcaggcgac tgcctatgct tttattgaat caggagaaat agcccagaat attcaattga 1501 ctgcaactgc cttaacttat ggaagtattg atattggtgg ttataataag gaatatctcc 1561 aagaattatt agatttagat gggctaggag agcatgtgat tcacatgaca ctcgtaggaa 1621 ctaaggagtc tcaatga SEQUENCE DESCRIPTION: SEQ ID N0:9 processing protein amino acid sequence MSFFTKEQQPKENCPPITVEKARQLFEFNTNHLSLSDYHHQTVL
KTSRQLVAQHLMPNATDNLSQHFLMNYKANNNYLGFQASIVDFFTDSAVANFSSSYVY
ESQEKIIRLPKPTKISTALSTCIIKRRSHRQFSDRQMPLQDLSNILYYACGVSSQASI
RDGASDKITLRNCASGGGLYPIHLVFYARNISKLIDGFYEYLPYQHALRCYRHSSEEN
VRDFAEYGAINAENCNIIIIYVYHYMKNTRKYGNQATAYAFIESGEIAQNIQLTATAL
TYGSIDIGGYNKEYLQELLDLDGLGEHVIHMTLVGTKESQ
SUBSTITUTE SHEET (RULE 26) SEQUENCE DESCRIPTION: SEQ ID NOS:10 AND 11 Transporter na sequence and amino acid sequence x912 atqagttttqtaeaattaacaaacgttgtcaagtcctacaaaaac M S F Y Q L T N V V K S Y K N
:95~ ggcaagaaagetgtcaatgacgcctcettgtctactgaagcaggt 5002 aatatttatggtttgttaggsccaaatggtgccggtaagtccaec N I Y G L L G P N G A G K S T
5017 ctgattaatettstcttaggcttgatccctttgagttccqgcaaa L I N L I L G L I P L S S G K
5092 attaetgttttagggcsatcccaaaagactattcgaasaacsagt I T V L G Q S Q K T I R K I S
5137 tcgcagataggttatgttccteasgacattgccgtttatecagac S Q I G Y V P Q D I A V y p p 5182 etaactgcttacgaaaatgcagaaciatttgggtcactttatqge L t A Y E N V E L F G S L Y G
5227 ttssagggagctcagcttaaaaaaeaagttctassaagtttagas L K G A Q L K K Q V L K S L E
5172 ettgtqgggccacactcccaagctsagcagtttccsagtcsaccc F V G L H S Q A K Q F P S Q f 5317 tcagqaggsatgaagagacggttasatategcttgcgcqetagtt S G G N K R R L N I A C A L V
5362 catteacccaaattsatcatttttqsegaaecgactgtagqgact H S P K L I I f D E P T V G I
5147 gatectcaatcaegtaatcatattttagagtcgattcgtttgcts D P Q S R N N I L E S I R L L
5152 aseaaagaaggcgetacagttatttatacgacecactstatgqss N K E G A T V I Y T T N Y PI E
5197 gsagtaqaggctetttgtgatcatstttttattatggatcatggt E V E A L C D Y I F I M D N G
551? caagttattgaagasggacctaastttgaaetggsasaaegttae Q V I E E G P K F E L E K R Y
5587 gttgesaatctagcaaaccagaccattgtsaetctaacagsctea 5632 eqteatttggaaetggeagataagcctgsctggtctttgatsqas R H L E L A D K P D YI S L I E
5677 gatqgagaaaascteatgttgaagsttgatastagtgatatgaca D G E K L N L K I D N S D !1 1 5722 ccagttgttcsteagcteaescaggecaststtacttttagcgsg S V V H Q L T Q A N I T F S E
5767 attagacataaccatttgaatttagasgasattttcttacactta I R N N H L N L E E I F L N L
5812 acsgqtasgaagttscgagatcag 5A35 T G K K L R D
SEQUENCE DESCRIPTION: SEQ ID N0:12 Sequence of the originally cloned 3.8 kb insert.
SU6ST'ITUTE SHEET (RULE 26) 351 AAGATTACAA CTGATGCTAN ATTGACTGAA GCTCAARA.AG CTGAACAATC

SUBSTITUTE SHEET (RULE 26) S.D. sagA (1529-1691) saga (1914-2866) SUBSTfTUTE SHEET (RULE 26~

SUBSTITUTE SHEET (RULE 26) -35 p S.D.
Start M L K F T S

N I L A T S V A E
T T Q V A P G G

C C C C C T T C C
F S I A T G S
Stop G N S Q G G S G S
Y T P G K

(The highest degree of homology was observed with epidermin and peps (from Staphylococcus epidermidis) matching 44% and 40%
similarity respectively, and 22% and 20% identity respectively.
Calculations of homology are done using the FASTA (Pearson W.R.
and Lipman D.J., 1988, PNAS 85: 2444-2448) and BLAST (Altschul S.F. and Lipman D.J., 1990 PNAS
87: 5509-5513) algorithms.) SUBSTITUTE SHEET (RULE 26) *rB

Claims

We Claim:

1. An isolated nucleic acid molecule which comprises:
i. a nucleic acid sequence encoding a polypeptide having substantial sequence identity to the amino acid sequence of SEQ. ID. NO. 2, 4 or 6;
ii. a nucleic acid sequence having at least 95% identity to a nucleic acid molecule encoding a polypeptide comprising the amino acid sequence of SEQ. ID. NO. 2, 4 or 6;
iii. a nucleic acid molecule encoding a polypeptide comprising the amino acid sequence of SEQ. ID. NO. 2, 4 or 6;
iv. a nucleic acid sequence complementary to (i), (ii), or (iii);
v. a nucleic acid sequence differing from any of (i),(ii), or (iii), in codon sequences due to the degeneracy of the genetic code;
vi. a nucleic acid sequence comprising at least 5 nucleotides capable of hybridizing to a nucleic acid sequence in SEQ. ID.
NO. 1, 3, or 5 or to a degenerate form thereof;
vii. a nucleic acid sequence encoding a truncation, an analog, an allelic or species variation of a polypeptide comprising the amino acid sequence shown in SEQ. ID. NO. 2, 4, or 6; or viii. a fragment, or allelic or species variation of (i), (ii) or (iii).

2. An isolated nucleic acid molecule which comprises:
i. a nucleic acid sequence having substantial sequence identity with a nucleic acid sequence shown in SEQ. ID. NO. 1, 3 or 5;
ii. nucleic acid sequences complementary to (i), preferably complementary to the full nucleic acid sequence shown in SEQ.
ID. NO. 1, 3, or 5;
iii. nucleic acid sequences differing from any of the nucleic acid sequences of (i) or (ii) in codon sequences due to the degeneracy of the genetic code; or iv. a fragment, or allelic or species variation of (i), (ii) or (iii).

3. An isolated nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 1, 3, or 5.

4. An isolated nucleic acid molecule comprising a nucleotide sequence selected from the group having at least: 65% homology, 75% homology, 85% homology, 95% homology and 98% homology to the nucleotide sequence of SEQ ID NO: 1, 3, or 5.

5. An isolated nucleic acid molecule which hybridizes to the nucleic acid molecule of claim 1 under stringent hybridization conditions.

6. A nucleic acid molecule of any of claims 1 to 3, wherein the molecule is selected from the group consisting of DNA and RNA.

7. The nucleic acid molecule of any of claims 1 to 4, wherein the nucleic acid molecule encodes a lantibiotic.

8. A nucleic acid molecule of claim 1, encoding a peptide comprising the amino acid sequence of SEQ ID NO: 2.

9. A nucleic acid molecule of any of claims 1 to 6, wherein the nucleic acid molecule is isolated from a group A streptococci cell.

10. An isolated nucleic acid molecule comprising a sequence selected from the group consisting of 8 to 10 nucleotides of the nucleic acid molecule of any of claims 1 to 7, 11 to 25 nucleotides of the nucleic acid molecule of any of claims 1 to 7 and 26 to 50 nucleotides of the nucleic acid molecule of any of claims 1 to 7.

11. An isolated nucleic acid molecule of claim 8, wherein the nucleic acid molecule hybridizes to the nucleic acid molecule of any of claims 1 to 7 under stringent hybridization conditions.

12. An isolated nucleic acid molecule comprising a DNA sequence obtained by screening an appropriate library containing the complete gene encoding an amino acid sequence of SEQ ID NO:2 under stringent hydridization conditions with a probe having a nucleic acid sequence encoding the amino acid sequence of SEQ ID No:2 or a fragment therof, which fragment retains binding and/or biological activity and isolating the DNA sequence.

13. An isolated nucleic acid molecule encoding the complementary nucleotide sequence of any of the nucleic acid molecules of claims 1 to 9.

14. An expression vector comprising the nucleic acid molecule of any of claims 1 to 13.

15. An isolated peptide produced from the nucleic acid molecule of any of claims 1 to 13.

16. An isolated peptide produced from the expression vector of claim 14.

17. An isolated peptide comprising the amino acid sequence in SEQ

ID NO: 2, 4, or 6.

18. An isolated peptide comprising an amino acid sequence selected from the group having at least 65% homology, 75%
homology, 85% homology, 95% homology and 98% homology to the peptide of SEQ ID NO: 2, 4, or 6.

19. A peptide of any of claims 15 to 18, Wherein the peptide has the characteristics of a lantibiotic.

20. A peptide of any of claims 15 to 19, wherein the peptide is isolated from a Group A Streptococci cell

21. An isolated peptide comprising at least 5 amino acids of the peptide of any of claims 15 to 20.

22. An isolated peptide comprising 6 to 15 amino acids of the peptide of any of claims 15 to 20.

23. An antibody directed against the peptide of any of claims 15 to 22.

24. A cell comprising the expression vector of claim 14.

25. Food products comprising the peptide of any of claims 15 to 22.

26. A pharmaceutical composition comprising the peptide of any of claims 15 to 22.

27. A vaccine comprising the peptide of any of claims 15 to 22.

28. A method for producing a polypeptide having the characteristics of a lantibiotic comprising inserting the expression vector of claim 14 in a cell and expressing the peptide.

29. A method for diagnosing disease, preferably bacterial infections, more preferably infections caused by group A
streptococci, comprising determining from a sample derived from an individual an increased level of expression of a nucleic acid comprising the nucleic acid sequence of of SEQ ID NO:1 or 5 or a polypeptide comprising the amino acid sequence of SEQ ID NO: 2 or 6.

30. A method for identifying compounds which bind to or otherwise interact with and inhibit or activate an activity of a peptide as claimed in any one of claims 15 to 22 or a nucleic acid molecule as claimed in any one of claims 1 to 13 comprising contacting the peptide or nucleic acid molecule with a compound to be screened under conditions to permit binding to or other interaction between the compound and the peptide or nucleic acid molecule to assess the binding to or other interaction with the compound, such binding or interaction being associated with a second component capable of providing a detectable signal in response to the binding or interaction of the peptide or nucleic acid molecule with the compound, and determining whether the compound binds to or otherwise interacts with and activates or inhibits an activity of the peptide or nucleic acid molecule by detecting the presence or absence of a signal generated from the binding or interaction of the compound with the peptide or nucleic acid molecule.

31. A chimeric toxin comprising a SAG-A polypeptide having cytolytic activity operatively linked to a targeting agent.