AU740481B2 - Defining epitopes of the outer membrane protein CopB of moraxella catarrhalis - Google Patents

Description

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DESCRIPTION

DEFINING EPITOPES OF THE OUTER MEMBRANE PROTEIN CopB OF MORAXELLA CA TARRHALIS BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates generally to the fields of microbiology and clinical bacteriology. In particular, sequences of the CopB outer membrane protein from various strains of Moraxella catarrhalis provide useful targets in immunodiagnosis and immunoprophylaxis.

2. Description of Related Art It was previously thought that M. catarrhalis, previously known as Branhamella 15 catarrhalis or Neisseria catarrhalis was a harmless saprophyte of the upper respiratory tract (Catlin, 1990; Berk, 1990). However, during the previous decade, it has been determined that this organism is an important human pathogen. Indeed, it has been established, that this Gram-negative diplococcus is the cause of a number of human infections (Murphy, 1989).

20 M. catarrhalis is now known to be the third most common cause of both acute a and chronic otitis media in children and accounts for up to 20% of cases (Aspin et al., 1994; Del Beccaro et al., 1992; Gan et al., 1991; Catlin, 1990; Faden et al., 1990;1991; Marchant, 1990), the most common disease for which infants and children receive health care according to the 1989 Consensus Report. This organism also causes acute maxillary IA sinusitis, generalized infections of the lower respiratory tract (Murphy and Loeb, 1989), WO 98/06851 PCT/US97/14221 -2and is an important cause of bronchopulmonary infections in patients with underlying chronic lung disease and, less frequently, of systemic infections in immunocompromised patients (Melendez and Johnson, 1990; Sarubbi et al., 1990; Schonheyder and Ejlertsen, 1989; Wright and Wallace, 1989).

In a recent report, M. catarrhalis DNA could be detected by polymerase chain reaction (PCR T M in middle ear fluid from 46% of patients with chronic otitis media with effusion (Post et al., 1995). In adults, M. catarrhalis is a frequent cause of acute exacerbations of chronic obstructive pulmonary disease (Davies and Maesen, 1988; Hager et al., 1987; McLeod et al., 1986; Nicotra et al., 1986). Invasive infections with this organism, such as bacteremia, meningitis, skeletal infections and endocarditis, are rare and occur mainly in immunocompromised individuals (Doern et al., 1981; Malkamaki et al., 1983).

The 1989 Consensus Report further concluded that prevention of otitis media is an important health care goal due to both its occurrence in infants and children, as well as certain populations of all age groups. In fact, the total financial burden of otitis media has been estimated to be at least 2.5 billion annually, or approximately 3% of the health care budget. Vaccines were identified as the most desired approach to the prevention of this disease for a number of reasons. For example, it was estimated that if vaccines could reduce the incidence of otitis media by 30%, this outcome could bring about an annual health care savings of at least $400 million. However, while some progress has been made in the development of vaccines for 2 of the 3 common otitis media pathogens, Streptococcus pneumoniae and Haemophilus influenzae, there is no indication that similar progress has been made with respect to M. catarrhalis. This is particularly troublesome in that M. catarrhalis now accounts for approximately 17-20% of all otitis media infection (Murphy, 1989).

Despite its recognized virulence potential, little is known about the mechanisms employed by M. catarrhalis in the production of disease or about host factors governing immunity to this pathogen. It has been documented that infections caused by M.

catarrhalis induce an antibody response directed against this pathogen (Chapman et al., WO 98/06851 PCT/US97/14221 -3- 1985; Chi et al., 1990; Faden et al., 1994; 1992; Goldblatt et al., 1990a; 1990b; Sethi et al., 1995) and that some of these antibodies have the potential to exert biologic activity via complement-dependent killing (Chapman et al., 1985) or opsonophagocytosis (Faden et al., 1994). For example, an antibody response to M catarrhalis otitis media has been documented by means of an ELISA system using whole M catarrhalis cells as antigen and acute and convalescent sera or middle ear fluid as the source of antibody (Leinonen et al., 1981). However, with a few exceptions (Goldblatt et al., 1990b; Sethi et al., 1995), the identity of the target antigen(s) remains unclear because, as in the preceding example, most studies used whole bacteria or crude outer membrane preparations as antigens to detect M. catarrhalis-directed antibodies.

The development of serum bactericidal antibody during M catarrhalis infection in adults was shown to be dependent on the classical complement pathway (Chapman et al., 1985). And more recently, it was reported that young children with M. catarrhalis otitis media develop an antibody response in the middle ear but fail to develop systemic antibody in a uniform manner (Faden et al., 1992). To date, the only M. catarrhalis outer membrane antigens that have been shown to be targets for antibodies that can exert protective effects in an animal model are the CopB and UspA proteins (Chen et al., 1996; Helminen et al., 1993a; 1994) while antibodies to protein CD have been reported to be bactericidal in vitro (Yang et al., 1997).

The wide occurrence of M. catarrhalis infections and the rapid spread of P-lactamase production among clinical isolates have stimulated efforts to develop a vaccine against this pathogen (Anonymous, 1989). Several lines of evidence suggest that the induction of appropriate humoral immunity will likely be protective against respiratory tract disease caused by M catarrhalis. Acute M catarrhalis infection induces the production of both serum and secretory antibodies against various antigenic determinants of this pathogen (Faden et al., 1992; Helminen et al., 1995; Sethi et al., 1995). (ii) The age-dependent development of the humoral response against M catarrhalis is inversely related to the prevalence of nasopharyngeal colonization and incidence of otitis media involving M. catarrhalis (Goldblatt et al., 1990b; Vaneechoutte et al., 1990). (iii) Passive immunization with M catarrhalis-directed antibodies as well WO 98/06851 PCT/US97/14221 -4as active immunization with M. catarrhalis outer membrane proteins enhanced pulmonary clearance of M catarrhalis in an animal model (Helminen et al., 1993a; 1994; Maciver et al., 1993).

Previous attempts have been made to identify and characterize M. catarrhalis antigens that would serve as potentially important targets of the human immune response to infection (Murphy, 1989; Goldblatt et al., 1990; Murphy et al., 1990). Generally speaking, the surface of M catarrhalis is composed of outer membrane proteins (OMPs), lipooligosaccharide (LOS) and fimbriae. M. catarrhalis appears to be somewhat distinct from other Gram-negative bacteria in that attempts to isolate the outer membrane of this organism using detergent fractionation of cell envelopes has generally proven to be unsuccessful in that the procedures did not yield consistent results (Murphy, 1989; Murphy and Loeb, 1989). Moreover, preparations were found to be contaminated with cytoplasmic membranes, suggesting an unusual characteristic of the M. catarrhalis cell envelope.

Isolation procedures have been reported for obtaining M. catarrhalis outer membrane components which result in what are said to be less-contaminated membrane preparations (Murphy and Loeb, 1989). Although this has allowed M. catarrhalis outer membrane protein profiles to be assessed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS/PAGE), these techniques did not lead to the isolation or characterization of OMPs (Murphy and Loeb, 1989). Seven or eight major OMP groups have been identified in this manner and appear to be fairly consistent between diverse M. catarrhalis strains. For example, OMPs have been grouped into classes A-H, beginning with bands of molecular weight around 98 kD (OMP-A) and proceeding to bands with molecular weights of about 21 kD (OMP-H) (Murphy and Loeb, 1989; Murphy, 1989).

Recently, one OMP designated CopB, was cloned and its genomic sequence and inferred amino acid sequence have been reported Patent Application S.N. 08/025,363). The M catarrhalis CopB outer membrane protein appears to be fairly well conserved among strains of M. catarrhalis, with the CopB-specific monoclonal WO 98/06851 PCT/US97/14221 antibody (MAb) 10F3 binding to the majority of 23 M. catarrhalis strains tested, suggesting that a strain-common epitope is present in many, but not all, strains of this pathogen. Southern blot analysis results also suggest some degree of conservation of the copB gene at the nucleotide sequence level among different strains. Moreover, polyclonal antisera raised against outer membrane vesicles from two MAb 10F3unreactive strains, TTA24 and B21, reacted with the recombinant CopB protein encoded by the copB gene which was derived from the M. catarrhalis 10F3-reactive strain 035E, indicating some conservation of the protein structure of the CopB protein among the strains.

The lack of a polysaccharide capsule surrounding M. catarrhalis indicates that surface-exposed outer membrane antigens are the likely targets for a protective immune response. Different M. catarrhalis strains share remarkably similar outer membrane protein profiles (Bartos and Murphy, 1988; Murphy and Bartos, 1989), and at least three surface-exposed proteins of this organism appear to be well-conserved antigenically (Helminen et al., 1993a; 1994; Hsiao et al., 1995; Murphy et al., 1993). One of these, the 80 kDa CopB protein (OMP B2), is a potential vaccine candidate, based on its reactivity with M catarrhalis strains and enhanced pulmonary clearance of M catarrhalis in a murine model (Helminen et al., 1993a). It has been established that CopB expression is iron-regulated (Aebi et al., 1996; Campagnari et al., 1994) and that CopB is involved at some level in the ability of M. catarrhalis to acquire iron from human transferrin and lactoferrin (Aebi et al., 1996). Expression of CopB is apparently essential for virulence of M catarrhalis, at least in an animal model, because an isogenic copB mutant was less able than its wild-type parent strain to resist clearance from the lungs of mice (Helminen et al., 1993b).

Passive immunization with polyclonal antisera raised against M. catarrhalis strain 035E outer membrane vesicles was also found to protect against pulmonary challenge with the heterologous M. catarrhalis strain TTA24. In addition, active immunization with M. catarrhalis outer membrane vesicles resulted in enhanced clearance of this organism from the lungs alter challenge. The positive effect of immunization in pulmonary clearance indicates that antibodies play a major role in 6 imrunoprotection from this pathogen. In addition, the protection observed against pulmonary challenge with a heterologous M.

catarrhalis strain demonstrates that one or more conserved surface antigens are targets for antibodies which function to enhance clearance of M. catarrhalis from the lungs.

With the rising importance of this pathogen in respiratory tract infections, identification of the surface components of this bacterium involved in virulence expression and inmunity is becoming more important. To date, there are no vaccines available for use in humans, against any other OMP, LOS or fimbriae, that induce protective antibodies against M. catarrhalis. Thus, it is clear that there remains a need to identify useful antigens and which can be employed in the preparation of immunoprophylactic reagents. Additionally, once such an antigen or antigens is identified, there is a need for providing methods and compositions which will allow the preparation of these vaccines and quantities that will allow their use on a wide scale basis in prophylactic protocols.

For the purposes of this specification it will be clearly understood that the word "comprising" means "including but not limited to", and that the word "comprises" has a corresponding meaning.

It will be clearly understood that, although a number of prior art publications are referred to herein, this reference does not constitute an admission that any of these documents forms part of the common general knowledge in the art, in Australia or in any other country.

SUMMARY OF THE INVETION S: It is a goal of the present invention to provide polypeptides and nucleic acids for CopB of M. catarrhalis. It is also a goal to provide methods for the diagnosis and prevention of M. catarrhalis infections using these polypeptide and nucleic acids, and 35 derivatives thereof. It is a further goal of the present invention to screen for agents that may be used both in diagnosis and imnunoprophylaxis of M. catarrhalis infections.

There is provided, in accordance with one aspect of the invention, an isolated peptide of about 5 to about 60 amino acids S 40 comprising the consecutive amino acid sequence KYAGK (SEQ ID which is reactive with the antibody 10F3. The consecutive residues of the isolated peptide may further comprise the amino acid residues KYAGKG (SEQ ID NO:36), KYAGKGY (SEQ ID ND:37), NKYAGK (SEQ ID NO:38), NKYAGKG (SEQ ID NO:39) or NKYAGKGY (SEQ ID 45 In a further embodiment, the isolated peptide may corrprise at least about 20 consecutive residues of the amino acid sequence H:\janel\Keep\Speci\41500-97.doc 31/01/01 WO 98/06851 PCT/US97/14221 -7- LDIEKDKKKRTDEQLQAELDNKYAGKGY (SEQ ID NO:41) or LDIKKDDKTLTETELQAELDNKYAGKGY (SEQ ID NO:42).

The isolated peptide may be about 5, 7, 10, 15, 20, 30, 40, 50 or 60 amino acids in length.

In another embodiment, there is provided an isolated peptide of about 20 to about amino acids comprising at least about 20 consecutive residues of the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID Again, the isolated peptide may be about 20, 30, 40, 50 or 60 amino acids in length.

In yet another embodiment, there is provided an antigenic composition comprising an isolated peptide of about 5 to about 60 amino acids comprising the amino acid sequence KYAGK (SEQ ID NO:35) and a pharmaceutically acceptable buffer or diluent. Alternatively the an antigenic composition comprises an isolated peptide of about 20 to about 60 amino acids comprising the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID and a pharmaceutically acceptable buffer or diluent. The antigenic composition may further comprise a carrier conjugated to said peptide. The carrier may be KLH. The antigenic composition may further comprise an adjuvant. The antigenic composition may comprise a peptide is covalently linked to a second antigen. The second antigen may be a peptide antigen or a non-peptide antigen.

In still yet another embodiment, there is provided a vaccine composition comprising an isolated peptide of about 5 to about 60 amino acids comprising the amino acid sequence KYAGK (SEQ ID NO:35) and a pharmaceutically acceptable WO 98/06851 PCT/US97/14221 -8buffer or diluent. Alternatively the an antigenic composition comprises an isolated peptide of about 20 to about 60 amino acids comprising the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID and a pharmaceutically acceptable buffer or diluent.

In still yet another embodiment, there is provided a method for inducing an immune response in a mammal comprising the step of providing to said mammal an antigenic composition comprising an isolated peptide of about 5 to about 60 amino acids comprising the amino acid sequence KYAGK (SEQ ID NO:35) and a pharmaceutically acceptable buffer or diluent. Alternatively the an antigenic composition comprises an isolated peptide of about 20 to about 60 amino acids comprising the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID and a pharmaceutically acceptable buffer or diluent.

In still yet another embodiment, there is provided an isolated and purified M. catarrhalis CopB antigen comprising the amino acid sequence KYAGK (SEQ ID NO:35), or in still a further embodiment LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID or at least about 20 consecutive residues thereof.

In still yet another embodiment, there is provided a nucleic acid encoding the CopB antigen of the M. catarrhalis isolates TTA24, 012E and 046E. Also provided are WO 98/06851 PCT/US97/14221 -9copB DNA sequences of the M. catarrhalis isolates TTA24 (SEQ ID NO:34), 012E (SEQ ID NO:28) and 046E (SEQ ID NO:32).

In still yet another embodiment, there is provided a method for generating a strain-specific antibody to M. catarrhalis CopB antigen comprising the step of providing to a mammal an antigenic composition comprising an isolated peptide comprising an amino acid sequence corresponding to residues of variable regions of said CopB antigen and a pharmaceutically acceptable buffer or diluent.

In still yet another embodiment, there is provided a method for diagnosing M. catarrhalis infection comprising the step of determining the presence, in a sample, of an M. catarrhalis, amino acid sequence corresponding to residues of variable regions of said CopB antigen. The step of determining may comprise PCR or immunologic reactivity of an antibody with an M. catarrhalis antigen.

In still yet another embodiment, there is provided a method for generating a strain-common antibody to M. catarrhalis CopB antigen comprising the step of providing to a mammal an antigenic composition comprising an isolated peptide comprising an amino acid sequence corresponding to residues of common regions of said CopB antigen and a pharmaceutically acceptable buffer or diluent.

In still yet another embodiment, there is provided a method for diagnosing M. catarrhalis infection comprising the step of determining the presence, in a sample, of an M. catarrhalis amino acid sequence corresponding to residues of common regions of said CopB antigen. The step of determining may comprise PCR or comprises immunologic reactivity of an antibody with an M. catarrhalis antigen.

In still yet another embodiment, there is provided a method for treating an individual having an M. catarrhalis infection comprising providing to said individual an isolated peptide of about 20 to about 60 amino acids comprising at least the consecutive residues KYAGK (SEQ ID NO:35) or about 20 consecutive residues of the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), WO 98/06851 PCT/US97/14221 LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID In still yet another embodiment, there is provided a method for preventing or limiting an M. catarrhalis infection comprising providing to a subject an antibody that reacts immunologically with an epitope formed by the amino acid sequence KYAGK (SEQ ID LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID In still yet another embodiment, there is provided a method for screening a peptide for reactivity with a CopB antibody comprising the steps of providing said peptide; contacting said peptide with an antibody that binds immunogically to CopB; and determining the binding of said antibody to said peptide. The antibody may be 10F3, and the determining may comprise an immunoassay selected from the group consisting of a Western blot, an ELISA, an RIA and immunoaffinity separation.

In still yet another embodiment, there is provided a method for screening a peptide for the ability to induce a protective immune response against M. catarrhalis comprising the steps of providing said peptide; administering a peptide in a suitable form to an experimental animal; challenging said animal with M. catarrhalis; and assaying the infection of said animal with M. catarrhalis. The animal may be a mouse, the challenge is a pulmonary challenge, and the assaying comprises assessing the degree of pulmonary clearance by said mouse. Preferably, the peptide is a CopB peptide, and more preferably, the CopB peptide encompasses residues 296-300 of M. catarrhalis strain 035E. Alternatively, the preferred embodiment may employ a CopB peptide is a peptide having at least 6 consecutive amino acids from M. catarrhalis strain 035E, including residue 295.

In still yet another embodiment, there is provided an isolated peptide having at least about 5 consecutive amino acids from the CopB protein of M. catarrhalis and WO 98/06851 PCT/US97/14221 -11 including residues 296-300, or the analogous position thereof when compared to strain 035E or having about 6 consecutive amino acids from the CopB protein of M. catarrhalis, wherein said peptide includes residue 295, or the analogous position thereof when compared to strain 035E. The isolated peptide may be between 5 and amino acids in length. The peptide may comprise non-CopB sequences and even non-M catarrhalis sequences.

In still yet another embodiment, there is provided an antigen composition comprising an isolated peptide having at least about 6 consecutive amino acids from the CopB protein of M. catarrhalis, wherein said peptide includes residue 295, or the analogous position thereof when compared to strain 035E and (ii) a pharmaceutically acceptable buffer or diluent.

BRIEF DESCRIPTION OF THE DRAWINGS The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

FIG. 1A and FIG. 1B Western blot of oligopeptide (region 1) antisera against CopB antigen from each of strains 035E, 01 2E, 046E and TTA24. Outer membrane vesicles of the M. catarrhalis strains 035E (lane 012E (lane TTA24 (lane 3) and 046E (lane 4) probed with MAb 10F3 (FIG. 1A) or mouse antiserum raised against peptide from region 1 conjugated with KLH (FIG. 1B).

FIG. 2 Amino acid sequence and reactivity with antibodies of both region 1 from CopB of four different M catarrhalis strains and synthetic peptides derived from these sequences. The numbers 275-300) above the region 1 sequences indicate the amino acid positions in the intact CopB protein. The numbers 1-26) above the R1 synthetic peptide indicate residue positions in the R1 peptide and its derivatives. Boxes indicates residues differing from those in 035E (SEQ ID NO:1). The reactivity of MAb 10F3, GST-26 antiserum, and GST antiserum with the CopB proteins of these strains in WO 98/06851 PCT/US97/14221 -12western blot analysis is indicated on the right; these two antisera were diluted 1:100 for use in this assay. The reactivity of the synthetic peptides with these same antibody preparations in the ELISA is indicated on the right opposite these peptides. The asterisk indicates that the ELISA with MAb 10F3 was performed after adsorption of the peptides to the microtiter wells in the presence of glutaraldehyde. The ELISA readings (OD 4 10 were recorded after 30 min as described in the Materials and Methods of Example V.

FIG. 3 Fine mapping of the MAb 10F3-reactive epitope using a dot blot assay involving immobilized synthetic decapeptides. Binding of MAb 10F3 to individual peptides was detected by incubating the membrane with radioiodinated goat anti-mouse immunoglobulin. The autoradiograph of the dot blot (peptides 1-8) is shown on the left, the corresponding amino acid sequence of each of the overlapping decapeptides with their respective positions in the CopB protein is listed in Table V. The numbers written vertically denote the amino acid positions in the intact CopB protein; the R1 region is underlined.

FIG. 4 Hydropathy plot and secondary structure analysis of region 1 from the CopB protein of M catarrhalis strain 035E. The hydropathy plot was generated by the method of Kyte and Doolittle (1982) using a window size of seven residues and secondary structure predictions were made using the method of Chou and Fasman (1978) as found in MacVector® sequence analysis software (Version The numbers on the horizontal scale denote the amino acid positions in the intact CopB protein; the RI region is underlined.

FIG. 5A and FIG. 5B Western blot analysis of the reactivity of MAbs and polyclonal serum antibodies with outer membrane proteins of M. catarrhalis strains, the GST-26 fusion protein, and GST alone. Proteins present in outer membrane vesicles from strains 035E (lane 012E (lane TTA24 (lane and 046E (lane purified GST-26 (lane 5) and GST (lane 6) were resolved by SDS-PAGE, transferred to nitrocellulose, and probed with MAb 10F3 (FIG. 5A) or with mouse GST-26 antiserum (dilution 1:1000) (FIG. 5B). The CopB protein from strain 035E gave rise to a doublet WO 98/06851 PCT/US97/14221 13reactive with MAb 10F3 in this study. Molecular weight position markers are shown on the left sides of the blots.

FIGS. 6A-6D Bactericidal activity of MAb 10F3 against M. catarrhalis strains.

Suspensions of the MAb 10F3-reactive strains 035E (FIG. 6A) and 012E (FIG. 6B) and the MAb 10F3-unreactive strains TTA24 (FIG. 6C) and 046E (FIG. 6D) were incubated with: normal human serum (closed triangles), normal human serum and MAb 10F3 (open squares), heat-inactivated normal human serum and MAb 10F3 (closed squares), normal human serum and GST-26 antiserum (open circles) or normal human serum and GST antiserum (closed circles). Portions of the reaction mixture were removed over time and spread on BHI agar plates to determine the number of viable bacteria. Note that the open circles and open squares in FIG. 6B are superimposed.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS The present invention relates to the identification of CopB outer membrane protein sequences from multiple strains of M. catarrhalis, and the nucleic acid sequences corresponding thereto. In addition, the present invention provides insights into the antigenic structure of CopB, based on an analysis of the amino acid sequences. This information is useful in developing both strain-specific and strain-common reagents for the diagnosis of M. catarrhalis infection. In addition, an understanding of which regions of the molecule are conserved permits the development of agents that will be useful in protecting against M. catarrhalis infections, in the preparation of vaccine reagents.

Particular embodiments relate to peptides, polypeptides and nucleic acids corresponding to the CopB molecules, peptides and antigenic compositions derived therefrom, and methods for the diagnosis and treatment ofM. catarrhalis disease.

As stated above, M. catarrhalis infections present a serious health challenge, especially to the young. CopB represents an important antigenic determinant, as the monoclonal antibody (MAb) termed 10F3 has been shown to protect experimental animals, as measured in a pulmonary clearance model, when provided in passive immunizations. The present invention, by virtue of new information regarding the structure of CopB provides such improved compositions and methods.

WO 98/06851 PCT/US97/14221 -14- In a first embodiment, the present invention provides for the identification of conserved and non-conserved portions of the CopB polypeptide. A homology comparison illustrates at least ten discrete regions of low homology. These regions are designated region 1 (about residues 275-302), region 2 (about residues 322-329), region 3 (about residue 348), region 4 (about residues 400-416), region 5 (about residues 437- 450), region 6 (about residues 485-486), region 7 (about residues 526-541), region 8 (about residues 583-596), region 9 (about residues 637-640) and region 10 (about residues 683-695). The numbering is based on the amino acid sequence of 035E strain (SEQ ID NO:29) which is encoding by SEQ ID NO:30 beginning at position 14.

The remaining regions of the molecule may be considered "conserved." Of particular note in this regard are the regions from about residue 10 to about residue 270, from about residue 350 to about residue 395, from about residue 455 to about residue 480, from about residue 490 to about residue 520, from about residue 545 to about residue 580, from about residue 600 to about residue 635 and from about residue 645 to about residue 680. Again, the numbering is based on the 035E strain (SEQ ID NO:29).

In a second embodiment, the present invention has identified the specific epitope to which 10F3 binds. A peptide sequence, found between residues 275-302 (region 1; SEQ ID NO:1) of the CopB protein of M. catarrhalis strain 035E, is sufficient to be bound by 10F3. In addition, this same region from the CopB protein from M. catarrhalis strain 012E (SEQ ID NO:2) is bound by 10F3, although there are differences in the identified region between these two strains. Two other strains, 046E and TTA24, are not bound by 10F3. The sequences from the identified region of these strains, SEQ ID NO:4 from strain TTA24 and SEQ ID NO:5 from strain 035E, respectively, contain differences in common to each other but not in common with 035E or 012E. It is clear that this region plays an important role in the biology of the pathogen and, from this information, one can deduce amino acids residues that are critical to and not critical to 10F3 antibody binding.

In a third embodiment of the invention, the specific epitope to which 10F3 binds is even further defined. Peptides LDNKYAGKGY (SEQ ID NO:25; peptide 7; residues WO 98/06851 PCT/US97/14221 293-302 of the CopB protein of strain 035E) and KYAGKGYKLG (SEQ ID NO:26; peptide 8; residues 296-305 of the CopB protein of strain 035E) specifically bind 10F3; whereas, peptides 1 6 (FIG. 3; Table V) exhibit non-specific binding in the presence of 10F3 and do not appear to have any specific affinity for 10F3. Thus, the small peptide KYAGK (SEQ ID NO:35) is preferred for binding to 10F3, a more preferred peptide is KYAGKG (SEQ ID NO:36) and an even more preferred peptide is KYAGKGY (SEQ ID NO:37).

In a fourth embodiment of the invention, the peptide sequence, LDNKYAGKGY (SEQ ID NO:25) allows maximal binding of MAb 10F3 compared to other peptides examined herein. The asparagine residue (position 3 of SEQ ID NO:25) appears to improve binding. Although it is recognized that other residues may be inserted at this position and also provide similar or even greater binding to 10F3, it is also clear that this position influences the binding kinetics of the epitope, because when aspartic acid is substituted for N at this position, reactivity with 10F3 is abolished. Thus, based on the data presented in FIG. 2 and FIG. 3, another preferred small peptide for binding to 10F3 is NKYAGK (SEQ ID NO:38), a more preferred peptide is NKYAGKG (SEQ ID NO:39) and an even more preferred peptide is NKYAGKGY (SEQ ID NO:40). Further embodiments of the present invention are discussed below.

Several lines of evidence indicate that portions of the CopB protein are exposed on the surface of M catarrhalis. These include the reactivity of the CopB-specific MAb 10F3 with a surface-exposed epitope (Helminen et al., 1993a), (ii) the bactericidal activity of MAb 10F3 against strains that react with this MAb (FIGS. 6A-6D), and (iii) the likely function of the CopB protein in a TonB-dependent physiologic process (Aebi et al., 1996). In addition, FrpB, an iron-regulated outer membrane protein of Neisseria meningitidis that is 49% identical to the CopB protein of strain 035E, has also been shown to be a target for bactericidal antibody (Pettersson et al., 1990; 1995).

Comparison of the deduced amino acid sequence of the CopB proteins from the four M. catarrhalis strains revealed that reactivity with MAb 10F3 was not an indicator of similarity between CopB proteins. Furthermore, the primary amino acid sequence of WO 98/06851 PCT/US97/14221 -16this protein was very well conserved among these four strains. The level of identity among these four CopB proteins proved to be greater than 90%, a finding which is somewhat encouraging from the standpoint of vaccine development. A similar level of amino acid sequence conservation has been reported for the CD outer membrane protein of M. catarrhalis (Hsiao et al., 1995).

The facts that the MAb 10F3-reactive epitope was detected in the majority of M. catarrhalis strains (Helminen et al., 1993a) and that this epitope induced the synthesis of antibodies that were biologically active both in vivo (Helminen et al., 1993a) and in vitro (FIGS. 6A-6D) made the determination of this epitope's location within the CopB protein an important step in the evaluation of CopB as a potential vaccine candidate.

This task was facilitated considerably by the finding that the deduced amino acid sequence differences between the CopB protein of the MAb 10F3-reactive strain 035E and that of the MAb 10F3-unreactive strain TTA24 were limited to five well-defined regions, one of which had to contain the MAb 10F3-reactive epitope. The analyses of the copB genes from two other M catarrhalis strains reinforced the likelihood that one of these five regions bound MAb 10F3 and prompted the synthesis of oligopeptides that contained the corresponding amino acid sequences from the CopB protein of strain 035E.

The use of synthetic peptides in an ELISA clearly identified region 1 as the sequence containing the MAb 10F3-reactive epitope. Unexpectedly, binding of MAb 10F3 to peptide RI (SEQ ID NO:1; FIG. 2) required the presence of the cross-linking agent glutaraldehyde during coating of this peptide to the polystyrene surface of the ELISA plate. At first, it was thought that either inherently poor binding of R1 (SEQ ID NO:1) to the microtiter well or binding of RI (SEQ ID NO:1) to the well via the MAb 10F3-reactive residues was responsible for this finding. However, the failure of soluble R1 (SEQ ID NO:1) to bind MAb 10F3 in an inhibition assay as well as the subsequent observation that GST-26 antiserum readily bound to microtiter wells coated with R1 (SEQ ID NO:1) in the absence of glutaraldehyde invalidated these hypotheses and made conformational changes of R1 (SEQ ID NO:1) caused by glutaraldehyde a more plausible explanation. Glutaraldehyde preferentially cross-links amino groups of lysine residues such as those present in both the N- and C-terminal portions of R1 (SEQ ID WO 98/06851 PCT/US97/14221 -17- NO: 1; FIG. Crosslinking of these lysine residues may have led to the formation of a loop-like structure that more closely resembled the native conformation of the MAb 10F3-reactive epitope. This hypothesis is supported by the lack of binding of MAb 10F3 by peptide R1E (SEQ ID NO:6; FIG. 2) which, as was subsequently determined, contained the binding site for MAb 10F3 but lacked the lysine-rich N-terminal portion of R1.

Differential binding of MAb 10F3 to the peptides RIA (SEQ ID NO:7; FIG. 2) and RIB (SEQ ID NO:3; FIG. 2) indicated that this MAb likely bound the C-terminal portion of R1 (SEQ ID NO:1) and that the asparagine residue in position 21 was essential for binding. This assumption was confirmed by fine mapping of the MAb 10F3-reactive epitope using overlapping decapeptides (FIG. 3) which demonstrated optimal binding of MAb 10F3 to a decapeptide (peptide 7; SEQ ID NO:25) that corresponded to the residues 19-28 of region 1 residues 293-302 of the CopB protein). This epitope comprises the C-terminal portion of a highly hydrophilic domain when analyzed by means of the hydropathy algorithm of Kyte and Doolittle (1982) (FIG.

This finding is in keeping with the proven, bacterial cell surface-exposed location of the binding site for MAb 10F3. It is also noteworthy that the MAb 10F3-reactive epitope appears to be part of the largest variable region of the otherwise highly conserved CopB proteins studied here. This finding is reminiscent of other well-studied bacterial outer membrane proteins, such as the major outer membrane protein P2 of nontypeable Haemophilus influenzae, for which it has been demonstrated that some surface-exposed domains exhibit strain-specific antigenicity (Duim et al., 1994; 1996).

Characterization of the immune response directed against the GST-26 fusion protein containing the MAb 10F3 binding site revealed that, in western blot analysis, antibodies in the GST-26 antiserum bound the CopB protein of strain 035E, but not the CopB protein of the equally MAb 10F3-reactive strain 012E (FIG. 5B). This result suggested that these polyclonal antibodies did not possess the same antigenic specificity as MAb 10F3. In fact, the strong reactivity of the GST-26 antiserum with the MAb 10F3-unreactive peptides RIB (SEQ ID NO:3; FIG. 2) and R1-TTA24 (SEQ ID NO:4; FIG. 2) suggested that most of these polyclonal antibodies are directed against epitopes WO 98/06851 PCT/US97/14221 -18of peptide R1 (SEQ ID NO:1) other than that which binds MAb 10F3. The reduced reactivity of GST-26 antiserum with peptide R1E (SEQ ID NO:6), which consisted of the C-terminal residues of peptide R1, indicated that, not unexpectedly, some of the antibodies in the GST-26 antiserum are directed against epitopes located in the N-terminal portion of peptide R1.

Antibodies raised against GST-26 bound to the surface of whole cells of M catarrhalis strains 035E, 012E and TTA24 (Table VI), but exerted bactericidal activity against only strain 012E (FIGS. 6A-6D). That these polyclonal antibodies, raised against this strain 035E-derived region 1 sequence (FIG. 2) could bind to strains 012E and TTA24 is not surprising when one considers that this same region of the CopB proteins of these other two strains was about 73%-80% identical to that of strain 035E (FIG. It is also likely that these polyclonal antibodies had relatively low binding affinities which precluded their detection in western blot analysis. However, the fact that these same surface-directed antibodies killed only strain 012E and not the homologous strain 035E or the heterologous strain TTA24 is more difficult to explain. One possibility is the presence of an immunodominant determinant in the RI region that induced the synthesis of blocking antibodies that bound to the RI region of CopB of strains 035E and TTA24 but which were unreactive with the RI region of CopB of strain 012E. Alternatively, there may have been other blocking antibodies in the mouse antiserum or in the normal human serum used as the source of complement in these studies; these blocking antibodies could be directed against a surface determinant of strains 035E and TTA24 that was absent on strain 012E.

In summary, comparison of the deduced amino acid sequences of the CopB proteins from four strains of M catarrhalis revealed a striking degree of identity among these macromolecules. This conservation of the primary amino acid sequence of the CopB protein among strains of this pathogen was crucial for localization of the protective epitope on the CopB protein of M catarrhalis strain 035E that is recognized by the bactericidal MAb 10F3. Immunization with a fusion protein reactive with MAb 10F3 induced the synthesis of CopB-specific antibodies bactericidal for at least one MAb 10F3-reactive strain of M catarrhalis.

WO 98/06851 PCTfUS9714221 -19- It is important to note that screening methods for diagnosis and prophylaxis are readily available, as set forth below. Thus, the ability to test peptides, mutant peptides and antibodies for their reactivity with each other and (ii) test peptides and antibodies for the ability to prevent infections in vivo, provide powerful tools to develop clinically important reagents.

1. CopB Peptides and Polypeptides The present invention, in one embodiment, encompasses the three new amino acid sequences presented in SEQ ID NO:27, SEQ ID NO:31 and SEQ ID NO:33. Also encompassed in the present invention are hybrid molecules containing portions from the CopB of one strain fused with portions of the CopB from another strain. For example, one may fuse residues 1-350 of strain TTA24 CopB with residues 351-759 of strain 035E CopB. Alternatively, a fusion could be generated with sequences from three or even four strains represented in a single CopB molecule, thus combining epitopes from each of the various strains. Also encompassed are fragments of the disclosed CopB molecules, as well as insertion, deletion or replacement mutants in which non-CopB sequences are introduced, CopB sequences are removed, or CopB sequences are replaced by or fused with non-CopB sequences, respectively. For example, in order to improve expression in certain systems, it is necessary to "fuse" amino-terminal regulatory sequences to the peptide of interest.

CopB, according to the present invention, may be advantageously cleaved into fragments for use in further structural or functional analysis, or in the generation of reagents such as CopB-related polypeptides and CopB-specific antibodies. This can be accomplished by treating purified or unpurified CopB with a peptidase such as endoproteinase glu-C (Boehringer, Indianapolis, IN). Treatment with CNBr is another method by which CopB fragments may be produced from natural CopB. Recombinant techniques also can be used to produce specific fragments of CopB.

More subtle modifications and changes may be made in the structure of the encoded CopB polypeptides of the present invention while retaining a molecule that encodes a protein or peptide with characteristics of natural or "wild-type" CopB WO 98/06851 PCT/US97/14221 polypeptide. The following is a discussion based upon changing of the amino acids of a CopB protein to create an equivalent, or even an "improved," second-generation molecule. The amino acid changes may be achieved by changing the codons of the DNA sequence, according to the following codon table: Table I Amino Acid Names and Codons abbreviations Alanine Ala A GCA GCC GCG GCU Cysteine Cys C UGC UGU Aspartic acid Asp D GAC GAU Glutamic acid Glu E GAA GAG Phenylalanine Phe F UUC UUU Glycine Gly G GGA GGC GGG GGU Histidine His H CAC CAU Isoleucine Ile I AUA AUC AUU Lysine Lys K AAA AAG Leucine Leu L UUA UUG CUA CUC CUG CUU Methionine Met M AUG Asparagine Asn N AAC AAU Proline Pro P CCA CCC CCG CCU Glutamine Gin Q CAA CAG Arginine Arg R AGA AGG CGA CGC CGG CGU Serine Ser S AGC AGU UCA UCC UCG UCU Threonin e Thr T ACA ACC ACG ACU Valine Val V GUA GUC GUG GUU Tryptophan Trp W UGG Tyrosine Tyr Y UAC UAU Generally, it is known that certain amino acids may be substituted for other amino acids in a protein structure in order to modify or improve its antigenic or immunogenic activity (see, Kyte Doolittle, 1982; Hopp, U.S. Patent 4,554,101, incorporated herein by reference). For example, through the substitution of alternative amino acids, small conformational changes may be conferred upon a polypeptide which result in increased activity or stability. Alternatively, amino acid substitutions in certain polypeptides may be utilized to provide residues which may then be linked to other molecules to provide peptide-molecule conjugates which retain enough antigenicity of WO 98/06851 PCT/US97/14221 -21the starting peptide to be useful for other purposes. For example, a selected CopB peptide that may be covalently bound to a solid support may be constructed which would have particular advantages in diagnostic embodiments.

The importance of the hydropathic index of amino acids in conferring interactive biological function on a protein has also been discussed generally by Kyte Doolittle (1982), wherein it is found that certain amino acids may be substituted for other amino acids having a similar hydropathic index or core and still retain a similar biological activity. As displayed in Table II below, amino acids are assigned a hydropathic index on the basis of their hydrophobicity and charge characteristics. It is believed that the relative hydropathic character of the amino acid determines the secondary structure of the resultant protein, which in turn defines the interaction of the protein with substrate molecules. Preferred substitutions which result in an antigenically equivalent CopB peptide or CopB protein will generally involve amino acids having index scores within ±2 units of one another, and more preferably within ±1 unit, and even more preferably, within ±0.5 units. Thus, for example, isoleucine, which has a hydropathic index of will preferably be exchanged with an amino acid such as valine or leucine Alternatively, at the other end of the scale, lysine will preferably be substituted for arginine and so on.

WO 98/06851 PCT/US97/14221 -22- TABLE II Amino Acid Isoleucine Valine Leucine Phenylalanine Cysteine/cystine Methionine Alanine Glycine Threonine Tryptophan Serine Tyrosine Proline Histidine Glutamic Acid Glutamine Aspartic Acid Asparagine Lysine Arginine Hydropathic Index 4.2 3.8 2.8 1.9 1.8 -0.4 -0.7 -0.9 -0.8 -1.3 -1.6 -3.2 -3.9 Substitution of like amino acids may also be made on the basis of hydrophilicity, particularly where the biological functional equivalent protein or peptide thereby created is intended for use in immunological embodiments. U.S. Patent 4,554,101, incorporated herein by reference, states that the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with its immunogenicity and antigenicity, i.e. with an important ,biological property of the protein.

WO 98/06851 PCTIUS97/14221 -23- As detailed in U.S. Patent 4,554,101, each amino acid has also been assigned a hydrophilicity value. These values are detailed below in Table III.

TABLE III Amino Acid Amino Acid arginine lysine aspartate glutamate serine asparagine glutamine glycine threonine alanine histidine proline cysteine methionine valine leucine isoleucine tyrosine phenylalanine tryptophan Hydropathic Index +3.0 1 +3.0 1 +0.3 +0.2 +0.2 0 -0.4 0.5 1 -1.3 -1.8 -1.8 -2.3 -3.4 It is understood that one amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent, and in particular, an immunologically equivalent CopB peptide or protein. In such changes, the substitution of amino acids whose hydrophilicity values are within ±2 is preferred, those WO 98/06851 PCT/US97/14221 -24which are within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred.

Accordingly, these amino acid substitutions are generally based on the relative similarity of R-group substituents, for example, in terms of size, electrophilic character, charge, and the like. In general, preferred substitutions which take various of the foregoing characteristics into consideration will be known to those of skill in the art and include, for example, the following combinations: arginine and lysine; glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.

In addition, peptides derived from these polypeptides, including peptides of at least about 6 consecutive amino acids from these sequences, are contemplated.

Alternatively, such peptides may comprise about 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59 or 60 consecutive residues. For example, a peptide that comprises 6 consecutive amino acid residues may comprise residues 1 to 6, 2 to 7, 3 to 8 and so on of the CopB protein. Such peptides may be represented by the formula x to (x n) amino to carboxy residues of the first and last consecutive residues where x is equal to any number from 1 to the full length of the CopB protein minus n, and n is equal to the length of the peptide minus 1. So, for CopB of TTA24, x 1 to (759 for CopB of 012E, x 1 to (758 for CopB of 035E, x 1 to (759 n) and for CopB of046E, x 1 to (767 Where the peptide is 10 residues long (n 10-1), the formula represents every 10-mer possible for each antigen., For example, where x is equal to 1 the peptide would comprise residues 1 to (1 or 1 to 10. Where x is equal to 2, the peptide would comprise residues 2 to (2 or 2 to 11, and so on, until the peptide would comprise residues 750 to (750 [759 750]), or 750 to 759.

Syntheses of CopB peptides are readily achieved using conventional synthetic techniques such as the solid phase method through the use of a commercially WO 98/06851 PCTUS97/14221 available peptide synthesizer such as an Applied Biosystems Model 430A Peptide Synthesizer). Peptides synthesized in this manner may then be aliquoted in predetermined amounts and stored in conventional manners, such as in aqueous solutions or, even more preferably, in a powder or lyophilized state pending use.

In general, due to the relative stability of peptides, they may be readily stored in aqueous solutions for fairly long periods of time if desired, up to six months or more, in virtually any aqueous solution without appreciable degradation or loss of antigenic activity. However, where extended aqueous storage is contemplated it will generally be desirable to include agents including buffers such as Tris or phosphate buffers to maintain a pH of 7.0 to 7.5. Moreover, it may be desirable to include agents which will inhibit microbial growth, such as sodium azide or Merthiolate. For extended storage in an aqueous state it will be desirable to store the solutions at 4 0 C, or more preferably, frozen. Of course, where the peptide(s) are stored in a lyophilized or powdered state, they may be stored virtually indefinitely, in metered aliquots that may be rehydrated with a predetermined amount of water (preferably distilled, deionized) or buffer prior to use.

Of particular interest are peptides that represent epitopes that lie within the CopB antigens of the present invention. An "epitope" is a region of a molecule that stimulates a response from a T-cell or B-cell, and hence, elicits an immune response from these cells. An epitopic core sequence, as used herein, is a relatively short stretch of amino acids that is structurally and biochemically "complementary" to, and therefore will bind to, binding sites on antibodies or T-cell receptors.

Antibody binding sites also may be termed "linear" epitopes, as the residues that are involved in the actual physical interaction of antigen and antibody are linear, or at least in a discrete region of the molecule. Other epitopes may be non-linear in that widely separated regions of the molecule participate in the interaction. Operationally, these two types of epitopes may be distinguished on the basis of binding in denaturing Western blot analysis positive binding indicates linear, negative binding indicates nonlinear.

WO 98/06851 PCT/US97/14221 -26- The identification of epitopic core sequences is known to those of skill in the art.

For example U.S. Patent 4,554,101 teaches identification and preparation of epitopes from amino acid sequences on the basis of hydrophilicity, and by Chou-Fasman analyses.

Numerous computer programs are available for use in predicting antigenic portions of proteins, examples of which include those programs based upon Jameson-Wolf analyses (Jameson and Wolf, 1988; Wolf et al., 1988), the program PepPlot® (Brutlag et al., 1990; Weinberger et al., 1985), and other new programs for protein tertiary structure prediction (Fetrow Bryant, 1993) that can be used in conjunction with computerized peptide sequence analysis programs. Epitopic core sequences of the present invention also may be operationally defined in terms of their ability to compete with or perhaps displace the binding of the corresponding CopB antigen to the corresponding CopBdirected antisera.

For any of the variant molecules described above, immunoassays may be employed to screen for reactivity of these molecules with previously developed immunoreagents. Similarly, new antibodies and antisera, based on these variants, may be generated in order test their reactivity with existing "native" or "wild-type" molecules.

Moreover, the availability of an art-recognized model for M. catarrhalis provides a ready means for testing variant in vivo for their ability to protect subjects from M.

catarrhalis infections.

2. A Structural Analysis of the 10F3 Epitope of CopB Based on the foregoing discussion, it is clear that it should be possible to substitute specific amino acids of the 10F3 epitope of region 1 with other amino acids and still retain, and possibly even improve upon, the reactivity of the epitope with 1 0F3 or other antibodies that recognize the CopB protein of Moraxella. Which amino acids may be interchanged is dependent upon several factors, including but not limited to, the hydropathicity, hydrophilicity, polarity and tertiary structure of the targeted amino acid as well as other amino acids proximal to the targeted residue which may influence its characteristics. In order to illustrate how one would begin to determine which amino acids are likely candidates for substitution in order to create new peptides, polypeptides WO 98/06851 PCT/US97/14221 -27or proteins that are either strain-specific or strain-common antigens for Moraxella, the analysis of variable region 1 is described below.

It appears that the fourth position of region 1 may be at least either glutamate or lysine and not adversely affect reactivity with 10F3. Both of these amino acids are charged residues, but glutamate is negative and lysine is positive; therefore, it is reasonable to speculate that any charged residue may be present in this position and still result in a protein or peptide that binds to the 10F3 antibody. This data suggests that the residue at position 4 is unlikely to be critical for strain-specific antibody binding. But as indicated above, other factors may affect the ability of one amino acid to be substituted for another without causing an undesired effect. Mutated peptides, polypeptides and proteins resulting from such substitutions could be easily screened for reactivity using the immunoassays described in the instant specification.

In strains 035E and 012E that bind 10F3, position 6 is occupied by aspartate, a negatively charged amino acid. In strains TTA24 and 046E which do not bind 10F3, the homologous position is occupied by either a positively charged lysine or a weakly basic asparagine. If one were to only consider the charge of the amino acids with regard to antibody binding then one would deduce that position 6 may be critical to reactivity with 10F3; however, data disclosed herein show that position 6 alone does not determine reactivity with 10F3. Other factors appear to be more important for 10F3 binding. But amino acids at position 6 could have a synergistic effect upon reactivity with 10F3 or other antibodies. Such an assertion could be tested as indicated.

Position 7 may be occupied by either lysine or aspartate and still result in a peptide that binds to 10F3. Given the analysis of positively and negatively charged residues described previously, it is reasonable to deduce that any one of lysine, arginine, histidine, aspartate or glutamate could also be present at the seventh position of a 10F3binding peptide. Further residues may also occupy this position and still result in a peptide that retains 10F3 antibody binding.

Position 9 is occupied by either a positively charged lysine or a neutral amino acid in both strains that react or do not react with 10F3. It is possible that other WO 98/06851 PCT/US97/14221 -28positively charged or even neutral amino acids may occupy position 9. At position 10 of each of the currently known 10F3-binding species there is a positively charged amino acid. However, as 035E contains arginine at this position and 012E contains lysine, it seems reasonable to propose that histidine, another positively charged amino acid, could also be present at this position in a 10F3-binding peptide.

Similarly, at position 12 there are one of two negatively charged amino acids.

Therefore, interchange of aspartate or glutamate at this position is contemplated to be acceptable. Furthermore, it is not unreasonable to at least propose that a positively charged amino acid may be present at this position. Although not representing the type of change that is already supported from data generated from a known CopB strain, the effect of inserting a positively charged residue at this position can be easily addressed. In these circumstances all that would be required would be to simply insert a positively charged amino acid at this position and to test the resultant peptide in any one of a number of acceptable immunobinding assays and to determine whether the resultant peptide retained the capability to bind to the MAb 10F3.

Variability also occurs around position 13 of the region where a negatively charged glutamate or neutral threonine is present and 10F3 binding reactivity is still retained. As neutral amino acids are also present in TTA24 and 046E it is likely that position 13 does not play a critical role in determining reactivity with 10F3, and any one of several neutral amino acids, including the aromatic phenylalanine and tryptophan, or negatively charged residues may occupy position 13 without causing undesirable effects.

The same may be true of positions 14, 16 and 24 which are also occupied by either negatively charged or neutral residues in all four strains.

Position 20 is occupied by either the negatively charged aspartate or by the weakly basic asparagine in strains that bind 10F3, but as this position is also occupied by aspartate in the strains that do not bind 10F3 little can be deduced about its importance in the reactivity of the region. But as indicated earlier, its role could be easily determined by preparing mutant peptides, polypeptides or proteins and screening them for reactivity with 10F3 or another antibody as described in the instant specification.

WO 98/06851 PCT/US97/14221 -29- Position 21 is occupied by only the weakly basic asparagine in the 035E and 012E strains. In TTA24 and 046E it is occupied by the negatively charged aspartate and the positively charged lysine, respectively. Although there are significant differences in charge between the residues, there is no pattern other than charge. Nonetheless, data described herein indicate that position 21 does indeed contain the key residue for determining maximal binding to 10F3.

Positions 22 and 26 of the region are both occupied by either the positively charged lysine or by one of two negatively charged residues. As there is no apparent relationship to 10F3 binding associated with either positively or negatively charged residues at this position. It is. reasonable to assume that these residue do not play a important roles in strain-specific reactivity given their current, surrounding residues. But if proximal residues are altered, then residues at either of these positions may exert an effect on antibody binding.

3. CopB Nucleic Acids In addition to polypeptides, the present invention also encompasses nucleic acids encoding the CopB antigens of SEQ ID NO:27, SEQ ID NO:31 and SEQ ID NO:33 which are provided as SEQ ID NO:28, SEQ ID NO:32 and SEQ ID NO:34, respectfully.

Because of the degeneracy of the genetic code, many other nucleic acids also may encode a given CopB, however. For example, four different three-base codons encode the amino acids alanine, glycine, proline, threonine and valine, while six different codons encode arginine, leucine and serine. Only methionine and tryptophan are encoded by a single codon. Table I provides a list of amino acids and their corresponding codons for use in such embodiments. In order to generate any nucleic acid encoding a given CopB, one need only refer to the codon table provided herein. Substitution of the natural codon with any codon encoding the same amino acid will result in a distinct nucleic acid that encodes CopB. As a practical matter, this can be. accomplished by site-directed mutagenesis of an existing copB gene or de novo chemical synthesis of one or more nucleic acids.

WO 98/06851 PCTIUS97/14221 These observations regarding codon selection, site-directed mutagenesis and chemical synthesis apply with equal force to the discussion of substitutional mutants CopB peptides and polypeptides, as set forth above. More specifically, substitutional mutants generated by site-directed changes in the nucleic acid sequence that are designed to alter one or more codons of a given polypeptide or epitope may provide a more convenient way of generating large numbers of mutants in a rapid fashion.

The nucleic acids of the present invention provide for a simple way to generate fragments trunications) of CopB, CopB-CopB fusion molecules (discussed above) and CopB fusions with other molecules. For example, utilization of restriction enzymes and nuclease in the copB gene permits one to manipulate the structure of these genes, and the resulting gene products. Vectors and cloning strategies are well known to those of skill in the art.

The nucleic acid sequence information provided by the present disclosure also allows for the preparation of relatively short DNA (or RNA) sequences that have the ability to specifically hybridize to gene sequences of the selected copB gene. In these aspects, nucleic acid probes of an appropriate length are prepared based on a consideration of the coding sequence of the copB gene, or flanking regions near the cop B gene, such as regions downstream and upstream in the M. catarrhalis chromosome.

The ability of such nucleic acid probes to specifically hybridize to copB gene sequences lends them particular utility in a variety of embodiments. For example, the probes can be used in a variety of diagnostic assays for detecting the presence of pathogenic organisms in a given sample. In addition, these oligonucleotides can be inserted, in frame, into expression constructs for the purpose of screening the corresponding peptides for reactivity with existing antibodies or for the ability to generate diagnostic or prophylactic reagents. Finally, as discussed above, they may be utilized to generate mutants by sitedirected mutagenesis.

To provide certain of the advantages in accordance with the invention, the preferred nucleic acid sequence employed for hybridization studies or assays includes sequences that are complementary to at least a 10 to 20, or so, nucleotide stretch of the WO 98/06851 PCT/US97/14221 -31 sequence, although sequences of 30 to 60 or so nucleotides are also envisioned to be useful. Such molecules may be term oligonucleotides or probes. A size of at least 9 nucleotides in length helps to ensure that the fragment will be of sufficient length to form a duplex molecule that is both stable and selective. Molecules having complementary sequences over stretches greater than 10 bases in length are generally preferred, in order to increase stability and selectivity of the hybrid, and thereby improve the quality and degree of the specific hybrid molecules obtained. Thus, one will generally prefer to design nucleic acid molecules having copB gene-complementary stretches of 15 to nucleotides, or even longer, such as 30 to 60, where desired. Such fragments may be readily prepared by, for example, directly synthesizing the fragment by chemical means, by application of nucleic acid reproduction technology, such as the PCR technology of U.S. Patent 4,603,102, or by introducing selected sequences into recombinant vectors for recombinant production.

The oligos or probes that would be useful may be derived from any portion of the sequences of strains TTA24 (SEQ ID NO:34), 012E (SEQ ID NO:28) or 046E (SEQ ID NO:32). Therefore, oligos or probes are specifically contemplated that comprise nucleotides 1 to 9, or 2 to 10, or 3 to 11 and so forth up to a probe comprising the last 9 nucleotides of the nucleotide sequence of TTA24 (SEQ ID NO:34), 012E (SEQ ID NO:28) or 046E (SEQ ID NO:32). Thus, each probe would comprise at least about 9 linear nucleotides of the nucleotide sequence of TTA24 (SEQ ID NO:34), 012E (SEQ ID NO:28) or 046E (SEQ ID NO:32), designated by the formula "n to n where n is an integer from 1 to the number of nucleotides in the sequence, less the length of the probe 1. Longer probes that hybridize to the copB gene trader low, medium, medium-high and high stringency conditions are also contemplated, including those that comprise the entire nucleotide sequence of TTA24 (SEQ ID NO:34), 012E (SEQ ID NO:28) or 046E (SEQ ID NO:32). This hypothetical may be repeated for probes having lengths of about 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90, 100 and greater bases.

In that the CopB proteins and antigenic epitopes of the present invention are believed to be indicative of pathogenic Moraxella species, the probes of the present WO 98/06851 PCT/US97/14221 -32invention will find particular utility as the basis for diagnostic hybridization assays for detecting copB genes in clinical samples. Exemplary clinical samples that can be used in the diagnosis of infections are thus any samples which could possibly include Moraxella nucleic acid, including middle ear fluid, sputum, mucus, bronchoalveolar fluid, amniotic fluid or the like. A variety of hybridization techniques and systems are known which can be used in connection with the hybridization aspects of the invention, including diagnostic assays such as those described in Falkow et al., U.S. Patent 4,358,535.

Depending on the application envisioned, one will desire to employ varying conditions of hybridization to achieve varying degrees of selectivity of the probe toward the target sequence. For applications requiring a high degree of selectivity, one will typically desire to employ relatively stringent conditions to form the hybrids, for example, one will select relatively low salt and/or high temperature conditions, such as provided by 0.02M-0.15M NaC1 at temperatures of 50'C to 70 0 C. These conditions are particularly selective, and tolerate little, if any, mismatch between the probe and the template or target strand.

Of course, for some applications, where one desires to prepare mutants employing a mutant primer strand hybridized to an underlying template (discussed above), less stringent hybridization conditions are called for in order to allow formation of the heteroduplex. In these circumstances, one would desire to employ conditions such as 0. 15M-0.9M salt, at temperatures ranging from 20'C to 55 0 C. In any case, it is generally appreciated that conditions can be rendered more stringent by the addition of increasing amounts of formamide, which serves to destabilize the hybrid duplex in the same manner as increased temperature. Thus, hybridization conditions can be readily manipulated, and the method of choice will generally depend on the desired results.

In certain embodiments, one may desire to employ nucleic acid probes to isolate variants from clone banks containing mutated clones. In particular embodiments, mutant clone colonies growing on solid media which contain variants of the copB nucleic acid sequence could be identified on duplicate filters using hybridization conditions and methods, such as those used in colony blot assays, to obtain hybridization only between probes containing sequence variants and nucleic acid sequence variants contained in WO 98/06851 PCTIUS97/14221 -33 specific colonies. In this manner, small hybridization probes containing short variant sequences of the copB gene may be utilized to identify those clones growing on solid media which contain sequence variants of the entire copB gene. These clones can then be grown to obtain desired quantities of the variant copB nucleic acid sequences or the corresponding CopB antigen.

In clinical diagnostic embodiments, nucleic acid sequences of the present invention are used in combination with an appropriate means, such as a label, for determining hybridization. A wide variety of appropriate indicator means are known in the art, including radioactive, enzymatic or other ligands, such as avidin/biotin, which are capable of giving a detectable signal. In preferred diagnostic embodiments, one will likely desire to employ an enzyme tag such as urease, alkaline phosphatase or peroxidase, instead of radioactive or other environmental undesirable reagents. In the case of enzyme tags, colorimetric indicator substrates are known which can be employed to provide a means visible to the human eye or spectrophotometrically, to identify specific hybridization with pathogen nucleic acid-containing samples. Biotin/avidinbased reagents also may be employed, where one of these binding partners is attached to the probe.

In general, it is envisioned that the hybridization probes described herein will be useful both as reagents in solution hybridizations as well as in embodiments employing a solid phase. In embodiments involving a solid phase, the test DNA (or RNA) from suspected clinical samples, such as exudates, body fluids amniotic fluid, middle ear effusion, bronchoalveolar lavage fluid) or even tissues, is adsorbed or otherwise affixed to a selected matrix or surface. This fixed, single-stranded nucleic acid is then subjected to specific hybridization with selected probes under desired conditions. The selected conditions will depend on the particular circumstances based on the particular criteria required (depending, for example, on the G+C contents, type of target nucleic acid, source of nucleic acid, size of hybridization probe, etc.). Following washing of the hybridized surface so as to remove nonspecifically bound probe molecules, specific hybridization is detected, or even quantified, by means of the label.

WO 98/06851 PCT/US97/14221 -34- The nucleic acid sequences which encode for the CopB antigens, or their variants, may be useful in conjunction with polymerase chain reaction (PCR) methodology to detect M. catarrhalis. In general, by applying the PCR technology as set out, in U.S. Patent 4,60,102, one may utilize various portions of the copB gene sequence as oligonucleotide primers for the PCR amplification of a defined portion of a copB nucleic acid in a sample. The amplified portion of the copB sequence may then be detected by hybridization with a hybridization probe containing a complementary sequence. In this manner, extremely small concentrations of M. catarrhalis nucleic acid may detected in a sample utilizing CopB sequences.

4. Vectors, Host Cells and Cultures for Producing CopB Antigens In another embodiment, nucleic acids of the present invention may be used advantageously to produce recombinant CopB protein. M. catarrhalis cells may be grown on agar plates using brain heart infusion broth as a medium. Plates are incubated at 37 0 C in candle extinction jars. Outer membrane fragments may be subsequently prepared from these cells by the EDTA-based extraction procedure of Murphy et al.

(1989).

To assist those of skill in carrying out more particular aspects of the invention, recombinant clones bearing DNA segments encoding CopB were deposited with the American Type Culture Collection (ATCC) on August 4, 1992, under the provisions of the Budapest Treaty. In particular, plasmid pMEH 120 (ATCC accession number 75285) bearing a nucleic segment encoding the CopB antigen of strain 035E was deposited in the form of purified plasmid DNA. Further the nucleotide sequences of the copB genes from M. catarrhalis strains TTA24, 012E and 046E have been submitted to GenBank and assigned the accession numbers U69980 (SEQ ID NO:34), U69981 (SEQ ID NO:28), and U69982 (SEQ ID NO:32), respectively.

The gene copB, encoding the CopB protein of strain 035E, was originally cloned in a pBR322-based recombinant plasmid, designated pMEH100. Subsequently, this gene was subcloned in pBluescript for sequencing analysis. This new plasmid, designated is what was deposited with the ATCC. Recombinant plasmid pMEH120 is a WO 98/06851 PCT/US97/14221 pBluescript II SK+ vector containing an insert of M. catarrhalis chromosomal NA approximately 4.5 kb in size, and encodes a protein of about 80 kD that is reactive with monoclonal antibody 10F3. As will be appreciated by those of skill in the art in light of the detailed disclosure set forth herein, that the invention is in no way intended to be limited by the foregoing or other specific embodiments that were deposited with the

ATCC.

Though CopB protein may be isolated from cultures of M. catarrhalis, it may prove more efficient to generate the protein in other host cell systems. In addition, the synthesis of mutant polypeptides, the nucleic acids for which must be generated outside the M catarrhalis genome, also will likely be produced most effectively in a recombinant system.

In order to express a recombinant CopB polypeptide, it is necessary to provide an copB gene in an expression cassette. The expression cassette contains a CopB-encoding nucleic acid trader transcriptional control of a promoter. A "promoter" refers to a DNA sequence recognized by the synthetic machinery of the cell, or introduced synthetic machinery, required to initiate the specific transcription of a gene. The phrase "under transcriptional control" means that the promoter is in the correct location and orientation in relation to the nucleic acid to control RNA polymerase initiation and expression of the gene. Those promoters most commonly used in prokaryotic recombinant DNA construction include the B-lactamase (penicillinase) and lactose promoter systems (Chang et al., 1978; Itakura et al., 1977; Goeddel et al., 1979) and a tryptophan (trp) promoter system (Goeddel et al., 1980; EPO Appl. Publ. No. 0036776). While these are the most commonly used, other microbial promoters have been discovered and utilized, and details concerning their nucleotide sequences have been published, enabling a skilled worker to ligate them functionally with plasmid vectors (EPO Appl. Publ. No.

0036776).

The appropriate expression cassette can be inserted into a commercially available expression vector by standard subcloning techniques. For example, the E. coli vectors pUC or pBluescript T M may be used according to the present invention to produce WO 98/06851 PCT/US97/14221 -36recombinant CopB polypeptide in vitro. The manipulation of these vectors is well known in the art. In general, plasmid vectors containing replicon and control sequences which are derived from species compatible with the host cell are used in connection with these hosts. The vector ordinarily carries a replication site, as well as marking sequences which are capable of providing phenotypic selection in transformed cells. For example, E. coli is typically transformed using pBR322, a plasmid derived from an E. coli species (Bolivar et al., 1977). pBR322 contains genes for ampicillin and tetracycline resistance and thus provides easy means for identifying transformed cells. The pBR plasmid, or other microbial plasmid or phage must also contain, or be modified to contain, promoters which can be used by the microbial organism for expression of its own proteins.

In addition, phage vectors containing replicon and control sequences that are compatible with the host microorganism can be used as a transforming vector in connection with these hosts. For example, the phage lambda GEMTM- 11 may be utilized in making recombinant phage vector which can be used to transform host cells, such as E. coli LE392.

In one embodiment, the protein is expressed as a fusion protein with (3-gal, allowing rapid affinity purification of the protein. Examples of such fusion protein expression systems are the glutathione S-transferase system (Pharmacia, Piscataway, NJ), the maltose binding protein system (NEB, Beverley, MA), the FLAG system (IBI, New Haven, CT), and the 6xHis system (Qiagen, Chatsworth, CA). Some of these fusion systems produce recombinant protein bearing only a small number of additional amino acids, which are unlikely to affect the functional capacity of the recombinant protein.

For example, both the FLAG system and the 6xHis system add only short sequences, both of which are known to be poorly antigenic and which do not adversely affect folding of the protein to its native conformation. Other fusion systems produce proteins where it is desirable to excise the fusion partner from the desired protein. In another embodiment, the fusion partner is linked to the recombinant protein by a peptide sequence containing a specific recognition sequence for a protease. Examples of suitable WO 98/06851 PCT/US97/14221 -37sequences are those recognized by the Tobacco Etch Virus protease (Life Technologies, Gaithersburg, MD) or Factor Xa (New England Biolabs, Beverley, MA).

E coli is a preferred prokaryotic host. For example, E coli strain RRI is particularly useful. Other microbial strains which may be used include E coli strains such as Ecoli LE392, E. coli B, and Ecoli X 1776 ,(ATCC No. 31537). The aforementioned strains, as well as E coli W3110 lambda-, prototrophic, ATCC No.

273325), bacilli such as Bacillus subtilis, or other enterobacteriaceae such as Salmonella typhimurium or Serratia marcescens, and various Pseudomonas species may be used.

These examples are, of course, intended to be illustrative rather than limiting.

Recombinant bacterial cells, for example E coli, are grown in any of a number of suitable media, for example LB, and the expression of the recombinant polypeptide induced by adding IPTG to the media or switching incubation to a higher temperature. After culturing the bacteria for a further period of between 2 and 24 hours, the cells are collected by centrifugation and washed to remove residual media. The bacterial cells are then lysed, for example, by disruption in a cell homogenizer and centrifuged to separate the dense inclusion bodies and cell membranes from the soluble cell components. This centrifugation can be performed trader conditions whereby the dense inclusion bodies are selectively enriched by incorporation of sugars such as sucrose into the buffer and centrifugation at a selective speed.

If the recombinant protein is expressed in the inclusion bodies, as is the case in many instances, these can be washed in any of several solutions to remove some of the contaminating host proteins, then solubilized in solutions containing high concentrations of urea 8M) or chaotropic agents such as guanidine hydrochloride in the presence of reducing agents such as P-mercaptoethanol or dithiothreitol (DTT).

Under some circumstances, it may be advantageous to incubate the polypeptide for several hours under conditions suitable for the protein to undergo a refolding process into a conformation which more closely resembles that of the native protein. Such conditions generally include low protein concentrations less than 500 g/ml, low levels of reducing agent, concentrations of urea less than 2 M and often the presence of reagents WO 98/06851 PCT/US97/14221 -38such as a mixture of reduced and oxidized glutathione which facilitate the interchange of disulphide bonds within the protein molecule.

The refolding process can be monitored, for example, by SDS-PAGE or with antibodies which are specific for the native molecule. Following refolding, the protein can then be purified further and separated from the refolding mixture by chromatography on any of several supports including ion exchange resins, gel permeation resins or on a variety of affinity columns.

Alternatively, the expression system may be eukaryotic in origin. For example, in one such embodiment, the expression system used is the insect baculovirus system, and the expression cassette comprises the baculovirus polyhedron promoter. The gene encoding the protein can be manipulated by standard techniques in order to facilitate cloning into the baculovirus vector. A preferred baculovirus vector is the pBlueBac vector (Invitrogen, Sorrento, CA). The vector carrying the copB gene is transfected into Spodoptera afrugiperda Sf9) cells by standard protocols, and the cells are cultured and processed to produce the recombinant protein.

There are a variety of other eukaryotic vectors that provide a suitable vehicle in which recombinant CopB can be produced. In various embodiments of the invention, the expression construct may comprise a virus or engineered construct derived from a viral genome. The ability of certain viruses to enter cells via receptor-mediated endocytosis and to integrate into host cell genome and express viral genes stably and efficiently have made them attractive candidates for the transfer of foreign genes into mammalian cells (Ridgeway, 1988; Nicolas and Rubenstein, 1988; Baichwal and Sugden, 1986; Temin, 1986). The first viruses used as vectors were DNA viruses including the papovaviruses (simian virus 40, bovine papilloma virus, and polyoma) (Ridgeway, 1988; Baichwal and Sugden, 1986) and adenoviruses (Ridgeway, 1988; Baichwal and Sugden, 1986) and adenoassociated viruses. Retroviruses also are attractive gene transfer vehicles (Nicolas and Rubenstein, 1988; Temin, 1986) as are vaccina virus (Ridgeway, 1988) adenoassociated virus (Ridgeway, 1988) and HSV (Glorioso et al., 1995). Such vectors may WO 98/06851 PCT/US97/14221 -39be used to transform cell lines in vitro for the purpose of expressing proteins of interest or (ii) to transform cells in vitro or in vivo to provide protective polypeptides.

With respect to eukaryotic vectors, the term promoter will be used here to refer to a group of transcriptional control modules that are clustered around the initiation site for RNA polymerase II. Much of the thinking about how promoters are organized derives from analyses of several viral promoters, including those for the HSV thymidine kinase (tk) and SV40 early transcription units. These studies, augmented by more recent work, have shown that promoters are composed of discrete functional modules, each consisting of approximately 7-20 bp of DNA, and containing one or more recognition sites for transcriptional activator or repressor proteins.

At least one module in each promoter functions to position the start site for RNA synthesis. The best known example of this is the TATA box, but in some promoters lacking a TATA box, such as the promoter for the mammalian terminal deoxynucleotidyl transferase gene and the promoter for the SV40 late genes, a discrete element overlying the start site itself helps to fix the place of initiation.

Additional promoter elements regulate the frequency of transcriptional initiation.

Typically, these are located in the region 30-110 bp upstream of the start site, although a number of promoters have recently been shown to contain functional elements downstream of the start site as well. The spacing between promoter elements frequently is flexible, so that promoter function is preserved when elements are inverted or moved relative to one another. In the tk promoter, the spacing between promoter elements can be increased to 50 bp apart before activity begins to decline. Depending on the promoter, it appears that individual elements can function either co-operatively or independently to activate transcription.

The particular promoter that is employed to control the expression of a nucleic acid is not believed to be critical, so long as it is capable of expressing the nucleic acid in the targeted cell. Thus, where a human cell is targeted, it is preferable to position the nucleic acid coding region adjacent to and under the control of a promoter that is capable of being expressed in a human cell. Generally speaking, such a promoter might include WO 98/06851 PCT/US97/14221 either a human or viral promoter. Preferred promoters include those derived from HSV, including x4 promoter. Another preferred embodiment is the tetracycline controlled promoter.

In various other embodiments, the human cytomegalovirus (CMV) immediate early gene promoter, the SV40 early promoter and the Rous sarcoma virus long terminal repeat can be used to obtain high-level expression of transgenes. The use of other viral or mammalian cellular or bacterial phage promoters which are well-known in the art to achieve expression of a transgene is contemplated as well, provided that the levels of expression are sufficient for a given purpose. Tables II and III list several elements/promoters which may be employed, in the context of the present invention, to regulate the expression of a transgene. This list is not intended to be exhaustive of all the possible elements involved in the promotion of transgene expression but, merely, to be exemplary thereof.

Enhancers were originally detected as genetic elements that increased transcription from a promoter located at a distant position on the same molecule of DNA.

This ability to act over a large distance had little precedent in classic studies of prokaryotic transcriptional regulation. Subsequent work showed that regions of DNA with enhancer activity are organized much like promoters. That is, they are composed of many individual elements, each of which binds to one or more transcriptional proteins.

The basic distinction between enhancers and promoters is operational. An enhancer region as a whole must be able to stimulate transcription at a distance; this need not be true of a promoter region or its component elements. On the other hand, a promoter must have one or more elements that direct initiation of RNA synthesis at a particular site and in a particular orientation, whereas enhancers lack these specificities.

Promoters and enhancers are often overlapping and contiguous, often seeming to have a very similar modular organization.

Additionally any promoter/enhancer combination (as per the Eukaryotic Promoter Data Base EPDB) could also be used to drive expression of a transgene. Use of a T3, T7 or SP6 cytoplasmic expression system is another possible embodiment. Eukaryotic cells WO 98/06851 PCT/US97/14221 -41can support cytoplasmic transcription from certain bacterial promoters if the appropriate bacterial polymerase is provided, either as part of the delivery complex or as an additional genetic expression construct.

Host cells include eukaryotic microbes, such as yeast cultures may also be used.

Saccharomyces cerevisiae, or common baker's yeast is the most commonly used among eukaryotic microorganisms, although a number of other strains are commonly available.

For expression in Saccharomyces, the plasmid YRp7, for example, is commonly used (Stinchcomb et al., 1979; Kingsman et al., 1979; Tschemper et al., 1980). This plasmid already contains the trpl gene which provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example ATCC No. 44076 or PEP4-1 (Jones, 1977). The presence of the trpl lesion as a characteristic of the yeast host cell genome then provides an effective environment for detecting transformation by growth in the absence of tryptophan.

Suitable promoting sequences in yeast vectors include the promoters for 3phosphoglycerate kinase (Hitzeman et al., 1980) or other glycolytic enzymes (Hess et al., 1968; Holland et al., 1978), such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase. In constructing suitable expression plasmids, the termination sequences associated with these genes are also ligated into the expression vector 3' of the sequence desired to be expressed to provide polyadenylation of the mRNA and termination. Other promoters, which have the additional advantage of transcription controlled by growth conditions are the promoter region for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, and the aforementioned glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Any plasmid vector containing a yeast-compatible promoter, origin of replication and termination sequences is suitable.

WO 98/06851 PCT/US97/14221 -42- In addition to eukaryotic microorganisms, cultures of cells derived from multicellular organisms may also be used as hosts. In principle, any such cell culture is workable, whether from vertebrate or invertebrate culture. However, interest has been greatest in vertebrate cells, and propagation of vertebrate cells in culture has become a routine procedure in recent years. Examples of such useful host cell lines are VERO and HeLa cells, Chinese hamster ovary (CHO) cell lines, and W138, BHK, COS-7, 293 and MDCK cell lines. Expression vectors for such cells ordinarily include (if necessary) an origin of replication, a promoter located in from of the gene to be expressed, along with any necessary ribosome binding sites, RNA splice sites, polyadenylation site, and transcriptional terminator sequences.

Preparation of Antibodies to CopB Antibodies that react immunologically with CopB polypeptides or peptides derived therefrom may be readily prepared through use of well-known techniques, such as those exemplified in U.S. Patent 4,196,265. Typically, this technique involves immunizing a suitable animal with a selected immunogen composition, purified or partially purified protein, synthetic protein or fragments thereof, as discussed in the section on vaccines. Animals to be immunized are mammals such as cats, dogs and horses, although there is no limitation other than that the subject be capable of mounting an immune response of some kind. The immunizing composition is administered in a manner effective to stimulate antibody producing cells. Rodents such as mice and rats are preferred animals, however, the use of rabbit, sheep or frog cells is possible. The use of rats may provide certain advantages, but mice are preferred, with the BALB/c mouse being most preferred as the most routinely used animal and one that generally gives a higher percentage of stable fusions.

For generation of monoclonal antibodies (MAbs), following immunization, somatic cells with the potential for producing antibodies, specifically B lymphocytes (B cells), are selected for use in the MAb generating protocol. These cells may be obtained from biopsied spleens, tonsils or lymph nodes, or from a peripheral blood sample.

Spleen cells and peripheral blood cells are preferred, the former because they are a rich WO 98/06851 PCT/US97/14221 -43source of antibody-producing cells that are in the dividing plasmablast stage, and the latter because peripheral blood is easily accessible. Often, a panel of animals will have been immunized and the spleen of the animal with the highest antibody titer removed.

Spleen lymphocytes are obtained by homogenizing the spleen with a syringe. Typically, a spleen from an immunized mouse contains approximately 5 x 107 to 2 x 10 8 lymphocytes.

The antibody-producing B cells from the immunized animal are then fused with cells of an immortal myeloma cell line, generally one of the same species as the animal that was immunized. Myeloma cell lines suited for use in hybridoma-producing fusion procedures preferably are non-antibody-producing, have high fusion efficiency and enzyme deficiencies that render them incapable of growing in certain selective media which support the growth of only the desired fused cells, called "hybridomas." Any one of a number of myeloma cells may be used and these are known to those of skill in the art. For example, where the immunized animal is a mouse, one may use P3-X63/Ag8, X63-Ag8.653, NS1/1.Ag 4 1, Sp210-Agl4, FO, NSO/U, MPC-11, MPC11-X45-GTG 1.7 and S194/5XXO Bul; for rats, one may use R210.RCY3, Y3-Ag 1.2.3, IR983F and 4B210; and U-266, GM1500-GRG2, LICR-LON-HMy2 and UC729-6 are all useful in connection with human cell fusions.

One preferred murine myeloma cell line is the NS-1 myeloma cell line (also termed P3-NS-1-Ag4-1), which is readily available from the NIGMS Human Genetic Mutant Cell Repository by requesting cell line repository number GM3573. Another mouse myeloma cell line that may be used is the 8-azaguanine-resistant mouse murine myeloma SP2/0 non-producer cell line.

Methods for generating hybrids of antibody-producing spleen or lymph node cells and myeloma cells usually comprise mixing somatic cells with myeloma cells in a 2:1 proportion, though the proportion may vary from about 20:1 to about 1:1, respectively, in the presence of an agent or agents (chemical or electrical) that promote the fusion of cell membranes. Fusion methods using Sendai virus have been described by Kohler Milstein (1975; 1976), and those using polyethylene glycol (PEG), such as 37% (v/v) WO 98/06851 PCT/US97/14221 -44- PEG, by Gefter et al. (1977). The use of electrically induced fusion methods is also appropriate.

Fusion procedures usually produce viable hybrids at low frequencies, about 6 8 1 x 10 to 1 x 10- This does not pose a problem, however, as the viable, fused hybrids are differentiated from the parental, unfused cells (particularly the unfused myeloma cells that would normally continue to divide indefinitely) by culture in a selective medium.

The selective medium generally is one that contains an agent that blocks the de novo synthesis of nucleotides in the tissue culture media. Exemplary and preferred agents are aminopterin, methotrexate and azaserine. Aminopterin and methotrexate block de novo synthesis of both purines and pyrimidines, whereas azaserine blocks only purine synthesis. Where aminopterin or methotrexate is used, the media is supplemented with hypoxanthine and thymidine as a source of nucleotides (HAT medium). Where azaserine is used, the media is supplemented with hypoxanthine.

The preferred selection medium is HAT. Only cells capable of operating nucleotide salvage pathways are able to survive in HAT medium. The myeloma cells are defective in key enzymes of the salvage pathway, hypoxanthine phosphoribosyl transferase (HPRT), and they cannot survive. The B cells can operate this pathway, but they have a limited life span in culture and generally die within about two weeks.

Therefore, the only cells that can survive in the selective media are those hybrids formed from myeloma and B cells.

This culturing provides a population of hybridomas from which specific hybridomas are selected. Typically, selection of hybridomas is performed by singleclone dilution in microtiter plates, followed by testing the individual clonal supernatants (after about two to three weeks) for the desired reactivity. The assay should be sensitive, simple and rapid, such as radioimmunoassays, enzyme immunoassays, cytotoxicity assays, plaque assays, dot immunobinding assays, and the like.

The selected hybridomas are then serially diluted and cloned into individual antibody-producing cell lines, which clones can then be propagated indefinitely to provide MAbs. The cell lines may be exploited for MAb production in two basic ways.

WO 98/06851 PCT/US97/14221 A sample of the hybridoma can be injected, usually in the peritoneal cavity, into a histocompatible animal of the type that was used to provide the somatic and myeloma cells for the original fusion. The injected animal develops tumors secreting the specific monoclonal antibody produced by the fused cell hybrid. The body fluids of the animal, such as serum or ascites fluid, can then be tapped to provide MAbs in high concentration.

The individual cell lines could also be cultured in vitro, where the MAbs are naturally secreted into the culture medium from which they can be readily obtained in high concentrations. MAbs produced by either means may be further purified, if desired, using filtration, centrifugation and various chromatographic methods such as HPLC or affinity chromatography.

Monoclonal antibodies of the present invention also include anti-idiotypic antibodies produced by methods well-known in the art. Monoclonal antibodies according to the present invention also may be monoclonal heteroconjugates, hybrids of two or more antibody molecules. In another embodiment, monoclonal antibodies according to the invention are chimeric monoclonal antibodies. In one approach, the chimeric monoclonal antibody is engineered by cloning recombinant DNA containing the promoter, leader, and variable-region sequences from a mouse antibody producing cell and the constant-region exons from a human antibody gene. The antibody encoded by such a recombinant gene is a mouse-human chimera. Its antibody specificity is determined by the variable region derived from mouse sequences. Its isotype, which is determined by the constant region, is derived from human DNA.

In another embodiment, monoclonal antibodies according to the present invention is a "humanized" monoclonal antibody, produced by techniques well-known in the art.

That is, mouse complementary determining regions ("CDRs") are transferred from heavy and light V-chains of the mouse Ig into a human V-domain, followed by the replacement of some human residues in the framework regions of their murine counterparts.

"Humanized" monoclonal antibodies in accordance with this invention are especially suitable for use in in vivo diagnostic and prophylactic methods for treating Moraxella infections.

WO 98/06851 PCT/US97/14221 -46- As stated above, the monoclonal antibodies and fragments thereof according to this invention can be multiplied according to in vitro and in vivo methods well-known in the art. Multiplication in vitro is carried out in suitable culture media such as Dulbecco's modified Eagle medium or RPMI 1640 medium, optionally replenished by a mammalian serum such as fetal calf serum or trace elements and growth-sustaining supplements, e.g., feeder cells, such as normal mouse peritoneal exudate cells, spleen cells, bone marrow macrophages or the like. In vitro production provides relatively pure antibody preparations and allows scale-up to give large amounts of the desired antibodies.

Techniques for large scale hybridoma cultivation under tissue culture conditions are known in the art and include homogenous suspension culture, in an airlift reactor or in a continuous stirrer reactor or immobilized or entrapped cell culture.

Large amounts of the monoclonal antibody of the present invention also may be obtained by multiplying hybridoma cells in vivo. Cell clones are injected into mammals which are histocompatible with the parent cells, syngeneic mice, to cause growth of antibody-producing tumors. Optionally, the animals are primed with a hydrocarbon, especially oils such as Pristane (tetramethylpentadecane) prior to injection.

In accordance with the present invention, fragments of the monoclonal antibody of the invention can be obtained from monoclonal antibodies produced as described above, by methods which include digestion with enzymes such as pepsin or papain and/or cleavage of disulfide bonds by chemical reduction. Alternatively, monoclonal antibody fragments encompassed by the present invention can be synthesized using an automated peptide synthesizer, or they may be produced manually using techniques well known in the art.

The monoclonal conjugates of the present invention are prepared by methods known in the art, by reacting a monoclonal antibody prepared as described above with, for instance, an enzyme in the presence of a coupling agent such as glutaraldehyde or periodate. Conjugates with fluorescein markers are prepared in the presence of these coupling agents, or by reaction with an isothiocyanate. Conjugates with metal chelates are similarly produced. Other moieties to which antibodies may be conjugated include WO 98/06851 PCT/US97/14221 -47radionuclides such as H, 125I, 131 32P, 3S, 14C, 5Cr 36C, 57CO 5Co, 59Fe, 75Se, 52Eu, and 9 9 mTc, are other useful labels which can be conjugated to antibodies. Radioactively labeled monoclonal antibodies of the present invention are produced according to wellknown methods in the art. For instance, monoclonal antibodies can be iodinated by contact with sodium or potassium iodide and a chemical oxidizing agent such as sodium hypochlorite, or an enzymatic oxidizing agent, such as lactoperoxidase. Monoclonal antibodies according to the invention may be labeled with technetium- 99 m by ligand exchange process, for example, by reducing pertechnate with stannous solution, chelating the reduced technetium onto a Sephadex column and applying the antibody to this column or by direct labeling techniques, by incubating pertechnate, a reducing agent such as SNCl 2 a buffer solution such as sodium-potassium phthalate solution, and the antibody.

6. Use of Peptides and Monoclonal Antibodies in Immunoassays It is proposed that the monoclonal antibodies of the present invention will find useful application in standard immunochemical procedures, such as ELISA and western blot methods, as well as other procedures which may utilize antibodies specific to CopB epitopes. While ELISAs are preferred forms of immunoassays, it will be readily appreciated that assays also include RIAs and other non-enzyme linked antibody binding assays or procedures. Additionally, it is proposed that monoclonal antibodies specific to the particular CopB epitope may be utilized in other useful applications. For example, their use in immunoabsorbent protocols may be useful in purifying native or recombinant CopB species or variants thereof.

It also is proposed that the disclosed CopB peptides of the invention will find use as antigens for raising antibodies and in immunoassays for the detection of anti-CopB antigen-reactive antibodies and CopB antigens (competitive assays). Alternatively, immunoassays may be exploited to determine the antigen relationship between certain CopB mutant peptides. Such screening assays may involve the generation of antisera or antibodies against mutant peptides, the reactivity of which can then be checked against other peptides, or (ii) the testing of mutant peptide reactivity with a battery of WO 98/06851 PCT/US97/14221 -48immunoreagents developed against heterologous antigens, such as antibody 10F3. In this way, a mutational analysis of various epitopes may be performed.

Diagnostic immunoassays include direct culturing of bodily fluids, either in liquid culture or on a solid support such as nutrient agar. A typical assay involves collecting a sample of bodily fluid from a patient and, optionally, placing the sample in conditions optimum for growth of the pathogen. A determination can then be made as to whether a particular microbe exists in the sample. Further analysis can be carried out to determine the properties of the microbe, whether or not it is hemolyzing.

Immunoassays encompassed by the present invention include, but are not limited to those described in U.S. Patent No. 4,367,110 (double monoclonal antibody sandwich assay) and U.S. Patent No. 4,452,901 (western blot). Other assays include immunoprecipitation of labeled ligands and immunocytochemistry, both in vitro and in vivo.

Immunoassays, in their most simple and direct sense, are binding assays. Certain preferred immunoassays are the various types of enzyme linked immunosorbent assays (ELISAs) and radioimmunoassays (RIAs) known in the art. Immunohistochemical detection using tissue sections is also particularly useful. However, it will be readily appreciated that detection is not limited to such techniques, and western blotting, dot blotting, FACS analyses, and the like may also be used.

In one exemplary ELISA, the anti-CopB antibodies of the invention are immobilized onto a selected surface exhibiting protein affinity, such as a well in a polystyrene microtiter plate. Then, a test composition suspected of containing the desired antigen, such as a clinical sample, is added to the wells. After binding and washing to remove non-specifically bound immune complexes, the bound antigen may be detected. Detection is generally achieved by the addition of another antibody, specific for the desired antigen, that is linked to a detectable label. This type of ELISA is a simple "sandwich ELISA." Detection also may be achieved by the addition of a second antibody specific for the desired antigen, followed by the addition of a third antibody that WO 98/06851 PCT/US97/14221 -49has binding affinity for the second antibody, with the third antibody being linked to a detectable label.

In another exemplary ELISA, the samples suspected of containing the CopB antigen are immobilized onto the well surface and then contacted with the anti-CopB antibodies. After binding and appropriate washing, the bound immune complexes are detected. Where the initial antigen specific antibodies are linked to a detectable label, the immune complexes may be detected directly. Again, the immune complexes may be detected using a second antibody that has binding affinity for the first antigen specific antibody, with the second antibody being linked to a detectable label.

Competition ELISAs are also possible in which test samples compete for binding with known amounts of labeled antigens or antibodies. The amount of reactive species in the unknown sample is determined by mixing the sample with the known labeled species before or during incubation with coated wells. (Peptide antigen or antibodies may also be linked to a solid support, such as in the form of beads, dipstick, membrane or column matrix, and the sample to be analyzed applied to the immobilized peptide or antibody.) The presence of reactive species in the sample acts to reduce the amount of labeled species available for binding to the well, and thus reduces the ultimate signal.

Irrespective of the format employed, ELISAs have certain features in common, such as coating, incubating or binding, washing to remove non-specifically bound species, and detecting the bound immune complexes. These are described below.

In coating a plate with either antigen or antibody, one will generally incubate the wells of the plate with a solution of the antigen or antibody, either overnight or for a specified period. The wells of the plate will then be washed to remove incompletely adsorbed material. Any remaining available surfaces of the wells are then "coated" with a nonspecific protein that is antigenically neutral with regard to the test antisera. These include bovine serum albumin (BSA), casein and solutions of milk powder. The coating allows for blocking of nonspecific adsorption sites on the immobilizing surface and thus reduces the background caused by nonspecific binding of antisera onto the surface.

WO 98/06851 PCT/US97/14221 After binding of material to the well, coating with a non-reactive material to reduce background, and washing to remove unbound material, the immobilizing surface is contacted with the antisera or clinical or biological extract to be tested in a manner conducive to immune complex (antigen/antibody) formation. Such conditions preferably include diluting the antisera with diluents such as BSA, bovine gamma globulin (BGG) and phosphate buffered saline (PBS)/Tween. These added agents also tend to assist in the reduction of nonspecific background. The layered antisera is then allowed to incubate for from 2 to 4 hours, at temperatures preferably on the order of 250 to 27 0

C.

Following incubation, the antisera-contacted surface is washed so as to remove nonimmunocomplexed material. A preferred washing procedure includes washing with a solution such as PBS/Tween, or borate buffer.

Following formation of specific immunocomplexes between the test sample and the bound antigen or antibody, followed by subsequent washing, the occurrence and even amount of immunocomplex formation may be determined by subjecting same to a second antibody having specificity for the first or for a distinct epitope of the bound antigen. Of course, in a test sample suspected of containing antibodies of human origin, the second antibody will preferably be an antibody having specificity in general for human IgG. To provide a detecting means, the detecting antibody will preferably have an associated enzyme that will generate a color development upon incubating with an appropriate chromogenic substrate. Thus, for example, one will desire to contact and incubate the antisera-bound surface with a urease or peroxidase-conjugated anti-human IgG for a period of time and under conditions which favor the development of immunocomplex formation incubation for 2 hours at room temperature in a PBScontaining solution such as PBS-Tween).

After incubation with the enzyme-tagged antibody, and subsequent to washing to remove unbound material, the amount of label is quantified by incubation with a chromogenic substrate such as urea and bromocresol purple or 2,2'-azino-di-(3-ethylbenzthiazoline-6-sulfonic acid [ABTS] and H 2 0 2 in the case of peroxidase as the enzyme label. Quantification is then achieved by measuring the degree of color generation, using a visible spectra spectrophotometer. Alternatively, the label may WO 98/06851 PCT/US97/14221 -51 be a chemiluminescent one. The use of such labels is described in U.S. Patent Nos.

5,310,687, 5,238,808 and 5,221,605.

In competitive formats, one may use labeled or unlabeled peptide as a competitor for the antigen in a sample. Alternatively, competing antibodies will require that the binding of two different antibodies be distinguishable. This can be accomplished by labeling species and not the other, or by labeling both species with differential labels rhodamine and fluorescein).

7. Use of CopB Peptide and CopB-Specific Antibody In Vivo In a further embodiment of the present invention, there are provided methods for active and passive immunoprophylaxis. Active immunoprophylaxis will be discussed first, followed by a discussion of passive immunoprophylaxis. It should be noted that the discussion of formulating vaccine compositions in the context of active immunoprophylaxis is relevant to raising antibodies in experimental animals for passive immunoprophylaxis and for the generation of diagnostic methods.

A. Active Immunoprophylaxis According to the present invention, CopB polypeptides or CopB-derived peptides, as discussed above, may be used as vaccine formulations to generate protective anti-M. catarrhalis antibody responses in vivo. By protective, it is meant only that the immune system of a treated individual is capable of generating a response that reduces, to any extent, the clinical impact of the bacterial infection. This may range from a minimal decrease is bacterial burden to outright prevention of infection. Ideally, the treated subject will not exhibit the more serious clinical manifestations of M catarrhalis infection.

Generally, immunoprophylaxis involves the administration, to a subject at risk, a vaccine composition. In the instant case, the vaccine composition will contain a CopB polypeptide or immunogenic derivative thereof in a pharmaceutically acceptable carrier, diluent or excipient. As stated above, those of skill in the art are able, through a variety of mechanisms, to identify appropriate antigenic characteristics of CopB and, in so WO 98/06851 PCT/US97/14221 -52doing, develop vaccines that will achieve certain goals. These goals include (i) generation of immune responses against specific strains of M. catarrhalis, (ii) generation of immune responses against certain groups of M catarrhalis strains and (iii) generation of immune responses against all M. catarrhalis strains.

The stability and immunogenicity of CopB antigens may vary and, therefore, it may be desirable to couple the antigen to a carrier molecule. Exemplary carriers are keyhole limpet hemocyanin (KLH) and human and bovine serum albumin, myoglobin, Pgalactosidase, penicillinase and bacterial toxoids. Those of skill in the art are aware of proper methods by which peptides can be linked to carriers without destroying their immunogenic value. Synthetic carriers such as multi-poly-DL-alanyl-poly-L-lysine and poly-L-lysine also are contemplated. Coupling generally is accomplished through amino-or carboxy-terminal residues of the antigen, thereby affording the peptide or polypeptide the greatest chance of assuming a relatively "native" conformation following coupling.

It also may be desirable to include in the composition any of a number of different substances referred to as adjuvants, which are known to stimulate the appropriate portion of the immune system of the vaccinated animal. Suitable adjuvants for the vaccination of subjects (including experimental animals; see above) include, but are not limited to oil emulsions such as Freund's complete or incomplete adjuvant (not suitable for livestock use), Marcol 52:Montanide 888 (Marcol is a Trademark of Esso, Montanide is a Trademark of SEPPIC, Paris), squalane or squalene, Adjuvant (containing peanut oil, mannide monooleate and aluminum monostearate), mineral gels such as aluminum hydroxide, aluminum phosphate, calcium phosphate and alum, surfactants such as hexadecylamine, octadecylamine, lysolecithin, dimethyldioctadecylammonium bromide, N,N-dioctadecyl-N,N'- bis(2-hydroxyethyl)propanediamine, methoxyhexadecylglycerol and pluronic polyols, polyanions such as pyran, dextran sulfate, polyacrylic acid and carbopol, peptides and amino acids such as muramyl dipeptide, dimethylglycine, tuftsin and trehalose dimycolate. Agents include synthetic polymers of sugars (Carbopol), emulsion in physiologically acceptable oil WO 98/06851 PCT/US97/14221 -53vehicles such as mannide mono-oleate (Aracel A) or emulsion with 20 percent solution of a perfluorocarbon (Fluosol-DA) also may be employed.

The preparation of vaccines which contain peptide sequences as active ingredients is generally well understood in the art, as exemplified by U.S. Patents 4,608,251, 4,601,903, 4,599,231, 4,599,230, 4,596,792 and 4.578,770, all of which are incorporated herein by reference. Typically, such vaccines are prepared as injectables.

Liquid solutions are preferred; solid forms suitable for solution or suspension in liquid prior to injection also may be prepared. The preparation further may be emulsified. The active immunogenic ingredient is often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof. In addition, if desired, the vaccine may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, or adjuvants which enhance the effectiveness of the vaccines.

The vaccine preparations of the present invention also can be incorporated into non-toxic carriers such as liposomes or other microcarrier substances, or by conjugation to polysaccharides, proteins or polymers or in combination with Quil-A to form "iscoms" (immunostimulating complexes). These complexes can serve to reduce the toxicity of the antigen, delay its clearance from the host and improve the immune response by acting as an adjuvant. Other suitable adjuvants for use in this embodiment of the present invention include INF, IL-2, IL-4, IL-8, IL-12 and other immunostimulatory compounds.

Further, conjugates comprising the immunogen together with an integral membrane protein of prokaryotic origin, such as TraT (see PCT/AU87/00107) may prove advantageous.

The vaccines are conventionally administered parenterally, by injection, for example, either subcutaneously or intramuscularly. Additional formulations which are suitable for other modes of administration include suppositories and, in some cases, oral formulations. For suppositories, traditional binders and carriers may include, for example, polyalkalene glycols or triglycerides: such suppositories may be formed from WO 98/06851 PCT/US97/14221 -54mixtures containing the active ingredient in the range of 0.5% to 10%, preferably 1-2%.

Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders and contain 10-95% of active ingredient, preferably 25-70%.

The peptides may be formulated into the vaccine as neutral or salt forms.

Pharmaceutically acceptable salts, include the acid addition salts (formed with the free amino groups of the peptide) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups may also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.

The vaccines are administered in a manner compatible with the dosage formulation, and in such amount as will be prophylactically effective and immunogenic.

The quantity to be administered depends on the subject to be treated, including, the capacity of the individual's immune system to synthesize antibodies, and the degree of protection desired. Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner. However, suitable dosage ranges are of the order of several hundred micrograms active ingredient to one milligram or so per vaccination. Suitable regimes for initial administration and booster shots are also variable, but are typified by an initial administration followed by subsequent inoculations or other administrations.

The manner of application may be varied widely. Any of the conventional methods for administration of a vaccine are applicable. These are believed to include oral application on a solid physiologically acceptable base or in a physiologically acceptable dispersion, parenterally, by injection or the like. The dosage of the vaccine will depend on the route of administration and will vary according to the size of the host.

WO 98/06851 PCT/US97/14221 In many instances, it will be desirable to have multiple administrations of the vaccine, usually not exceeding six vaccinations, more usually not exceeding four vaccinations and preferably one or more, usually at least about three vaccinations. The vaccinations will normally be at from two to twelve week intervals, more usually from three to five week intervals. Periodic boosters at intervals of 1-5 years, usually three years, will be desirable to maintain protective levels of the antibodies. The course of the immunization may be followed by assays for antibodies for the supemrnatant antigens.

The assays may be performed by labeling with conventional labels, such as radionuclides, enzymes, fluorescers, and the like. These techniques are well known and may be found in a wide variety of patents, such as U.S. Patent Nos. 3,791,932, 4,174,384 and 3,949,064, as illustrative of these types of assays.

B. Passive Immunoprophylaxis Passive immunity is defined, for the purposes of this application, as the transfer to one organism of an immune response effector that was generated in another organism.

The classic example of establishing passive immunity is to transfer antibodies produced in one organism into a second, immunologically compatible animal. By "immunologically compatible," it is meant that the antibody can perform at least some of its immune functions in the new host animal. More recently, as a better understanding of cellular immune functions has evolved, it has become possible to accomplish passive immunity by transferring other effectors, such as certain kinds of lymphocytes, including cytotoxic and helper T cells, NK cells and other immune effector cells. The present invention contemplates both of these approaches.

Antibodies, antisera and immune effector cells are raised using standard vaccination regimes in appropriate animals, as discussed above. The primary animal is vaccinated with at least CopB polypeptide or peptide product according to the present invention, with or without an adjuvant, to generate an immune response. The immune response may be monitored, for example, by measurement of the levels of antibodies produced, using standard ELISA methods.

WO 98/06851 PCTIUS97/14221 -56- Once an adequate immune response has been generated, immune effector cells can be collected on a regular basis, usually from blood draws. The antibody fraction can be purified from the blood by standard means, by protein A or protein G chromatography. In an alternative preferred embodiment, monoclonal antibodyproducing hybridomas are prepared by standard means (Coligan et al., 1991).

Monoclonal antibodies are then prepared from the hybridoma cells by standard means. If the primary host's monoclonal antibodies are not compatible with the animal to be treated, it is possible that genetic engineering of the cells can be employed to modify the antibody to be tolerated by the animal to be treated. In the human context, murine antibodies, for example, may be "humanized" in this fashion.

Antibodies, antisera or immune effector cells, prepared as set forth above, are injected into hosts to provide passive immunity against microbial infection. For example, an antibody composition is prepared by mixing, preferably homogeneously mixing, at least one antibody with at least one pharmaceutically or veterinarally acceptable carrier, diluent, or excipient using standard methods of pharmaceutical or veterinary preparation. The amount of antibody required to produce a single dosage form will vary depending upon the microbial species being vaccinated against, the individual to be treated and the particular mode of administration. The specific dose level for any particular individual will depend upon a variety of factors including the age, body weight, general health, sex, and diet of the individual, time of administration, route of administration, rate of excretion, drug combination and the severity of the microbial infectation.

The antibody composition may be administered intravenously, subcutaneously, intranasally, orally, intramuscularly, vaginally, rectally, topically or via any other desired route. Repeated dosings may be necessary and will vary, for example, depending on the clinical setting, the particular microbe, the condition of the patient and the use of other treatments.

WO 98/06851 PCT/US97/14221 -57- C. Animal Modelfor Testing Efficacy of Therapies The evaluation of the functional significance of antibodies to surface antigens of M. catarrhalis has been hampered by the lack of a suitable animal model. The relative lack of virulence of this organism for animals rendered identification of an appropriate model system difficult (Doere, 1986). Attempts to use rodents, including chinchillas, to study middle ear infections caused by M catarrhalis were unsuccessful, likely because this organism cannot grow or survive in the middle ear of these hosts (Doyle, 1989).

Murine short-term pulmonary clearance models have now been developed which permit an evaluation of the interaction of bacteria with the lower respiratory tract as well as assessment of pathologic changes in the lungs. This model reproducibly delivers an inoculum of bacteria to a localized peripheral segment of the murine lung. Bacteria multiply within the lung, but are eventually cleared as a result of resident defense mechanisms, (ii) the development of an inflammatory response, and/or (iii) the development of a specific immune response. Using this model, it has been demonstrated that serum IgG antibody can enter the alveolar spaces in the absence of an inflammatory response and enhance pulmonary clearance of non-typable H. influenzae (McGehee et al., 1989), a pathogen with a host range and disease spectrum nearly identical to those of M. catarrhalis.

The above model has been successfully adapted for use as a model of M catarrhalis infection and prophylaxis (Unhanand et al., 1992; Verghese et al., 1990).

Thus, there is a ready model with which one can test the efficacy of a peptide-based vaccine or an antibody, polyclonal or monoclonal, in passive immunoprophylaxis.

Demonstration of efficacy for an anti-bacterial prophylaxis in this model would be accepted by those in the field of medical microbiology as predictive of efficacy in humans due to the similarity in pulmonary clearance mechanisms between mice and humans.

8. Examples The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques WO 98/06851 PCT/US97/14221 -58disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

EXAMPLE I: Nucleotide Sequence Analysis of Four copB Genes from M. catarrhalis To begin to address the issue of antigenic heterogeneity of CopB surface epitopes among M. catarrhalis strains, the inventors isolated and sequenced the copB genes from clinical isolates ofM. catarrhalis that either do or do not react with MAb 10F3. Isolates TTA24 and 046E do not bind to MAb 10F3; whereas, the 012E and 035E isolates do bind MAb 10F3. In addition, TTA24 is a serum-resistant strain and can be used in the mouse model for pulmonary clearance. (Helminen et al., 1994) M. catarrhalis TTA24 chromosomal DNA was partially digested with PstI (Gibco BRL, Gaithersburg, MD) and fragments ranging from 6 to 9 kb were purified from a 0.7% agarose gel using the GeneCleanII TM kit (BIO 101 Inc., La Jolla, CA).

These fragments were ligated overnight at 16 0 C into PstI-digested and alkaline phosphatase-treated plasmid pBR322 (New England Biolabs Inc., Beverly, MA) using T4 DNA ligase (Gibco BRL). The ligation reaction mixture was transformed into competent E. coli RR1 cells.

Using a colony blot method, transformants were transferred to nitrocellulose pads, cross-linked using the UV Stratalinker 1800 TM (Stratagene Inc., La Jolla, CA) and hybridized with a 32P-labeled 1.3 kb PvuII/XbaI copB gene fragment from M catarrhalis 035E. This gene probe was shown to hybridize with a 7.8 kb PstI fragment of M.

catarrhalis TTA24 chromosomal DNA in a Southern blot analysis. Reactive clones were tested for expression of the CopB protein by western blot analysis of whole cell lysates with polyclonal antiserum raised against M. catarrhalis TTA24 outer membrane vesicles.

A recombinant plasmid containing a 7.8 kb insert that encoded the CopB protein was WO 98/06851 PCT/US97/14221 -59designated pTFA100. This plasmid was purified using an alkaline lysis protocol and digested with Hinfl.

A 2.6 kb fragment known to hybridize with the 1.3 kb copB gene probe and expected to contain the complete copB gene open reading frame of M. catarrhalis TTA24 was purified from the agarose gel as described above. Using BglII linkers (New England Biolabs Inc), this fragment was ligated into a BamHI digested and alkaline phosphatase-treated pBluescript II SK+ (Stratagene Inc.) and transformed into competent E. coli HB101 cells. Recombinant strains were screened as described above. A recombinant plasmid containing a 2.6 kb insert and encoding the CopB protein in the host strain was designated pTTA 150.

The 012E and 046E chromosomal DNAs were extracted from whole cell isolates as follows. One to two loopfuls of cells of each respective isolate was resuspended into 1 ml of lysis buffer (150 mM NaCI, 50mM Tris, pH 8.0, 10 mM EDTA, pH Sodium dodecyl sulfate (SDS) and RNase were added to yield final concentrations of 1% SDS and 50 4pg/ml RNase. Resuspended cells were incubated for 1 to 10 minutes at 55-65 0

C

until cell lysis. DNAs were extracted from cell lysates with an equal volume of a mixture of phenol, chloroform and isoamyl alcohol. The upper phase of the extract was separated and DNAs were precipitated with two volumes of 100% ethanol. The isolated DNAs were resuspended in 300-500 pl of Tris EDTA (TE) buffer. SDS and NaCI were added to each resuspension for final concentrations of 0.1 and 50 mM, respectively.

One microliter of a 1 mg/ml solution of proteinase K was also added to each resuspension. The DNAs were then incubated for 1 hour at 50-55 0 C. Each was extracted once with an equal volume of phenol:chloroform mixture and then precipitated and resuspended in TE buffer as before.

An aliquot of isolated 012E or 046E chromosomal DNA was amplified using PCR with the 5' primer 5'-CAAGCCTCATAATCGGAG-3' (SEQ ID NO:9) and the 3' primer 5'-CCTCCAGTGAAATCGAATC-3' (SEQ ID NO:10) in order to obtain DNA fragments containing the copB gene. The PCR reactions were cycled as follows: 1 minute 30 seconds at 94 0 C; 1 minute 30 seconds at 51°C; 1 minute 30 seconds at 72 0

C.

WO 98/06851 PCT/US97/14221 These steps were repeated 29 times. The reactions were held for 10 minutes at 72 0

C

after the final cycle. The PCR reactions were then electrophoresed in a 0.7% agarose gel and the respective 2.5 kb bands were cut out and stored at -20 0 C. The respective DNAs in the frozen gel slices were extracted by spinning in a CoStar Spin-X column, followed by an isopropanol precipitation of the column flow through liquid. The DNAs were resuspended in distilled water and quantitated on a UV spectrophotometer.

The 2.5 kb PCR products of 012E and 046E were sequenced using the ABI PRISM Dye Terminator Cycle Sequencing Ready Reaction Kit With AmpliTaq DNA Polymerase, FS, in a ABI 373A automated sequencer following the manufacturer's protocol. Sequencing primers were designed from the 035E copB DNA sequence or were derived from the individual DNA sequences of 012E or 046E. The chromosomal DNA isolated from TTA24 was sequenced using standard methods by Lark Sequencing Technologies Inc., Houston, TX.

The copB DNA gene sequences cloned from TTA24, 012E and 046E are SEQ ID NO:34, SEQ ID NO:28 and SEQ ID NO:32, respectively. The deduced CopB amino acid sequences from TTA24, 012E and 046E are SEQ ID NO:33, SEQ ID NO:27 and SEQ ID NO:31, respectively.

EXAMPLE II: Identification of a CopB Epitope for 10F3 MAb Using the computerized DNA sequence analysis program MacVectorTM (IBI, New Haven, CT) the inventors aligned the CopB amino acid sequences from 035E, 012E, TTA24, and 046E with each other. Comparative analysis revealed that the CopB proteins from 035E and TTA24 are 98% identical to each other, the CopB proteins from 012E and 035E are 92% identical and the CopB proteins from 046E and 035E are 89% identical. Variability between the protein sequences was localized to relatively small regions. Based on the sequence variability between TTA24 and 035E and the hydrophilicity of the variants, five regions were identified as potentially comprising strain-specific epitopic core sequences of the CopB protein.

WO 98/06851 PCT/US97/14221 -61 Variable region 1 comprised about 26 amino acids corresponding to about positions 275-300 of 035E. Region 2 comprised about 19 amino acids corresponding to about positions 318-336 of 035E. Region 3 comprised about 14 amino acids corresponding to about positions 343-356 of 035E. Region 4 comprised about 19 amino acids corresponding to about positions 392-410 of 035E. Region 5 comprised about 11 amino acids corresponding to about positions 445455 of 035E.

Alignment of the CopB protein sequences of 035E and TTA24 with those from 012E and 046E revealed that not only does variation occur in these five regions but other relatively small regions also show variability. But the variation in the other areas either does not correlate with reactivity, or the lack thereof, of the isolates to MAb 10F3 or the hydrophilicity of the varied amino acids suggests that these areas do not contain strain-specific epitopes to MAb 10F3; however, these regions may contain strain-specific epitopes to other antibodies for the CopB protein.

EXAMPLE III: Reactivity of a CopB Epitopic Peptide with MAb 10F3 To test whether or not any of the five variable regions identified above contain epitopes specific to MAb 10F3, the inventors synthesized oligopeptides from the CopB protein of 035E that encompassed the five regions of variability identified above using standard methods.

Using a direct ELISA system as described below, the inventors tested the ability of the synthesized oligopeptides to bind to MAb 10F3. Of the five, only the oligopeptide corresponding to variable region 1 (SEQ ID NO:1), specifically bound to MAb 10F3.

Comparing the CopB protein sequences of 035E and TTA24 in region 1 revealed a limited number of amino acid differences between the two. Oligopeptides containing the variations between the two proteins were synthesized and utilizing the direct ELISA system as before, the ability of each oligopeptide to bind to MAb 10F3 was tested. Only replacement of the asparagine residue at about position 295 in the CopB protein of 035E and corresponding to about position 21 of the peptide from variable region 1, by an WO 98/06851 PCT/US97/14221 -62aspartate residue was associated with the loss of MAb 10F3 binding activity. Indicating that region 1 contains a strain-specific epitope for MAb 10F3.

Direct ELISAs were conducted as follows. Flat-bottomed microtiter ELISA plates (Coming Glass Ware, Coming, NY) were coated with outer membrane vesicles of M. catarrhalis strain O35E (5 mg) or synthetic peptides (0.3-300 mg) in coating buffer mM sodium carbonate, pH 9.6) with or without 2% glutaraldehyde and incubated overnight at 4 0 C. After washing three times with PBS-Tween (0.05% v/v) containing sodium azide (0.025% w/v) and blocking with PBS-Tween containing 1% of bovine serum albumin (BSA), MAb 10F3 or MAb 17C7 (control) were added and plates were incubated for one hour at 37 0 C. After washing, antibody binding was detected using alkaline-phosphatase-conjugated goat anti-mouse IgG (Organon Teknika Corp., West Chester, PA) with p-nitrophenylphosphate (Sigma Co., St. Louis, MO) in diethanolamine buffer (pH 9.8) as enzyme substrate. Absorbance was measured at 410 nm using a MR700 Microplate reader (Dynatech Laboratories, Chantilly, VA).

EXAMPLE IV: Generation of Antibodies with a CopB Epitope The oligopeptide from variable region 1 (SEQ ID NO:1) which was shown to lack cross-reactivity with MAb 10F3 in the preceding example was covalently coupled to keyhole limpet hemocyanin (KLH) using glutaraldehyde.

BALB/c mice were either immunized intraperitoneally with 50 pg of oligopeptide-KLH conjugate in Freund's complete adjuvant and boosted with the same dose of oligopeptide-KLH conjugate in Freund's incomplete adjuvant on day 28 of the test or they were immunized with a peptide-KLH conjugate containing an unrelated and non-cross-reacting peptide from Borrelia burgdorferi. Blood was drawn from the mice on day 42 post-primary immunization and antisera was isolated from it.

Western blot analysis was performed by standard methods. Antisera raised against the oligopeptide-KLH conjugate contained high titers of IgG antibodies which specifically react with the M. catarrhalis CopB protein compared to controls in a western WO 98/06851 PCT/US97/14221 -63blot system. As can be seen in FIG. 1A and FIG. 1B, the antisera bound to both the CopB protein of strain 035E (FIG. 1B, lane 1) and, less apparently, to the CopB protein of strain 012E (FIG. 1B, lane The antisera did not bind to the CopB proteins from strains TTA24 and 046E (FIG. 1B, lanes 3 and 4, respectively).

EXAMPLE V: Further Identification of a CopB Epitope for 10F3 MAb In this study, MAb 10F3 was shown to be bactericidal against MAb 10F3reactive strains. Further comparison of the deduced amino acid sequences of the CopB proteins from four strains of M. catarrhalis revealed a high degree of identity among these proteins which in turn facilitated mapping of the MAb 10F3-reactive epitope.

These data allowed construction of a fusion protein which bound MAb 10F3 and induced the synthesis of antibodies directed against the surface of M catarrhalis.

Materials and Methods Bacterial strains, plasmids and growth conditions. The bacterial strains and plasmids used in this study are listed in Table IV, below. M catarrhalis strain 035E has been described in detail (Helminen et al., 1993a; 1993b). M. catarrhalis strains were routinely cultured at 37 0 C on Brain-Heart Infusion (BHI) agar plates (Difco Laboratories, Detroit, MI) in an atmosphere of 95% air-5% CO 2 or in BHI broth. The Escherichia coli cloning strains RR1, HB101, DH5a and recombinant strains were grown on Lubria- Bertani (LB) medium (Sambrook et al., 1989) supplemented, when necessary, with an appropriate antimicrobial compound.

WO 98/06851 PCT/US97/14221 -64- TABLE IV Bacterial Strains and Plasmids Used in This Study Strain or plasmid Description Source or Reference Moraxella catarrhalis 035E Wild-type isolate from middle ear fluid (Helminen et al., 1993a) 012E Wild-type isolate from middle ear fluid J. Nelson 046E Wild-type isolate from middle ear fluid J. Nelson TTA24 Wild-type isolate from transtracheal S. Berk; (Helminen aspirate et al., 1994) Escherichia coli HB101 Host for cloning experiments (Sambrook et al., 1989) RR1 Host for cloning experiments (Sambrook et al., 1989) Host for cloning experiments (Sambrook et al., 1989) Plasmids pBR322 Cloning vector; Ampr Tetr (Sambrook et al., 1989) pBluescript II Cloning vector; Ampr Stratagene

SK+

pTTA100 pBR322 with a 7.8 kb PstI fragment of This study M catarrhalis strain TTA24 chromosomal DNA containing the copB gene pTTA150 pBluescript II SK+ with a 2.6 kb Hinfi This study fragment from pTTA100 containing the copB gene pGEX-4T-2 Cloning vector Pharmacia pEP 10F3 pGEX-4T-2 with a 78-bp insert encoding This study amino acids 275-300 of the CopB protein of M catarrhalis strain 035E Outer membrane protein preparations and western blot analysis. Outer membrane vesicles were prepared from BHI broth-grown M catarrhalis strains as described (Murphy and Loeb, 1989). Proteins present in these outer membrane vesicles were resolved by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) and detected by western blot analysis as described (Helminen et al., 1993a).

WO 98/06851 PCTUS97/14221 Monoclonal antibodies (MAbs) and polyclonal antisera. MAb 10F3 is a murine IgG 2 a antibody reactive with a surface-exposed epitope of the CopB outer membrane protein of the M. catarrhalis strains 035E and 012E (Helminen et al., 1 9 93a). This MAb does not bind to the CopB protein expressed by M. catarrhalis strains TTA24 and 046E (Helminen et al., 1993a). This MAb was used in the form of hybridoma culture supernatant fluid for ELISA assays, epitope mapping, western blot analysis and in the indirect antibody-accessibility assay. For use in bactericidal assays, MAb 10F3 was purified using protein A-Sepharose CL-4B (Pharmacia, Piscataway, NJ) as described (Ey et al., 1978). MAb 17C7 is a murine IgG antibody directed against the UspA surface antigen of M catarrhalis (Helminen et al., 1994). MAb 3F12 is a murine IgG antibody directed against the UspA surface antigen of M catarrhalis (Helminen et al., 1994).

MAb 3F12 is a murine IgG antibody specific for the major outer membrane protein (MOMP) of H. ducreyi (Gulig et al., 1982). These latter two MAbs were used as negative controls in the ELISA and, indirect antibody-accessibility assays, respectively.

Polyclonal rabbit antiserum raised against M. catarrhalis strain TTA24 outer membrane vesicles was described previously (Helminen et al., 1993a).

Cloning and nucleotide sequence analysis of the copB gene of M catarrhalis strain-TTA24. Chromosomal DNA obtained from this strain was partially digested with PstI (Gibco BRL, Gaithersburg, MD) and then subjected to agarose gel electrophoresis.

Fragments (6-9 kb) were purified by using the GeneCleanlI kit (BIO 101 Inc., La Jolla, CA); these fragments were ligated overnight at 16 0 C into PstI-digested and alkaline phosphatase-treated pBR322 (New England Biolabs Inc., Beverly, MA) using T4 DNA ligase (Gibco BRL Inc., Gaithersburg, MD). The ligation reaction mixture was used to transform competent E. coli RR1 cells. Colony material from tetracycline-resistant transformants was transferred to nitrocellulose pads and treated with UV light (UV Stratalinker, Stratagene, La Jolla, CA) to bind DNA to the nitrocellulose. These membranes were probed with a 32P-labeled 1.3 kb PvuII-XbaI fragment from the copB gene ofM. catarrhalis strain 035E (Helminen et al., 1993a). Clones that hybridized this copB gene probe were tested for expression of the CopB protein by western blot analysis.

WO 98/06851 PCT/US97/14221 -66- PCRTM-based amplification and nucleotide sequence of the cooB genes of M catarrhalis strains 012E and 046E. Chromosomal DNA from M. catarrhalis strains 012E and 046E was extracted by standard methods and used as template DNA in a PCRTM system together with primers derived from the nucleotide sequence of the copB gene from M. catarrhalis strain 035E (Helminen et al., 1993a). Using a PTC 100 Programmable Thermal Controller (MJ Research, Inc., Cambridge, MA) and the GeneAmp PCR T M kit (Roche Molecular Systems Inc., Branchburg, NJ), a 2.5 kb DNA fragment containing the copB gene was amplified from each strain. Using Spin-X centrifuge tube filters (Coming Costar Corp., Cambridge, MA), these 2.5 kb PCR

TM

products were extracted from 0.7% agarose gel slices and resuspended in water. The nucleotide sequence of these two PCRTM products was determined by the use of an Applied Biosystems Model 373 DNA sequencer (Applied Biosystems, Inc., Foster City, CA) according to the manufacturer's protocol. The sequencing reactions were performed with the Applied Biosystems PRISM Ready Reaction DiDeoxy Terminator Cycle Sequencing Kit with AmpliTaq DNA Polymerase according to the manufacturer's directions (Applied Biosystems, Inc., Foster City, CA). Sequencing primers were designed from the nucleotide sequence of the copB gene from M. catarrhalis strain 035E (Helminen et al., 1993a) or from the individual copB sequences.

Nucleotide sequence accession numbers. The nucleotide sequences of the copB genes from M catarrhalis strains TTA24, 012E and 046E have been submitted to GenBank and assigned the accession numbers U69980 (SEQ ID NO:34), U69981 (SEQ ID NO:28), and U69982 (SEQ ID NO:32), respectively.

Oligopeptide synthesis. Oligopeptides were synthesized on a Symphony Peptide Synthesizer (Rainin Instrument Co., Inc., Woburn, MA). Molecular weight and purity of the peptides were determined by high performance liquid chromatography and mass spectrometry.

ELISA. Flat-bottom microtiter ELISA plates (Coming Glass Ware, Coming, NY) were coated with outer membrane vesicles (5 gg) from M. catarrhalis strain 035E or with synthetic peptides (10 pig) in 50 mM sodium carbonate buffer (pH 9.6) with or WO 98/06851 PCTIUS97/14221 -67without 2% fresh glutaraldehyde and incubated overnight at 4°C. After washing three times with PBS-Tween (PBS containing 0.05% Tween-20 and 0.025% [w/v] sodium azide) and blocking with PBS-Tween containing 1% bovine serum albumin (BSA) for 1 hr, 100pl portions of MAb 10F3 or MAb 17C7 (negative control) or antiserum in dilutions of 1:10 to 1:1000 in blocking buffer were added and the plates were incubated at 37 0 C for 1 hr. After washing, antibody binding to outer membrane vesicles or peptides was detected by using alkaline phosphatase-conjugated goat antimouse IgG (Organon Teknika Corp., West Chester, PA) with p-nitrophenylphosphate (Sigma Co., St. Louis, MO) in 10% diethanolamine buffer (pH 9.8) as enzyme substrate. Absorbance was measured at 410 nm using a MR 700 Microplate reader (Dynatech Laboratories, Chantilly, VA).

Fine mapping of the MAb 10F3-reactive epitope. Overlapping synthetic decapeptides that were N-terminally bound to a membrane composed of derivatized cellulose were obtained from Research Genetics Inc., Huntsville, AL. After five washes with PBS-Tween, the membrane was blocked for 1 hr at room temperature in PBS- Tween containing 10% (wt/vol) non-fat dry milk, and subsequently incubated with MAb 10F3 overnight at 4 0 C. Following three washes with PBS-Tween, the membrane was incubated overnight at 4 0 C with gentle rocking with 106 cpm of radioiodinated (specific activity 2 x 107 cpm/pg protein), affinity-purified goat anti-mouse immunoglobulin. The membrane was then washed as before and exposed to X-ray film (Fuji RX safety film; Fuji Industries, Tokyo, Japan).

Construction of a glutathione-S-transferase (GST) fusion protein expressing, the MAb 10F3-reactive epitope. The pGEX-4T-2 expression vector system (Pharmacia Biotech Inc., Piscataway, NJ) was used to construct a fusion protein containing the MAb 10F3-reactive epitope at the C-terminus of GST. Using the oligonucleotide primers 5'-CGGGATCCCTAGATATAGAAAAAGAT-3' (SEQ ID NO:11) and 5'-CCGCTCGAGCTTGCCTCGATATTTGTTATC-3' (SEQ ID NO:12) derived from the copB gene sequence of M catarrhalis strain 035E and containing a BamHI or a XhoI restriction site at their 5'-end, respectively, a 78 bp-fragment encoding amino acid residues 275-300 of the CopB protein peptide R1, SEQ ID NO:1, in FIG. 2) was WO 98/06851 PCT/US97/14221 -68amplified from M. catarrhalis strain 035E chromosomal DNA by PCR T M digested with BamHI and Xhol, and ligated into BamHI- and Xhol-digested pGEX-4T-2 using T4 DNA ligase. The ligation product was transformed into competent E. coli DH5a and recombinant clones were screened for reactivity with MAb 10F3 using a colony blot assay described elsewhere (Gulig et al., 1982). The plasmid construct present in one of the MAb 10F3-reactive clones was designated pEP10F3. The correct in-frame position and orientation of the 78 bp-insert with respect to the GST open reading frame were confirmed by nucleotide sequence analysis of the relevant region of pEP10F3 using the vector-derived sequencing primers 5'-CAATGTGCCTGGATGCGTTC-3' (SEQ ID NO:13) and 5'-CAGACAAGCTGTGACCGTCTCC-3' (SEQ ID NO:14). Large quantities of this fusion protein, designated GST-26, and of GST alone were produced and purified according to the manufacturer's directions for purification of GST fusion proteins.

Immunization protocol. Groups of five two-month-old female BALB/c mice (Charles River Breeding Laboratories, Wilmington, Mass.) were immunized on day 1 by intraperitoneal injection with 50/pg GST-26 suspended in 0.2 ml of Freund's complete adjuvant (Difco Laboratories, Detroit, MI) that had been diluted 1:1 in PBS. Control animals were immunized with GST only in adjuvant. These animals were given an intraperitoneal injection on day 28 with the same amount of protein in Freund's incomplete adjuvant (Difco Laboratories, Detroit, MI) that had been diluted 1:1 in PBS.

Blood for serum preparation was obtained by standard methods on day 42. All procedures involving animals received approval from the Institutional Animal Care and Use Committee; all animals were housed in accordance with guidelines from the United States Department of Agriculture and the Association for Assessment and Accreditation of Laboratory Animal Care International.

Indirect antibody-accessibility assay. An overnight BHI broth culture of M catarrhalis strain 035E was diluted in PBS buffer containing 10% fetal bovine serum and 0.025% sodium azide to a density of 110 Klett units (ca. 10 9 colony forming units [cfu]/ml) as measured with a Klett-Summerson colorimeter (Klett Manufacturing Co., New York, Identical portions (100 .tl) of this suspension WO 98/06851 PCT/US97/14221 -69were added to 1 ml of MAb 10F3 or MAb 3F12 hybridoma culture supernatant or to 1 ml of the PBS buffer described above containing antiserum at a dilution of 1:500. After incubation at 4°C with gentle agitation for 1 hr, the bacterial cells were washed once and then resuspended in 1 ml of the buffer solution. Radioiodinated goat anti-mouse immunoglobulin was added and the mixture was incubated for 1 hr at 4 0 C with gentle agitation. The cells were then washed four times with 1 ml of the buffer solution, resuspended in 500 ptl of triple detergent (Gulig et al., 1982) and transferred to a 12 x mm glass tube. The radioactivity present in each sample was determined by using a gamma counter.

Bactericidal assay. Complement-sufficient normal adult human serum was prepared by standard methods. Complement inactivation was achieved by heating the serum for 30 min at 56 0 C. An M catarrhalis BHI broth culture was grown to early logarithmic phase and diluted in Veronal-buffered saline containing 0.15% gelatin (Sigma Chemicals Co., St. Louis, MO) to a concentration of 2.5 x 104 cfu/ml (Helminen et al., 1993b). Portions (100 p1) of this cell suspension were added to 100 pl of native or heat-inactivated normal human serum containing either 15 pg of purified MAb 10F3 or heat-inactivated antiserum in final dilutions of 1:20 to 1:2000. This mixture was then incubated at 37 0 C. At time 0 and at 60 and 120 min after the start of the assay, 10 ptl aliquots were removed, suspended in 75 pl of BHI broth and spread onto prewarmed BHI agar plates which were then incubated overnight to determine the number of cfu in each sample.

Results Cloning of the copB gene from M catarrhalis strain TTA24. As a first step in localizing the epitope that bound MAb 10F3, the amino acid sequence of the CopB protein from a M catarrhalis strain unreactive with this MAb strain TTA24) was determined. A 1.3 kb PvuII-XbaI fragment from the M. catarrhalis strain 035E copB gene (Helminen et al., 1993a) was used to screen a genomic library constructed from M. catarrhalis strain TTA24 in the plasmid vector pBR322. Whole cell lysates prepared from recombinant E. coli clones that hybridized this DNA probe were probed in western WO 98/06851 PCT/US97/14221 blot analysis with antiserum raised against outer membrane vesicles from M catarrhalis strain TTA24. One of these recombinant clones which expressed an 80 kDa protein reactive with this antiserum was shown to contain a 7.8 kb PstI DNA insert, as was expected from previous Southern blot-based analysis of the conservation of the copB gene among M. catarrhalis strains (Helminen et al., 1993a). The recombinant plasmid was designated pTTA100 and a 2.6 kb Hinfl fragment from this plasmid that was predicted to contain the entire copB gene was subcloned into pBluescript to obtain the recombinant plasmid pTTA150. Nucleotide sequence analysis of both strands of this 2.6 kb DNA fragment confirmed that it contained the complete copB gene from strain TTA24.

Nucleotide sequence analysis of copB genes from additional M catarrhalis strains. To obtain information about the amino acid sequence of other CopB proteins, the copB genes from a MAb 10F3-reactive strain (012E) and a MAb 10F3-unreactive strain (046E) were amplified from the chromosome of each strain by PCRTM. The oligonucleotide primers (5'-CAAGCCTCATAATCGGAG-3' (SEQ ID NO:9) and CCTCCAGTGAAATCGAATC-3' (SEQ ID NO:10) were derived from the sequence of the copB gene of strain 035E (Helminen et al., 1993a) and were located just outside the open reading frame. Both strands of these two PCRTM products were sequenced in their entirety.

Comparison of the CopB proteins from MAb 10F3-reactive and -unreactive strains. In an attempt to further localize the epitope for MAb 10F3 within the CopB protein, the deduced amino acid sequences of the CopB proteins from these four strains were again aligned and compared as in Example II. These sequences included the leader peptide, the existence of which was confirmed previously by N-terminal amino acid sequence analysis of the mature CopB protein from M catarrhalis strain 035E (Helminen et al., 1993a). The overall identities among these four proteins were striking, with the level of identity between the two most dissimilarproteins those of strains 035E and 046E) being about 89%-91%. Interestingly, the reactivity of these CopB proteins with MAb 10F3 was not indicative of the degree of identity among these proteins. For example, the MAb 10F3-reactive protein from strain 035E was about 98% WO 98/06851 PCT/US97/14221 -71 identical to the MAb 10F3-unreactive CopB protein from strain TTA24 and only about 92%-94% identical to the MAb 10F3-reactive protein from strain 012E.

The fact that the CopB proteins of strains 035E and TTA24 shared the highest degree of identity but differed in their ability to bind MAb 10F3 provided the necessary information to begin localizing the MAb 10F3-reactive epitope. Sequence deviations between these two CopB proteins were confined to five distinct regions (designated located between amino acid residues 280 and 450. Because MAb 10F3 was known to bind to both native and denatured CopB (Helminen el al., 1993a) and thus in all likelihood to a linear epitope, only one of these five regions was expected to be involved in the binding of this MAb.

Mapping of the MAb 10F3-reactive epitope. Oligopeptides spanning the five regions of dissimilarity between the CopB proteins of strains 035E and TTA24 were synthesized; these contained the amino acid sequences from the MAb 10F3-reactive CopB protein of strain 035E. These peptides were designated RI through R5 and had the following amino acid sequences: RI, LDIEKDKKKRTDEQLQAELDNKYAGK (SEQ ID NO:1); R2, DANGKLVADLDRNNPTQRE (SEQ ID R3, NLEWTGKNLGFANE (SEQ ID NO: 16); R4, DSPSNMHVVATGANINFDK (SEQ ID NO:17); and R5, RPGFQNQEKTD (SEQ ID NO: 18).

The ability of these peptides to bind MAb 10F3 was investigated by means of a direct ELISA assay. When sodium carbonate coating buffer was used to affix the five peptides to the microtiter wells, none of them bound MAb 10F3. Variations in the pH and salt concentration of this coating buffer, and variation of the coating temperature did not result in detectable binding of MAb 10F3 to any of these peptides. When 100 pl portions of MAb 10F3 hybridoma culture supernatant were preincubated with various concentrations of the five peptides and then used to probe microtiter wells coated with WO 98/06851 PCT/US97/14221 -72outer membrane vesicles of strain 035E, there was no concentration-dependent reduction of MAb 10F3-binding by any of the five peptides. However, when glutaraldehyde was added to a final concentration of 2% to the five peptides dissolved in coating buffer, wells coated with the 26-residue peptide R1 (SEQ ID NO:1; FIG. 2, table at lower right) readily bound MAb 10F3. In contrast, none of the other four peptides bound this MAb.

The negative control MAb 17C7 did not bind any of these peptides.

Amino acid sequence differences between strains 035E and TTA24 within region 1 corresponded to the residues 6, 12, 13, 14 and 21 of peptide R1 (SEQ ID NO:1; FIG.

Because the amino acids in positions 12, 13 and 14 also varied among the two 16 MAb 10F3-reactive strains 035E and 012E (FIG. these residues were considered less likely to be essential for binding this MAb. The peptides R1A (SEQ ID NO:7) and RIB (SEQ ID NO:3; FIG. 2) were synthesized to determine whether the aspartic acid in position 6 or the asparagine in position 21 were required for binding of MAb 10F3.

As shown in FIG. 2, changing N to D in position 21 (peptide RIB; SEQ ID NO:3) resulted in loss of MAb 10F3 reactivity, while replacing D with N in position 6 (peptide R1A; SEQ ID NO:7) did not affect binding of this MAb. The presence of N in position 21 of peptide RI (SEQ ID NO:1) (corresponding to residue 295 in the CopB protein) thus appeared critical for binding of MAb 10F3. As expected, a peptide (R1-TTA24; SEQ ID NO:4) containing the amino acid sequence from the same region of the CopB protein from M catarrhalis strain TTA24 did not bind this MAb (FIG. 2).

Based on the assumption that sequential B-cell epitopes are typically 5 to 7 amino acids in length (Kabat, 1970; Schechter, 1971), an oligopeptide (R1E; SEQ ID NO:6 in FIG. 2) which contained 5 amino acids of the CopB sequence of strain 035E on either side of the N in position 21 of peptide RI (SEQ ID NO:1) was expected to bind MAb 10F3. However, peptide R1E (SEQ ID NO:6) exhibited no binding of this MAb (FIG.

Therefore, the binding site for MAb 10F3 within R1 (SEQ ID NO:1) was mapped using 8 overlapping decapeptides (FIG. 3; Table V) bound (via the N-terminus) to a solid phase support composed of derivatized cellulose. Probing of these 8 decapeptides with MAb 10F3 revealed that peptide 7 (SEQ ID NO: 25) and peptide 8 (SEQ ID NO:26) readily bound MAb 10F3, with peptide 7 (SEQ ID NO: 25) exhibiting the strongest WO 98/06851 PCT/US97/14221 -73binding. The sequence LDNKYAGKGY (SEQ ID NO:25) (residues 293-302 of the CopB protein of strain 035E) thus allowed maximal binding of MAb 10F3 compared to the other decapeptides.

TABLE V Decapeptide as shown Amino Acid Sequence Sequence Listing in FIG. 3 Designation PEPTIDE 1 LDIEKDKKKR SEQ ID NO:19 PEPTIDE 2 EKDKKKRTDE SEQ ID PEPTIDE 3 KKKRTDEQLQ SEQ ID NO:21 PEPTIDE 4 RTDEQLQAEL SEQ ID NO:22 PEPTIDE 5 EQLQAELDNK SEQ ID NO:23 PEPTIDE 6 QAELDNKYAG SEQ ID NO:24 PEPTIDE 7 LDNKYAGKGY SEQ ID PEPTIDE 8 KYAGKGYKLG SEQ ID NO:26 Using the method of Kyte and Doolittle (1982), further analysis of region 1 within the context of the CopB protein of strain 035E revealed that this region is part of a highly hydrophilic domain (FIG. Use of the Chou-Fasman method (1978) for predicting secondary structure indicated that this region likely displays a primarily oahelical structure, while the binding site for MAb 10F3 is predicted to form a p-tur (FIG.

4).

Immunogenicity of the GST-26 fusion protein. To determine whether the peptide sequence of R1 (SEQ ID NO:1) could induce the synthesis of antibodies to CopB that would bind to the surface of M. catarrhalis, this 26-residue peptide was expressed in a fusion construct (GST-26) at the C-terminus of the 26 kDa GST protein and used to immunize mice. As expected, the molecular weight of purified GST-26 was approximately 30 kDa (FIG. 5A and FIG. 5B, lane 5) and was strongly reactive with WO 98/06851 PCT/US97/14221 -74- MAb 10F3 in western blot analysis (FIG. 5A, lane while GST alone was unreactive with this MAb (FIG. 5A, lane GST-26 was also strongly reactive with MAb 10F3 when used as antigen in the direct ELISA system.

The presence of CopB-specific antibody in mouse antiserum raised against GST- 26 was assessed by ELISA using the synthetic peptides R1 (SEQ ID NO:1), RIA (SEQ ID NO:7), R1E (SEQ ID NO:6), RIB (SEQ ID NO:3) and R1-TTA24 (SEQ ID NO:4) (see FIG. 2) and by western blot analysis using outer membrane vesicles of M. catarrhalis strains 035E, 012E, TTA24 and 046E, as well as GST-26 and GST as antigens. In the ELISA assay, the GST-26 antiserum, but not the GST antiserum, reacted strongly with R1 (SEQ ID NO:1), RIA (SEQ ID NO:7), R1E (SEQ ID NO:6), RIB (SEQ ID NO:3) and R1-TTA24 (SEQ ID NO:4) (see FIG. Interestingly, GST-26 antiserum also reacted with R1-TTA24 (SEQ ID NO:4; FIG. Binding occurred regardless of whether glutaraldehyde was included with the peptides for coating of the microtiter plate wells (described above).

In western blot analysis, both the CopB-specific MAb 10F3 (FIG. 5A, lane 1) and antibodies in the GST-26 antiserum (FIG. 5B, lane 1) bound to an 80 kDa antigen of strain 035E. MAb 10F3 also bound to an 82 kDa antigen from strain 012E (FIG. lane the CopB protein of strain 012E is known to migrate slightly more slowly in SDS-PAGE than the CopB protein of strain 035E. The GST-26 antiserum did not react with any antigens in the 80-82 kDa range from strains 012E, TTA24, and 046E (FIG. lanes 2-4, respectively). As expected, antibodies in the GST-26 antiserum bound to both GST-26 and GST (FIG. 5B, lane 5 and 6, respectively).

Binding of GST-26 antibodies to the cell surface of M catarrhalis. The MAb 10F3-reactive epitope of CopB has been shown to be expressed on the bacterial surface (Helminen et al., 1993a). Because the GST-26 antiserum was shown to contain antibodies specifically binding to the CopB protein from strain 035E and also to region 1 of strain TTA24 (ELISA with R1-TTA24 in FIG. it was of interest to determine whether antibodies derived from this antiserum would bind to the cell surface of M. catarrhalis. The use of the indirect antibody-accessibility assay with whole cells of WO 98/06851 PCT/US97/14221 M. catarrhalis strains 035E, TTA24, 012E and 046E as antigen demonstrated that, as expected, MAb 10F3 readily bound to the surface of strains 035E and 012E, but not to strains TTA24 and 046E (Table VI). Similarly, antibodies in the GST-26 antiserum exhibited specific binding to whole cells of strain 035E, while antibodies present in the control antiserum raised against GST did not (Table VI).

TABLE VI Binding of Antibodies to Surface Determinants of Whole Cells of M catarrhalis Strains Binding of secondary l'I-labeled goat anti-mouse IgG to murine primary antibody attached to whole cells of M. catarrhalis strains a Primary antibody 035E 012E TTA24 046E GST-26 antiserum 62,712 50,099 40,480 14,223 GST antiserumb 6,081 4,293 4,795 16,205 MAb 10F3 c 107,332 63,830 4,231 3,952 MAb 3F12d 3,437 3,817 2,651 3,544 aCounts per minute of lI-labeled goat anti-mouse immunoglobulin bound to murine antibodies attached to the bacterial cell surface, as determined by the indirect antibodyaccessibility assay. These results are the means of two independent studies.

Antiserum raised in mice against GST was included as a negative control.

CMAb 10F3 is included as a positive control.

dMAb 3F12, a murine IgG antibody specific for a H. ducreyi major outer membrane protein, is included as a negative control.

As expected from the ELISA data, antibodies in the GST-26 antiserum also reacted with whole cells of strains 012E and TTA24 (Table VI), although no binding of the same antiserum to outer membrane vesicles of these strains was detected in western blot analysis (FIG. 5B, lanes 2 and 3, respectively). High levels of binding of the GST control antiserum to whole cells of strain 046E (Table VI) precluded determination of whether the GST-26 antiserum would bind specifically to this organism.

Bactericidal activity of MAb 10F3 and of GST-26 antiserum. MAb 10F3 was previously shown to enhance pulmonary clearance of M catarrhalis from the lungs of mice passively immunized with this MAb (Helminen et al., 1993a). However, the functional basis for this MAb-accelerated elimination of bacteria from the lower WO 98/06851 PCT/US97/14221 -76respiratory tract was not determined. Therefore, the ability of MAb 10F3 to kill M. catarrhalis in the presence of human complement was evaluated by performing bactericidal assays with the MAb 10F3-reactive strains 035E and 012E and with the MAb 10F3-unreactive strains TTA24 and 046E. Similarly, the antisera raised against GST-26 and GST (negative control) were tested for their bactericidal activity because GST-26 contained antibodies directed at the surface of strains 035E, 012E and TTA24.

All four M. catarrhalis strains were resistant to killing by complement-sufficient normal human serum in the absence of specific antibody (FIGS. 6A-6D, closed triangles). In the presence of normal human serum, strains 035E (FIG. 6A, open squares) and 012E (FIG. 6B, open squares) were readily killed by MAb 10F3. The MAb 10F3unreactive strains TTA24 and 046E were not killed by MAb 10F3 (FIG. 6C and FIG. 6D, open squares). MAb 10F3 did not kill any of these four strains when heat-inactivated normal human serum was used in place of complement-sufficient normal human serum (FIGS. 6A-6D, closed squares).

The GST-26 antiserum did not exert detectable bactericidal activity against strains 035E, TTA24 and 046E (FIG. 6A, FIG. 6C and FIG. 6D, open circles). However, this same GST-26 antiserum did kill strain 012E (FIG. 6B, open circles). The possibility that a prozone effect had prevented killing of strain 035E by the GST-26 antiserum was addressed by incubating the M catarrhalis strain 035E cells with dilutions of the GST- 26 antiserum ranging from 1:20 to 1:2000, none of which showed bactericidal activity.

Control antiserum raised against GST did not cause complement-mediated killing of any of these M. catarrhalis strains (FIGS. 6A-6D, closed circles).

WO 98/06851 PCTIUS97/14221 -77-

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WO 98/06851 PCT/US97/14221 -84- SEOUENCE LISTING GENERAL INFORMATION:

APPLICANT:

NAME: Board of Regents, The University of Texas System STREET: 201 West 7th Street CITY: Austin STATE: TX COUNTRY: USA POSTAL CODE (ZIP): 78701 TELEPHONE: (512) 418-3000 TELEFAX: (512) 474-7577 (ii) TITLE OF INVENTION: DEFINING EPITOPES OF THE OUTER MEMBRANE PROTEIN COPB OF MORAXELLA CATARRHALIS (iii) NUMBER OF SEQUENCES: (iv) COMPUTER READABLE FORM: MEDIUM TYPE: Floppy disk COMPUTER: IBM PC compatible OPERATING SYSTEM: PC-DOS/MS-DOS SOFTWARE: PatentIn Release Version #1.30 (EPO) CURRENT APPLICATION DATA: APPLICATION NUMBER: Unknown (vi) PRIOR APPLICATION DATA: APPLICATION NUMBER: US 60/023,832 FILING DATE: 12-AUG-1996 INFORMATION FOR SEQ ID NO: 1: SEQUENCE CHARACTERISTICS: LENGTH: 26 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 1: Leu Asp Ile Glu Lys Asp Lys Lys Lys Arg Thr Asp Glu Gln Leu Gln 1 5 10 Ala Glu Leu Asp Asn Lys Tyr Ala Gly Lys INFORMATION FOR SEQ ID NO: 2: SEQUENCE CHARACTERISTICS: LENGTH: 26 amino acids TYPE: amino acid

STRANDEDNESS:

.WO 98/06851 PCT/US97/14221 TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 2: Leu Asp Ile Lys Lys Asp Asp Lys Thr Leu Thr Glu Thr Glu Leu Gin 1 5 10 Ala Glu Leu Asp Asn Lys Tyr Ala Gly Lys INFORMATION FOR SEQ ID NO: 3: SEQUENCE CHARACTERISTICS: LENGTH: 26 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 3: Leu Asp Ile Glu Lys Asp Lys Lys Lys Arg Thr Asp Glu Gln Leu Gin 1 5 10 Ala Glu Leu Asp Asp Lys Tyr Ala Gly Lys INFORMATION FOR SEQ ID NO: 4: SEQUENCE CHARACTERISTICS: LENGTH: 26 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 4: Leu Asp Ile Glu Lys Asn Lys Lys Lys Arg Thr Glu Ala Glu Leu Gin 1 5 10 Ala Glu Leu Asp Asp Lys Tyr Ala Gly Lys INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 26 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear WO 98/06851 PCT/US97/14221 -86- (xi) SEQUENCE DESCRIPTION: SEQ ID NO: Ile Asp Ile Glu Lys Lys Gly Lys Ile Arg Thr Glu Ala Glu Leu Leu 1 5 10 Ala Glu Leu Asn Lys Asp Tyr Pro Gly Gin INFORMATION FOR SEQ ID NO: 6: SEQUENCE CHARACTERISTICS: LENGTH: 15 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 6: Asp Glu Gin Leu Gin Ala Glu Leu Asp Asn Lys Tyr Ala Gly Lys 1 5 10 INFORMATION FOR SEQ ID NO: 7: SEQUENCE CHARACTERISTICS: LENGTH: 26 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 7: Leu Asp Ile Glu Lys Asn Lys Lys Lys Arg Thr Asp Glu Gin Leu Gin 1 5 10 Ala Glu Leu Asp Asn Lys Tyr Ala Gly Lys INFORMATION FOR SEQ ID NO: 8: SEQUENCE CHARACTERISTICS: LENGTH: 18 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 8: CAAGCCTCAT AATCGGAG WO 98/06851 PCT/US97/14221 -87- INFORMATION FOR SEQ ID NO: 9: SEQUENCE CHARACTERISTICS: LENGTH: 19 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 9: CCTCCAGTGA AATCGAATC 19 INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 26 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: CGGGATCCCT AGATATAGAA AAAGAT 26 INFORMATION FOR SEQ ID NO: 11: SEQUENCE CHARACTERISTICS: LENGTH: 30 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 11: CCGCTCGAGC TTGCCTCGAT ATTTGTTATC INFORMATION FOR SEQ ID NO: 12: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 12: CAATGTGCCT GGATGCGTTC INFORMATION FOR SEQ ID NO: 13: SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs WO 98/06851 PCT/US97/14221 -88- TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 13: CAGACAAGCT GTGACCGTCT CC 22 INFORMATION FOR SEQ ID NO: 14: SEQUENCE CHARACTERISTICS: LENGTH: 19 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 14: Asp Ala Asn Gly Lys Leu Val Ala Asp Leu Asp Arg Asn Asn Pro Thr 1 5 10 Gln Arg Glu INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 14 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: Asn Leu Glu Trp Thr Gly Lys Asn Leu Gly Phe Ala Asn Glu 1 5 INFORMATION FOR SEQ ID NO: 16: SEQUENCE CHARACTERISTICS: LENGTH: 19 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 16: Asp Ser Pro Ser Asn Met His Val Val Ala Thr Gly Ala Asn Ile Asn 1 5 10 Phe Asp Lys WO 98/06851 PCT/US97/14221 -89- INFORMATION FOR SEQ ID NO: 17: SEQUENCE CHARACTERISTICS: LENGTH: 11 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 17: Arg Pro Gly Phe Gin Asn Gin Glu Lys Thr Asp 1 5 INFORMATION FOR SEQ ID NO: 18: SEQUENCE CHARACTERISTICS: LENGTH: 10 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 18: Leu Asp Ile Glu Lys Asp Lys Lys Lys Arg 1 5 INFORMATION FOR SEQ ID NO: 19: SEQUENCE CHARACTERISTICS: LENGTH: 10 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 19: Glu Lys Asp Lys Lys Lys Arg Thr Asp Glu 1 5 INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 10 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: Lys Lys Lys Arg Thr Asp Glu G1n Leu Gin 1 5 WO 98/06851 PCT/US97/14221 INFORMATION FOR SEQ ID NO: 21: SEQUENCE CHARACTERISTICS: LENGTH: 10 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 21: Arg Thr Asp Glu Gin Leu Gin Ala Glu Leu 1 5 INFORMATION FOR SEQ ID NO: 22: SEQUENCE CHARACTERISTICS: LENGTH: 10 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 22: Glu Gin Leu Gin Ala Glu Leu Asp Asn Lys 1 5 INFORMATION FOR SEQ ID NO: 23: SEQUENCE CHARACTERISTICS: LENGTH: 10 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 23: Gin Ala Glu Leu Asp Asn Lys Tyr Ala Gly 1 5 INFORMATION FOR SEQ ID NO: 24: SEQUENCE CHARACTERISTICS: LENGTH: 10 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 24: Leu Asp Asn Lys Tyr Ala Gly Lys Gly Tyr 1 5 WO 98/06851 PCT/US97/14221 -91- INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 10 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: Lys Tyr Ala Gly Lys Gly Tyr Lys Leu Gly 1 5 INFORMATION FOR SEQ ID NO: 26: SEQUENCE CHARACTERISTICS: LENGTH: 31 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 26: Leu Asp Ile Glu Lys Asp Lys Lys Lys Arg Thr Asp Glu Gin Leu Gln 1 5 10 Ala Glu Leu Asp Asn Lys Tyr Ala Gly Lys Gly Tyr Lys Leu Gly 25 INFORMATION FOR SEQ ID NO: 27: SEQUENCE CHARACTERISTICS: LENGTH: 758 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 27: Met Asn Lys Phe Gin Leu Leu Pro Leu Thr Leu 1 5 10 Phe Thr Thr Thr Ala Phe Ala Ala Val Ser Gin 25 Ala Gly Asp Thr Val Val Ser Asp Arg Gin Gly 40 Asn Val Val Thr Leu Arg Glu Lys Asp Glu Ser 55 Arg Gly Leu Leu Gin Asp Glu Pro Ala Ile Gly 70 Ala Val Ser Ala Ala Pro Lys Val Val Leu Ala Lys Ile Lys Thr Thr Ala Thr Asp Leu Phe Gly Gly Gly WO 98/06851 WO 9806851PCTIUS97/14221 92 Gly Thr Asp Leu Gin Gly Gin Lys 130 Ala Ile 145 Asp Lys Gly His Gly Gin Tyr Lys 210 Thr Arg 225 Thr Ala Lys Gly Leu Thr Leu Gin 290 Gly Ser 305 Gly Lys Thr Tyr Phe Ala Ser Lys Arg 115 Gly Val Asp Ser Val 195 Gly Ser Gly Ile Leu 275 Al a Lys Leu Gin Asn 355 Gin Ile 100 Phe Ala Thr Tyr Tyr 180 Asp Gly Al a Asp Arg 260 Asp Glu Thr Val Lys 340 Glu Phe Asp Met Gly Lys Gly 165 His Ala Lys Leu His 245 Gly Ile Leu Pro Al a 325 Leu Val Ile Asn Leu Phe Thr 150 Phe Gly Leu Gly Asp 230 Arg Val Lys Asp Asp 310 Asp Thr Thr Ser Ala Asp Al a 135 Leu Lys Ser Val Tyr 215 Lys Phe Arg Lys Asn 295 Gly Leu Asn Ala Ile Arg Tyr Gin 105 Pro Gin 120 Ser Ala Asp Ala Val Gly Ala Phe 185 Ser Tyr 200 Thr Asn Ser Ser Val Val Glu Glu 265 Asp Asp 280 Lys. Tyr Lys Lys Asp Arg Leu Glu 345 Asn Val 360 Gly 90 Asp Met Gly Asp Al a 170 Gly Asn Leu Tyr Ser 250 Phe Lys Ala Tyr Asn 330 Trp Tyr Met Gly Val Ile Glu 155 Gly Lys Gin Leu Leu 235 His Asp Thr Gly Asn 315 Asn Thr Lys Gly Gin Lys Gly 140 Leu Leu Al a Val Gly 220 Vai Leu Phe Leu Lys 300 Val Pro Gly Leu His Leu Val 125 Ala Leu Ser Gin Asn 205 Asn Lys Asn Ala Thr 285 Gly Val Thr Lys Giu 365 Asn His 110 Val Thr Arg Thr Thr 190 Asp Asp Ala Glu Asn 270 Glu Tyr Asp Gin Asn 350 His Ala Tyr Ser Asn Asn Asn 175 Gly Ser Val Gly Val 255 Arg Thr Lys Ala Arg 335 Leu Gly Ile His Val Gly Ser 160 Lys Phe Asp Val Leu 240 His Ala Glu Leu Asn 320 Glu Gly Arg WO 98/06851 PCT/US97/14221 -93- Asn Ser Ser Ser Asp Gin Gly Asn Thr Tyr Ile Thr Lys Asp Val Pro 370 375 380 Lys Glu Ile Ile Asp Asn Val Asp Thr Pro Ser Asn Met His Val Val 385 390 395 400 Ala Thr Gly Ala Asn Ile Asn Phe Asp Lys Glu Phe Asn His Ser Pro 405 410 415 Leu Lys Gly Phe Gly Val Asp His Thr Leu Leu Lys Tyr Gly Ile Asn 420 425 430 Tyr Arg His Gin Lys Ala Val Pro Pro Arg Ser Leu Lys Pro Gly Val 435 440 445 Val His Gin Glu Lys Thr Asp Ala Gly Ile Tyr Leu Glu Ala Val Asn 450 455 460 Gin Ile Asn Asp Phe Thr Ile Asn Thr Gly Val Arg Val Asp Arg Phe 465 470 475 480 Asp Phe Lys Ala Met Asp Gly Lys Lys Val Gly Lys Thr Asp Ile Asn 485 490 495 Pro Ser Phe Gly Val Ile Tyr Asp Val Asn Pro Asn Leu Ser Val Ser 500 505 510 Gly Asn Leu Ile Tyr Ala Thr Arg Ser Pro Arg Phe Ala Asp Ala Ile 515 520 525 Leu Ser Arg Gly Tyr Arg Gly Gly Val Ile Ser Ile Asp Asp Asn Ala 530 535 540 Lys Ala Glu Lys Ala Arg Asn Thr Glu Ile Gly Phe Asn Tyr Asn Asn 545 550 555 560 Gly Pro Tyr Thr Ala Phe Gly Ser Tyr Phe Trp Gin Arg Val Asp Asn 565 570 575 Ala Arg Ala Thr Ala Asp Ile Thr Arg His Gly Thr Thr Asp Ala Asn 580 585 590 Gly Lys Pro Ile Lys Val Pro Thr Leu Gly Asn Gin Gly His Gin Thr 595 600 605 Asn Gin Gly Tyr Glu Leu Gly Val Gly Tyr Thr Glu Gly Ala Trp Arg 610 615 620 Ala Arg Ala Gly Val Ala His Ser Lys Pro Thr Met His Asn Val Lys 625 630 635 640 Phe Ser Gly Asn Pro Glu Tyr Ala Val Arg Thr Gly Arg Thr Trp Thr 645 650 655 Ala Asp Val Ala Tyr Arg Leu Pro Asn Pro Ser Val Glu Leu Gly Val 660 665 670 WO 98/06851 WO 98/685 1PCT/US97/14221 94 Arg His Thr 675 Ser Gly Giu Leu Val Glu Gly Val 680 Asn Asp Ala Lys Asp Thr 685 Asn Ser Ile Ile Val Ser Asp Val. Ser Lys 690 Ile Tyr Ala Asn Trp 705 Phe Lys 710 Val Leu 695 Pro Phe Arg Giu Giy Ala Val Asn Asn 725 Tyr 700 Lys Tyr Giy Asn Asn Lys Asn 730 Pro Gly Ala 745 Asp 715 Tyr Val Asn Val Asn 720 Arg Pro His Thr Gin 735 Arg Val Arg Ala Ser Ile Asp Thr 740 Gly Val Asn Phe Thr Tyr 755 Leu Gly Arg Asp Phe 750 INFORMATION FOR SEQ ID NO: 28: SEQUENCE CHARACTERISTICS: LENGTH: 2451 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 28: AATCGGAGTT ATTATGAATA AGTTTCAATT ATTACCGCTG ACATTGGCGG TGAGTGCCGC

TTTTACAACC

AGTGGTCAGT

AGACGAAAGC

TGGCGGTGGT

TGACCTAAAA

TATGCTAGAC

TGCAGGCATT

TTTAAGAAAC

AGGTCATTCT

TGCCCTTGTC

CAATCTGTTG

CAAGGCAGGG

ACTGCTTTTG

GATCGCCAAG

ACGGCTACAG

AATGGTACTT

ATTGACAACG

CCCCAGATGG

GGGGCAACCA

AGCGACAAAG

TATCATGGCA

TCTTATAATC

GGCAATGATG

CTAACTGCTG

CAGCTGTTAG

GTGCAAAAAT

ATTTGCGTGG

CTCAATTTAT

CTTATCAAGA

TCAAAGTCGT

ATGGTGCGAT

ATTATGGCTT

GTGCCTTTGG

AAGTAAATGA

TGGTTACAAG

GCGATCATCG

CCAGCCTAAG

TAAAACCAAT

TTTGTTAC!AA

CAGCATTCGT

TGGTCAATTA

TTCGGTACA.A

TGTTACCAAA~

TAAAGTTGGT

TAAAGCACAG

CAGCGACTAT

AAGTGCCTTG

ATTTGTGGTC

GTTGTCTTGG

GTTGTTACCT

GATGAACCTG

GGCATGGGTC

CACTACCACC

AAAGGGGCAG

ACCTTAGATG

GCAGGCTTAT

ACAGGATTTG

AAAGGCGGTA

GATAAATCCA

AGCCATCTAA

CAGGCGATAC

TACGAGAAAA

CCATCGGTTT

ATAATGCCAT

AAGGTCGCTT

GCTTTGCCAG

CTGATGAGCT

CAACCAACAA

GTCAGGTAGA

AAGGGTACAC

GTTACCTTGT

ATGAAGTTCA

120 180 240 300 360 420 480 540 600 660 720 780 WO 98106851 WO 9806851PCTIUS97/14221 95

TAAAGGCATT

TATAAAAAA

ATATGCAGGC

GGTTGATGCC

AACCTACCAG

AGTTACTGCC

CACCTATATC

CATGCATGTG

ATTAAAAGGC

AAAAGCTGTA

TGGCATTTAT

TGTTGACCGT

CCCAAGCTTT

CTATGCCACT

TGTGATTAGT

TAACTATAAT

TGCCAGAGCG

TAAAGTACCA

AGGCTATACC

GCACAATGTC

AGCAGATGTC

GGTTGAAGGG

CCGTGAAGGC

GGTGAATGTA

GCGTGCTTCC

CACTTACTAA

GTTCTTTTTA

CGTGGTGTGC

GATGATAAAA

AAGGGTTACA

AATGGTAAAT

AAGTTAACTA

AATGTCTATA

ACCAAAGATG

GTAGCCACAG

TTTGGTGTTG

CCGCCCAGAA

CTAGAAGCGG

TTTGACTTTA

GGGGTGATTT

CGTAGCCCAC

ATTGATGACA

AATGGACCAT

ACCGCTGATA

ACGCTTGGCA

GAAGGTGCGT

AAATTTAGTG

GCCTATCGCC

GTAGATGCCA

TATAATGTCA

AACTTTGCGG

ATAGATACCT

TACTTACCGA

TGGGTATGAG

GTGAAGAGTT

CCCTTACCGA

AACTTGGCAG

TGGTGGCTGA

ACCTTGAATG

AGTTAGAACA

TGCCCAAAGA

GGGCTAATAT

ACCATACTTT

GTCTAAAACC

TTAACCAAAT

AAGCCATGGA

ATGATGTCAAI

GCTTTGCTGA

ATGCAAAAGC

ATACCGCCTT

TAACTCGTCA

ACCAAGGTCA

GGCGTGCGCG

GCAATCCTGA

TGCCAAACCC

AAGACACATC

GTGACATCTA

TGAATAATGT

TACCTGGGGC

TTTATCGGTA

TGGATAAAAA

TGACTTCGCC

AACTGAGCTT

TAAAACACCA

TTTAGATAGG

GACAGGTAAA

TGGACGCAAC

GATAATAGAT

TAATTTTGAT

ATTAAAATAT

TGGTGTGGTG

TAATGACTTT

TGGTAAAAAG

TCCTAATCTT

TGCTATCCTA

AGAAAAAGCA

TGGCAGTTAT

TGGTACAACA

TCAGACCAAC

TGCTGGCGTT

ATATGCCGTG

CAGTGTAGAG

CAT CATAAGT

TGCCAACTGG

CTTTAATAAA

AGGTCGTGAT

TAATACTGAA

CGATAAAAAA

AATCGTGCCT

CAGGCAGAGT

GATGGTAAAA

AACAACCCAA

AACCTTGGTT

TCTTCTAGCG

AATGTTGATA

AAAGAATTTA

GGCATCAACT

CATCAAGAAA

ACCATCAATA

GTTGGAAAAA

AGCGTCAGCG

AGCCGTGGTT

CGCAATACCG

TTTTGGCAGC

GATGCTAATG

CAAGGCTATG

GCTCACAGCA

CGTACAGGTC

CTTGGTGTGA

GGTGAAGTTA

AAGCCTTATG

AACTATCGCC

TTCCGTGTTG

CACTCAAGCA

CCAATCGTAT

TGACGCTAGA

TAGATAACAA

AGTATAATGT

CTCAGCGTGA

TTGCAAATGA

ATCAAGGTAA

CACCATCAAA

ATCACAGCCC

ATCGCCATCA

AAACCGATGC

CAGGCGTGCG

CCGACATCAA

GTAACCTAAT

ATCGTGGTGG

AGATTGGTTT

GTGTGGATAA

GTAAGCCTAT

AGCTGGGTGT

AACCAACCAT

GTACATGGAC

GACACACATT

GCAAACTTAA

GTAATGATAA

CACACACTCA

GCGTGAACTT

CTGCTTGGGT

CATATTGATT

840 900 960 1020 1080 1140 1200 1260 1320 1380 1440 1500 1560 1620 1680 1740 1800 1860 1920 1980 2040 2100 2160 2220 2280 2340 2400 2451 GGCTATAATG ATAAAATTAA ATCATTACTG.ATTTAAAAAC CACGCATTGG C WO 98/06851 PCTIUS97/14221 -96- INFORMATION FOR SEQ ID NO: 29: SEQUENCE CHARACTERISTICS: LENGTH: 759 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 29: Met Asn Lys Phe Gin Leu Leu Pro Leu Thr Leu Ala Val Ser Ala Ala 1 5 10 Phe Thr Thr Thr Ala Phe Ala Ala Val Ser Gin Pro Lys Val Val Leu 25 Ala Gly Asp Thr Val Val Ser Asp Arg Gin Gly Ala Lys Ile Lys Thr 40 Asn Val Val Thr Leu Arg Glu Lys Asp Glu Ser Thr Ala Thr Asp Leu 55 Arg Gly Leu Leu Gin Asp Glu Pro Ala Ile Gly Phe Gly Gly Gly Asn 70 75 Gly Thr Ser Gin Phe Ile Ser Ile Arg Gly Met Gly His Asn Ala Ile 90 Asp Leu Lys Ile Asp Asn Ala Tyr Gin Asp Gly Gin Leu His Tyr His 100 105 110 Gin Gly Arg Phe Met Leu Asp Pro Gin Met Val Lys Val Val Ser Val 115 120 125 Gln Lys Gly Ala Gly Phe Ala Ser Ala Gly Ile Gly Ala Thr Asn Gly 130 135 140 Ala Ile Val Thr Lys Thr Leu Asp Ala Asp Glu Leu Leu Arg Asn Ser 145 150 155 160 Asp Lys Asp Tyr Gly Phe Lys Val Gly Ala Gly Leu Ser Thr Asn Lys 165 170 175 Gly His Ser Tyr His Gly Ser Ala Phe Gly Lys Ala Gin Thr Gly Phe 180 185 190 Gly Gin Val Asp Ala Leu Val Ser Tyr Asn Gin Val Asn Asp Ser Asp 195 200 205 Tyr Lys Gly Gly Lys Gly Tyr Thr Asn Leu Leu Gly Asn Asp Val Val 210 215 220 Thr Arg Ser Ala Leu Asp Lys Ser Ser Tyr Leu Val Lys Ala Gly Leu 225 230 235 240 WO 98/06851 PCT/US97/14221 -97- Thr Ala Gly Asp His Arg Phe Val Val Ser His Leu Asn Glu Val His 245 250 255 Lys Gly Ile Arg Gly Val Arg Glu Glu Phe Asp Phe Ala Asn Arg Ala 260 265 270 Leu Thr Leu Asp Ile Glu Lys Asp Lys Lys Lys Arg Thr Asp Glu Gin 275 280 285 Leu Gin Ala Glu Leu Asp Asn Lys Tyr Ala Gly Lys Gly Tyr Lys Leu 290 295 300 Gly Ser Lys Thr Pro Asp Gly Lys Lys Tyr Asn Val Val Asp Ala Asn 305 310 315 320 Gly Lys Leu Val Ala Asp Leu Asp Arg Asn Asn Pro Thr Gin Arg Glu 325 330 335 Thr Tyr Gin Lys Leu Thr Asn Leu Glu Trp Thr Gly Lys Asn Leu Gly 340 345 350 Phe Ala Asn Glu Val Thr Ala Asn Val Tyr Lys Leu Glu His Gly Arg 355 360 365 Asn Ser Ser Ser Asp Lys Gly Asn Ser Tyr Ile Leu Arg Asp Val Pro 370 375 380 Asn Thr Ile Asn Asp Asn Gly Asp Ser Pro Ser Asn Met His Val Val 385 390 395 400 Ala Thr Gly Ala Asn Ile Asn Phe Asp Lys Glu Phe Asn His Gly Leu 405 410 415 Leu Lys Gly Phe Gly Val Asp His Thr Leu Leu Lys Tyr Gly Ile Asn 420 425 430 Tyr Arg His Gin Glu Ala Val Pro Pro Arg Gly Ile Arg Pro Gly Phe 435 440 445 Gin Asn Gin Glu Lys Thr Asp Ala Gly Ile Tyr Leu Glu Ala Val Asn 450 455 460 Gin Ile Asn Asp Phe Thr Ile Asn Thr Gly Val Arg Val Asp Arg Phe 465 470 475 480 Asp Phe Lys Ala Met Asp Gly Lys Lys Val Gly Lys Thr Asp Ile Asn 485 490 495 Pro Ser Phe Gly Val Ile Tyr Asp Val Asn Pro Asn Leu Ser Val Ser 500 505 510 Gly Asn Leu Ile Tyr Ala Thr Arg Ser Pro Arg Phe Ala Asp Ala Ile 515 520 525 Leu Ser Arg Gly Phe Arg Asp.Gly Val Val Ser Ile Ala Asp Asn Ala 530 535 540 WO 98/06851 PCT/US97/14221 -98- Lys Ala Glu Lys Ala Arg Asn Thr Glu Ile Gly Phe Asn Tyr Asn Asn 545 550 555 560 Gly Pro Tyr Thr Ala Phe Gly Ser Tyr Phe Trp Gin Arg Val Asp Asn 565 570 575 Ala Arg Ala Thr Ala Asp Ala Val Gin His Pro Thr Val Thr Thr Ala 580 585 590 Lys Ile Thr Tyr Leu Gly Asn Gin Gly His Gin Thr Asn His Gly Tyr 595 600 605 Glu Leu Gly Val Gly Tyr Thr Glu Gly Ala Trp Arg Ala Arg Ala Gly 610 615 620 Val Ala His Ser Lys Pro Thr Met His Asn Val Lys Phe Lys Ala Asn 625 630 635 640 Pro Glu Tyr Ala Val Arg Thr Gly Arg Thr Trp Thr Ala Asp Val Ala 645 650 655 Tyr Arg Leu Pro Asn Pro Ser Val Glu Leu Gly Val Arg His Thr Leu 660 665 670 Val Glu Gly Val Asp Ala Lys Asp Thr Ser Ile Leu Ser Gly Lys Phe 675 680 685 Asp Asp Lys Asp Gly Ala Ile Leu Asn Arg Glu Gly Tyr Asn Val Ser 690 695 700 Asp Ile Tyr Ala Asn Trp Lys Pro Tyr Gly Asn Asp Lys Val Asn Val 705 710 715 720 Asn Phe Ala Val Asn Asn Val Phe Asn Lys Asn Tyr Arg Pro His Thr 725 730 735 Gin Arg Ala Ser Ile Asp Thr Leu Pro Gly Ala Gly Arg Asp Phe Arg 740 745 750 Val Gly Val Asn Phe Thr Tyr 755 INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 2407 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: AATCGGAGTT ATTATGAATA AGTTTCAATT ATTACCGCTG ACATTGGCGG TGAGTGCCGC .WO 98/06851 .WO 9806851PCT[US97/14221 99

TTTTACAACC

AGTGGTCAGT

AGACGAAAGC

TGGCGGTGGT

TGACCTAAAA

TATGCTAGAC

TGCAGGCATT

TTTAAGAAAC

AGGTCATTCT

TGCCCTTGTC

CAATCTGTTG

CAAGGCAGGG

TAAAGGCATT

TATAGAAAAA

ATATGCAGGC

GGTTGATGCC

AACCTACCAA

AGTTACTGCC

CAGCTATATT

TATGCATGTG

ATTAAAAGGC

AGAAGCTGTA

TGGCATTTAT

TGTTGACCGT

CCCAAGCTTT

CTATGCCACT

CGTTGTGAGT

TAACTATAAT

ACTGCTTTTG

GATCGCCAAG

ACGGCTACAG

AATGGTACTT

ATTGACAACG

CCCCAGATGG

GGGGCAACCA

AGCGACAAAG

TATCATGGTA

TCTTATAATC

GGCAATGATG

CTAACTGCTG

CGTGGCGTGC

GATAAGAAAA

AAGGGTTACA

AATGGTAAAT

AAGTTAACCA

AATGTCTATA

CTTCGTGATG

GTAGCCACAG

TTTGGCGTTG

CCGCCTAGAG

CTAGAAGCGG

TTTGACTTTA

GGGGTGATTT

CGCAGCCCAC

ATTGCTGATA

AATGGGCCAT

CAGCTGTTAG

GTGCAAAAAT

ATTTGCGTGG

CTCAATTTAT

CTTATCAAGA

TCAAAGTCGT

ATGGTGCGAT

ATTATGGCTT

GTGCCTTTGG

AAGTAAATGA

TGGTTACAAG

GCGATCATCG

GTGAAGAGTT

AACGTACTGA

AACTTGGCAG

TGGTGGCTGA

ACCTTGAATG

AGTTAGAACA

TACCTAATAC

GGGCTAATAT

ACCATACTTT

GTATTAGACC

TTAACCAAAT

AAGCTATGGA

ATGATGTCAA

GCTTTGCTGA

ACGCAAAAGC

ATACCGCCTT

CCAGCCTAAG

TAAAACCAAT

TTTGTTACAA

CAGCATTCGT

TGGTCAATTA

TTCGGTACAA

TGTTACCAAA

TAAAGTTGGT

TAAAGCACAG

CAGCGACTAT

AAGTGCCTTG

ATTTGTGGTC

TGACTTCGCC

CGAACAGCTT

TAA.AACACCA

TTTAGATAGG

GACAGGTAAA

TGGACGCAZAC

CATCAATGAT

TAATTTTGAT

ATTAAAATAT

TGGTTTTCAA

CAATGACTTT

CGGTAAAAAG

TCCTAATCTT

TGCTATCCTA

AGAAAAAGCA

TGGCAGCTAT

GTTGTCTTGG

GTTGTTACCT

GATGAACCTG

GGCATGGGTC

CACTACCACC

AAAGGGGCAG

ACCTTAGATG

GCAGGCTTAT

ACAGGATTTG

AAAGGCGGTA

GATAA.ATCCA

AGCCATCTAA

AATCGTGCCT

CAGGCAGAGT

GATGGTAAAA

AACAACCCAA

AACCTTGGTT

TCCTCTAGCG

AACGGTGATA

AAAGAATTTA

GGCATCAACT

AACCAAGAAA

ACCATCAATA

GTTGGAAAAA

AGCGTCAGCG

AGCCGTGGCT

CGCAATACCG

TTTTGGCAGC

CAGGCGATAC

TACGAGAAAA

CCATCGGTTT

ATAATGCCAT

AAGGTCGCTT

GCTTTGCCAG

CTGATGAGCT

CAACCAACAA

GTCAGGTAGA

AAGGGTACAC

GTTACCTTGT

ATGAAGTTCA

TGACGCTAGA

TAGATAACAA

AGTATAATGT

CTCAGCGTGA

TTGCAAATGA

ATAAAGGTAA

GCCCATCAAA

ATCACGGTCT

ATCGCCATCA

AAACCGATGC

CAGGCGTGCG

CCGACATCAA

GTAACCTAAT

TCCGTGATGG

AGATTGGTTT

GTGTGGATAA

120 180 240 300 360 420 480 540 600 660 720 780 840 900 960 1020 1080 1140 1200 1260 1320 1380 1440 1500 1560 1620 1680 1740 WO 98/06851 WO 9806851PCT[US97/14221 -100-

TGCCAGAGCT

TCTTGGCAAC

AGGTGCGTGG

ATTTAAAGCC

CTATCGCCTG

AGATGCCAAA

TAACCGTGAA

TAAGGTGAAT

TCAGCGTGCT

CTTCACTTAC

GTGTTCTTTT

GATTGGC

ACTGCCGATG

CAAGGTCATC

CGTGCGCGTG

AACCCTGAAT

CCAAACCCCA

GACACTTCTA

GGCTATAATG

GTAAACTTTG

TCCATAGATA

TAATACTTGC

CTGTACAACA

AGACCAACCA

CTGGCGTTGC

ATGCCGTGCG

GTGTAGAGCT

TCCTTAGCGG

TCAGTGACAT

CGGTGAATAA

CCTTACCTGG

CGATTTATCG

CCCCACAGTT ACAACAGCTA AGATTACCTA

CGGTTATGAG

TCACAGCAAG

TACAGGTCGT

TGGTGTGAGA

TAAATTTGAT

CTATGCCAAC

TGTCTTTAAT

GGCAGGTCGT

GTATAATACT

CTGGGCGTAG

CCAACCATGC

ACATGGACAG

CACACATTGG

GATAAAGATG

TGGAAGCCTT

AAAAACTATC

GATTTCCGTG

GAACACTCAA

GCTATACCGA

ACAATGTCAA

CAGATGTCGC

TTGAAGGGGT

GTGCTATTCT

ATGGCAATGA

GCCCACACAC

TTGGCGTGAA

GCACGCTTGG

1800 1860 1920 1980 2040 2100 2160 2220 2280 2340 2400 2407 TATGGGTATG AGTGGATAAA AACGATAAAA AAAGCCAATC GTATCATATT INFORMATION FOR SEQ ID NO: 31: Wi SEQUENCE CHARACTERISTICS: LENGTH: 767 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 31: Met Asn Lys Phe Gin Leu Leu Pro Met Thr Leu Ala Val Ser 1 Phe Ala Ala Thr Thr Thr Ala Phe Ala Ala Val 25 Arg Gin Pro Lys Ala Gly Asp Asn Val Val Thr Val Val Ser Gin Gly Ala Lys Ala Val Val Leu Ile Lys Thr Thr Asp Leu Thr Leu Arg Arg Gly Giu 55 Glu Asp Glu Ser Thr Phe Leu Leu Gin Gly Asp 70 Val Pro Ala Ile Gly 75 Met Gly Giy Gly Asn Ile Thr Ser Gin Phe Ser Ile Arg Gly His Asn Ala Asp Leu Lys Ile Asp Asn Ala Tyr Gin Asp Giy Gin Leu His Tyr His 100 10S 110 WO 98/06851 WO 9806851PCT[US97/14221 101 Gin Gin Al a 145 Asp Gly Gly Tyr Thr 225 Thr Lys Leu Leu Gly 305 Val Thr Lys Glu Lys 385 Met Gly Lys 130 Ile Lys His Gin Lys 210 Arg Ala Gly Thr Leu 290 Lys Asp Gin Asn His 370 Asp His Arg 115 Gly Val Asp Ser Val 195 Gly Ser Gly Ile Ile 275 Ala Lys Al a Arg Leu 355 Gly Val Val Phe Ala Thr Tyr Tyr 180 Asp Gly Ala Asp Arg 260 Asp Glu Ile Asn Glu 340 Gly Arg Pro Val Met Gly Lys Gly 165 His Ala Lys Leu His 245 Gly Ile Leu Asn Gly 325 Thr Phe Asn Lys Ala 405 Leu Phe Thr 150 Phe Gly Leu Gly Asp 230 Arg Val Giu Asn Asp 310 Arg Tyr Ala Ser Glu 390 Thr Asp Al a 135 Leu Lys Ser Val1 Tyr 215 Lys Phe Arg Lys Lys 295 Lys Gin Gin Asn Ser 375 Ile Gly Pro Gin 120 Ser Ala Asp Ala Val Gly Ala Phe 185 Ser Tyr 200 Thr Asn Ser Ser Val Val Giu Giu 265 Lys Gly 280 Asp Tyr Asp Asn Val Pro Lys Leu 345 Giu Val 360 Ser Asp Ile Asp Ala Asn Met Gly Asp Ala 170 Gly Asn Leu Tyr Ser 250 Phe Lys Pro Lys Asn 330 Thr Thr Gin Asn Ile 410 Val Ile Giu 155 Gly Lys Gin Leu Leu 235 His Asp Ile Gly Val 315 Leu Asn Ala Gly Val 395 Asn Lys Gly 140 Leu Leu Ala Val Gly 220 Val Leu Phe Arg Gin 300 Val Asn Leu Asn Asn 380 Asp Phe Val 125 Ala Leu Ser Gin Asn 205 Asn Lys Asn Al a Thr 285 Giy Gly Arg Giu Val 365 Thr Thr Asp Val Thr Arg Thr Thr 190 Asp Asp Al a Glu Asn 270 Glu Tyr Tyr Asn Trp 350 Tyr Tyr Pro Lys Ser Asn Asn Asn 175 Gly Ser Val Gly Val 255 Arg Ala Lys His Asn 335 Thr Lys Ile Ser Glu 415 Val Gly Ser 160 Lys Phe Asp Val Leu 240 His Al a Giu Leu Val 320 Pro Ala Leu Thr Asn 400 Phe WO 98/06851 WO 9806851PCTIUS97/14221 102 Asn His Tyr Gly Lys Pro 450 Glu Ala 465 Vai Asp Thr Asp Leu Ser Val Asp 530 Asp Asp 545 Asn Tyr Arg Val Thr Asp Gly His 610 Gly Ala 625 His Asn Arg Thr Giu Leu Thr Ser 690 Ser Ile 435 Gly Val Arg Ile Val 515 Ala Asn Asn Asp Ala 595 Gin Trp Val Trp Gly 675 Ile Pro Leu 420 Asn Tyr Vai Val Asn Gin Phe Asp 485 Asn Pro 500 Ser Gly Ile Leu Ala Lys Asn Gly 565 Asn Ala 580 Asn Gly Thr Asn Arg Ala Thr Leu 645 Thr Ala 660 Val Arg Leu Ser Lys Arg His Ile 470 Phe Ser Asn Ser Ala 550 Pro Arg Lys Gin Arg 630 Asp Asp His Gly Giy His Gin 455 Asn Lys Phe Leu Arg 535 Giu Tyr Ala Ser Giy 615 Ala Gly Val Thr Lys 695 Phe Gin 440 Giu Asp Ala Gly Ile 520 Gly Lys Thr Thr Ile 600 Tyr Gly Asn Ala Leu 680 Phe Gly 425 Lys Lys Phe Leu Val 505 Tyr Tyr Ala Al a Al a 585 Lys Giu Val Pro Tyr 665 Val Asp Vai Al a Thr Thr Gly 490 Ile Al a Arg Arg Phe 570 Asp Val Leu Ala Giu 650 Arg Glu Asp Asp Val Asp Ile 475 Gly Tyr Thr Gly Asn 555 Gly Ile Pro Gly Tyr 635 Tyr Leu Gly Lys His Pro Ala 460 Asn Lys Asp Arg Gly 540 Thr Ser Thr Ala Val 620 Ser Ala Pro Val Asp 700 Thr Pro 445 Gly Thr Lys Val Ser 525 Val Giu Tyr Arg Leu 605 Gly Lys Val Asn Asp 685 Giy Leu 430 Arg Ile Gly Val Asn 510 Pro Ile Ile Phe His 590 Gly Tyr Pro Arg Pro 670 Ala Al a Leu Ser Tyr Val1 Gly 495 Pro Arg Ser Gly Trp 575 Gly Asn Thr Thr Thr 655 Ser Lys Ile Lys Leu Leu Arg 480 Lys Asn Phe Ile Phe 560 Gin Thr Gin Giu Met 640 Gly Val Asp Leu WO 98/06851 WO 9806851PCTIUS97/14221 103 Asn Arg Glu Gly Tyr Asn Val Ser Asp 705 710 Tyr Gly Asn Asp Lys Val Asn Val Asn 725 Asn Lys Asn Tyr Arg Pro His Thr Gin 740 745 Pro Gly Ala Gly Arg Asp Phe Arg Val 755 760 Ile Tyr Ala 715 Phe Ala Val 730 Arg Ala Ser Gly Val Asn Asn Trp, Lys Pro 720 Asn Asn Val Phe 735 Ile Asp Thr Leu 750 Phe Thr Tyr 765 INFORMATION FOR SEQ ID NO: 32: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 2479 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 32: AATCGGAGTT ATTATGAATA AGTTTCAATT ATTACCGATG ACATTGGCGG TGAGTGCCGC

TTTTACAACC

AGTGGTCAGT

AGACGAAAGC

TGGCGGTGGT

TGACCTAAAA

TATGCTAGAC

TGCAGGCATT

TTTAAGAAAC

AGGTCATTCT

TGCCCTTGTC

CAATCTGTTG

CAAGGCAGGG

TAAAGGCATT

CATAGAAAAA

TTATCCAGGT

CGGTTATCAT

ACTGCTTTTG

GATCGCCAAG

ACGGCTACAG

AATGGTACTT

ATTGACAACG

CCCCAGATGG

GGGGCAACCA

AGCGACAAAG

TATCATGGCA

TCTTATAATC

GGCAATGATG

CTAACTGCTG,

CGTGGTGTGC

AAAGGTAAAA

CAGGGCTATA

GTGGTCGATG

CAGCTGTTAG

GTGCAAAAAT

ATTTGCGTGG

CTCAATTTGT

CTTATCAAGA

TCAAAGTCGT

ATGGTGCGAT

ATTATGGCTT

GTGCCTTTGG

AAGTAAATGA

TGGTTACAAG

GCGATCATCG

GTGAAGAGTT

TCCGTACCGA

AGCTTGGTAA

CCAATGGCAG

CCAGCCTAAG

TAAAACCAAT

TTTGTTACAA

CAGCATTCGT

TGGTCAATTA

TTCGGTACAA

TGTTACCAAA

TAAAGTTGGT

TAAAGCACAG

CAGCGACTAT

AAGTGCCTTG

ATTTGTGGTC

TGACTTCGCC

AGCAGAGCTT

AAAAATAAAT

ACAGGTACCT

GTTGTCTTGG

GTTGTTACCT

GATGAACCTG

GGCATGGGTC

CACTACCACC

AAAGGGGCAG

ACCTTAGATG

GCAGGCTTAT

ACAGGATTTG

AAAGGCGGTA

GATAAATCCA

AGCCATCTAA

AATCGTGCCT

TTGGCAGAAT

GATAAAGATA

AATTTAAATA

CAGGCGATAC

TACGAGAAAA

CCATCGGTTT

ATAATGCCAT

AAGGTCGCTT

GCTTTGCCAG

CTGATGAGCT

CAACCAACAA

GTCAGGTAGA

AAGGGTACAC

GTTACCTTGT

ATGAAGTTCA

TGACAATAGA

TAAATAAAGA

ATAAGGTGGT

GGAACAACCC

120 180 240 300 360 420 480 540 600 660 720 780 840 900 960 1020 WO. 98/06851 WO 98/685 1PCTIUS97/14221 104

AACTCAGCGT

TTTTGCAAAT

CGATCAAGGT

TACACCATCA

TAATCACAGC

CTATCGCCAT

AAAAACCGAT

TACAGGCGTG

AACCGACATC

CGGTAACCTA

TTATCGTGGT

TGAGATAGGT

GCGTGTGGAT

TGGTAAGTCT

TGAGTTGGGC

CAAACCAACC

TCGTACATGG

GAGACACACC

TGATGATAAA

CAACTGGAAG

TAATAAAAAC

TCGTGATTTC

TACTGAACAC

AAAAAAAGCC

TTAAAAACCA

GAAACCTACC

GAAGTTACTG

AACACCTATA

AACATGCATG

CCATTAAAAG

CAAAAAGCTG

GCTGGCATTT

CGTGTTGACC

AACCCAAGCT

ATCTATGCCA

GGTGTGATTA

TTTAACTATA

AACGCCAGAG

ATTAAAGTAC

GTAGGTTATA

ATGCACAATG

ACAGCAGATG

TTGGTTGAAG

GATGGTGCTA

CCTTATGGCA

TATCGCCCAC

CGTGTTGGCG

TCAAGCACGC

AATCGTATCA

CGCATTGGC

AGAAGTTAAC

CCAATGTCTA

TCACCAAAGA

TGGTAGCCAC

GCTTTGGTGT

TACCGCCCAG

ATCTAGAAGC

GTTTTGACTT

TTGGGGTGAT

CTCGCAGTCC

GTATTGATGA

ATAATGGACC

CCACCGCTGA

CAGCGCTTGG

CCGAAGGTGC

TCACATTGGA

TCGCCTATCG

GGGTAGATGC

TTCTTAACCG

ATGATAAGGT

ACACTCAGCG

TGAACTTCAC

TTGGGTGTTC

CAATCTTGAA

TAAGTTAGAA

TGTGCCCAAA

AGGGGC!TAAT

TGACCATACT

AAGTCTAAAA

GGTTAACCAA

TAAAGCCTTG

TTATGATGTC

ACGCTTTGTT

CAATGCAAAA

ATATACCGCC

TATAACTCGT

CAACCAAGGT

GTGGCGTGCG

CGGTAACCCT

CCTGCCAAAC

CAAAGACACT

TGAAGGCTAT

GAATGTAAAC

TGCTTCCATA

TTACTAATAC

TTTTTATGGG

TGGACAGCTA

CATGGACGCA

GAGATAATAG

ATTAATTTTG

TTATTAAAAT

CCTGGTGTGG

ATTAATGACT

GGCGGTAAAA

AATCCTAATC

GATGCCATCC

GCAGAAAAAG

TTTGGCAGTT

CATGGTACAA

CATCAGACCA

CGTGCTGGCG

GAATATGCCG

CCCAGTGTAG

TCTATCCTTA

AATGTCAGTG

TTTGCGGTGA

GATACCTTAC

TTACCGATTT

TATGAGTGGA

AAAACCTTGG

ACTCTTCTAG

ATAATGTTGA

ATAAAGAATT

ATGGCATCAA

TGCATCAAGA

TTACCATCAA

AGGTTGGAAA

TTAGCGTCAG

TAAGCCGTGG

CGCGTAATAC

ATTTTTGGCA

CAGATGCTAA

ACCAAGGCTA

TTGCTTACAG

TGCGTACAGG

AGCTTGGTGT

GCGGTAAATT

ACATCTATGC

ATAATGTCTT

CTGGGGCAGG

ATCGGTATAA

TAAAAACGAT

1080 1140 1200 1260 1320 1380 1440 1500 1560 1620 1680 1740 1800 1860 1920 1980 2040 2100 2160 2220 2280 2340 2400 2460 2479 TATTGATTGG CTATAATGAT AAAATTAAAT CATTACTGAT INFORMATION FOR SEQ ID NO: 33: SEQUENCE CHARACTERISTICS: LENGTH: 759 amino acids WO 98/06851 WO 9806851PCT/US97/14221 105- TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID, NO: 33: Met Asn Lys Phe Gin Leu Leu Pro Leu Thr Leu Ala Val Ser Ala Ala 1 Phe Ala Asn Arg Gly Asp Gin Gin Al a 145 Asp Gly Gly Tyr Thr 225 Thr Thr Gly Val Gly Thr Leu Gly Lys 130 Ile Lys His Gin Lys 210 Arg Ala Thr Asp Val Leu Ser Lys Arg 115 Gly Val Asp Ser Val 195 Gly Ser Gly 5 Thr Ala Thr Val Thr Leu Leu Gin Gin Phe Ile Asp 100 Phe Met Ala Gly Thr Lys Tyr Gly 165 Tyr His 180 Asp Ala Gly Lys Ala Leu Asp His 245 Phe Val Arg Asp 70 Ile Asn Leu Phe Thr 150 Phe Gly Leu Gly Asp 230 Arg Al a Ser Giu.

55 Glu Ser Ala Asp Al a 135 Leu Lys Ser Val Tyr 215 Lys Phe Al a Asp 40 Lys Pro Ile Tyr Pro 120 Ser Asp Val Ala Ser 200 Thr Ser Val Val 25 Arg Asp Ala Arg Gin 105 Gin Ala Ala Gly Phe 185 Tyr Asn Ser Val 10 Ser Gin Glu Ile Gly 90 Asp Met Gly Asp Ala 170 Gly Asn Leu Tyr Ser 250 Gin Gly Ser Gly 75 Met Gly Val Ile Glu 155 Gly Lys Gin Leu Leu 235 His Pro Al a Thr Phe Giy Gln Lys Gly 140 Leu Leu Ala Val Gly 220 Val Leu Lys Lys Ala Gly His Leu Val 125 Ala Leu Ser Gin Asn 205 Asn Lys Asn Val Ile Thr Gly Asn His 110 Val Thr Arg Thr Thr 190 Asp Asp Ala Glu Val Lys Asp Gly Ala Tyr Ser Asn Asn Asn 175 Gly Ser Val Gly Val 255 Leu Thr Leu Asn Ile His Val Gly Ser 160 Lys Phe Asp Val Leu 240 His Lys Gly Ile Arg 260 Gly Val Arg Giu Glu Phe Asp Phe Ala Asn Arg Ala 270 WO 98/06851 PCT/US97/14221 -106- Leu Thr Leu Asp Ile Glu Lys Asn Lys Lys Lys Arg Thr Glu Ala Glu 275 280 285 Leu Gin Ala Glu Leu Asp Asp Lys Tyr Ala Gly Lys Gly Tyr Lys Leu 290 295 300 Gly Ser Lys Thr Pro Asp Gly Lys Lys Tyr Asn Val Val Asp Ala Asn 305 310 315 320 Gly Lys Leu Val Asp Asn Leu Val Gly Asn Asn Pro Thr Gin Arg Glu 325 330 335 Thr Tyr Gin Lys Leu Thr Asn Leu Glu Trp Thr Ala Lys Asn Leu Gly 340 345 350 Phe Ala Asn Glu Val Thr Ala Asn Val Tyr Lys Leu Glu His Gly Arg 355 360 365 Asn Ser Ser Ser Asp Lys Gly Asn Ser Tyr Ile Leu Arg Asp Val Pro 370 375 380 Asn Thr Ile Asn Asp Asn Gly Asp Ser Pro Ser Asn Met His Val Ser 385 390 395 400 Ala Lys Gly Ala Asn Ile Asn Phe Asp Lys Glu Phe Asn His Gly Leu 405 410 415 Leu Lys Gly Phe Gly Val Asp His Thr Leu Leu Lys Tyr Gly Ile Asn 420 425 430 Tyr Arg His Gin Glu Ala Val Pro Pro Arg Gly Ile Arg Pro Gly Phe 435 440 445 Gin His Gin Glu Lys Thr Asp Ala Gly Ile Tyr Leu Glu Ala Val Asn 450 455 460 Gin Ile Asn Asp Phe Thr Ile Asn Thr Gly Val Arg Val Asp Arg Phe 465 470 475 480 Asp Phe Lys Ala Met Asp Gly Lys *Lys Val Gly Lys Thr Asp Ile Asn 485 490 495 Pro Ser Phe Gly Val Ile Tyr Asp Val Asn Pro Asn Leu Ser Val Ser 500 505 510 Gly Asn Leu Ile Tyr Ala Thr Arg Ser Pro Arg Phe Ala Asp Ala Ile 515 520 525 Leu Ser Arg Gly Phe Arg Asp Gly Val Val Ser Ile Ala Asp Asn Ala 530 535 540 Lys Ala Glu Lys Ala Arg Asn Thr Glu Ile Gly Phe Asn Tyr Asn Asn 545 550 555 560 WO 98/06851 PCT/US97/14221 107- Gly Ala Lys Glu Val 625 Pro Tyr Val Asp Asp 705 Asn Gin Val Pro Arg Ile Leu 610 Ala Glu Arg Glu Asp 690 Ile Phe Arg Gly Tyr Ala Thr 595 Gly His Tyr Leu Gly 675 Lys Tyr Ala Ala Val 755 Thr Thr 580 Tyr Val Ser Ala Pro 660 Val Asp Ala Val Ser 740 Asn Ala 565 Ala Leu Gly Lys Val 645 Asn Asp Gly Asn Asn 725 Ile Phe Phe Asp Gly Tyr Pro 630 Arg Pro Ala Ala Trp 710 Asn Asp Thr Gly Ala Asn Thr 615 Thr Thr Ser Lys Ile 695 Lys Val Thr Tyr Ser Val Gin 600 Glu Met Gly Val Asp 680 Leu Pro Phe Leu Tyr Gin 585 Gly Gly His Arg Glu 665 Thr Asn Tyr Asn Pro 745 Phe 570 His His Ala Asn Thr 650 Leu Ser Arg Gly Lys 730 Gly Trp Pro Gin Trp Val 635 Trp Gly Ile Glu Asn 715 Asn Ala Arg Val Asn 605 Ala Phe Ala Arg Ser 685 Tyr Lys Arg Arg Asp 575 Thr Gly Ala Ala Val 655 Thr Lys Val Asn His 735 Phe Asn Ala Tyr Gly Asn 640 Ala Leu Phe Ser Val 720 Thr Arg INFORMATION FOR SEQ ID NO: 34: SEQUENCE CHARACTERISTICS: LENGTH: 2455 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 34: AATCGGAGTT ATTATGAATA AGTTTCAATT ATTACCGCTG ACATTGGCGG TGAGTGCCGC TTTTACAACC ACTGCTTTTG CAGCTGTTAG CCAGCCTAAG GTTGTCTTGG CAGGCGATAC AGTGGTCAGT GATCGCCAAG GTGCAAAAAT TAAAACCAAT GTTGTTACCT TACGAGAAAA WO 98/06851 WO 98/685 1PCTIUS97/14221 108

AGACGAAAGC

TGGCGGTGGT

TGACCTAAAA

TATGCTAGAC

TGCAGGCATT

TTTAAGAAAC

AGGTCATTCT

TGCCCTTGTC

CAATCTGTTG

CAAGGCAGGG

TAAAGGCATT

TATAGAGAAA

ATATGCAGGC

GGTTGATGCC

AACCTACCAG

AGTTACTGCC

CAGCTATATT

TATGCATGTT

ATTAAAAGGC

AGAAGCTGTA

TGGCATTTAT

TGTTGACCGT

CCCAAGCTTT

CTATGCCACT

CGTTGTGAGT

TAACTATAAT

TGCCAGAGCT

TCTTGGCAAC

ACGGCTACAG

AATGGTACTT

ATTGACAACG

CCCCAGATGG

GGGGCAACCA

AGCGACAAAG

TATCATGGCA

TCTTATAATC

GGCAATGATG

CTAACTGCTG

CGTGGCGTGC

AATAAGAAAA

AAGGGTTACA

AATGGTAAGT

AAGTTAACCA

AATGTCTATA

CTTCGTGATG

AGTGCCAAAG

TTTGGCGTTG

CCGCCTAGAG

CTAGAAGCGG

TTTGACTTTA

GGGGTGATTT

CGCAGCCCAC

ATTGCTGATA

AATGGGCCAT

ACTGCCGATG

CAAGGTCATC

ATTTGCGTGG

CTCAATTTAT

CTTATCAAGA

TCAAAGTCGT

ATGGTGCGAT

ATTATGGCTT

GTGCCTTTGG

AAGTAAATGA

TGGTTACAAG

GCGATCATCG

GTGAAGAGTT

AACGTACCGA

AACTTGGCAG

TGGTGGATAA

ACCTTGAATG

AGTTAGAACA

TACCTAATAC

GGGCTAATAT

ACCATACTTT

GTATTAGACC

TTAA~CCAAAT

AAGCCATGGA

ATGATGTCAA

GCTTTGCTGA

ACGCAAAAGC

ATACCGCCTT

CTGTACAACA

AGACCAACCA

TTTGTTACAA GATGAACCTG CCATCGGTTT

CAGCATTCGT

TGGTCAATTA

TTCGGTACAA

TGTTACCAAA

TAAAGTTGGT

TAAAGCACAG

CAGCGACTAT

AAGTGCCTTG

ATTTGTGGTC

TGACTTCGCC

AGCAGAGCTT

TAAAACACCA

TTTAGTTGGG

GACAGCTAAA

TGGACGCAAC

CATCAATGAT

TAATTTTGAT

ATTAAAATAT

TGGTTTTCAA

CAATGACTTT

CGGTAAAAAG

TCCTAATCTT

TGCTATCCTA

AGAAAAAGCA

TGGCAGCTAT

CCCCACAGTT

CGGTTATGAG

GGCATGGGTC

CACTACCACC

AAAGGGGCAG

ACCTTAGATG

GCAGGCTTAT

ACAGGATTTG

AAAGGCGGTA

GATAAATCCA

AGCCATCTAA

AATCGTGCCT

CAGGCAGAGT

GATGGTAAAA

AACAACCCAA

AACCTTGGTT

TCCTCTAGCG

AACGGTGATA

AAAGAATTTA

GGCATCAACT

CACCAAGAAA

ACCATCAATA

GTTGGAAAAA

AGCGTCAGCG

AGCCGTGGCT

CGCAATACCG

TTTTGGCAGC

ACAACAGCTA

CTGGGCGTAG

ATAATGCCAT

AAGGTCGCTT

GCTTTGCCAG

CTGATGAGCT

CAACCAACAA

GCCAGGTAGA

AAGGGTACAC

GTTACCTTGT

ATGAAGTTCA

TGACGCTAGA

TAGATGACAA

AGTATAATGT

CTCAGCGTGA

TTGCGAATGA

ATAAAGGTAA

GCCCATCAAA

ATCACGGTCT

ATCGCCATCA

AAACCGATGC

CAGGCGTGCG

CCGACATCAA

GTAACCTAAT

TCCGTGATGG

AGATTGGTTT

GTGTGGATAA

AGATTACCTA

GCTATACCGA

240 300 360 420 480 540 600 660 720 780 840 900 960 1020 1080 1140 1200 1260 1320 1380 1440 1500 1560 1620 1680 1740 1800 1860 WO 98/06851 WO 9806851PCTIUS97/14221 109

AGGTGCGTGG

ATTTAAAGCC

CTATCGCCTG

AGATGCCAAA

TAACCGTGAA

TAAGGTGAAT

TCAGCGTGCT

CTTCACTTAC

GTGTTCTTTT

GATTGGCTAT

CGTGCGCGTG

AACCCTGAAT

CCAAACCCCA

GACACTTCTA

GGCTATAATG

GTAAACTTTG

TCCATAGATA

TAATACTTGC

TATGGGTATG

AATGATAAAA

CTGGCGTTGC

ATGCCGTGCG

GTGTAGAGCT

TCCTTAGCGG

TCAGTGACAT

CGGTGAATAA

CCTTACCTGG

CGATTTATCG

AGTGGATAAA

TTAAATCATT

TCACAGCAAG

TACAGGTCGT

TGGTGTGAGA

TAAATTTGAT

CTATGCCAAC

TGTCTTTAAT

GGCAGGTCGT

GTATAATACT

AACGATAAAA

ACTGATTTAA

CCAACCATGC

ACATGGACAG

CACACATTGG

GATAAAGATG

TGGAAGCCTT

AAAAACTATC

GATTTCCGTG

GAACACTCAA

AAAGCCAATC

AAACCACGCA

ACAATGTCAA

CAGATGTCGC

TTGAAGGGGT

GTGCTATTCT

ATGGCAATGA

GCCCACACAC

TTGGCGTGAA

GCACGCTTGG

GTATCATATT

TTGGC

1920 1980 2040 2100 2160 2220 2280 2340 2400 2455 INFORMATION FOR SEQ ID NO: Wi SEQUENCE CHARACTERISTICS: LENGTH: 5 amino acids TYPE: amino acid

STRAN'DEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: Lys Tyr Ala Gly Lys 1 INFORMATION FOR SEQ ID NO: 36: Wi SEQUENCE CHARACTERISTICS: LENGTH: 6 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 36: Lys Tyr Ala Gly Lys Gly 1 INFORMATION FOR SEQ ID NO: 37: SEQUENCE CHARACTERISTICS: LENGTH: 7 amino acids TYPE: amino acid

STRAN~DEDNESS:

TOPOLOGY: linear WO 98/06851 PCT/US97/14221 -110- (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 37: Lys Tyr Ala Gly Lys Gly Tyr 1 INFORMATION FOR SEQ ID NO: 38: SEQUENCE CHARACTERISTICS: LENGTH: 6 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 38: Asn Lys Tyr Ala Gly Lys 1 INFORMATION FOR SEQ ID NO: 39: SEQUENCE CHARACTERISTICS: LENGTH: 7 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 39: Asn Lys Tyr Ala Gly Lys Gly 1 INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 8 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: Asn Lys Tyr Ala Gly Lys Gly Tyr 1 INFORMATION FOR SEQ ID NO: 41: SEQUENCE CHARACTERISTICS: LENGTH: 28 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear WO 98/06851 PCT/US97/14221 -111- (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 41: Leu Asp Ile Glu Lys Asp Lys Lys Lys Arg Thr Asp Glu Gin Leu Gin 1 5 10 Ala Glu Leu Asp Asn Lys Tyr Ala Gly Lys Gly Tyr INFORMATION FOR SEQ ID NO: 42: SEQUENCE CHARACTERISTICS: LENGTH: 28 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 42: Leu Asp Ile Lys Lys Asp Asp Lys Thr Leu Thr Glu Thr Glu Leu Gin 1 5 10 Ala Glu Leu Asp Asn Lys Tyr Ala Gly Lys Gly Tyr INFORMATION FOR SEQ ID NO: 43: SEQUENCE CHARACTERISTICS: LENGTH: 28 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 43: Leu Asp Ile Glu Lys Asp Lys Lys Lys Arg Thr Asp Glu Gin Leu Gin 1 5 10 Ala Glu Leu Asp Asp Lys Tyr Ala Gly Lys Gly Tyr INFORMATION FOR SEQ ID NO: 44: SEQUENCE CHARACTERISTICS: LENGTH: 28 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 44: Leu Asp Ile Glu Lys Asn Lys Lys Lys Arg Thr Glu Ala Glu Leu Gin 1 5 10 WO 98/06851 PCT/US97/14221 112- Ala Glu Leu Asp Asp Lys Tyr Ala Gly Lys Gly Tyr INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 28 amino acids TYPE: amino acid

STRANDEDNESS:

TOPOLOGY: linear (xi) SEQUENCE DESCRIPTION: SEQ ID NO: Ile Asp Ile Glu Lys Lys Gly Lys Ile Arg Thr Glu Ala Glu Leu Leu 1 5 10 Ala Glu Leu Asn Lys Asp Tyr Pro Gly Gin Gly Tyr

Claims (53)

1. An isolated peptide of about 5 to about 60 amino acid residues comprising at least the consecutive residues KYAGK (SEQ ID NO:35), wherein the isolated peptide is reactive with the antibody 10F3.

2. The isolated peptide of claim 1, wherein the consecutive residues comprise at least KYAGKG (SEQ ID NO:36).

3. The isolated peptide of claim 2, wherein the consecutive residues comprise at least KYAGKGY (SEQ ID NO:37).

4. The isolated peptide of claim 1, wherein the consecutive residues comprise at least NKYAGK (SEQ ID NO:38). The isolated peptide of claim 4, wherein the consecutive residues comprise at least NKYAGKG (SEQ ID NO:39).

6. The isolated peptide of claim 5, wherein the consecutive residues comprise at least NKYAGKGY (SEQ ID

7. The isolated peptide of claim 1, wherein said peptide comprises at least about consecutive residues of the amino acid sequence LDIEKDKKKRTDEQLQAELDNKYAGKGY (SEQ ID NO:41) or LDIKKDDKTLTETELQAELDNKYAGKGY (SEQ ID NO:42).

8. The isolated peptide of claim 7, wherein said peptide comprises at least about consecutive residues of the amino acid sequence LDIEKDKKKRTDEQLQAELDNKYAGKGY (SEQ ID NO:41).

9. The isolated peptide of claim 7, wherein said peptide comprises at least about consecutive residues of the amino acid sequence LDIKKDDKTLTETELQAELDNKYAGKGY (SEQ ID NO:42). WO 98/06851 PCT/US97/14221 -114- The isolated peptide of claim 1, wherein said peptide is about 5 amino acids in length.

11. The isolated peptide of claim 1, wherein said peptide is about 7 amino acids in length.

12. The isolated peptide of claim 1, wherein said peptide is about 10 amino acids in length.

13. The isolated peptide of claim 1, wherein said peptide is about 15 amino acids in length.

14. The isolated peptide of claim 1, wherein said peptide is about 20 amino acids in length. The isolated peptide of claim 1, wherein said peptide is about 30 amino acids in length.

16. The isolated peptide of claim 1, wherein said peptide is about 40 amino acids in length.

17. The isolated peptide of claim 1, wherein said peptide is about 50 amino acids in length.

18. The isolated peptide of claim 1, wherein said peptide is about 60 amino acids in length.

19. An isolated peptide of about 20 to about 60 amino acids comprising at least about consecutive residues of the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID WO 98/06851 PCT/US97/14221 -115- The isolated peptide of claim 19, wherein said peptide comprises at least about consecutive residues of the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43).

21. The isolated peptide of claim 19, wherein said peptide comprises at least about consecutive residues of the amino acid sequence LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44).

22. The isolated peptide of claim 19, wherein said peptide comprises at least about consecutive residues of the amino acid sequence IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID

23. The isolated peptide of claim 19, wherein said peptide is about 20 amino acids in length.

24. The isolated peptide of claim 19, wherein said peptide is about 30 amino acids in length. The isolated peptide of claim 19, wherein said peptide is about 40 amino acids in length.

26. The isolated peptide of claim 19, wherein said peptide is about 50 amino acids in length.

27. The isolated peptide of claim 19, wherein said peptide is about 60 amino acids in length.

28. An antigenic composition comprising an isolated peptide of about 5 to about amino acids comprising the amino acid sequence KYAGK (SEQ ID and a pharmaceutically acceptable buffer or diluent. 116

29. The antigenic composition of claim 28, wherein said antigenic composition further comprises a carrier conjugated to said peptide.

30. The antigenic composition of claim 29, wherein said carrier is KLH.

31. The antigenic composition according to any one of claims 28 to 30, further comprising an adjuvant.

32. The antigenic composition of claim 31, wherein said adjuvant comprises a lipid.

33. The antigenic composition of claim 28, wherein said peptide is covalently linked to a second antigen.

34. The antigenic composition of claim 33, wherein said second antigen is a peptide antigen.

35. The antigenic composition of claim 34, wherein said second antigen is a non-peptide antigen.

36. An antigenic composition comprising: an isolated peptide of about 20 to about 25 amino acids comprising the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID NO:45); and a pharmaceutically acceptable buffer or diluent.

37. The antigenic composition of claim 36, further comprising a carrier conjugated to said peptide. 35 38. The antigenic composition of claim 37, wherein said carrier is KLH.

39. The antigenic composition according to any one of claims 36 to 38, further comprising an adjuvant. H:\janel\Keep\Speci\41500-97.doc 31/01/01 WO 98/06851 PCT/US97/14221 -117- The antigenic composition of claim 39, wherein said adjuvant comprises a lipid.

41. The antigenic composition of claim 36, wherein said peptide is covalently linked to a second antigen.

42. The antigenic composition of claim 41, wherein said second antigen is a peptide antigen.

43. The antigenic composition of claim 41, wherein said second antigen is a non- peptide antigen.

44. A vaccine composition comprising an isolated peptide of about 20 to about amino acids comprising the amino acid sequence KYAGK (SEQ ID NO:35) and a pharmaceutically acceptable buffer or diluent. A vaccine composition comprising an isolated peptide of about 20 to about amino acids comprising the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID NO:45) and a pharmaceutically acceptable buffer or diluent.

46. A vaccine composition of claim 45, wherein said vaccine composition comprises at least about 20 consecutive residues of the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43).

47. A vaccine composition of claim 45, wherein said vaccine composition comprises at least about 20 consecutive residues of the amino acid sequence LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44). WO 98/06851 PCT/US97/14221 -118-

48. A vaccine composition of claim 45, wherein said vaccine composition comprises at least about 20 consecutive residues of the amino acid sequence IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID

49. A method for inducing an immune response in a mammal comprising the step of providing to said mammal an antigenic composition comprising an isolated peptide of about 5 to about 60 amino acids comprising the amino acid sequence KYAGK (SEQ ID NO:35) and a pharmaceutically acceptable buffer or diluent. A method for inducing an immune response in a mammal comprising the step of providing to said mammal an antigenic composition comprising an isolated peptide of about 20 to about 60 amino acids comprising the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID NO:45) and a pharmaceutically acceptable buffer or diluent.

51. The isolated peptide of claim 50, wherein said peptide comprises at least about consecutive residues of the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43).

52. The isolated peptide of claim 50, wherein said peptide comprises at least about consecutive residues of the amino acid sequence LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44).

53. The isolated peptide of claim 50, wherein said peptide, comprises at least about consecutive residues of the amino acid sequence IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID WO 98/06851 PCT/US97/14221 -119-

54. An isolated and purified M. catarrhalis CopB antigen comprising the amino acid sequence sequence KYAGK (SEQ ID An isolated and purified M. catarrhalis CopB antigen comprising the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID

56. The CopB antigen of claim 55, wherein said antigen comprises at least about consecutive residues of the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43).

57. The CopB antigen of claim 55, wherein said antigen comprises at least about consecutive residues of the amino acid sequence LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44).

58. The CopB antigen of claim 55, wherein said antigen comprises at least about consecutive residues of the amino acid sequence IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID

59. A nucleic acid encoding the CopB antigen of the M catarrhalis isolate TTA24. A nucleic acid having the copB DNA sequence, SEQ ID NO:34, of the M catarrhalis isolate TTA24.

61. A nucleic acid encoding the CopB antigen of the M catarrhalis isolate 012E.

62. A nucleic acid having the copB DNA sequence, SEQ ID NO:28, of the M catarrhalis isolate 012E.

63. A nucleic acid encoding the Cop B antigen of the M catarrhalis isolate 046E.

120- 64. A nucleic acid having the copB DNA sequence, SEQ ID NO:32, of the M. catarrhalis isolate 046E. A method for generating a strain-specific antibody to M catarrhalis CopB antigen comprising the step of providing to a mammal an antigenic composition comprising an isolated peptide comprising an amino acid sequence corresponding to residues of variable regions of said CopB antigen and a pharmaceutically acceptable buffer or diluent. 66. A method for diagnosing M. catarrhalis infection comprising the step of determining the presence, in a sample, of an M. catarrhalis, amino acid sequence corresponding to residues of variable regions of said CopB antigen. 67. The method of claim 66, wherein said determining comprises PCR. 68. The method of claim 66, wherein said determining comprises immunologic reactivity of an antibody with an M catarrhalis antigen. 69. A methpd for generating a strain-common antibody to M. catarrhalis CopB 20 antigen comprising the step of providing to a mammal an antigenic composition comprising an isolated peptide comprising an amino acid sequence of from 6 to 60 amino acid residues corresponding to residues of common regions of said CopB antigen and a pharmaceutically acceptable buffer of diluent. 25 70. A method for diagnosing M. catarrhalis infection comprising the step of i determining the presence, in a sample, of an M catarrhalis amino acid sequence corresponding to residues of common regions of said CopB antigen. 71. The method of claim 70, wherein said determining comprises PCR. 2 7 AUG 2001 WO 98/06851 PCT/US97/14221 -121 72. The method of claim 70, wherein said determining comprises immunologic reactivity of an antibody with an M catarrhalis antigen. 73. A method for treating an individual having an M catarrhalis infection comprising providing to said individual an isolated peptide of about 20 to about amino acids comprising at least the consecutive residues KYAGK (SEQ ID 74. A method for preventing or limiting an M catarrhalis infection comprising providing to a subject an isolated peptide of about 20 to about 60 amino acids comprising at least about 20 consecutive residues of the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID The peptide of claim 74, wherein the said peptide comprises at least about consecutive residues of the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43). 76. The peptide of claim 74, wherein the said peptide comprises at least about consecutive residues of the amino acid sequence LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44). 77. The peptide of claim 74, wherein the said peptide comprises at least about consecutive residues of the amino acid sequence IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID 78. A method for preventing or limiting an M. catarrhalis infection comprising providing to a subject an antibody that reacts immunologically with an epitope formed by the amino acid sequence KYAGK (SEQ ID 122 79. A method for preventing or limiting an M. catarrhalis infection comprising providing to a subject an antibody that reacts immunologically with an epitope formed by the amino acid sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43), LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44) or IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID The epitope of claim 79, wherein said epitope comprises at least about 20 consecutive residues of the amino acid sequence sequence LDIEKDKKKRTDEQLQAELDDKYAGKGY (SEQ ID NO:43). 81. The epitope of claim 79, wherein said epitope comprises at least about 20 consecutive residues of the amino acid sequence sequence LDIEKNKKKRTEAELQAELDDKYAGKGY (SEQ ID NO:44). 82. The epitope of claim 79, wherein said epitope 20 comprises at least about 20 consecutive residues of the amino acid sequence sequence IDIEKKGKIRTEAELLAELNKDYPGQGY (SEQ ID S83. A method for screening a peptide for reactivity 25 with a CopB antibody comprising the steps of: providing said peptide comprising an amino acid sequence of from 6 to 60 amino acid residues corresponding to the residues of variable and/or common regions of CopB antigen, or conservative substitutions, 30 additions or deletions thereof; contacting said peptide with an antibody that binds immunologically to CopB; and S. i determining the binding of said antibody to said peptide. 84. The method of claim 83, wherein said antibody is 10F3. The method of claim 83, wherein said determining comprises an immunoassay selected from the group consisting of a Western blot, an ELISA, an RIA and immunoaffinity H:\evonnee\Keep\Speci\41500.97.doc 27/08/01 123 separation. 86. A method for screening a peptide for the ability to induce a protective immune response against M. catarrhalis comprising the steps of: providing said peptide comprising an amino acid sequence of from 6 to 60 amino acid residues corresponding to residues of variable and/or common regions of CopB antigen, or conservative substitutions, additions or deletions thereof; administering a peptide in a suitable form to an experimental animal; challenging said animal with M. catarrhalis; and assaying the infection of said animal with M. catarrhalis. 87. The method of claim 86, wherein said animal is a mouse, said challenging is a pulmonary challenge, and said 20 assaying comprises assessing the degree of pulmonary clearance by said mouse. 88. The method of claim 86, wherein said peptide is a CopB peptide. 89. The method of claim 88, wherein said CopB peptide encompasses residues 296-300 of M. catarrhalis strain 035E. The method of claim 89, wherein said CopB peptide is a peptide having at least 6 consecutive amino acids from M. catarrhalis strain 035E, including residue 295. 91. An isolated peptide having at least about 5 to about 60 consecutive amino acids from the CopB protein of M. catarrhalis, wherein said peptide includes residue 296- 300, or the analogous positions thereof when compared to strain 035E. 92. The isolated peptide of claim 91, wherein said CopB peptide is a peptide having at least 6 consecutive amino acids and includes residue 295, or the analogous H: \evonnee\Keep\Speci\41500.97.doc 27/08/01 124 position thereof when compared to strain 035E. 93. The isolated peptide of claim 91, wherein said peptide is between 6 and 60 amino acids in length. 94. The isolated peptide of claim 93, wherein said peptide comprises non-CopB sequences. The isolated peptide of claim 94, wherein said peptide comprises non-M. catarrhalis sequences. 96. An antigen composition comprising an isolated peptide having at least about 6 to about 60 consecutive amino acids from the CopB protein of M. catarrhalis, wherein said peptide includes residue 295, or the analogous position thereof when compared to strain 035E, and (ii) a pharmaceutically acceptable buffer or diluent. 2 97. Use of a composition according to any one of claims 28 to 35, in the preparation of a medicament for the treatment of an M. catarrhalis infection. 25 98. Use of a composition according to any one of claims 36 to 43, in the preparation of a medicament for use in the treatment or limiting of an M. catarrhalis infection. 30 99. Use of an antibody according to claim 78, in the preparation of a medicament for use in preventing or limiting an M. catarrhalis infection. 100. Use of an antibody according to claim 79, in the preparation of a medicament for use in preventing or limiting an M. catarrhalis infection. 101. An isolated peptide according to claim 1, substantially as herein described with reference to the examples and figures. H:\evonnee\Keep\Speci\4150 0 .97.doc 27/08/01 124a 102. Anisolated peptide according to claim 19, substantially as herein described with reference to the examples and figures. S S. S S S .SSSSS S S 9 S S. S S S S. S S *5 S. \melb-files\home$\ evormee\ Keep\ Speci \41500. 97. doc 27/08/01 125 103. A vaccine composition according to claim 44, substantially as herein described with reference to the examples and figures. 104. A vaccine composition according to claim substantially as herein described with reference to the examples and figures. 105. A method according to claim 49, substantially as herein described with reference to the examples and figures. 106. A method according to claim 50, substantially as herein described with reference to the examples and figures. 107. A nucleic acid according to claim 59, substantially as herein described with reference to the examples and figures. 108. A nucleic acid according to claim 61, substantially as herein described with reference to the examples and figures. 109. A nucleic acid according to claim 63, substantially as herein described with reference to the examples and figures. 110. A method according to claim 65, substantially as herein described with reference to the examples and figures. 111. A method according to claim 66, substantially as S 35 herein described with reference to the examples and figures. 112. A method according to claim 69, substantially as herein described with reference to the examples and 40 figures. H:\janel\Keep\Speci\41500-97.doc 31101/01 126 113. A method according to claim 70, substantially as herein described with reference to the examples and figures. 114. A method according to claim 83, substantially as herein described with reference to the examples and figures. 115. A method according to claim 86, substantially as herein described with reference to the examples and figures. 116. An isolated peptide according to claim 91, substantially as herein described with reference to the examples and figures. Dated this 31st day of January 2001 BOARD OF REGENTS, THE UNIVERSITY OF TEXAS SYSTEM By their Patent Attorneys GRIFFITH HACK Fellows Institute of Patent and Trade Mark Attorneys of Australia *ee .e a e a H:\janel\Keep\Speci\41500-97.doc 31/01/01