# Patent

## Title
Chlamydia PMP proteins, gene sequences and uses thereof

## Abstract

The invention discloses the Chlamydia PMPE and PMPI polypeptide, polypeptides derived therefrp, (PMP-derived polypeptides), nucleotide sequences encoding said polypeptides, antibodies that specifically bind the PMP polypeptides and PMP-derived polypeptides and T-cells specific for PMP polypeptides and PMP-derived polypeptides. Also disclosed are prophylactic and therapeutic compositions, including immunogenic compositions, e.g., vaccines, comprising PMP polypeptides or PMP-derived polypeptides or antibodies thereto. The invention additionally discloses methods of inducing in animals an immune response to Chlamydia cells, Chlamydia elementary bodies, and/or cells expressing Chlamydial proteins, e.g., cell infected with Chlamydia.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
The present application is a divisional application of U.S. application Ser. No. 10/398,248, which is a national stage application of International Application No. PCT/U01/30345, filed on Sep. 28, 2001, which is a continuation-in-part of U.S. application Ser. No. 09/677,752, filed Oct. 2, 2000, which is hereby incorporated by reference in its their entireties.


1. FIELD OF THE INVENTION
The present invention generally relates to polymorphic membrane proteins or PMPs of Chlamydia, amino acid and nucleotide sequences thereof, antibodies specific for such Chlamydia PMP polypeptides, prophylactic and therapeutic compositions, including vaccines, and to methods of preventing, treating or ameliorating disorders in mammals and birds related to Chlamydia infections and for inducing immune responses in animals to Chlamydia. 
2. BACKGROUND OF THE INVENTION
Chlamydiae are obligate intracellular bacteria that infect animals, including mammals and birds, particularly at the epithelial lining of the lung, conjunctivae or genital tract. The most common species of Chlamydia include Chlamydia trachomatis, Chlamydia psittaci, Chlamydia pecorum and Chlamydia pneumoniae. Recently, the newly designated species of Chlamydia, C. pneumoniae (formerly C. trachomatis TWAR), has been implicated as a major cause of epidemic human pneumonitis and perhaps may play a role in atherosclerosis.
There are currently 18 recognized C. trachomatis serovars, causing trachoma and a broad spectrum of sexually transmitted diseases, with the A, B and C serovars being most frequently associated with trachoma, while the D-K serovars are the most common cause of genital infections.
Chlamydia are prevalent human pathogens causing disorders such as sexually transmitted diseases, respiratory diseases, including pneumonia, neonatal conjunctivitis, and blindness. Reactive inflammatory arthritis is a common sequel to sexually acquired non-gonococcal genital tract infection. Approximately 50% of reactive inflammatory arthritis cases are associated with Chlamydia trachomatis infection of the genital tract.
C. trachomatis is the major cause of sexually transmitted disease in many industrialized countries, including the United States. While the exact incidence of C. trachomatis infection in the United States is not known, current epidemiological studies indicate that more than 4 million chlamydial infections occur each year, compared to an estimated 2 million gonococcal infections. While all racial, ethnic and socioeconomic groups are affected, the greatest number of chlamydial infections occurs among young, 12 to 20 year-old, sexually active individuals. Most genitourinary chlamydial infections are clinically asymptomatic. Prolonged carriage in both men and women is common. As many as 25% of men and 75% of women diagnosed as having chlamydial infections have no overt signs of infection. As a consequence, these asymptomatic individuals constitute a large reservoir that can sustain transmission of the agent within the community.
Far from being benign, serious disease can develop from these infections including: urethritis, lymphogranuloma venereum (LGV), cervicitis, and epididymitis in males. Ascending infections from the endocervix commonly gives rise to endometritis, pelvic inflammatory disease (PID) and salpingitis which can cause tubal occlusion and lead ultimately to infertility in females. Recently, Chlamydia infections have been linked to heart disease (Bachaier et al. Science:283:1335, 1999; Fan et al. Inf. and Imm. 67:6145, 1999).
C. trachomatis infection of neonates results from perinatal exposure to the mother's infected cervix. Nearly 70% of neonates born vaginally to mothers with chlamydial cervicitis become infected during delivery. The mucus membranes of the eye, oropharynx, urogenital tract and rectum are the primary sites of infection. Chlamydial conjunctivitis has become the most common form of ophthalmia neonatorum. Approximately 20-30% of exposed infants develop inclusion conjunctivitis within 14 days of delivery even after receiving prophylaxis with either silver nitrate or antibiotic ointment. C. trachomatis is also the leading cause of infant pneumonia in the United States. Nearly 10-20% of neonates delivered through an infected cervix will develop chlamydial pneumonia and require some type of medical intervention.
In developing countries, ocular infections of C. trachomatis cause trachoma, a chronic follicular conjunctivitis where repeated scar formation leads to distortion of the eyelids and eventual loss of sight. Trachoma is the world's leading cause of preventable blindness. The World Health Organization estimates that over 500 million people worldwide, including about 150 million children, currently suffer from active trachoma and over 6 million people have been blinded by this disease.
In industrialized countries, the costs associated with treating chlamydial infections are enormous. In the United States, the annual cost of treating these diseases was estimated at $2.5-3 billion in 1992 and has been projected to exceed $8 billion by the year 2000.
One potential solution to this health crisis would be an effective chlamydial vaccine. Several lines of evidence suggest that developing an effective vaccine is feasible.
Studies in both humans and primates have shown that short-term protective immunity to C. trachomatis can be produced by vaccinating with whole Chlamydia. However, protection was characterized as short lived, serovar specific, and due to mucosal antibody production. Additionally, in some vaccinees disease was exacerbated when these individuals became naturally infected with a serovar different from that used for immunization. This adverse reaction was ultimately demonstrated to be due to a delayed-type hypersensitivity response. Thus, the need exists to develop a subunit-based chlamydial vaccine capable of producing an efficacious but nonsensitizing immune response. Such a subunit vaccine may need to elicit both mucosal neutralizing secretory IgA antibody and/or cellular immune response to be efficacious.
Subunit vaccine development efforts to date have focused almost exclusively on the major outer membrane protein (MOMP). MOMP is an integral membrane protein of approximately 40 kDa in size and comprises up to about 60% of the infectious elementary body (EB) membrane protein (Caldwell et al. 1981. Infect. Immun., 31:1161-1176). MOMP imparts structural integrity to the extracellular EB and is thought to function as a porin-like molecule when the organism is growing intracellularly and is metabolically active. With the exception of four surface exposed variable domains (VDI-VDIV), MOMP is highly conserved among all 18 serovars. MOMP is highly immunogenic and can elicit a local neutralizing anti-Chlamydia antibody. However, problems exists with this approach.
To date, most MOMP-specific neutralizing epitopes that have been mapped are located within the VD regions and thus give rise only to serovar-specific antibody. Attempts to combine serovar-specific epitopes in various vaccine vectors (e.g., poliovirus) to generate broadly cross-reactive neutralizing antibodies have been only marginally successful (Murdin et al. 1993. Infect. Immun., 61:4406-4414; Murdin et al. 1995. Infect. Immun., 63:1116-1121).
Two other major outer membrane proteins in C. trachomatis, the 60 kDa and 12 kDa cysteine-rich proteins, as well as the surface-exposed lipopolysaccharide, are highly immunogenic but, unlike MOMP, have not been shown to induce a neutralizing antibody (Cerrone et al., 1991, Infect Immun., 59:79-90). Therefore, there remains a need for a novel subunit-based chlamydial vaccine.
Citation or identification of any reference in this section or any other section of this application shall not be construed as an indication that such reference is available as prior art to the present invention.
3. SUMMARY OF THE INVENTION
This invention is directed to PMP proteins (referred to hereafter and in the claims as PMP polypeptides or PMP proteins) from Chlamydia spp. More particularly, the present invention encompasses the family of PMPE and PMPI polypeptides of Chlamydia trachomatis and other Chlamydia spp., including but not limited to, Chlamydia pneumonia, Chlamydia pecorum, and Chlamydia psittaci, having a molecular weight of 90 to 115 kD, and an amino acid sequence of SEQ ID NO:2 or 73 (PMPE) or SEQ ID NO.:4 (PMPI) or a sequence homologous thereto, in isolated, purified or recombinantly produced form. SEQ ID NOs.:2 and 4 represent the amino acid sequences of the Chlamydia trachomatis L2 serovar PMPE and PMPI proteins, respectively, encoded by the pmpE and pmpI genes. SEQ ID NO:73 represents the amino acid sequence of the Chlamydia trachomatis L2 serovar PMPE protein encoded by plasmid M15 pREP (pQE-PmpE-Ct#37), which is derived from a different strain than is SEQ ID NO:2. Preferably, the PMPE and PMPI polypeptides of the invention are encoded by a nucleic acid comprising a nucleotide sequence that hybridizes under low, moderate or, more preferably, highly stringent conditions to a nucleic acid comprising a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:2, 4, or 73 or a nucleotide sequence of SEQ ID NO.:1,3, or 73. Also, preferably, the PMPE and PMPI polypeptides of the invention do not cross react with or bind specifically to the monoclonal antibody secreted by hybridoma ATCC No. HB10861 available from the American Type Tissue Collection (ATCC).
The nucleotide sequences for the pmpE and pmpI Chlamydia trachomatis L2 serovar coding regions are SEQ ID NOs.:1 and 3, respectively. The nucleotide sequence of the portion of plasmid M15 pREP (pQE-PmpE-Ct#37) encoding the PMPE polypeptide also of the Chlamydia trachomatis L2 serovar is SEQ ID NO:72. The present invention encompasses all Chlamydia PMPE and PMPI polypeptides, particularly those of the Chlamydia trachomatis L2 serovar, and also including PMPI and PMPE polypeptides from other Chlamydia trachomatis serovars and other Chlamydia species. Identification of these homologs can be accomplished by methods well known in the art, for example, but not limited to, nucleic acid hybridization and PCR based techniques. The present invention encompasses isolated and/or purified PMPE and PMPI polypeptides, and polypeptides derived therefrom (“PMP-derived polypeptides”, e.g., derivatives, fragments and analogs thereof), preferably, that elicit an immune reaction against whole Chlamydia cells and/or are specifically bound by antibodies raised against polypeptides having an amino acid sequence of SEQ ID NO.: 2, 4, or 73. The invention further comprises methods for making said PMP polypeptides and PMP-derived polypeptides.
Preferably, the PMP protein has the amino acid sequence of SEQ ID NO.:2, 4 or 73 or is homologous to any of SEQ ID NO.:2, 4-34, or 73, preferably having an amino acid sequence identity of at least 70% or 80%, more preferably greater than 90%, and most preferably greater than 95% or 99%. These proteins preferably elicit an immune reaction against whole Chlamydia cells and/or are specifically bound by antibodies raised against polypeptides having an amino acid sequence of SEQ ID NO.: 2, 4, or 73. Preferred fragments of the protein comprise an amino acid sequence of any of SEQ ID NOs.:5-34.
Preferably, the PMP protein is an outer membrane protein. More preferably, the PMP protein is surface localized. Preferably, the PMP protein has at least one GGAI (Gly Gly Ala Ile) domain. It is intended that PMP proteins from all species of Chlamydia are included in this invention; however, preferred species include Chlamydia trachomatis, Chlamydia psittaci, Chlamydia pecorum and Chlamydia pneumoniae. 
The invention also provides PMP fusion peptides having B and/or T-cell stimulating activity, preferably comprising at least two T or B cell epitopes derived from the same or from different Chlamydia PMP proteins which proteins, or portions thereof, are arranged in a contiguous polypeptide in a configuration different from a naturally occurring configuration of the regions of a Chlamydia PMP protein.
A preferred polypeptide of the invention is a fusion polypeptide comprising at least two peptides, said at least two peptides, each consisting of amino acid sequences selected from the group consisting of SEQ ID NOs.:5, 6, 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, and 34, with the proviso that the peptides of the polypeptide are arranged in a contiguous polypeptide configuration that is different from the configuration of a naturally occurring PMPE or PMPI polypeptide (e.g., is not a naturally occurring PMPE or PMPI polypeptide or fragment thereof).
Other preferred PMP-derived polypeptides of the invention are isolated or purified fusion polypeptides wherein the polypeptide comprises one or more of the amino acid sequences of SEQ ID NO.:5, 6, 7, 8, 9, 10 or 11 or an isolated or purified fusion polypeptide wherein the polypeptide comprises an amino acid sequence of SEQ ID NO.:23, 24, 25, 26, 27, 28, or 29, with the proviso that the peptides of the polypeptide are arranged in a configuration that is different from the configuration of a naturally occurring PMPE or PMPI polypeptide. A preferred PMP-derived polypeptide is an isolated or purified fusion polypeptide, wherein the polypeptide comprises an amino acid sequence of SEQ ID NO.:5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28 or 29, with the proviso that the peptides are arranged in a configuration that is different from the configuration of a naturally occurring PMPE or PMPI polypeptide.
Preferably, the PMP-derived polypeptides of the invention are immunologically cross-reactive with the PMP protein from which they are derived and are capable of eliciting in an animal an immune response to Chlamydia. A preferred PMP polypeptide or PMP-derived polypeptide of the invention induces IgM, IgG, IgA, and/or IgE antibodies, delayed hypersensitivity T-cell responses and/or cytotoxic T-cell responses to cells expressing Chlamydial antigens (including but not limited to cells infected with Chlamydia and antigen presenting cells such as macrophages, dendritic cells, B cells, or synthetic antigen presenting cells which display Chlamydial antigens), native PMP proteins from which the polypeptide is derived, Chlamydia cells, or Chlamydia elemental bodies (EB). In a more preferred embodiment, the PMP polypeptide or PMP-derived polypeptide is capable of eliciting an immune response against other Chlamydia serovars and, more preferably, other Chlamydia species along with the Chlamydia serovar or species in which the PMP polypeptide occurs naturally.
The invention also encompasses antisera and antibodies, including but not limited to, cytotoxic or bactericidal polyclonal and monoclonal antibodies, which bind to and are specific for the PMP polypeptide, PMP-derived polypeptides and/or fragments thereof.
Preferably the antibodies bind a PMP protein (preferably a PMPE or PMPI polypeptide) having the amino acid sequence of SEQ ID NOs.:2, 73, or 4 or an amino acid sequence homologous thereto. Also included are monoclonal antibodies that specifically bind a PMP or PMP-derived polypeptide, including but not limited to monoclonal antibodies that specifically bind a polypeptide comprising an amino acid sequence of any of SEQ ID NOs.:2, 4-34 or 73. Also included are antigen binding fragments of polyclonal or monoclonal antibodies, e.g., Fv, Fab, Fab′ and F(ab′)2 fragments. A further aspect of the invention are chimerized or humanized antibodies in which one or more of the antigen binding regions of the anti-PMP antibody is introduced into the framework region of a heterologous (e.g., human) antibody. In a preferred aspect, the antibodies are human antibodies.
Another aspect of the invention is directed to T-cells raised against an antigenic or immunogenic composition of the invention or T-cells specific for antigenic or immunogenic polypeptides of the invention or specific for cells expressing Chlamydial antigens (including but not limited to cells infected with Chlamydia or antigen presenting cells presenting PMP polypeptides such as dendritic cells, B cells, or synthetic antigen presenting cells), Chlamydia cells, or Chlamydia elemental bodies (EB).
The invention further provides isolated nucleic acid molecules (DNA or RNA) encoding the PMPE polypeptides, PMPI polypeptides, PMPE-derived polypeptides, PMPI-derived polypeptides, vectors comprising said sequences, host cells containing said vectors or having the sequences operably linked to a heterologous promoter, recombinant polypeptides produced therefrom, and pharmaceutical compositions comprising the nucleic acid molecules, vectors, and cells.
A preferred aspect of the invention is a nucleotide sequence encoding a PMP protein comprising the amino acid sequence of any of SEQ ID NOs.:2, 4-34, or 73 or an amino acid sequence substantially homologous thereto. Also included is an isolated nucleic acid molecule comprising a DNA sequence of SEQ ID NOs.:1, 3 or 72 or a complementary sequence thereof; a fragment of the DNA molecule having the nucleotide sequence of SEQ ID NOs.:1, 3 or 72, or a complementary sequence thereof; or a nucleic acid molecule which hybridizes under low or moderate stringency conditions or, more preferably, highly stringent (or stringent) conditions to any one of the sequences described above. The nucleic acid molecule that hybridizes under stringent conditions preferably has a sequence identity of about 70%, 80%, 90%, 95%, or 99% with any of the sequences identified above, more preferably about 90%.
The invention further encompasses pharmaceutical compositions including prophylactic or therapeutic compositions, which may be immunogenic compositions, including vaccines, comprising one or more of the PMP polypeptides of the invention, optionally in combination with, fused to, or conjugated to one or more other component(s), including a lipid, phospholipid, a carbohydrate, including a lipopolysaccharide, any proteins either novel or known to those skilled in the art, inactivated whole or attenuated organisms, including but not limited to viruses, yeasts, fungi and bacteria. Particularly preferred bacteria include, but are not limited to Neisseria, Chlamydia, Moraxella, Pseudomonas, Streptococcus or Haemophilus bacteria.
In a specific embodiment, the invention encompasses pharmaceutical compositions, including prophylactic or therapeutic compositions, which may be immunogenic compositions including vaccines, comprising one or more of the PMP polypeptides and/or PMP-derived polypeptides and an attenuated or inactivated Chlamydia cultivar or an attenuated or inactivated Chlamydia cultivar expressing PMP polypeptide in a greater amount when compared to wild-type Chlamydia. 
The invention further encompasses pharmaceutical compositions comprising isolated nucleic acid molecules encoding PMP polypeptides and PMP-derived polypeptides of the present invention which can be used in methods to detect Chlamydia infection or to prevent, treat or reduce the severity of a disease or disorder related to infection with Chlamydia. Such compositions include but are not limited to vectors or recombinant host cells comprising such nucleic acid molecules or having a nucleotide sequence of the invention operably linked to a heterologous promoter.
The invention also includes diagnostic reagents, that may include any one or more of the above mentioned aspects, such as native PMP proteins, recombinant PMP proteins, PMP-derived polypeptides, nucleic acid molecules, immunogenic compositions, antigenic compositions, antisera, T-cells, antibodies, vectors comprising the nucleic acids, and transformed cells comprising the vectors.
A further aspect of the present invention provides methods for determining the presence of nucleic acids encoding a PMP protein or a PMP-derived polypeptide in a test sample, and diagnostic kits and reagents therefor, for determining the presence of a nucleic acid encoding a PMP polypeptide or PMP-derived polypeptide.
Also included in this invention are methods of inducing an immune response to Chlamydia spp. and methods of preventing, treating or ameliorating disorders or diseases related to Chlamydia in an animal, including mammals and birds and, preferably, in humans, in need of such treatment comprising administering an effective amount of the pharmaceutical or vaccine composition of the invention. Preferred disorders or diseases include a Chlamydia bacterial infection, including those infections that cause trachoma, conjunctivitis, urethritis, lymphogranuloma venereum (LGV), cervicitis, epididymitis, or endometritis, pelvic inflammatory disease (PID), salpingitis, tubal occlusion, infertility, cervical cancer, reactive arthritis, inflammatory heart disease, dilated/cardiomyopathy, autoimmune myocarditis, or atherosclerosis.
A further aspect of the invention provides antagonists or agonists which inhibit or enhance, respectively, the activity or expression of the polypeptides or nucleic acid molecules of the invention. In particular embodiments, the agonists or antagonists kill Chlamydia cells or arrest Chlamydia cell growth, i.e., can be used to treat or prevent Chlamydia infection.
A further aspect of the invention is a method for identifying compounds which interact with and inhibit or activate an activity of the polypeptides or nucleic acid molecules of the invention comprising contacting a composition comprising the polypeptide or the nucleic acid molecule with the compound to be screened under conditions that permit interaction between the compound and the polypeptide or nucleic acid molecule to assess the interaction of a compound and to detect interaction of the compound with the polypeptide of nucleic acid. The interaction of the compound with the polypeptide or nucleic acid molecule is determined by the association of a second component (e.g., an antibody) capable of providing a detectable signal in response to the interaction of the polypeptide or nucleic acid molecule with the compound; and determining the presence or absence of a signal generated from the interaction of the compound with the polypeptide or nucleic acid molecule. Alternatively, the interaction of the compound with the polypeptide or nucleic acid molecule is determined by the ability of the compound to inhibit the activity of the polypeptide or the nucleic acid molecule.
3.1. Abbreviations

    
    
        anti-PMP=PMP polypeptide antibody or antiserum
        ATCC=American Type Culture Collection
        immuno-reactive=capable of provoking a cellular or humoral immune response
        kD or kDa=kilodaltons
        OG=n-octyl-D-glucopyranoside or octyl glucoside
        OMP=outer membrane protein
        OMPs=outer membrane proteins
        PBS=phosphate buffered saline
        PAGE=polyactylamide gel electrophoresis
        polypeptide=a peptide of any length, preferably having eight or more amino acid residues
        SDS=sodium dodecylsulfate
        SDS-PAGE=sodium dodecylsulfate polyacrylamide gel electrophoresis
    
    


Nucleotide sequences defined herein are represented by one-letter symbols for the bases as follows:

    
    
        A (adenine)
        C (cytosine)
        G (guanine)
        T (thymine)
        U (uracil)
        M (A or C)
        R (A or G)
        W (A or T/U)
        S (C or G)
        Y (C or T/U)
        K (G or T/U)
        V (A or C or G; not T/U)
        H (A or C or T/U; not G)
        D (A or G or T/U; not C)
        B (C or G or T/U; not A)
        N (A or C or G or T/U) or (unknown)
    
    


Peptide and polypeptide sequences defined herein are represented by one-letter symbols for amino acid residues as follows:

    
    
        A (alanine)
        R (arginine)
        N (asparagine)
        D (aspartic acid)
        C (cysteine)
        Q (glutamine)
        E (glutamic acid)
        G (glycine)
        H (histidine)
        I (isoleucine)
        L (leucine)
        K (lysine)
        M (methionine)
        F (phenylalanine)
        P (proline)
        S (serine)
        T (threonine)
        W (tryptophan)
        Y (tyrosine)
        V (valine)
        X (unknown)
    
    


The present invention may be more fully understood by reference to the following detailed description of the invention, non-limiting examples of specific embodiments of the invention and the appended figures.



4. BRIEF DESCRIPTION OF DRAWINGS
FIG. 1. Schematic map of the C. trachomatis PMPE expression plasmid M15 pREP (pQE-PmpE-Ct#37). The mature form of the C. trachomatis PMPE protein is expressed in E. coli as a fusion protein carrying the MRGS-(H)6 domain encoded by the vector plasmid pQE-30 at the N-terminus.
FIG. 2. Schematic map of the C. trachomatis PMPI expression plasmid TOP10 (pBAD-pmpI-Ct-Uni#7). The C. trachomatis PMPI protein is expressed in E. coli as a fusion protein carrying the HP-Thio domain encoded by the vector plasmid pBAD/Thio-E at the N-terminus.
FIG. 3. A Coomassie blue-stained SDS-PAGE gel of the gel-purified C. trachomatis PMPE protein expressed from the pQE-pmpE-Ct #37 plasmid. The PMPE protein migrates as an  ̃100 kDa protein. Pre-stained molecular weight markers (Lane 1) are Myosin ( ̃250 kDa), Phosphorylase B ( ̃148 kDa), BSA ( ̃98 kDa), GDH ( ̃64 kDa), ADH ( ̃50 kDa), CAH ( ̃36 kDa), Myoglobulin (30 kDa), Lysozyme (16 kDa), Aprotinin ( ̃6 kDa), Insulin B chain ( ̃4 kDa) (See Blue prestained standard Novex LC5625).
FIG. 4. A Coomassie blue-stained SDS-PAGE gel of E. coli Top10 cell extracts carrying the C. trachomatis PMPI expression plasmid pBAD-pmpI-ct-Uni#7. Lane 1, pre-stained molecular weight markers (Novex MultiMark LC5725); lane 2, non-induced cells; lane 3, arabinose induced cells. The C. trachomatis PMPI protein in the arabinose-induced lane is indicated by an arrow. Molecular weight markers (Lane 1) are Myosin ( ̃250 kDa), Phosphorylase B ( ̃148 kDa), GDH ( ̃60 kDa), CAH ( ̃42 kDa), Myoglobulin-Blue ( ̃30 kDa), Myoglobulin-Red ( ̃22 kDa), Lysozyme ( ̃17 kDa).
FIGS. 5A-E. Full length nucleotide sequence and corresponding deduced amino acid sequence of the PMPE polypeptide of Chlamydia trachomatis L2 (SEQ ID NOs.:1 and 2).
FIGS. 6A-D. Full length nucleotide sequence and corresponding deduced amino acid sequence of the PMPI polypeptide of Chlamydia trachomatis L2 (SEQ ID NOs.:3 and 4).
FIG. 7. In vitro antigen-specific spleen cell proliferative response in animals immunized with recombinant PMPE and an adjuvant. Spleens were harvested from immunized C3H HeOuJ female mice approximately 14 days after a three dose immunization regimen. Single cell suspensions were prepared and the cells from two animals were pooled for analysis. Aliquots of the pooled cell samples were incubated for 72-96 hours in the presence of a test stimulant and pulsed with 3H-thymidine for the last 18-24 hours. Pooled samples incubated and pulsed labeled in parallel but in the absence of any stimulant served as the baseline 3H-thymidine uptake control. Represented is the stimulation index of cells stimulated with ConA (concanavalin A) (positive stimulation control); adjuvant (adjuvant employed in immunizations); PMPE (recombinant pmpE protein); EB (UV-inactivated C. trachomatis elementary bodies). 1 μg/ml (open bars), 4 μg/ml (solid bars) and 8 μg/ml (hatched bars) denote the three concentrations of in vitro stimulant used in the experiment. Stimulation index (SI) denotes the difference in 3H-thymidine incorporation of stimulated cells minus the background incorporation of the unstimulated controls. Bars denote the mean±standard deviation in SI.
FIGS. 8A-D. Full length nucleotide and corresponding deduced amino acid sequence of the PMPE polypeptide of Chlamydia trachomatis serovar L2 contained in plasmid M15pREP (PQE-PmpE-Ct#37) (SEQ ID Nos.:72 and 73).



5. DETAILED DESCRIPTION OF THE INVENTION
5.1. Chlamydia PMP Polypeptides
The present invention is generally directed to compositions and methods for the diagnosis, prevention, and treatment of Chlamydial infection. In one aspect, the composition of the subject invention provides pure native (wildtype) or recombinantly produced PMP polypeptides that comprise at least one immunogenic portion of a Chlamydia antigen.
The terms “treatment” or “therapy” as used herein and in the claims encompasses elimination, reduction or amelioration of disease symptoms caused directly or indirectly by the organism or numbers of organisms present.
In particular embodiments, the term “Chlamydia” refers to any Chlamydial species (spp.) including but not limited to Chlamydia trachomatis, Chlamydia pneumonia, Chlamydia psittaci and Chlamydia pecorum. 
Strains from any of these organism may be obtained worldwide from any biologicals depository, particularly strains of Chlamydia ATCC VR-346, VR-347, VR-348B, VR-571B, VR-572, VR-573, VR-577, VR-578, VR-878, VF-879, VP-880, VR-885, VR-886, VR-887, VR-901B, VR-902B, VR-903, VR-1355, VR-1474, VR-1477, VR-2282, which may be obtained from the ATCC.
In a particular embodiment, the Chlamydia PMP protein is a PMPE polypeptide comprising or consisting of the amino acid sequence of SEQ ID NO.:2 or SEQ ID NO:73. In another embodiment, the PMPE polypeptide comprises residues 32-965 of SEQ ID NO:2 or residues 23-956 of SEQ ID NO:73
In another particular embodiment, the PMPE polypeptide is encoded by the nucleotide sequence of SEQ ID NO.:1 or SEQ ID NO:72. In another embodiment, the Chlamydia PMPE polypeptide comprises or consists of an amino acid sequence which is homologous to SEQ ID NO.:2 or 73, or a portion thereof or is encoded by a nucleotide sequence homologous to (for example, that hybridizes under low, moderate or high stringency conditions to) the nucleotide sequence of SEQ ID NO.:1 or 72, or a portion thereof.
In another particular embodiment, the Chlamydia PMP protein is a PMPI protein comprising or consisting of the amino acid sequence of SEQ ID NO.:4. In another embodiment, the Chlamydia polypeptide is a PMPI polypeptide encoded by the nucleotide sequence of SEQ ID NO.:3 or the nucleotide sequence (specifically, the PMPI encoding portion) of plasmid TOP10 (pBAD-pmpI-Ct-Uni)#7. In another embodiment, the Chlamydia polypeptide comprises or consists of an amino acid sequence which is homologous to SEQ ID NO.:4, or a portion thereof, or is encoded by a nucleotide sequence homologous to (for example, that hybridizes under low, moderate or high stringency conditions to) the nucleotide sequence of SEQ ID NO.:3, or a portion thereof.
The present invention provides the family of Chlamydia PMPE and PMPI proteins. The amino acid sequences of SEQ ID NOs.:2, 4, and 73 and the nucleotide sequences of SEQ ID NOs.:1, 3, and 72 represent the amino acid and nucleotide sequences, respectively, of the PMPE and PMPI polypeptides, respectively, of the Chlamydia trachomatis L2 serovar (SEQ ID NOs.:72 and 73 being variants from a different strain of the Chlamydia trachomatis L2 serovar than SEQ ID NOs.:1-4). The invention also relates to PMPE and PMPI polypeptides from other Chlamydia trachomatis serovars and strains and other Chlamydia species, as well as other derivatives and fragments thereof (i.e., PMPE- and PMPI-derived polypeptides). In a preferred embodiment, immunization with the polypeptide of the invention elicits antibodies that specifically bind to PMPE or PMPI polypeptides from other Chlamydia serovars and, preferably, species (preferably all species, but may be a subset of species) besides the serovar and species from which the polypeptide was isolated or derived.
As used herein a “homologous” sequence is at least 70%, preferably greater than 80%, more preferably greater than 90%, most preferably 95% or 99% identical in sequence to a reference amino acid or nucleotide sequence of identical size or when compared to a reference sequence when the alignment or comparison is conducted by a computer homology program or search algorithm known in the art. By way of example and not limitation, useful computer homology programs include the following: Basic Local Alignment Search Tool (BLAST) (Altschul et al., 1990, J. of Molec. Biol., 215:403-410, “The BLAST Algorithm”; Altschul et al., 1997, Nuc. Acids Res. 25:3389-3402) a heuristic search algorithm tailored to searching for sequence similarity which ascribes significance using the statistical methods of Karlin and Altschul 1990, Proc. Nat'l Acad. Sci. USA, 87:2264-68; 1993, Proc. Nat'l Acad. Sci. USA 90:5873-77. Five specific BLAST programs perform the following tasks:
1) The BLASTP program compares an amino acid query sequence against a protein sequence database.
2) The BLASTN program compares a nucleotide query sequence against a nucleotide sequence database.
3) The BLASTX program compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database.
4) The TBLASTN program compares a protein query sequence against a nucleotide sequence database translated in all six reading frames (both strands).
5) The TBLASTX program compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
Smith-Waterman (Smith-Waterman, 1981, J. of Molec. Biol., 147:195-197) is a mathematically rigorous algorithm for sequence alignments.
FASTA (see Pearson et al., 1988, Proc. Nat'l Acad. Sci. USA, 85:2444-2448) is a heuristic approximation to the Smith-Waterman algorithm.
By further way of example and not limitation, useful computer homology algorithms and parameters for determining percent identity include the following:
To determine the percent identity of two amino acid sequences or of two nucleotide sequences, e.g., between PMP sequences and other known sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity=# of identical positions/total # of positions (e.g., overlapping positions)×100). In one embodiment, the two sequences are the same length.
The determination of percent identity between two sequences can be accomplished using a mathematical algorithm, a preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, 1990, Proc. Nat'l Acad. Sci. USA, 87:2264-68; as modified by 1993, Proc. Nat'l Acad. Sci. USA 90:5873-77. Such algorithm is incorporated into the NBLAST and XBLAST programs of Altschul, 1990, J. of Molec. Biol., 215:403-410. BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12 to obtain nucleotide sequences homologous to a nucleic acid molecule of the invention. BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to a protein molecule of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul, 1997, Nuc. Acids Res. 25:3389-3402. Alternatively, PSI-BLAST can be used to perform an iterated search which detects distant relationships between molecules (Id.). When utilizing BLAST, Gapped BLAST, and PSI-BLAST programs, the default parameters of the respective programs can be used. Another preferred, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, CABIOS (1989). Such an algorithm is incorporated into the ALIGN program (version 2.0) which is part of the CGC sequence alignment software package. When using the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table a gap length penalty of 12, and a gap penalty of 4 can be used. Additional algorithms for sequence analysis are known in the art and include ADVANCE and ADAM as described in Torellis and Robotti (1994) Comput. Appl. Biosc., 10:3-5; and FASTA described in Pearson and Lipman, 1988, Proc. Nat'l Acad. Sci. USA, 85:2444-2448. Within FASTA, ktup is a control option that sets the sensitivity and speed of the search. If ktup=2, similar regions in the two sequences being compared are found by looking at pairs of aligned residues; if ktup=1, single aligned amino acids are examined. Ktup can be set to 2 or 1 for protein sequences, or from 1 to 6 for nucleotide sequences. The default, if ktup is not specified, is 2 for proteins and 6 for nucleotides. Alternatively, protein sequence alignment may be carried out using the CLUSTAL W algorithm as described by Higgins et al., 1996, Methods Enzymol., 266:383-402.
The percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, only exact matches are counted.
According to various aspects of the invention, the polypeptides of the invention are characterized by their apparent molecular weights based on the polypeptides' migration in SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) relative to the migration of known molecular weight markers. While any molecular weight standards known in the art may be used with the SDS-PAGE, preferred molecular weight markers comprise pre-stained Myosin (250 kDa), Phosphorylase B (148 kDa), BSA (98 kDa) and GDH (64 kDa). One skilled in the art will appreciate that the polypeptides of the invention may migrate differently in different types of gel systems (e.g., different buffers; different types and concentrations of gel, crosslinkers or SDS, etc.). One skilled in the art will also appreciate that the polypeptides may have different apparent molecular weights due to different molecular weight markers used with the SDS-PAGE. Hence, the molecular weight characterization of the polypeptides of the invention is intended to be directed to cover the same polypeptides on any SDS-PAGE system and with any set of molecular weight markers which might indicate slightly different apparent molecular weights for the polypeptides than those disclosed herein.
In specific embodiments, the subject invention discloses PMP polypeptides comprising an immunogenic portion of a Chlamydia antigen, wherein the Chlamydia antigen comprises an amino acid sequence encoded by a nucleic acid molecule comprising a sequence selected from the group consisting of (a) nucleotide sequences of SEQ ID NO.:1, 3 and 72; (b) the complements of said nucleotide sequences; and (c) variants of such sequences.
5.2. Chlamydia PMP-Derived Polypeptides
The term “antigens” and its related term “antigenic” as used herein and in the claims refers to a substance to which an antibody or T-cell receptor specifically binds. As used herein, antisera, antibodies and T-cells are “antigen-specific” if they specifically bind to or react with an antigen and do not react detectably with unrelated proteins other than by non-specific interaction. Preferably said antigens are immunogenic.
The term “immunogenic” as used herein and in the claims refers to the ability to induce an immune response, e.g., an antibody and/or a cellular immune response in an animal, preferably a mammal or a bird.
In a specific embodiment of the invention, proteins consisting of or comprising a fragment of a PMPE protein consisting of at least 8 (contiguous) amino acids of the protein are provided. In other embodiments, the fragment consists of at least 5, 10, 20, 40, 50, 60, 80, 100, 150, 200, 300, 400 or 500 amino acids of SEQ ID NO.:2 or 73 or a sequence homologous thereto. In specific embodiments, such fragments are not larger than 10, 11, 12, 15, 20, 25, 35, 50, 75, 80, 90, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675 or 700 amino acids. In preferred embodiments, the PMPE-derived polypeptide contains a sequence forming an outer-surface epitope, i.e., a portion of the peptide located on the outside of the Chlamydia cell and that can be bound by anti-PMPE antibodies.
In a particular embodiment, the PMPE-derived polypeptide is a fragment of a PMPE polypeptide which fragment comprises or consists of an amino acid sequence of any of SEQ ID NOs.:5-22. In another particular embodiment, the PMPE-derived polypeptide is a fragment of a PMPE polypeptide, which fragment comprises or consists of an amino acid sequence of any of SEQ ID NOs.:5-22, but also comprises additional C-terminal or N-terminal PMPE sequences.
In a specific embodiment of the invention, proteins are provided that consist of or comprise a fragment of a PMPI protein consisting of at least 8 (continuous) amino acids of SEQ ID NO.:4 or a sequence homologous thereto. In other embodiments, the fragment consists of at least 5, 10, 15, 20, 25, 50, 75, 100, 150 or 200 amino acids of SEQ ID NO.:4. In specific embodiments, such fragments are not longer than 10, 11, 12, 15, 20, 25, 35, 50, 75, 80, 90, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675 or 700 amino acids. In preferred embodiments, PMPI-derived polypeptide contains a sequence forming an outer-surface epitope.
In a particular embodiment, the PMPI-derived polypeptide is a fragment of a PMPI peptide which comprises the amino acid sequence of any of SEQ ID NOs.:23-34.
In another particular embodiment, the PMPE-derived polypeptide is a fragment of a PMPE polypeptide which comprises the amino acid sequence of any of SEQ ID NOs.:5-22, but also comprises additional C-terminal or N-terminal PMPI sequences.
Preferably, the PMPE-derived polypeptides of the invention are immunologically cross-reactive with the PMPE polypeptide, and are capable of eliciting in an animal an immune response to Chlamydia, Chlamydia elemental bodies (EB), Chlamydia reticulate bodies (RBs), Chlamydia infected cells or antigen presenting cells expressing Chlamydial antigens and/or are able to be bound by anti-PMPE antibodies.
Preferably, the PMPI-derived polypeptides of the invention are immunologically cross-reactive with the PMPI polypeptide, and are capable of eliciting in an animal an immune response to Chlamydia, Chlamydia elemental bodies (EB), reticulocyte bodies (RBs), Chlamydia infected cells or antigen presenting cells expressing Chlamydial antigens and/or are able to be bound by anti-PMPI antibodies. More preferably, the PMP-derived polypeptides of the invention comprise sequences forming one or more epitopes of the native PMPE or PMPI polypeptide of Chlamydia (i.e., the epitopes of PMPE or PMPI polypeptide as they exist in intact Chlamydia cells). Such preferred PMPE-derived or PMPI-derived polypeptides can be identified by their ability to specifically bind polyclonal or monoclonal antibodies raised to intact Chlamydia cells (e.g., antibodies elicited by formaldehyde or glutaraldehyde fixed Chlamydia cells; such antibodies are referred to herein as “anti-whole cell” antibodies). For example, peptides from a limited or complete protease digestion of the PMPE or PMPI polypeptide are fractionated using standard methods and tested for their ability to bind anti-whole cell antibodies. Reactive polypeptides are isolated and their amino acid sequence determined by methods known in the art. In a preferred embodiment, the PMPE and/or PMPI-derived polypeptide comprises one or more portions of a PMPE or PMPI protein, or derivative thereof, that is a T-cell epitope.
Preferably, the PMP polypeptides and PMP-derived polypeptides of the invention are not bound specifically by the monoclonal antibody secreted by hybridoma ATCC No. HB10861 available from the ATCC.
PMP-derived polypeptides can also be constructed by making deletions that remove a part of the parent polypeptide, while retaining the desired specific antigenicity and/or immunogenicity. Deletions can also remove regions of high variability among strains.
Also preferably, the PMP-derived polypeptides of the invention comprise sequences that form one or more epitopes of a native PMP polypeptide, which epitopes elicit bactericidal or opsonizing antibodies. Such preferred PMP-derived polypeptides may be identified by their ability to generate antibodies that kill Chlamydia spp., particularly, Chlamydia trachomatis cells. For example, polypeptides from a limited or complete protease digestion or chemical cleavage of a PMP polypeptide are fractionated using standard methods (e.g., by limited proteolytic digestion using enzymes such as trypsin, papain, or related proteolytic enzymes or by chemical cleavage using agents such as cyanogen bromide and followed by fractionation of the digestion or cleavage products), injected into animals, and the antibodies produced therefrom are tested for the ability to interfere with or kill Chlamydia cells and/or Chlamydia infected cells. Once identified and isolated, the amino acid sequences of such preferred PMP-derived polypeptides are determined using standard sequencing methods. The determined sequence may be used to enable production of such polypeptides by synthetic chemical and/or genetic engineering means.
These preferred PMP-derived polypeptides also can be identified by using anti-whole cell antibodies to screen bacterial libraries expressing random fragments of Chlamydia genomic DNA or cloned nucleotide sequences encoding a PMPE or PMPI polypeptide or fragments thereof. See, e.g., Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, 2nd ed., Cold Spring Harbor Press, Cold Spring Harbor, N.Y., Vol. 1, Chapter 12. The reactive clones are identified and their inserts are isolated and sequenced to determine the amino acid sequences of such preferred PMP-derived polypeptides.
Examples of immunogenic portions of antigens contemplated by the present invention include polypeptides comprising or consisting of the fragments set forth in Tables 1 and 2, where the numbers following the PMPE (Table 1, column 1) or PMPI (Table 2, column 1) designation refer to the amino acid residues in SEQ ID NOs.:2 or 4, respectively. Polypeptides comprising at least an immunogenic portion of one or more Chlamydia antigens or immunogenic portions as described herein may generally be used, alone or in combination, to detect, prevent, treat or reduce the severity of Chlamydial infection.







TABLE 1







PREFERRED FRAGMENTS OF PMPE










FRAGMENT
SEO ID NO.:







PMPE15-56
 5



PMPE15-121
 6



PMPE45-125
 7



PMPE125-190
 8



PMPE195-261
 9



PMPE275-366
10



PMPE375-440
11



PMPE440-490
12



PMPE525-590
13



PMPE590-625
14



PMPE615-650
15



PMPE625-700
16



PMPE725-800
17



PMPE755-775
18



PMPE785-845
19



PMPE815-865
20



PMPE1-31
21



PMPE1-500
22

















TABLE 2







PREFERRED FRAGMENTS OF PMPI










FRAGMENT
SEQ ID NO.:







PMPI 13-40
23



PMPI 70-110
24



PMPI 150-225
25



PMPI 250-290
26



PMPI 370-455
27



PMPI 400-455
28



PMPI 470-520
29



PMPI 615-670
30



PMPI 710-775
31



PMPI 765-825
32



PMPI 830-860
33



PMP 1-500
34










Polypeptides having a sequence homologous to one of the PMP polypeptides of the invention, including naturally-occurring allelic variants, as well as mutants, variants or any other non-naturally occurring variants, preferably those that cross-react with antibodies against a PMP polypeptide of the present invention, are encompassed by the present invention.
Allelic variants are very common in nature. For example, a bacterial species e.g., C. trachomatis, is usually represented by a variety of strains or serovars that differ from each other by minor allelic variations. Indeed, a polypeptide that fulfills the same biological function in different strains can have an amino acid sequence that is not identical in each of the strains. Such an allelic variation may be equally reflected at the nucleic acid molecule level.
An allelic variant is an alternate form of a polypeptide that is characterized as having a substitution, deletion, or addition of one or more amino acids that does not substantially alter the biological function of the polypeptide. By “biological function” is meant the function of the polypeptide in the cells in which it naturally occurs, even if the function is not necessary for the growth or survival of the cells.
Nucleic acid molecules, e.g., DNA molecules, encoding allelic variants can easily be retrieved by the polymerase chain reaction (PCR) amplification of genomic bacterial DNA extracted by conventional methods. This involves the use of synthetic oligonucleotide primers matching upstream and downstream sequences of the 5′ and 3′ ends of the encoding domains. Typically, a primer can consist of 10 to 40, preferably 15 to 25 nucleotides. It may be also advantageous to select primers containing C and G nucleotides in a proportion sufficient to ensure efficient hybridization; e.g., an amount of C and G nucleotides of at least 40%, preferably 50% of the total number of nucleotides in the primer.
Variants of Chlamydia trachomatis PMP proteins, such as PMP proteins from the A, B, Ba, C, D, Da, E, F, G, H, I, Ia, J, K, MoPN, L1, L2, and L3 serovars, which share sequence homology to the PMP polypeptides and nucleic acid molecules described herein are also provided.
“Homolog” or “homologous” is defined as being at least 70, 80, 85, 90, 95 or 99% identical to a reference sequence of identical size or when the alignment or comparison is by a computer homology program or search algorithm known in the art (see Section 5.1 supra). Preferably, the serovar homologs show 70, 80, 85, 90, 95 or 99% identity to the corresponding polypeptide sequence or sequences described herein. Most preferably, the serovar homologs show 95-99% homology to the corresponding polypeptide sequence or sequences described herein. Also, homologous nucleotide sequences exhibit 70, 80, 85, 90, 95 or 99% identity to the corresponding nucleotide sequence or sequences described herein.
A PMP-derived polypeptide of the invention may also be a modified PMPE or PMPI polypeptide or fragment thereof (i.e., a Chlamydia PMP polypeptide or fragment having one or more amino acid substitutions, insertions and/or deletions of the wild-type Chlamydia PMP sequence or amino acids chemically modified in vivo or in vitro). Such modifications may enhance the immunogenicity of the resultant PMP-derived polypeptide product or have no effect on such activity.
As used herein, the term “enhance the immunogenicity” refers to an increased antibody titer or increased cellular immune response elicited by exposure to the modified polypeptide as compared to the immune response elicited by unmodified polypeptides or formalin or glutaraldehyde fixed Chlamydia. Modification techniques that may be used include, but are not limited to, those disclosed in U.S. Pat. No. 4,526,716.
As an illustrative, non-limiting example, one or more amino acid residues within the PMP-derived polypeptide sequence can be substituted by another amino acid of a similar polarity which acts as a functional equivalent, resulting, for example, in a silent alteration. Substitutes for an amino acid within the sequence may be selected from other members of the class to which the amino acid belongs. For example, the nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid.
Included within the scope of the invention are PMP-derived polypeptides which are Chlamydia PMP polypeptide fragments or other derivatives or analogs which are differentially modified during or after translation, e.g., by glycosylation, acetylation, phosphorylation, lipidation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule or other cellular ligand, etc. Any of numerous chemical modifications may be carried out by known techniques, including but not limited to, specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBH4, acetylation, formylation, oxidation, reduction, metabolic synthesis in the presence of tunicamycin, etc.
Furthermore, if desired, nonclassical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the PMP polypeptide sequence. Non-classical amino acids include but are not limited to the D-isomers of the common amino acids, α-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, γ-Abu, ε-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, β-alanine, fluoro-amino acids, designer amino acids such as β-methyl amino acids, Cα-methyl amino acids, Nα-methyl amino acids, PNA's and amino acid analogs in general. Furthermore, the amino acid can be D (dextrorotary) or L (levorotary).
A Chlamydia PMP-derived polypeptide may further be a chimeric polypeptide comprising one or more heterologous polypeptides, lipids, phospholipids or lipopolysaccharides of Chlamydia origin or of another bacterial or viral origin, fused (e.g., covalently bound) to the amino-terminus or carboxyl-terminus of or is within a complete PMPE or PMPI polypeptide or PMP-derived polypeptide. Useful heterologous polypeptides to be included within such a chimeric polypeptide include, but are not limited to, a) pre- and/or pro-sequences that facilitate the transport, translocation and/or processing of the PMP-derived polypeptide in a host cell, b) affinity purification sequences, and c) any useful immunogenic sequences (e.g., sequences encoding one or more epitopes of a surface-exposed protein of a microbial pathogen). One preferred heterologous protein of the chimeric polypeptide includes Hin47 (see U.S. Pat. Nos. 5,679,547 and 5,721,115, which are hereby incorporated by reference in their entirety). Another preferred chimeric polypeptide includes a High Molecular Weight (HMW) protein of Chlamydia or fragments thereof (see PCT publication WO 99/17741, entitled “Chlamydia Protein, Gene Sequence and Uses Thereof”, which is incorporated by reference herein in its entirety) or Chlamydia MOMP or fragments thereof (see U.S. Pat. No. 5,869,608, which is incorporated herein by reference in its entirety). The fragments of these proteins preferably contain an epitope specifically bound by an antibody raised against the protein. A particularly preferred chimeric protein comprises one or more of: SEQ ID NOs.:5-34, an N-terminal fragment of HMW protein and a fragment of MOMP. Other preferred chimeric proteins comprise fragments of PMPE, HMW protein, MOMP, PMPH, and C. trachomatis HtrA. The sequences of C. trachomatis HtrA and C. trachomatis PMPH are disclosed in Stephens et al., 1998, Science 282:754-759 and in Genbank accession nos. AAC68420 (HtrA) and AE001360 (PMPH), which are all hereby incorporated by reference in their entireties.
PMP-derived polypeptides also include but are not limited to fusion polypeptides comprising at least two regions derived from one or more Chlamydia proteins, each having T-cell or antibody stimulating activity. The regions may be derived from the same Chlamydia protein or may comprise one or more regions from more than one Chlamydia protein. The polypeptides are arranged in a nonsequential order or noncontiguous order (e.g., in an order different from the order of the amino acids of the native protein). A preferred polypeptide of the invention is a fusion polypeptide comprising at least two peptides, each of which peptides consists of an amino acid sequence selected from the group consisting of SEQ ID NOs.:5, 6, 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, and 34, with the proviso that the peptides are arranged in a configuration that is different from the configuration of a naturally occurring PMPE or PMPI polypeptide.
Other preferred PMP-derived polypeptides of the invention are fusion polypeptides wherein the polypeptide comprises all the peptides consisting of the amino acid sequences of SEQ ID NOs.:5, 6, 7, 8, 9, 10 and 11, or a fusion polypeptide wherein the polypeptide comprises all the peptides consisting of the amino acid sequences of SEQ ID NOs.:23, 24, 25, 26, 27, 28, and 29, with the proviso that the peptides are arranged in a configuration that is different from the configuration of a naturally occurring PMPE or PMPI polypeptide. A preferred PMP-derived polypeptide is a fusion polypeptide comprising a peptide consisting of an amino acid sequence of any of SEQ ID NOs.:5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28 or 29, with the proviso that the peptides are arranged in a configuration that is different from the configuration of a naturally occurring PMPE or PMPI polypeptide. In a preferred embodiment, the fusion proteins of the invention are isolated.
Other preferred PMP-derived polypeptides of the invention are fusion proteins comprising one or more peptides comprising or consisting of the amino acid sequences of SEQ ID NOs:5-34, and one or more fragments (preferably, epitope containing fragments) of one or more other C. trachomatis proteins, including but not limited to HMW protein, PMPH, HtrA, and MOMP. Preferred chimeric fusion proteins comprise an amino terminal fragment of HMW protein and one or more fragments of MOMP. Particularly preferred chimeric PMPE or PMPI polypeptides comprise one or more fragments of MOMP which comprise or consist of amino acid residues 273-333, 64-85, 139-160, 224-237, 288-317, 1-200, 64-350, 160-350, 240-333 or 80-105 (for sequence and numbering, see Batteiger et al., 1996, Infect. Immun. 64:542-547 and Yuan et al., 1989, Infect. Immun., 57:1040-1049, both of which are hereby incorporated by reference in their entireties). Preferred PMPE or PMPI chimeric polypeptides may also comprise fragments of HMW protein which comprises or consists of residues 1-500 or residues 23-500 or residues 1-100, 1-200, 1-300, or 1-400. The fragments of HMW protein, MOMP, HtrA and PMPH are at least 8, 10, 15, 20, 25, 30, 50, 75 or 100 amino acid fragments.
If desired, the amino acid sequences of the regions can be produced and joined by a linker.
Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their ability to adopt a secondary structure that could interact with functional epitopes of the first and second polypeptides; (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes; (4) the ability to increase solubility; and (5) the ability to increase sensitivity to processing by antigen-presenting cells. Such linkers can be any amino acid sequence or other appropriate link or joining agent.
Linkers useful in the invention include linkers comprising a charged amino acid pair such as KK or RR, linkers sensitive to cathepsin and/or other trypsin-like enzymes, thrombin or Factor Xa, or linkers which result in an increase in solubility of the polypeptide.
Preferred peptide linker sequences contain Gly, Asn and Ser residues. Amino acid sequences which may be usefully employed as linkers include those disclosed in Maratea et al. Gene 40:39-46 (1985); Murphy et al., Proc. Nat. Acad Sci USA 83:8258-8562 (1986); U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180. The linker sequence may be from 1 to about 50 amino acids in length.
Another particular example of fusion polypeptides of the invention includes a PMP polypeptide or PMP-derived polypeptide of the invention fused to a polypeptide having adjuvant activity, such as the subunit B of either cholera toxin or E. coli heat labile toxin. Another particular example of a fusion polypeptide encompassed by the invention includes a PMP polypeptide or PMP-derived polypeptide of the invention fused to a cytokine (such as, but not limited to, IL-2, IL-4, IL-10, IL-12, or interferon). A polypeptide of the invention can be fused to the N— or C-terminal end of a polypeptide having adjuvant activity. Alternatively, a polypeptide of the invention can be fused within the amino acid sequence of the polypeptide having adjuvant activity.
Also preferably, the PMP-derived fusion polypeptides of the invention comprise sequences that form one or more epitopes of a native Chlamydia PMP polypeptide that elicit bactericidal or opsonizing antibodies and/or T-cells. Such preferred PMP-derived polypeptides may be identified by their ability to generate antibodies and/or T-cells that kill cells infected with Chlamydia spp. cells particularly, Chlamydia trachomatis cells.
5.3. Isolation and Purification of PMP Polypeptides and PMP-Derived Polypeptides
The invention provides isolated PMPE and PMPI polypeptides, PMPE-derived and PMPI-derived polypeptides. As used herein, the term “isolated” means that the product has been removed from other biological materials with which it is naturally associated, or free from other biological materials derived, for example, from a recombinant host cell that has been genetically engineered to express the polypeptide of the invention. As used herein, the term “purified” means that the product is substantially free of other biological material with which it is naturally associated, or free from other biological materials derived, for example, from a recombinant host cell that has been genetically engineered to express the polypeptide of the invention. That is, a purified PMP polypeptide composition is at least 70-95% pure PMP polypeptide by weight, preferably at least 75% pure PMP polypeptide by weight, and more preferably at least 95% pure PMP polypeptide by weight, or most preferably 98% or 99% pure PMP polypeptide by weight. Thus, a Chlamydia lysate or membrane preparation on an acrylamide gel (with or without SDS), including a portion of the gel containing one or more protein bands, of a Chlamydia lysate or membrane preparation of Chlamydia is not a purified preparation or composition of PMPE or PMPI, since the gel comprises other Chlamydia proteins and by weight PMPE or PMPI does not constitute at least 70% pure PMP polypeptide by weight, preferably at least 75% pure PMP polypeptide by weight, and more preferably at least 95% pure PMP polypeptide by weight, or most preferably 98% or 99% pure PMP polypeptide by weight of the preparation or composition. However, a preparation of PMPE or PMPI obtained by eluting the PMPE or PMPI band from the acrylamide gel is a purified preparation of PMPE or PMPI.
The PMP polypeptide of the invention may be isolated from a protein extract, including a whole cell extract of any Chlamydia spp., including, but not limited to, Chlamydia trachomatis, Chlamydia pneumoniae, Chlamydia pecorum, and Chlamydia psittaci. Strains from any of these organisms may be obtained worldwide from any biologicals depository, for example, strains of ATCC VR-346, VR-347, VR-348B, VR-571B, VR-572, VR-573, VR-577, VR-578, VR-878, VF-879, VR-880, VR-885, VR-886, VR-887, VR-901B, VR-902B, VR-903, VR-1355, VR-1474, VR-1477, or VR-2282 maybe obtained from the American Type Culture Collection.
Another source of the PMP polypeptide is a protein preparation from a gene expression system (such as E. coli) engineered to express a cloned sequence encoding a PMP polypeptide or PMP-derived polypeptide (see Section 5.5, infra).
The PMP polypeptide can be isolated and purified from the source material using any biochemical technique and approach well known to those skilled in the art. In one approach, Chlamydia cellular envelope is obtained by standard techniques and inner membrane, periplasmic and outer membrane proteins are solubilized using a solubilizing compound such as a detergent or hypotonic solution. A preferred detergent solution is one containing octyl glucopyranoside (OG), sarkosyl or TRITON X100TM (t-octyl phenoxy-polyethoxy-ethanol). A preferred solubilizing hypotonic solution is one containing LiCl. The PMP polypeptide is in the solubilized fraction. Cellular debris and insoluble material in the extract are separated and removed preferably by centrifugation. The polypeptides in the extract are concentrated, incubated in SDS-containing Laemmli gel sample buffer at 100° C. for 5 minutes and then fractionated by electrophoresis in a denaturing sodium dodecylsulfate (SDS) polyacrylamide gel from about 6% to about 12%, with or without a reducing agent. See Laemmli, 1970, Nature 227:680-685. The band or fraction identified as a PMP polypeptide, having an apparent molecular weight of about 90-115 kDa, as described above, may then be purified directly from the fraction or gel slice containing the PMP polypeptide. In a preferred embodiment, the PMP polypeptide has an apparent molecular weight of about 90-115 kDa which can be determined by comparing its migration distance or rate in denaturing SDS-PAGE relative to the migration of known molecular weight markers such as of myosin (250 kDa), Phosphorylase B (148 kDa), BSA (98 kDa) and GDH (64 kDa) (weights for pre-stained markers).
Another method of purifying PMP polypeptide is by affinity chromatography using anti-PMP antibodies (see Section 5.4). The affinity chromatography may be carried out using either polyclonal or monoclonal anti-PMP antibodies, preferably, monoclonal antibodies. The antibodies are covalently linked to agarose gels activated by cyanogen bromide or succinamide esters (Affi-Gel, BioRad, Inc.) or by other methods known to those skilled in the art. The protein extract is loaded on the top of the gel and is left in contact with the gel for a period of time and under standard reaction conditions sufficient for PMP polypeptide to bind to the antibody. Preferably, the solid support is a material used in a chromatographic column. The affinity gel is washed to remove other proteins and cell materials not bound by the anti-PMP antibody. The PMP polypeptide is then removed from the antibody to recover the PMP polypeptide in isolated, or preferably, in purified form.
A PMP-derived polypeptide of the invention can be produced by chemical and/or enzymatic cleavage or degradation of an isolated or purified PMP polypeptide. A PMP-derived polypeptide can also be chemically synthesized based on the known amino acid sequence of the PMP polypeptide and, in the case of a chimeric polypeptide, the amino acid sequence of the heterologous polypeptide, by methods well known in the art. See, for example, Creighton, 1983, Proteins: Structures and Molecular Principles, W.H. Freeman and Co., NY.
A PMP-derived polypeptide can also be produced in a gene expression system expressing a recombinant nucleic acid construct comprising a sequence encoding a PMP-derived polypeptide. The nucleotide sequences encoding polypeptides of the invention may be synthesized, and/or cloned, and expressed according to techniques well known to those skilled in the art. See, for example, Sambrook, et al., 1989, Molecular Cloning A Laboratory Manual, Vols. 1-3, Cold Spring Harbor Press, NY, Chapter 9.
PMP-derived polypeptides of the invention can be fractionated and purified by the application of standard protein purification techniques, modified and applied in accordance with the discoveries and teachings described herein. In particular, preferred PMP polypeptides of the invention, those that form an outer-surface or exposed epitope of the native PMP polypeptide, may be isolated and purified according to the affinity procedures disclosed above for the isolation and purification of a PMP polypeptide (e.g., affinity purification using anti-PMP antibodies).
If desirable, the polypeptides of the invention may be further purified using standard protein or peptide purification techniques including but not limited to, electrophoresis, centrifugation, gel filtration, precipitation, dialysis, chromatography (including ion exchange chromatography, affinity chromatography, immunoadsorbent affinity chromatography, dye-binding chromatography, size exclusion chromatography, hydroxyapatite chromatography, reverse-phase high performance liquid chromatography, and gel permeation high performance liquid chromatography), isoelectric focusing, and variations and combinations thereof.
One or more of these techniques may be employed sequentially in a procedure designed to isolate and/or purify the PMP polypeptide or the PMP-derived polypeptides of the invention according to its/their physical or chemical characteristics. These characteristics include the hydrophobicity, charge, binding capability, and molecular weight of the protein. The various fractions of materials obtained after each technique are tested for binding to the PMP receptor or ligand or to anti-PMP antibodies or for functional activity (“test” activities). Those fractions showing such test activity are then pooled and subjected to the next technique in the sequential procedure, and the new fractions are tested again. The process is repeated until fractions are obtained that have one or more of the above described “test” activities and that contain only a single band (or a very predominant band) or entity when subjected to polyacrylamide gel electrophoresis or chromatography.
5.4. PMP Immunogens and Anti-PMP Antibodies
The present invention provides antibodies that specifically bind a PMP polypeptide and/or PMP-derived polypeptide. For the production of such antibodies, isolated or, preferably, purified preparations of a PMP polypeptide or PMP-derived polypeptide are used as immunogens in an immunogenic composition. The same immunogen can be used to immunize mice for the production of hybridoma lines that produce monoclonal anti-PMP antibodies. In particular embodiments, the immunogen is an isolated or purified PMP polypeptide or PMP-derived polypeptide from any Chlamydia strain, including, but not limited to, Chlamydia trachomatis, Chlamydia pneumoniae, Chlamydia pecorum, and Chlamydia psittaci. Particularly preferred are the strains of Chlamydia trachomatis from the American Type Culture Collection (ATCC): VR-346, VR-347, VR-348B, VR-571B, VR-572, VR-573, VR-577, VR-578, VR-878, VF-879, VR-880, VR-885, VR-886, VR-887, VR-901B, VR-902B, VR-903, VR-1355, VR-1474, VR-1477, VR-2282.
In other embodiments, peptide fragments of a PMP polypeptide are used as immunogens. Preferably, peptide fragments of a purified PMP polypeptide are used. The peptides may be produced by protease digestion, chemical cleavage of isolated or purified PMP polypeptide, chemical synthesis or by recombinant expression, after which they are then isolated or purified. Such isolated or purified peptides can be used directly as immunogens. In particular embodiments, useful peptide fragments are 8 or more amino acids in length.
Useful immunogens may also comprise such peptides or peptide fragments conjugated to a carrier molecule, preferably a carrier protein. Carrier proteins may be any commonly used in immunology, include, but are not limited to, bovine serum albumin (BSA), chicken albumin, keyhole limpet hemocyanin (KLH), tetanus toxoid and the like. For a discussion of hapten protein conjugates, see, for example, Harlow and Lane Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1988, or a standard immunology textbook such as Roitt, et al., IMMUNOLOGY, C.V. Mosby Co., St. Louis, Mo. (1985) or Klein, IMMUNOLOGY, Blackwell Scientific Publications, Inc., Cambridge, Mass. (1990).
In yet another embodiment, for the production of antibodies that specifically bind one or more epitopes (preferably, outer membrane epitopes) of a native PMP polypeptide, intact Chlamydia cells or elemental bodies (EBs) or reticulate bodies (RBs) prepared therefrom, or cells infected with Chlamydia are used as immunogen. The cells, EBs, RBs or cells infected with Chlamydia may be fixed with agents such as formaldehyde or glutaraldehyde before immunization. See Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1988, Chapter 15. It is preferred that such anti-whole cell antibodies be monoclonal antibodies. Hybridoma lines producing the desired monoclonal antibodies can be identified by using purified PMP polypeptide, intact Chlamydia cells, EBs, RBs or cells infected with Chlamydia as the screening ligand. The immunogen for inducing these antibodies may be whole Chlamydia cells, EBs, RBs, extracts or lysates of any Chlamydia, including, but not limited to, Chlamydia trachomatis, Chlamydia pneumoniae, Chlamydia pecorum, and Chlamydia psittaci. Particularly preferred are strains of Chlamydia strains ATCC VR-346, VR-347. VR-348B, VR-571B, VR-572, VR-573, VR-577, VR-578, VR-878, VF-879, VR-880, VR-885, VR-886, VR-887, VR-901B, VR-902B, VR-903, VR-1355, VR-1474, VR-1477, VR-2282.
Polyclonal antisera produced by immunization with cells infected with Chlamydia, whole cells, EBs or RBs contain antibodies that bind other Chlamydia proteins (“non-anti-PMP antibodies”) and thus are more cumbersome to use when it is known or suspected that the sample contains other Chlamydia proteins or materials that are cross-reactive with these other proteins. Under such circumstances, any binding by the anti-whole cell antibodies of a given sample or band must be verified by coincidental binding of the same sample or band by antibodies that specifically bind the PMP polypeptide (e.g., anti-PMPE antibodies or anti-PMPI antibodies) and/or a PMP-derived polypeptide, or by competition tests using anti-PMP antibodies, PMP polypeptides or PMP-derived polypeptides as the competitor (i.e., addition of anti-PMP antibodies, PMP polypeptide or PMP-derived polypeptide to the reaction mix lowers or abolishes sample binding by anti-whole cell antibodies). Alternatively, such polyclonal antisera containing “non-anti-PMP” antibodies, may be cleared of such non-anti-PMP antibodies by standard approaches and methods. For example, the non-anti-PMP antibodies may be removed by precipitation with cells having a deletion of the PMP coding sequence or Chlamydia strains known not to have the PMP polypeptide; or by absorption to columns comprising such cells or outer membrane proteins of such cells.
In further embodiments, useful immunogens for eliciting antibodies of the invention comprise mixtures of two or more of any of the above-mentioned individual immunogens.
Immunization of animals with the immunogens described herein, preferably of humans, rabbits, rats, ferrets, mice, sheep, goats, cows or horses, is performed following procedures well known to those skilled in the art, for purposes of obtaining antisera containing polyclonal antibodies or hybridoma lines secreting monoclonal antibodies.
Monoclonal antibodies can be prepared by standard techniques, given the teachings contained herein. Such techniques are disclosed, for example, in U.S. Pat. No. 4,271,145 and U.S. Pat. No. 4,196,265. Briefly, an animal is immunized with the immunogen. Hybridomas are prepared by fusing spleen cells from the immunized animal with myeloma cells. The fusion products are screened for those producing antibodies that bind to the immunogen. The positive hybridomas clones are isolated, and the monoclonal antibodies are recovered from those clones.
Immunization regimens for production of both polyclonal and monoclonal antibodies are well known in the art. The immunogen may be injected by any of a number of routes, including subcutaneous, intravenous, intraperitoneal, intradermal, intramuscular, mucosal, or a combination of these. The immunogen may be injected in soluble form, aggregate form, attached to a physical carrier, or mixed with an adjuvant, using methods and materials well known in the art. The antisera and antibodies may be purified using column chromatography methods well known to those of skill in the art.
The antibodies may also be used as probes for identifying clones in expression libraries that have or may have inserts encoding one or more PMP polypeptides or fragments thereof. The antibodies, PMP polypeptides or PMP-derived polypeptides may also be used in immunoassays (e.g., ELISA, RIA, Western Blots) to specifically detect and/or quantitate Chlamydia or anti-Chlamydia antibody in biological specimens. Anti-PMP antibodies of the invention specifically bind PMP polypeptide from Chlamydia trachomatis, Chlamydia pneumoniae, Chlamydia pecorum, and/or Chlamydia psittaci. Thus anti-PMP antibodies can be used to diagnose Chlamydia infections.
The antibodies of the invention, including but not limited to those that are cytotoxic, cytostatic, or neutralizing, may also be used in passive immunization to prevent or attenuate Chlamydia infections of animals, including humans. As used herein, a cytotoxic antibody is one that enhances opsonization and/or complement killing of the bacterium bound by the antibody. As used herein, neutralizing antibody is one that reduces the infectivity of the Chlamydia and/or blocks binding of Chlamydia to a target cell. An effective concentration of polyclonal or monoclonal antibodies raised against the immunogens of the invention may be administered to a host to achieve such effects. The exact concentration of the antibodies administered will vary according to each specific antibody preparation, but may be determined using standard techniques well known to those of ordinary skill in the art. Administration of the antibodies may be accomplished using a variety of techniques, including, but not limited to those described in Section 5.7 for the delivery of vaccines.
Another aspect of the invention is directed to antisera raised against an antigenic or immunogenic composition of the invention, and antibodies present in the antisera that specifically bind a PMP protein or a fragment or analogue thereof.
Preferably, the antibodies bind a PMP polypeptide having the amino acid sequence selected from the group consisting of SEQ ID NOs.:2, 4-34 and 73 and a PMP-derived polypeptide. Also included are monoclonal antibodies that specifically bind a PMP polypeptide having the amino acid sequence selected from the group consisting of SEQ ID NOs.:2, 4-34, and 73 and a PMP-derived polypeptide. The term “antibodies” is intended to include all forms, such as but not limited to polyclonal, monoclonal, purified IgG, IgM, or IgA antibodies and fragments thereof, including but not limited to antigen binding fragments such as Fv, single chain Fv (scFv), F(ab.)2, Fab, and F(ab)′ fragments (Harlow and Lane, 1988, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press); single chain antibodies (U.S. Pat. No. 4,946,778) and complementary determining regions (CDR), (see Verhoeyen and Winter, in Molecular Immunology 2ed., by B. D. Hames and D. M. Glover, IRL Press, Oxford University Press, 1996, at pp. 283-325), etc.
A further aspect of the invention are chimeric or humanized antibodies (Morrison et al., 1984, Proc. Nat'l Acad. Sci. USA 81:6851; Reichmann et al. Nature 332:323: U.S. Pat. Nos. 5,225,539; 5,585,089; and 5,530,101; Neuberger et al., 1984, Nature 81:6851 Riechmann et al., 1988, Nature 332:323; U.S. Pat. Nos. 5,225,539; 5,585,089; and 5,530,101) in which one or more of the antigen binding regions of the anti-PMP antibody is introduced into the framework region of a heterologous (e.g., human) antibody. The chimeric or humanized antibodies of the invention are less antigenic in humans than non-human antibodies but have the desired antigen binding and other activities, including but not limited to neutralizing activity, cytotoxic activity, opsonizing activity or protective activity.
In a preferred embodiment, the antibodies of the invention are human antibodies. Human antibodies may be isolated, for example, from human immunoglobulin libraries (see, e.g., PCT publications WO 98/46645, WO 98/50433, WO 98/24893, WO 98/16054, WO 96/34096, WO 96/33735, and WO 91/10741) by, preferably, phage display techniques (see, e.g., Brinkman et al., J. Immunol. Methods 182:41-50 (1995); Ames et al., J. Immunol. Methods 184:177-186 (1995); Kettleborough et al., Eur. J. Immunol. 24:952-958 (1994); Persic et al., Gene 187 9-18 (1997); Burton et al., Advances in Immunology 57:191-280 (1994); PCT application No. PCT/GB91/01134; PCT publications WO 90/02809; WO 91/10737; WO 92/01047; WO 92/18619; WO 93/11236; WO 95/15982; WO 95/20401; and U.S. Pat. Nos. 5,698,426; 5,223,409; 5,403,484; 5,580,717; 5,427,908; 5,750,753; 5,821,047; 5,571,698; 5,427,908; 5,616,637; 5,780,225; 5,658,727; 5,733,743 and 5,969,108; each of which is incorporated herein by reference in its entirety. Human antibodies may also be generated from animals transgenic for one or more human immunoglobulin and that do not express endogenous immunoglobulins, see, e.g., U.S. Pat. No. 5,939,598 by Kucherlapati et al.
A further aspect of the invention is T-cells specific for Chlamydia, Chlamydial EB, RBs, Chlamydia infected cells or antigen presenting cells displaying Chlamydial antigens. T-cell preparations enriched for T-cells specific for PMP or PMP-derived polypeptides can be produced or isolated by methods known in the art (See section 5.8).
5.5. Nucleic Acids Encoding the PMP Polypeptide and PMP Derived Polypeptides
The isolated nucleic acids of the present invention, including DNA and RNA, comprising a sequence encoding the PMP protein or PMP-derived polypeptide thereof, may be synthesized using methods known in the art, such as using conventional chemical approaches or polymerase chain reaction (PCR) amplification using convenient pairs of oligonucleotide primers and ligase chain reaction using a battery of contiguous oligonucleotides. The sequences also allow for the identification and cloning of the PMP protein gene from any species or serovar of Chlamydia, for instance for screening Chlamydial genomic libraries or expression libraries as described below.
In a particular embodiment, the PMP polypeptide comprises an amino acid sequence of either SEQ ID NO.:2,4 or 73 and the nucleic acids comprise nucleotide sequences encoding said amino acid sequences. Particularly preferred fragments of PMP have 8 or more amino acids of the amino acid sequences of SEQ ID NOs.:2, 4 or 73 or sequences substantially homologous thereto, and the invention encompasses nucleic acids comprising nucleotide sequences encoding said amino acid sequences. In another particular embodiment, the PMP polypeptide is encoded by the nucleotide sequence of SEQ ID NOs.:1, 3 or 72, with particularly preferred fragments having a nucleotide sequence of NOs.:36-65, or sequences substantially homologous thereto.
The term “isolated nucleic acid” or “isolated nucleic acid molecule” is defined as a nucleic acid molecule removed from the environment in which it naturally occurs. For example, a naturally-occurring DNA molecule present in the genome of a living bacteria or as part of gene bank is not isolated, but the same molecule separated from the remaining part of the bacterial genome, as a result of, e.g., a cloning event (amplification) is isolated. Typically, an isolated DNA molecule is free from DNA regions (e.g., coding regions) with which it is immediately contiguous at the 5′ or 3′ end, in the naturally occurring genome. Such isolated nucleic acids or nucleic acid molecules could be part of a vector or a composition and still be isolated in that such a vector or composition is not part of its natural environment. However, “isolated nucleic acid” or “isolated nucleic acid molecule” does not include a nucleic acid that is part of a recombinant library.
Nucleic acids of the present invention can be single or double stranded. The invention also provides nucleic acids hybridizable to or complementary to SEQ ID NO.:1, 3 or 72 or fragments thereof, as well as polypeptides encoded by these nucleic acids. In specific aspects, nucleic acids are provided which comprise a sequence fully complementary to or complementary to at least 10, 15, 25, 50, 100, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400 or 1500 contiguous nucleotides of a nucleic acid encoding a PMP polypeptide or an PMP-derived polypeptide. In a specific embodiment, a nucleic acid which is hybridizable to a nucleic acid encoding a PMP polypeptide (e.g., having a nucleotide sequence of SEQ ID NO.:1, 3 or 72 or to a nucleic acid encoding a PMP-derived polypeptide, under conditions of low, moderate or high stringency is provided). Also provided are fragments of nucleic acids encoding a PMP polypeptide or PMP-derived polypeptide of the invention (or complements thereof) where such fragments are at least 10, 15, 25, 50, 100, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400 or 1500 nucleotides and in certain embodiments no more than 50, 75, 100, 150, 200, 250, 300, 500, 600, 800, 1000, 1500, 2000, 2500 or 3000 nucleotides in length.
By way of example and not limitation, procedures using such conditions of low stringency are as follows (see also Shilo and Weinberg, 1981, Proc. Natl. Acad. Sci. USA 78:6789-6792): Filters containing DNA are pretreated for 6 h at 40° C. in a solution containing 35% formamide, 5×SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.1% PVP, 0.1% Ficoll, 1% BSA, and 500 μg/ml denatured salmon sperm DNA. Hybridizations are carried out in the same solution with the following modifications: 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 μg/ml salmon sperm DNA, 10% (wt/vol) dextran sulfate, and 5-20×106 cpm 32P-labeled probe is used. Filters are incubated in hybridization mixture for 18-20 h at 40° C., and then washed for 1.5 h at 55° C. in a solution containing 2×SSC, 25 mM Tris-HCl (pH 7.4), 5 mM EDTA, and 0.1% SDS. The wash solution is replaced with fresh solution and incubated an additional 1.5 h at 60° C. Filters are blotted dry and exposed for autoradiography. If necessary, filters are washed for a third time at 65-68° C. and re-exposed to film. Other conditions of low stringency which may be used are well known in the art (e.g., as employed for cross-species hybridizations).
In another specific embodiment, a nucleic acid which is hybridizable to a nucleic acid encoding a PMP polypeptide or a PMP-derived polypeptide under conditions of high stringency is provided. By way of example and not limitation, procedures using such conditions of high stringency are as follows: Prehybridization of filters containing DNA is carried out for 8 h to overnight at 65° C. in buffer composed of 6×SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 μg/ml denatured salmon sperm DNA. Filters are hybridized for 48 h at 65° C. in prehybridization mixture containing 100 μg/ml denatured salmon sperm DNA and 5-20×106 cpm of 32P-labeled probe. Washing of filters is done at 37° C. for 1 h in a solution containing 2×SSC, 0.01% PVP, 0.01% Ficoll, and 0.01% BSA. This is followed by awash in 0.1×SSC at 50° C. for 45 min before autoradiography. Other conditions of high stringency which may be used are well known in the art.
In another specific embodiment, a nucleic acid which is hybridizable to a nucleic acid encoding a PMP polypeptide or a PMP-derived polypeptide under conditions of moderate stringency is provided.
Various other stringency conditions which promote nucleic acid hybridization can be used. For example, hybridization in 6×SSC at about 45° C., followed by washing in 2×SSC at 50° C. may be used. Alternatively, the salt concentration in the wash step can range from low stringency of about 5×SSC at 50° C., to moderate stringency of about 2×SSC at 50° C., to high stringency of about 0.2×SSC at 50° C. In addition, the temperature of the wash step can be increased from low stringency conditions at room temperature, to moderately stringent conditions at about 42° C., to high stringency conditions at about 65° C. Other conditions include, but are not limited to, hybridizing at 68° C. in 0.5M NaHPO4 (pH7.2)/1 mM EDTA/7% SDS, or hybridization in 50% formamide/0.25M NaHPO4 (pH 7.2)/0.25 M NaCl/1 mM EDTA/7% SDS; followed by washing in 40 mM NaHPO4 (pH 7.2)/1 mM EDTA/5% SDS at 42° C. or in 40 mM NaHPO4 (pH7.2)/1 mM EDTA/1% SDS at 50° C. Both temperature and salt may be varied, or alternatively, one or the other variable may remain constant while the other is changed.
Low, moderate and high stringency conditions are well known to those of skill in the art, and will vary predictably depending on the base composition of the particular nucleic acid sequence and on the specific organism from which the nucleic acid sequence is derived. For guidance regarding such conditions see, for example, Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y.
In the preparation of genomic libraries, DNA fragments are generated, some of which will encode parts or the whole of a Chlamydia PMPE or PMPI protein. The DNA may be cleaved at specific sites using various restriction enzymes. Alternatively, one may use DNase in the presence of manganese to fragment the DNA, or the DNA can be physically sheared, as for example, by sonication. The DNA fragments can then be separated according to size by standard techniques, including but not limited to, agarose and polyacrylamide gel electrophoresis, column chromatography and sucrose gradient centrifugation. The DNA fragments can then be inserted into suitable vectors, including but not limited to plasmids, cosmids, bacteriophages lambda or T4, bacmids and yeast artificial chromosome (YAC). (See, for example, Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, 2d Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Glover, D. M. (ed.), 1985, DNA Cloning: A Practical Approach, MRL Press, Ltd., Oxford, U.K. Vol. I, II.) The genomic library may be screened by nucleic acid hybridization to labeled probe (Benton and Davis, 1977, Science 196:180; Grunstein and Hogness, 1975, Proc. Natl. Acad. Sci. U.S.A. 72:3961). The genomic libraries maybe screened with labeled degenerate oligonucleotide probes corresponding to the amino acid sequence of any peptide of PMP protein using optimal approaches well known in the art. Any probe used preferably is 15 nucleotides or longer.
The term “probe” as used herein refers to DNA (preferably single stranded) or RNA molecules that hybridize under stringent conditions as defined above, to nucleic acids having sequences homologous to SEQ ID NO.:1, SEQ ID NO.:3, or SEQ ID NO:72, or to a complementary or anti-sense sequence thereof. Generally, probes are significantly shorter than full-length sequences shown in SEQ ID NOs.:1, 3 or 72.
For example, they can contain from about 5 to about 100 nucleotides preferably from about 10 to about 80 nucleotides. In particular, probes have sequences that are at least 75% preferably at lest 85%, and more preferably 95%, homologous to a portion of a sequence of SEQ ID NOs.:1, 3 or 72, or complementary to such sequences. Probes can contain modified bases such as inosine, methyl-5-deoxycytidine, deoxyuridine, dimethylamino-5-deoxyuridine, or diamino-2,6 purine.
Clones in libraries with insert DNA encoding a PMP protein or a PMP-derived polypeptides will hybridize to one or more of the degenerate oligonucleotide probes. Hybridization of such oligonucleotide probes to genomic libraries is carried out using methods known in the art. For example, hybridization with the two above-mentioned oligonucleotide probes may be carried out in 2×SSC, 1.0% SDS at 50° C. and washed using the same conditions.
In yet another aspect, clones of nucleotide sequences encoding a part or the entire PMP protein or PMP-derived polypeptide may also be obtained by screening Chlamydia expression libraries. For example, Chlamydia DNA or Chlamydia cDNA generated from RNA is isolated and random fragments are prepared and ligated into an expression vector (e.g., a bacteriophage, plasmid, phagemid or cosmid) such that the inserted sequence in the vector is capable of being expressed by the host cell into which the vector is then introduced. Various screening assays can then be used to select for the expressed PMP-protein or PMP-derived polypeptides. In one embodiment, the various anti-PMP antibodies of the invention can be used to identify the desired clones using methods known in the art. See, for example, Harlow and Lane, 1988, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., Appendix IV. Clones or plaques from the library are brought into contact with the antibodies to identify those clones that bind.
In an embodiment, colonies or plaques containing DNA that encodes a PMP protein or PMP-derived polypeptide could be detected using DYNA Beads according to Olsvick et al., 29th ICAAC, Houston, Tex. 1989, incorporated herein by reference. Anti-PMP antibodies are crosslinked to DYNA Beads M280, and these antibody-containing beads are used to adsorb to colonies or plaques expressing a PMP protein or a PMP derived polypeptide. Colonies or plaques expressing a PMP protein or a PMP derived polypeptide are identified as any of those that bind the beads.
Alternatively, the anti-PMP antibodies can be nonspecifically immobilized to a suitable support, such as silica or CELITETM resin. This material is used to adsorb to bacterial colonies expressing a PMP protein or a PMP derived polypeptide as described in the preceding paragraph.
In another aspect, PCR amplification may be used to produce substantially pure DNA encoding a part of or the whole of a PMP protein from Chlamydia genomic DNA. Oligonucleotide primers, degenerate or otherwise, corresponding to known PMP protein sequences can be used as primers.
In particular embodiments, an oligonucleotide encoding a portion of SEQ ID NO.:2, 4 or 73 may be used as the 5′ primer. For fragment examples, a 5′ primer may be made from any one of the nucleotide sequences of SEQ ID NO.:66 or 69 or any portion thereof. For 3′ primers, a nucleotide sequence of SEQ ID NO.:67 or 70 or any portion thereof may be used.
As examples, an oligonucleotide encoding the N-terminal primer, and together with a 3′ reverse PCR oligonucleotide complementary to an internal, dow stream protein coding sequence may be used to amplify an N-terminal-specific PMP DNA fragment. Alternatively, an oligonucleotide encoding an internal PMP coding sequence may be used as the 5′ forward PCR primer together with a 3′ reverse PCR oligonucleotide complementary to downstream, internal PMP protein coding sequences may be used to PCR amplify an internal PMP specific DNA fragment. Alternatively, the forward primer can be combined together with an oligonucleotide complementary to the C-terminal PMP coding region to PCR amplify the PMP ORF. These PMP specific PCR products can be cloned into appropriate expression vectors to direct the synthesis of all or part of the PMP polypeptide as distinct proteins or fusion proteins. Alternatively, these PMP specific PCR products can be appropriately labeled and used as hybridization probes to identify all or part of the PMP gene from genomic DNA libraries.
PCR can be carried out, e.g., by use of a Perkin-Elmer thermal cycler and Taq polymerase (GENE AMPTM). One can choose to synthesize several different degenerate primers, for use in the PCR reactions. It is also possible to vary the stringency of hybridization conditions used in priming the PCR reactions, to allow for greater or lesser degrees of nucleotide sequence similarity between the degenerate primers and the corresponding sequences in Chlamydia DNA. After successful amplification of a segment of the sequence encoding a PMP protein, that segment may be molecularly cloned and sequenced, and utilized as a probe to isolate a complete genomic clone. This, in turn, will permit the determination of the gene's complete nucleotide sequence, the analysis of its expression, and the production of its protein product for functional analysis, as described infra.
Once a PMP polypeptide coding sequence has been isolated from one Chlamydia species, strain, or cultivar, it is possible to use the same approach to isolate PMP polypeptide coding sequences from other Chlamydia species, strains and cultivars. It will be recognized by those skilled in the art that the DNA or RNA sequence encoding PMP polypeptides (or fragments thereof) of the invention can be used to obtain other DNA or RNA sequences that hybridize with it under conditions of moderate to high stringency, using general techniques known in the art (see supra). Hybridization with a PMP sequence from one Chlamydia strain or cultivar under high stringency conditions will identify the corresponding sequences from other strains and cultivars. High stringency conditions vary with probe length and base composition. The formulae for determining such conditions are well known in the art. See Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, NY, Chapter 11. As an example, high stringency hybridization conditions as applied to probes of greater than 300 bases in length involve a final wash in 0.1×SSC/0.1% SDS at 68° C. for at least 1 hour (Ausubel, et al., Eds., 1989, Current Protocols in Molecular Biology, Vol. I, Greene Publishing Associates, Inc and John Wiley & Sons, Inc. New York, at page 2.10.2). See also, the description of high stringency conditions, supra.
One skilled in the art would be able to identify complete clones of a PMP polypeptide coding sequence using approaches well known in the art. The extent of the PMP polypeptide coding sequence contained in an isolated clone may be ascertained by sequencing the cloned insert and comparing the deduced size of the polypeptide encoded by the open reading frames (ORFs) with that of the PMP polypeptide and/or by comparing the deduced amino acid sequence with that of known amino acid sequence of the purified PMP polypeptide. Where a partial clone of the PMP polypeptide coding sequence has been isolated, complete clones may be isolated by using the insert of the partial clone as a hybridization probe. Alternatively, a complete PMP polypeptide coding sequence can be reconstructed from overlapping partial clones by splicing their cloned PMP inserts together or by using the sequence information in the partial clones to design primers for PCR to amplify the entire PMP coding region from an appropriate source such as Chlamydia genomic DNA or cDNA.
Complete clones may be any that an ORF with a deduced amino acid sequence matching or homologous to that of the PMP polypeptide or, where the complete amino acid sequence of the latter is not available, matching or homologous to that of a peptide fragment of a PMP polypeptide and having a molecular weight corresponding to that of the PMP polypeptide. Further, complete clones may be identified by the ability of their inserts, when placed in an expression vector, to produce a polypeptide that binds antibodies specific to the amino-terminus of the PMP polypeptide and antibodies specific to the carboxyl-terminus of the PMP polypeptide.
Nucleic acids encoding PMP-derived polypeptides and PMP fusion proteins may be produced by methods well known in the art. In one aspect, nucleic acids encoding PMP-derived polypeptides can be derived from PMP polypeptide coding sequences by recombinant DNA methods in view of the teachings disclosed herein. For example, the coding sequence of a PMP polypeptide may be altered creating amino acid substitutions that will not affect the immunogenicity of the PMP polypeptide or which may improve its immunogenicity, such as conservative or semi-conservative substitutions as described above. Various methods may be used, including but not limited to, oligonucleotide directed, site specific mutagenesis. This and other techniques known in the art may be used to create single or multiple mutations, such as replacements, insertions, deletions, and transpositions, for example, as described in Botstein and Shortle, 1985, Science 229:1193-1210.
In another preferred embodiment, the nucleic acid encoding a PMPE or PMPI protein is a synthetic nucleic acid in which the codons have been optimized for increased expression in the host cell in which it is produced. The degeneracy of the genetic code permits variations of the nucleotide sequence, while still producing a polypeptide having the identical amino acid sequence as the polypeptide encoded by the native DNA sequence. The frequency of individual synonymous codons for amino acids varies widely from genome to genome among eucaryotes and procaryotes. These differences in codon choice patterns appear to contribute to the overall expression levels of individual genes by modulating peptide elongation rates. For this reason it is desirable and useful to design nucleic acid molecules intended for a particular expression system where the codon frequencies reflect the tRNA frequencies of the host cell or organism in which the protein is expressed. Native codons are exchanged for codons of highly expressed genes in the host cells. For instance, the nucleic acid molecule can be optimized for expression of the encoded protein in bacterial cells (e.g., E. coli), yeast (e.g., Pichia), insect cells (e.g., Drosophila), or mammalian cells or animals (e.g., human, sheep, bovine or mouse cells or animals).
Restriction enzyme sites critical for gene synthesis and DNA manipulation are preserved or destroyed to facilitate nucleic acid and vector construction and expression of the encoded protein. In constructing the synthetic genes of the invention it may be desirable to avoid CpG sequences as these sequences may cause gene silencing. Thus, in a preferred embodiment the coding region of the synthetic nucleic acid molecule does not include the sequence “CG” or includes less than 5, 8, 10, 12, 15, 20 or 30 occurrences of the sequence “CG.” The codon optimized sequence is synthesized and assembled and inserted into an appropriate expression vector using conventional techniques well known to those of skill in the art.
In a particularly preferred embodiment, a synthetic nucleic acid encoding a PMPE or PMPI protein comprises at least one codon substitution in which non-preferred or less preferred codon in the natural gene encoding the protein has been replaced by a preferred codon encoding the same amino acid. For instance in humans the preferred codons are: Ala (GCC); Arg (CGC); Asn (AAC); Asp (GAC); Cys (TGC); Gln (CAG); Gly (GGC); His (CAC); Ile (ATC); Leu (CTG); Lys (AAG); Pro (CCC); Phe (TTC); Ser (AGC); Thr (ACC); Tyr (TAC); and Val (GTG). Less preferred codons are: Gly (GGG); Ile (ATT); Leu (CTC); Ser (TCC); Val (GTC); and Arg (AGG). All codons which do not fit the description of preferred codons or less preferred codons are non-preferred codons. In general, the degree of preference of a particular codon is indicated by the prevalence of the codon in highly expressed genes. Codon preference for highly expressed human genes are as indicated in Table 3. For example, “ATC” represents 77% of the Ile codons in highly expressed mammalian genes and is the preferred Ile codon; “ATT” represents 18% of the Ile codons in highly expressed mammalian genes and is the less preferred Ile codon. The sequence “ATA” represents only 5% of the Ile codons in highly expressed human genes and is a non-preferred Ile codon. Replacing a codon with another codon that is more prevalent in highly expressed human genes will generally increase expression of the gene in mammalian cells. Accordingly, the invention includes replacing a less preferred codon with a preferred codon as well as replacing a non-preferred codon with a preferred or less preferred codon.
The synthetic nucleic acid is optimized for expression of the encoded protein and at least one non-preferred or less preferred coding in a nucleic acid molecule encoding the protein is replaced by a preferred or more preferred codon encoding the same amino acid. The synthetic nucleic acid expresses the encoded protein at a level which is at least 110%, 125%, 150%, 200%, 500% of that expressed by the starting nucleic acid molecule (i.e., prior to optimization) in an in vitro cell culture system under identical conditions. In addition, preferably the synthetic nucleic acid molecule comprises fewer than 5, 8, 10, 12, 15, 20 or 30 occurrences of the sequence CG. Preferably at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% of the non-preferred codons and less preferred codons in the nucleic acid molecule have been replaced by preferred codons or more preferred codons.
In a particularly preferred embodiment, the nucleic acid has been optimized for expression of the encoded protein in human or mammalian cells or organisms.








TABLE 3





Codon Frequency (Percentage) in highly expressed



human genes





















Ala
GC
C
53






T
17





A
13





G
17



 



Arg
CG
C
37





T
7





A
6





G
21




AG
A
10





G
18



 



Asn
AA
C
78





T
22



 



Asp
GA
C
75





T
25



 



Leu
CT
C
26





T
5





A
3





G
58




TT
A
2





G
6



 



Lys
AA
A
18





G
82



 



Pro
CC
C
48





T
19





A
16





G
17



 



Phe
TT
C
80





T
20



 



Cys
TG
C
68





T
32



 



Gln
CA
A
12





G
88



 



Glu
GA
A
25





G
75



 



Gly
GG
C
50





T
12





A
14





G
24



 



His
CA
C
79





T
21



 



Ile
AT
C
77





T
18





A
5



 



Ser
TC
C
28





T
13





A
5





G
9




AG
C
34





T
10



 



Thr
AC
C
57





T
14





A
14





G
15



 



Tyr
TA
C
74





T
26



 



Val
GT
C
25





T
7





A
5





G
64










Further, nucleic acids containing PMP polypeptide coding sequences may be truncated by restriction enzyme or exonuclease digestions. Heterologous coding sequences may be added to the PMP polypeptide coding sequence by ligation or PCR amplification Moreover, DNA encoding the whole or a part of PMP-derived polypeptide may be synthesized chemically or using PCR amplification based on the known or deduced amino acid sequence of the PMP polypeptide and any desired alterations to that sequence.
The identified and isolated DNA containing the PMP polypeptide or PMP-derived polypeptide coding sequence can be inserted into an appropriate cloning vector. A large number of vector-host systems known in the art may be used. The term “host” as used herein and in the claims refers to either in vivo in an animal or in vitro in mammalian cell cultures.
Possible vectors include, but are not limited to, plasmids and modified viruses, but the vector system must be compatible with the host cell used. Such vectors include, but are not limited to, bacteriophage such as lambda derivatives, or plasmids such as pET, pBAD, pTrcHis, pBR322 or pUC plasmid derivatives. The insertion into a cloning vector can, for example, be accomplished by ligating the DNA fragment into a cloning vector which has complementary cohesive termini. However, if the complementary restriction sites used to fragment the DNA are not present in the cloning vector, the ends of the DNA molecules may be enzymatically modified. Alternatively, any site desired may be produced by ligating nucleotide sequences (linkers) onto the DNA termini; these ligated linkers may comprise specific chemically synthesized oligonucleotides encoding restriction endonuclease recognition sequences. In an alternative method, the cleaved DNA may be modified by homopolymeric tailing. Recombinant molecules can be introduced into host cells via transformation, transfection, infection, electroporation, etc., so that many copies of the gene sequence are generated.
In an alternative method, the desired DNA containing a PMP polypeptide or PMP-derived polypeptide coding sequence may be identified and isolated after insertion into a suitable cloning vector in a “shot gun” approach. Enrichment for the desired sequence, for example, by size fractionation, can be done before insertion into the cloning vector.
In specific embodiments, transformation of host cells with recombinant DNA molecules that contain a PMP polypeptide or PMP-derived polypeptide coding sequence enables generation of multiple copies of such coding sequence. Thus, the coding sequence may be obtained in large quantities by growing transformants, isolating the recombinant DNA molecules from the transformants and, when necessary, retrieving the inserted coding sequence from the isolated recombinant DNA.
The nucleotide sequences encoding the PMP polypeptides of the present invention are useful for their ability to selectively form duplex molecules with complementary stretches of other protein genes. Depending on the application, a variety of hybridization conditions may be employed to achieve hybridization with varying sequence identities. In specific aspects, nucleic acids are provided which comprise a sequence complementary to at least 10, 15, 25, 50, 100, 200 or 250 nucleotides of the PMP protein coding nucleic acid molecule. In specific embodiments, nucleic acids which hybridize to a PMP protein nucleic acid (e.g., having a nucleotide sequence of SEQ ID NO.:1, 3 or 72) under annealing conditions are provided.
For a high degree of selectivity, relatively stringent conditions are used to form the duplexes, such as, by way of example and not limitation, low salt and/or high temperature conditions, such as provided by 0.02 M to 0.15 M NaCl at temperatures of between about 50° C. to 70° C. For some applications, less stringent hybridization conditions are required, by way of example and not limitation, such as 0.15 M to 0.9 M salt, at temperatures ranging from between about 20° C. to 55° C. Hybridization conditions can also be rendered more stringent by the addition of increasing amounts of formamide, to destabilize the hybrid duplex. Thus, particular hybridization conditions can be readily manipulated, and will generally be a method of choice depending on the desired results.
5.6. Recombinant Production of PMP Polypeptide and PMP-Derived Polypeptides
In accordance with this invention, it is preferred to make the Chlamydia protein of the present invention by recombinant methods, particularly when the naturally occurring protein as isolated from a culture of a species of Chlamydia may include trace amounts of toxic materials or other contaminants. This problem can be avoided by using protein recombinantly produced in heterologous systems which can be isolated from the host in a manner to minimize contaminants in the isolated material. In this case, the PMP proteins are produced by an appropriate host cell that has been transformed by a DNA molecule that codes for the polypeptide.
The nucleic acids encoding the PMP polypeptides or PMP-derived polypeptides of the invention can be inserted into an appropriate expression vector, i.e., a vector that contains the necessary elements for the transcription and translation of the inserted polypeptide-coding sequence. The nucleotide sequences encoding the PMP polypeptides or PMP-derived polypeptides are inserted into the vectors in a manner such that they will be expressed under appropriate conditions (e.g., in proper orientation and correct reading frame). The recombinant expression vector also comprises an “expression means”. The term “expression means” refers to elements of a vector which are necessary for transcription and translation of the nucleic acid encoding the protein, including but not limited to promoter/enhancer elements, a replication site, an RNA polymerase binding sequence, a ribosomal binding sequence, sequences which are capable of providing phenotype selection (e.g., ampicillin or tetracycline resistance), peptide tags that permit isolation of the expressed protein, signal sequences that direct secretion of the expressed protein and replicon and control sequences that can be used to transform host cells. The expression means is operatively coupled to the nucleic acid molecule encoding the PMP protein by linking the inserted nucleic acid molecule into the expression vector.
Promoter/enhancer elements which may be used to control expression of inserted sequences include, but are not limited to the SV40 early promoter region (Bernoist and Chambon, 1981, Nature 290:304-310), the promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto et al., 1980, Cell 22:787-797), the herpes thymidine kinase promoter (Wagner et al., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:1441-1445), the regulatory sequences of the metallothionein gene (Brinster et al., 1982, Nature 296:39-42) for expression in animal cells; the promoters of lactamase (Villa-Kamaroff et al., 1978, Proc. Natl. Acad. Sci. U.S.A. 75:3727-3731), tac (DeBoer et al., 1983, Proc. Natl. Acad. Sci. U.S.A. 80:21-25), or trc for expression in bacterial cells (see also “Useful proteins from recombinant bacteria” in Scientific American, 1980, 242:74-94); the nopaline synthetase promoter region or the cauliflower mosaic virus 35S RNA promoter (Gardner et al., 1981, Nucl. Acids Res. 9:2871), and the promoter of the photosynthetic enzyme ribulose biphosphate carboxylase (Herrera-Estrella et al., 1984, Nature 310:115-120) for expression in plant cells; Gal4 promoter, the ADC (alcohol dehydrogenase) promoter, PGK (phosphoglycerol kinase) promoter, alkaline phosphatase promoter for expression in yeast or other fungi.
Depending on the host-vector system utilized, any one of a number of suitable transcription and translation elements may be used. In a preferred embodiment, a chimeric protein comprising a PMP protein or PMP-derived polypeptide sequence and a pre and/or pro sequence of the host cell is expressed. In other preferred embodiments, a chimeric protein comprising a PMP protein or PMP derived polypeptide sequence fused with, for example, an affinity purification peptide, including but not limited to, maltose binding protein, glutathione-S-transferase, thioredoxin or histidine tag, is expressed. In further preferred embodiments, a chimeric protein comprising a PMP protein or PMP-derived polypeptide sequence and a useful immunogenic peptide or protein is expressed.
Any method known in the art for inserting DNA fragments into a vector may be used to construct expression vectors containing a PMP or PMP-derived polypeptide encoding nucleic acid molecule consisting of appropriate transcriptional/translational control signals and the polypeptide coding sequences. These methods may include in vitro recombinant DNA and synthetic techniques and in vivo recombinantation (genetic recombination).
Methods of introducing exogenous DNA into yeast hosts include either the transformation of spheroplasts or of intact yeast cells treated with alkali cations. Transformation procedures usually vary with the yeast species to be transformed. See e.g., Kurtz et al. (1986) Mol. Cell. Biol. 6:142; Kunze et al. (1985) J. Basic Microbiol. 25:141; for Candida, Gleeson et al. (1986) J. Gen. Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet. 202:302; for Hansenula; Das et al. (1984) J. Bacteriol. 158:1165; De Louvencourt et al. (1983) J. Bacteriol. 154:1165; Van den Berg et al. (1990) Bio/Technology 8:135; for Kluyveromyces; Cregg et al. (1985) Mol. Cell. Biol. 5:3376; Kunze et al. (1985) J. Basic Microbiol. 25:141; U.S. Pat. No. 4,837,148 and U.S. Pat. No. 4,929,555; for Pichia; Hinnen et al. (1978) Proc. Natl. Acad. Sci. USA 75;1929; Ito et al. (1983) J. Bacteriol. 153:163; for Saccharomyces; Beach et al. (1981) Nature 300:706; for Schizosaccharomyces; Davidow et al. (1985) Curr. Genet. 10:39.
Expression vectors containing PMP polypeptide or PMP-derived polypeptide coding sequences can be identified by three general approaches: (a) nucleic acid hybridization; (b) presence or absence of “marker” gene functions; and (c) expression of inserted sequences. In the first approach, the presence of a foreign gene inserted into an expression vector can be detected by nucleic acid hybridization using probes comprising sequences that are homologous to the inserted PMP polypeptide or PMP-derived polypeptide coding sequence. In the second approach, the recombinant vector/host system can be identified and selected based upon the presence or absence of certain “marker” gene functions (e.g., thymidine kinase activity, resistance to antibiotics, transformation phenotype, occlusion body formation in baculovirus, etc.) caused by the insertion of foreign genes into the vector.
For example, E. coli may be transformed using pBR322 which contains genes for ampicillin and tetracycline resistance. If the PMP polypeptide or PMP-derived polypeptide coding sequence is inserted within the marker gene sequence of the vector, recombinants containing the insert can be identified by the absence of the marker gene function. In the third approach, recombinant expression vectors can be identified by assaying the foreign gene product expressed by the recombinant. Such assays can be based, for example, on the physical or functional properties of PMP polypeptide or PMP-derived polypeptide in vitro assay systems, e.g., binding of a His tag engineered into the expressed protein to a column, binding to a PMP ligand or receptor or binding with anti-PMP antibodies of the invention.
Commercially available vectors for expressing heterologous proteins in bacterial hosts include but are not limited to pZERO, pTrc99A, pUC19, pUC18, pKK223-3, pEX1, pCAL, pET, pSPUTK, pTrxFus, pFastBac, pThioHis, pTrcHis, pTrcHis2, and pLEx. For example, the phage in lambda GEMTM-11 may be utilized in making recombinant phage vectors which can be used to transform host cells, such as E. coli LE392. In a preferred embodiment, the vector is pQE30 or pBAD/ThioE, which can be used transform host cells, such as E. coli. 
Expression and transformation vectors for transformation into many yeast strains are available. For example, expression vectors have been developed for, the following yeasts: Candida albicans, Kurtz, et al. (1986) Mol. Cell. Biol. 6:142; Candida maltosa, Kunze, et al. (1985) J. Basic Microbiol. 25:141; Hansenula polymorpha, Gleeson, et al. (1986) J. Gen. Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet. 202:302; Kluyveromyces fragilis, Das, et al. (1984) J. Bacteriol. 158:1165; Kluyveromyces lactis, De Louvencourt et al. (1983) J. Bacteriol. 154:737; Van den Berg, et al. (1990) Bio/Technology 8:135; Pichia quillerimondii, Kunze et al. (1985) J. Basic Microbiol. 25:141; Pichia pastoris, Cregg, et al. (1985) Mol. Cell. Biol. 5:3376, U.S. Pat. No. 4,837,148 and U.S. Pat. No. 4,929,555; Saccharomyces cerevisiae, Hinnen et al. (1978) Proc. Natl. Acad. Sci. USA 75:1929, Ito et al. (1983) J. Bacteriol. 153:163; Schizosaccharomyces pombe, Beach et al. (1981) Nature 300:706; and Yarrowia lipolytica, Davidow, et al. (1985) Curr. Genet. 10:380-471, Gaillardin, et al. (1985) Curr. Genet. 10:49.
A variety of host-vector systems may be utilized to express the polypeptide-coding sequence. These include but are not limited to mammalian cell systems infected with virus (e.g., vaccinia virus, adenovirus, etc.); insect cell systems infected with virus (e.g., baculovirus); microorganisms such as yeast containing yeast vectors, or bacteria transformed with bacteriophage DNA, plasmid DNA, or cosmid DNA, plant cells or transgenic plants.
Hosts that are appropriate for expression of nucleic acid molecules of the present invention, fragments, analogues or variants thereof, may include E. coli, Bacillus species, Haemophilus, fungi, yeast, such as Saccharomyces, Pichia, Bordetella, or Candida, or the baculovirus expression system. Preferably, the host cell is a yeast or bacterium. In one embodiment, the host cell is an E. coli cell which has been genetically engineered to express epitopes of C. trachomatis LPS (see, e.g., U.S. Pat. No. 5,075,228, which is hereby incorporated by reference in its entirety). In a preferred embodiment, the PMP protein or PMP-derived protein is expressed in a heterologous, recombinant bacteria which has been engineered to express lpxA and/or Kdo transferase of C. trachomatis (for nucleotide and amino acid sequences see Genbank accession numbers AEOO1324 and AE001294, which are hereby incorporated by reference in their entirety) and is defective in its own lpxA or Kdo transferase gene. In other embodiments, the host also expresses one or more Chlamydia, preferably Chlamydia trachomatis, proteins, preferably an outer membrane protein, most preferably HMW protein, MOMP, PMPH or HtrA, or a fragment thereof.
Particularly desirable hosts for expression in this regard include Gram positive bacteria which do not have LPS and are, therefore endotoxin free. Most preferably the bacterium is E. coli, B. subtilis or Salmonella. 
In addition, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Expression from certain promoters can be elevated in the presence of certain inducers; thus, expression of the genetically engineered PMP polypeptide or PMP-derived polypeptide may be controlled. Furthermore, different host cells have characteristic and specific mechanisms for the translational and post-translational processing and modification of proteins. Appropriate cell lines or host systems can be chosen to ensure the desired modification and processing of the foreign protein expressed.
Once a suitable host system and growth conditions are established, recombinant expression vectors can be propagated and prepared in quantity. Upon expression, a recombinant polypeptide of the invention is produced and can be recovered in a substantially purified from the cell paste, the cell extract or from the supernatant after centrifugation of the recombinant cell culture using techniques well known in the art.
For instance, the recombinant polypeptide can be purified by antibody-based affinity purification, preparative gel electrophoresis, or affinity purification using tags (e.g., 6× histidine tag) included in the recombinant polypeptide. (See, Section 5.3 supra).
5.7. Compositions
The present invention also provides therapeutic and prophylactic compositions, which may be antigenic compositions, and preferably immunogenic compositions, including vaccines, for use in the treatment or prevention of Chlamydia infections of animals, including mammals and birds, and more specifically rodents and primates, including humans. Preferred immunogenic compositions include vaccines for use in humans. The antigenic, preferably immunogenic, compositions of the present invention can be prepared by techniques known to those skilled in the art and comprise, for example, an immunologically effective amount of any of the PMP immunogens disclosed in Sections 5.1. or 5.2, optionally in combination with or fused to or conjugated to one or more other immunogens, including lipids, phospholipids, carbohydrates, lipopolysaccharides, inactivated or attenuated whole organisms and other proteins, of Chlamydia origin or other bacterial origin, a pharmaceutically acceptable carrier, optionally an appropriate adjuvant, and optionally other materials traditionally found in vaccines. In one embodiment, the invention provides a cocktail vaccine comprising several immunogens, which has the advantage that immunity against one or several strains of a single pathogen or one or several pathogens can be obtained by a single administration. Examples of other immunogens include, but are not limited to, those used in the known DPT vaccines, HMW protein of C. trachomatis or fragments thereof, MOMP of C. trachomatis or fragments thereof, or PMPH or HtrA of C. trachomatis or fragments thereof (preferably epitope containing fragments), entire organisms or subunits therefrom of Chlamydia, Neisseria, HIV, Haemophilus influenzae, Moraxella catarrhalis, Human papilloma virus, Herpes simplex virus, Haemophilus ducreyi, Treponema pallidium, Candida albicans and Streptococcus pneumoniae, etc. Preferred are compositions comprising one or more fragments of C. trachomatis MOMP which comprise or consist of residues 273-333, 64-85, 139-160, 224-237, 288-317, 1-200, 64-350, 160-350, 240-333 or 80-105. The compositions may optionally comprise HMW protein or comprise an amino-terminal fragment of HMW protein, i.e., a fragment comprising or consisting of residues 1-100, 1-200, 1-300, 1-400, or 1-500 of the mature HMW protein. The compositions may optionally comprise Chlamydia trachomatis LPS or LPS from a recombinant bacteria which has been engineered to express lpxA or Kdo transferase of C. trachomatis and which is defective in its own lpxA or Kdo transferase gene. For instance, LPS from an E. coli mutant defective in its lpxA transfected with nucleic acid encoding lpxA protein of C. trachomatis can be isolated and purified according to techniques well known in the art (Sweet et al., J. Biol. Chem. 276:19565, 2001 or Rund et al. J. Biol. Chem. 274:16819, 1999, both of which are incorporated by referenced in their entireties).
In specific embodiments, the pharmaceutical or vaccine composition comprises a PMPE or PMPI polypeptide or PMPE-derived polypeptide or PMPI-derived polypeptide and an HMW protein, or fragment thereof (preferably an at least 5, 8, 10, 20, 40, 50, 60, 80, 100, 150, 200, 300, 400 or 500 amino acid fragment and preferably an epitope containing fragment thereof). In other specific embodiments, the composition comprises a PMPE or PMPI polypeptide or PMPE-derived polypeptide or PMPI-derived polypeptide and a MOMP, or fragment thereof (preferably an at least 5, 8, 10, 20, 40, 50, 60, 80, 100, 150, 200, 300, 400 or 500 amino acid fragment and preferably an epitope containing fragment thereof).
The term “immunogenic amount” is used herein to mean an amount sufficient to induce an immune response to produce antibodies, T-cells, and/or cytokines and other cellular immune response components. Preferably, the immunogenic composition is one that elicits an immune response sufficient to prevent Chlamydia infections or to attenuate the severity of any preexisting or subsequent Chlamydia infection. An immunogenic amount of the immunogen to be used in the vaccine is determined by means known in the art in view of the teachings herein. The exact concentration will depend upon the specific immunogen to be administered, but can be determined by using standard techniques well known to those skilled in the art for assaying the development of an immune response.
The vaccine compositions of the invention elicit an immune response in a subject. Compositions which induce antibodies, including anti-PMP protein antibodies and antibodies that are opsonizing or bactericidal are one aspect of the invention. In preferred non-limiting, embodiments of the invention, an effective amount of a composition of the invention produces an elevation of antibody titer to at least three times the antibody titer prior to administration. In a preferred, specific, non-limiting embodiment of the invention, approximately 0.01 to 2000 μg and, preferably, 0.1 to 500 μg, most preferably 50 to 250 μg of the PMP protein or PMP-derived protein is administered is to a host. Compositions which induce T-cell responses which are bactericidal or reactive with host cells infected with Chlamydia are also an aspect of the invention. Preferred are compositions additionally comprising an adjuvant.
The combined immunogen and carrier or diluent may be an aqueous solution, emulsion or suspension or may be a dried preparation. Appropriate carriers are known to those skilled in the art and include stabilizers, diluents, and buffers. Suitable stabilizers include carbohydrates, such as sorbitol, lactose, mannitol, starch, sucrose, dextran, and glucose, and proteins, such as albumin or casein. Suitable diluents include saline, Hanks Balanced Salts, and Ringers solution. Suitable buffers include an alkali metal phosphate, an alkali metal carbonate, or an alkaline earth metal carbonate. In preferred embodiments, the composition of the invention is formulated for administration to humans.
The pharmaceutical and immunogenic compositions, including vaccines, of the invention are prepared by techniques known to those skilled in the art, given the teachings contained herein. Generally, an immunogen is mixed with the carrier to form a solution, suspension, or emulsion. One or more of the additives discussed herein may be added in the carrier or may be added subsequently. The vaccine preparations may be desiccated or lyophilized, for example, by freeze drying or spray drying for storage or formulations purposes. They may be subsequently reconstituted into liquid vaccines by the addition of an appropriate liquid carrier or administered in dry formulation using methods known to those skilled in the art, particularly in capsules or tablet forms.
An effective amount of the antigenic, immunogenic, pharmaceutical, including, but not limited to vaccine, composition of the invention should be administered, in which “effective amount” is defined as an amount that is sufficient to produce a desired prophylactic, therapeutic or ameliorative response in a subject, including but not limited to an immune response. The amount needed will vary depending upon the immunogenicity of the PMP protein, PMP-derived polypeptide or nucleic acid used, and the species and weight of the subject to be administered, but maybe ascertained using standard techniques.
Immunogenic, antigenic, pharmaceutical and vaccine compositions may further contain one or more auxiliary substance, such as wetting or emulsifying agents, pH buffering agents, or adjuvants to enhance the effectiveness thereof. Immunogenic, antigenic, pharmaceutical and vaccine compositions may be administered to birds, humans or other mammals, including ruminants, rodents or primates, by a variety of administration routes, including parenterally, intradermally, intraperitoneally, subcutaneously or intramuscularly.
Alternatively, the immunogenic, antigenic, pharmaceutical and vaccine compositions formed according to the present invention, may be formulated and delivered in a manner to evoke an immune response at mucosal surfaces. Thus, the immunogenic, antigenic, pharmaceutical and vaccine compositions may be administered to mucosal surfaces by, for example, the nasal, oral (intragastric), ocular, bronchiolar, intravaginal or intrarectal routes. Alternatively, other modes of administration including suppositories and oral formulations may be desirable. For suppositories, binders and carriers may include, for example, polyalkalene glycols or triglycerides. Oral formulations may include normally employed incipients such as, for example, pharmaceutical grades of saccharine, cellulose and magnesium carbonate. These compositions can take the form of microspheres, solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders and contain about 0.001 to 95% of the PMP protein. Preferred dosage forms contain 50 μg to 250 μg of the PMP protein. The immunogenic, antigenic, pharmaceutical and vaccine compositions are administered in a manner compatible with the dosage formulation, and in such amount as will be therapeutically effective, protective or immunogenic. Preferred are compositions additionally comprising an adjuvant.
Further, the immunogenic, antigenic, pharmaceutical and vaccine compositions may be used in combination with or conjugated to one or more targeting molecules for delivery to specific cells of the immune system and/or mucosal surfaces. Some examples include but are not limited to vitamin B12, bacterial toxins or fragments thereof, monoclonal antibodies and other specific targeting lipids, proteins, nucleic acids or carbohydrates.
Suitable regimes for initial administration and booster doses are also variable, but may include an initial administration followed by subsequent administrations. The dose may also depend on the route(s) of administration and will vary according to the size of the host. The concentration of the PMP protein or PMP-derived polypeptide in an antigenic, immunogenic or pharmaceutical composition according to the invention is in general about 0.001 to 95%, preferably 0.01 to 5%.
The antigenic, immunogenic or pharmaceutical preparations, including vaccines, may comprise as the immunostimulating material a nucleic acid vector comprising at least a portion of the nucleic acid molecule encoding the PMP protein or PMP-derived polypeptide.
A vaccine comprising nucleic acid molecules encoding one or more PMP polypeptides, PMP-derived polypeptides or fusion proteins as described herein, such that the polypeptide is generated in situ is provided. In such vaccines, the nucleic acid molecules may be present within any of a variety of delivery systems known to those skilled in the art, including nucleic acid expression systems, bacterial and viral expression systems. Appropriate nucleic acid expression systems contain the necessary nucleotide sequences for expression in the patient such as suitable promoter and terminating signals. In a preferred embodiment, the nucleic acid molecules may be introduced using a viral expression system (e.g., vaccinia or other pox virus, alphavirus retrovirus or adenovirus) which may involve the use of non-pathogenic (defective) virus. Techniques for incorporating nucleic acid molecules into such expression systems are well known to those of ordinary skill in the art. The nucleic acid molecules may also be administered as “naked” plasmid vectors as described, for example, in Ulmer et al. Science 259:1745-1749 (1992) and reviewed by Cohen, Science 259:1691-1692 (1993). Techniques for incorporating DNA into such vectors are well known to those of ordinary skill in the art. A vector may additionally transfer or incorporate a gene for a selectable marker (to aid in the identification or selection of transduced cells) and/or a targeting moiety, such as a gene that encodes a ligand for a receptor on a specific target cell, to render the vector target specific. Targeting may also be accomplished using an antibody, by methods know to those skilled in the art.
Nucleic acid molecules (DNA or RNA) of the invention can be administered as vaccines for therapeutic or prophylactic purpose. Typically a DNA molecule is placed under the control of a promoter suitable for expression in a mammalian cell. The promoter can function ubiquitously or tissue-specifically. Examples of non-tissue specific promoters include the early cytomegalovirus (CMV) promoter (described in U.S. Pat. No. 4,168,062) and Rous Sarcoma virus promoter (described in Norton and Coffin, Molec. Cell Biol. 5:281 (1985)). The desmin promoter (Li et al. Gene 78:243 (1989); Li & Paulin, J. Biol Chem 266:6562 (1991); and Li & Paulin, J. Biol Chem 268:10401 (1993)) is tissue specific and drives expression in muscle cells. More generally, useful vectors are described in, e.g., WO 94/21797 and Hartikka et al., Human Gene Therapy 7:1205 (1996).
A composition of the invention can contain one or several nucleic acid molecules of the invention. It can also contain at least one additional nucleic acid molecule encoding another antigen or fragment derivative, including but not limited to, DPT vaccines, HMW protein of C. trachomatis or fragment thereof, MOMP of C. trachomatis or fragment thereof, entire organisms or subunits therefrom of Chlamydia, Neisseria, HIV, Haemophilus influenzae, Moraxella catarrhalis, Human papilloma virus, Herpes simplex virus, Haemophilus ducreyi, Treponema pallidium, Candida albicans and Streptococcus pneumoniae, etc. A nucleic acid molecule encoding a cytokine, such as interleukin-1 or interleukin-12 can also be added to the composition so that the immune response is enhanced. DNA molecules of the invention and/or additional DNA molecules may be on different plasmids or vectors in the same composition or can be carried in the same plasmid or vector.
Other formulations of nucleic acid molecules for therapeutic and prophylactic purposes include sterile saline or sterile buffered saline colloidal dispersion systems, such as macromolecule complexes, nanocapsules, silica microparticles, tungsten microparticles, gold microparticles, microspheres, beads and lipid based systems including oil-in-water emulsions, micelles, mixed micelles and liposomes. A preferred colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (i.e., an artificial vesicle). The uptake of naked nucleic acid molecules may be increased by incorporating the nucleic acid molecules into and/or onto biodegradable beads, which are efficiently transported into the cells. The preparation and use of such systems is well known in the art.
A nucleic acid molecule can be associated with agents that assist in cellular uptake. It can be formulated with a chemical agent that modifies the cellular permeability, such as bupivacaine (see, e.g., WO 94/16737).
Cationic lipids are also known in the art and are commonly used for DNA delivery. Such lipids include LIPOFECTINTM, also known as DOTMA (N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride), DOTAP (1,2-bis(oleyloxy)-3-(trimethylammonio)propane, DDAB (dimethyldioctadecylammonium bromide), DOGS (dioctadecylamidologlycy spermine) and cholesterol derivatives such as DC-Chol (3 beta-(N-(N′,N′-dimethyl aminomethane)-carbamoyl)cholesterol. A description of these cationic lipids can be found in EP 187,702, WO 90/11092, U.S. Pat. No. 5,283,185, WO 91/15501, WO 95/26356, and U.S. Pat. No. 5,527,928. Cationic lipids for DNA delivery are preferably used in association with a neutral lipid such as DOPE (dioleyl phosphatidylethanolamine) as described in, e.g., WO 90/11092.
Other transfection facilitation compounds can be added to a formulation containing cationic liposomes. They include, e.g., spermine derivatives useful for facilitating the transport of DNA through the nuclear membrane (see, for example, WO 93/18759) and membrane-permeabilizing compounds such as GALA, Gramicidine S and cationic bile salts (see, for example, WO 93/19768).
The amount of nucleic acid molecule to be used in a vaccine recipient depends, e.g., on the strength of the promoter used in the DNA construct, the immunogenicity of the expressed gene product, the mode of administration and type of formulation. In general, a therapeutically or prophylactically effective dose from about 1 μg to about 1 mg, preferably from about 10 μg to about 800 μg and more preferably from about 25 μg to about 250 μg can be administered to human adults. The administration can be achieved in a single dose or repeated at intervals.
The route of administration can be any conventional route used in the vaccine field. As general guidance, a nucleic acid molecule of the invention can be administered via a mucosal surface, e.g., an ocular, intranasal, pulmonary, oral, intestinal, rectal, vaginal, and urinary tract surface; or via a parenteral route, e.g., by an intravenous, subcutaneous, intraperitoneal, intradermal, intra-epidermal or intramuscular route. The choice of administration will depend on the formulation that is selected. For instance a nucleic acid molecule formulated in association with bupivacaine is advantageously administered into muscles.
Recombinant bacterial vaccines genetically engineered for recombinant expression of nucleic acid molecules encoding PMP or PMP-derived polypeptides include Shigella, Salmonella, Vibrio cholerae, and Lactobacillus. Recombinant BCG and Streptococcus expressing PMP or PMP-derived polypeptides can also be used for prevention or treatment of Chlamydia infections.
Non-toxicogenic Vibrio cholerae mutant strains that are useful as a live oral vaccine are described in Mekalanos et al. Nature 306:551 (1983) and U.S. Pat. No. 4,882,278. An effective vaccine dose of a Vibrio cholerae strain capable of expressing a polypeptide or polypeptide derivative encoded by a DNA molecule of the invention can be administered. Preferred routes of administration include all mucosal routes, most preferably intranasally or orally.
Attenuated Salmonella typhimurium strains, genetically engineered for recombinant expression of heterologous antigens or not and their use as oral vaccines are described in Nakayama et al. Bio/Technology 6:693 (1988) and WO 92/11361. Preferred routes of administration include all mucosal routes, most preferably intranasally or orally.
Other bacterial strains useful as vaccine vectors are described in High et al., EMBO 11:1991(1992); Sizemore et al., Science 270:299 (1995) (Shigella flexneri); Medaglini et al., Proc Natl. Acad. Sci. US 92:6868 (1995) (Streptococcus gordonii); and Flynn, Cell Mol. Biol. 40:31 (1994); WO 88/6626; WO 90/0594; WO 91/13157; WO 92/1796; and WO 02/21376 (Bacille Calmette Guerin).
In genetically engineered recombinant bacterial vectors, nucleic acid molecule(s) of the invention can be inserted into the bacterial genome, carried on a plasmid, or can remain in a free state.
When used as vaccine agents, recombinant bacterial or viral vaccines, nucleic acid molecules and polypeptides of the invention can be used sequentially or concomitantly as part of a multistep immunization process. For example, a mammal or bird can be initially primed with a vaccine vector of the invention such as pox virus or adenovirus, e.g., via the parenteral route or mucosally and then boosted several time with the a polypeptide e.g., via the mucosal route. In another example, a mammal can be vaccinated with polypeptide via the mucosal route and at the same time or shortly thereafter, with a nucleic acid molecule via intramuscular route.
An adjuvant can also be added to a composition containing a PMP vaccine. To efficiently induce humoral immune responses (HIR) and cell-mediated immunity (CMI), immunogens are typically emulsified in adjuvants. Immunogenicity can be significantly improved if the immunogen is co-administered with an adjuvant. Adjuvants may act by retaining the immunogen locally near the site of administration to produce a depot effect facilitating a slow, sustained release of antigen to cells of the immune system. Adjuvants can also attract cells of the immune system to an immunogen depot and stimulate such cells to elicit immune responses.
Many adjuvants are toxic, inducing granulomas, acute and chronic inflammations (Freund's complete adjuvant, FCA), cytolysis (saponins and Pluronic polymers) and pyrogenicity, arthritis and anterior uveitis (LPS and MDP). Although FCA is an excellent adjuvant and widely used in research, it is not licensed for use in human or veterinary vaccines because of its toxicity.
Immunostimulatory agents or adjuvants have been used for many years to improve the host immune responses to, for example, vaccines. Intrinsic adjuvants, such as lipopolysaccharides, normally are the components of the killed or attenuated bacteria used as vaccines. Extrinsic adjuvants are immunomodulators which are typically non-covalently linked to antigens and are formulated to enhance the host immune responses. Thus, adjuvants have been identified that enhance the immune response to antigens delivered parenterally. Aluminum hydroxide, aluminum oxide, and aluminum phosphate (collectively commonly referred to as alum) are routinely used as adjuvants in human and veterinary vaccines. The efficacy of alum in increasing antibody responses to diphtheria and tetanus toxoids is well established and a HBsAg vaccine has been adjuvanted with alum.
Other extrinsic adjuvants may include chemokines, cytokines (e.g., IL-2), saponins complexed to membrane protein antigens (immune stimulating complexes), pluronic polymers with mineral oil, killed mycobacteria in mineral oil, Freund's complete adjuvant, bacterial products, such as muramyl dipeptide (MDP) and lipopolysaccharide (LPS), as well as lipid A, and liposomes.
U.S. Pat. No. 6,019,982, incorporated herein by reference, describes mutated forms of heat labile toxin of enterotoxigenic E. coli (“mLT”). U.S. Pat. No. 5,057,540, incorporated herein by reference, describes the adjuvant, QS21, an HPLC purified non-toxic fraction of a saponin from the bark of the South American tree Quiliaja saponaria molina. 3D-MPL is described in Great Britain Patent 2,220,211, which is incorporated herein by reference.
U.S. Pat. No. 4,855,283 granted to Lockhoff et al. on Aug. 8, 1989, which is incorporated herein by reference, teaches glycolipid analogues including N-glycosylamides, N-glycosylureas and N-glycosylcarbamates, each of which is substituted in the sugar residue by an amino acid, as immuno-modulators or adjuvants. Lockhoff reported that N-glycosphospholipids and glycoglycerolipids are capable of eliciting strong immune responses in both herpes simplex virus vaccine and pseudorabies virus vaccine. Some glycolipids have been synthesized from long chain-alkylamines and fatty acids that are linked directly with the sugars through the anomeric carbon atom, to mimic the functions of the naturally occurring lipid residues.
U.S. Pat. No. 4,258,029 granted to Moloney, incorporated herein by reference, teaches that octadecyl tyrosine hydrochloride (OTH) functions as an adjuvant when complexed with tetanus toxoid and formalin inactivated type I, II and III poliomyelitis virus vaccine. Lipidation of synthetic peptides has also been used to increase their immunogenicity.
Therefore, according to the invention, the immunogenic, antigenic, pharmaceutical, including vaccine, compositions comprising a PMP protein, or a PMP derived polypeptide or a PMP encoding nucleic acid or fragment thereof, vector or cell expressing the same, may further comprise an adjuvant, such as, but not limited to alum, mLT, LTR192G, QS21, RIBI DETOXTM, MMPL, CpG DNA, MF59, calcium phosphate, PLG and all those listed above. Preferably, the adjuvant is selected from one or more of the following: alum, QS21, CpG DNA, PLG, LT, 3D-mPL, or Bacille Calmette-Guerine (BCG) and mutated or modified forms of the above, particularly mLT and LTR192G. The compositions of the present invention may also further comprise a suitable pharmaceutical carrier, including but not limited to saline, bicarbonate, dextrose or other aqueous solution. Other suitable pharmaceutical carriers are described in Remington's Pharmaceutical Sciences, Mack Publishing Company, a standard reference text in this field, which is incorporated herein by reference in its entirety.
Immunogenic, antigenic and pharmaceutical, including vaccine, compositions may be administered in a suitable, nontoxic pharmaceutical carrier, may be comprised in microcapsules, microbeads, and/or may be comprised in a sustained release implant.
Immunogenic, antigenic and pharmaceutical, including vaccine, compositions may desirably be administered at several intervals in order to sustain antibody levels and/or T-cell levels. Immunogenic, antigenic and pharmaceutical, including vaccine, compositions may be used in conjunction with other bacteriocidal or bacteriostatic methods.
Another embodiment of the vaccines of the present is a vaccine comprising one or more isolated or purified PMPE or PMPI polypeptides or PMPE-derived polypeptides or PMPI-derived polypeptides, or homologs thereof, of Chlamydia spp, having a molecular weight between 90 and 115 kDa as determined in SDS polyacrylamide gel electrophoresis, or isolated nucleic acids encoding a PMPE or PMPI polypeptide, or PMPE-derived polypeptide, or PMPI-polypeptide from Chlamydia spp., having a molecular weight between 90 and 115 kDa as determined in SDS polyacrylamide gel electrophoresis, and further comprising one or more components selected from the group consisting of alum, mLT, LTR192G, QS21, MF59, CpG DNA, MPL, calcium phosphate and PLG. Optionally, the vaccine may include HMW protein or fragments thereof, C. trachomatis MOMP or fragments thereof, C. trachomatis PMPH or fragments thereof, or C. trachomatis HtrA or fragments thereof, or a combination of the foregoing. The compositions may optionally comprise trachomatis LPS or LPS from a recombinant bacteria which has been engineered to express lpxA or Kdo transferase of C. trachomatis and which is defective in its own lpxA or Kdo transferase gene
Also included in the invention is a method of producing an immune response in an animal comprising immunizing the animal with an effective amount of one or more of the PMP polypeptides or nucleic acid molecules encoding the PMP polypeptides of the invention, compositions comprising the same and vaccines comprising the same. The PMP polypeptides, nucleic acids, compositions and vaccines comprising the PMP polypeptides of the invention may be administered simultaneously or sequentially. Examples of simultaneous administration include cases in which two or more polypeptides, nucleic acids, compositions, or vaccines, which maybe the same or different, are administered in the same or different formulation or are administered separately, e.g., in a different or the same formulation but within a short time (such as minutes or hours) of each other. Examples of sequential administration include cases in which two or more polypeptides, nucleic acids, compositions or vaccines, which may be the same or different, are not administered together or within a short time of each other, but may be administered separately at intervals of, for example, days, weeks, months or years.
The polypeptides, nucleic acid molecules or recombinant bacterial vaccines of the present invention are also useful in the generation of antibodies, as described supra, or T-cells. For T-cells, animals, including humans, are immunized as described above. Following immunization, PBL (peripheral blood lymphocytes), spleen cells or lymph node cells are harvested and stimulated in vitro by placing large numbers of lymphocytes in flasks with media containing human serum. A polypeptide of the present invention is added to the flasks, and T-cells are harvested and placed in new flasks with X-irradiated peripheral blood mononuclear cells. The polypeptide is added directly to these flasks, and cells are grown in the presence of IL-2. As soon as the cells are shown to be Chlamydia specific T-cells, they are changed to a stimulation cycle with higher IL-2 concentrations (20 units) to expand them.
Alternatively, one or more T-cells that proliferate in the presence of a polypeptide of the present invention can be expanded in number by cloning. Methods for cloning cells are well known in the art. For example, T-cell lines may be established in vitro and cloned by limiting dilution. Responder T-cells are purified from the peripheral blood established in culture by stimulating with the nominal antigen in the presence of irradiated autologous filler cells. In order to generate CD4+ T-cell lines, the Chlamydia polypeptide is used as the antigenic stimulus and autologous PBL or lymphoblastoid cell lines (LCL) immortalized by infection with Epstein Barr virus are used as antigen presenting cells. In order to generate CD8+ T-cell lines, autologous antigen-presenting cells transfected with an expression vector which produces the relevant Chlamydia polypeptide may be used as stimulator cells. T-cell lines are established following antigen stimulation by plating stimulated T-cells in 96-well flat-bottom plates with PBL or LCL cells and recombinant interleukin-2 (rIL2) (50 U/ml). Wells with established clonal growth are identified at approximately 2-3 weeks after initial plating and restimulated with appropriate antigen in the presence of autologous antigen-presenting cells, then subsequently expanded by the addition of low doses of IL2. T-cell clones are maintained in 24-well plates by periodic restimulation with antigen and IL2 approximately every two weeks.
T-cell preparations may be further enriched by isolating T-cells specific for antigen reactivity using the methods disclosed by Kendricks et al. in U.S. Pat. No. 5,595,881.
The vaccine compositions of the present inventions are useful in preventing, treating or ameliorating disease symptoms in an animal, preferably a human, with a disease or disorder associated with Chlamydia infection or to prevent the occurrence or progression of a disease or disorder associated with Chlamydia infection in an animal, preferably a human. Such diseases or disorders include, but are not limited to, Chlamydia bacterial infection, conjunctivitis, urethritis, lymphogranuloma venereum (LGV), cervicitis, epididymitis, salpingitis, tubal occlusion, infertility, cervical cancer, reactive arthritis, arteriosclerosis and atherosclerosis.
5.8. Immunoassays and Diagnostic Reagents
The PMP protein, PMP-derived polypeptide or nucleic acid encoding same, and fragments thereof, are useful as diagnostic reagents. Use of the proteins and nucleic acids of the invention as an antigen or immunogen for the generation of anti-PMP protein antibodies or as an antigen in immunoassays including enzyme-linked immunosorbent assays (ELISA), radioimmunoassays (RIA) and other non-enzyme linked antibody binding assays or procedures known in the art for the detection of anti-bacterial, anti-Chlamydia, and anti-PMP protein antibodies are encompassed by the invention.
ELISA is well-known and routine in the art. Generally, in ELISA, the PMP protein is immobilized onto a selected surface, for example, a surface capable of binding proteins such as the wells of a polystyrene microtiter plate. After washing to remove incompletely absorbed PMP protein, a nonspecific protein solution that is known to be antigenically neutral with regard to the test sample may be bound to the selected surface. This allows for blocking of nonspecific absorption sites on the immobilizing surface and thus reduces the background caused by nonspecific bindings of antisera onto the surface.
The immobilizing surface is then contacted with a sample, such as clinical or biological materials, to be tested in a manner conducive to immune complex (antigen/antibody) formation. This may include diluting the sample with diluents, such as solutions of bovine gamma globulin (BGG) and/or phosphate buffered saline (PBS)/Tween. The sample is then allowed to incubate for from 2 to 4 hours, at temperatures on the order of about 20° C. to 37° C. Following incubation, the sample-contacted surface is washed to remove non-immunocomplexed material. The washing procedure may include washing with a solution, such as PBS/Tween or a borate buffer. Following formation of specific immunocomplexes between the test sample and the bound PMP protein, and subsequent washing, the occurrence, and even amount, of immunocomplex formation may be determined by subjecting the immunocomplex to a second antibody having specificity for the first antibody. If the test sample is of human origin, the second antibody is an antibody having specificity for human immunoglobulins and in general IgG.
To provide detecting means, the second antibody may have an associated activity such as an enzymatic activity that will generate, for example, a color development upon incubating with an appropriate chromogenic substrate. Detection may then be achieved by detecting color generation. Quantification may then be achieved by measuring the degree of color generation using, for example, a visible spectrophotometer and comparing to an appropriate standard. Any other detecting means known to those skilled in the art are included.
In Western blot assays, the polypeptide, either as a purified preparation or a cell extract, is subjected to SDS-PAGE electrophoresis, for example, as described by Laemmli, Nature 227:690 (1970) or any other method known in the art. After transfer to a nitrocellulose membrane, the material is further incubated with the serum sample, polyclonal antibody preparation, or monoclonal antibody diluted in the range of from about 1:5 to 1:5000, preferably from about 1:100 to about 1:500, depending upon the titer and specification of the antibodies. Appropriate dilutions can be readily determined by methods known in the art. The reaction is revealed according to standard procedures. For example, when human antibody is used, the membrane is incubated in a goat anti-human peroxidase conjugate for an appropriate length of time. The membrane is washed. The reaction is developed with the appropriate substrate and stopped. The reaction is measured visually by the appearance of a colored band e.g., by colorimetry.
In a dot blot assay, the purified or partially purified polypeptide or cell extract can be used. Briefly, a solution of the antigen at about 100 μg/ml is serially two-fold diluted in 50 mM Tris-HCl (pH 7.5). 100 μl of each dilution is applied to a 0.45 μm nitrocellulose membrane set in a 96-well dot blot apparatus. The buffer is removed by applying vacuum to the system. Wells are washed by addition of 50 μM Tris-HCl (pH 7.5) and the membrane is air-dried. The membrane is saturated in block buffer (50 mM Tris-HCl (pH 7.5), 0.15 M NaCl and 10 g/L skim milk) and incubated with an antiserum dilution from about 1:50 to about 1:500. The reaction is revealed according to standard procedures. For example, a goat anti-rabbit peroxidase conjugate is added to the well when rabbit antibodies are used. Incubation is carried out 90 minutes at 37° C. and the blot is washed. The reaction is developed with the appropriate substrate and stopped. The reaction is measured visually by the appearance of a colored spot, e.g., by colorimetry.
The PMP proteins, PMP-derived polypeptides or nucleic acids encoding same, and fragments thereof, are also useful as antigens or immunogens for the generation of anti-PMP protein T-cell response or as an antigen in immunoassays, including T-cell proliferation assays, cytokine production, delayed hypersensitivity reactions or cytotoxic T-cells (CTL) reactions.
For analysis of Chlamydia peptide specific T-cell proliferative responses, fresh peripheral blood, spleen or lymph node cells are harvested. Cells are plated into 96-well round bottom microtiter plates and are incubated with peptides. Data is expressed as a stimulation index (SI) which is defined as the mean of the number of cells in experimental wells divided by the mean of the number of cells in control wells (no antigen).
For analysis of cytokine release of T-cells in response to Chlamydia polypeptides, responder cells are mixed with polypeptides. Supernatants are collected and added to an ELISA coated with antibody to the cytokine (e.g., anti-IFN-α or anti-IL-2 antibody). After washing, rabbit anti-cytokine polyclonal antibody (e.g., anti-IFN-α or anti-IL-2) is added. Labeled goat anti-rabbit IgG polyclonal is added. Substrate is added and the amount of cytokine released into the supernatant is determined based upon the amount of color developed in the ELISA.
Another embodiment includes diagnostic kits comprising all of the essential reagents required to perform a desired immunoassay according to the present invention. The diagnostic kit may be presented in a commercially packaged form as a combination of one or more containers holding the necessary reagents. Such a kit may comprise PMP protein, PMP-derived polypeptide or nucleic acid encoding same, or a monoclonal or polyclonal antibody of the present invention, in combination with several conventional kit components. Conventional kit components will be readily apparent to those skilled in the art and are disclosed in numerous publications, including, for example, Harlow and Lane, Antibodies A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 1988) which is incorporated herein by reference in its entirety. Conventional kit components may include such items as, for example, microtiter plates, buffers to maintain the pH of the assay mixture (such as, but not limited to Tris, HEPES, etc.), conjugated second antibodies, such as peroxidase conjugated anti-mouse IgG (or any anti-IgG to the animal from which the first antibody was derived) and the like, and other standard reagents.
The nucleic acid molecules containing the PMP encoding sequences of the present invention may be used in combination with an appropriate indicator 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 and digoxigenin-labeling, which are capable of providing a detectable signal. In some diagnostic embodiments, an enzyme tag, such as urease, alkaline phosphatase or peroxidase, instead of a radioactive tag, may be used. 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 samples containing PMP protein gene sequences.
Probes of the invention can be used in diagnostic tests, as capture or detection probes. Such capture probes can be conventionally immobilized on a solid support directly or indirectly, by covalent means or by passive adsorption. A detection probe can be labeled by a detection marker selected from radioactive isotopes, enzymes, such as peroxidase, alkaline phosphatase, and enzymes able to hydrolyze a chromogenic, fluorogenic or luminescent substrate; compounds that are chromogenic, fluorogenic or luminescent; nucleotide base analogs; and biotin.
Probes of the invention can be used in any conventional hybridization techniques, such as dot blot (Maniatis et al., Molecular Cloning: A Laboratory Manual (1982) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 1982), Southern blot (Southern, J. Mol. Biol. 98:503 1975), northern blot (identical to Southern blot to the exception that RNA is used as a target), or sandwich techniques (Dunn et al., Cell 12:23 1977).
In embodiments involving solid-phase procedures, the test DNA (or RNA) from samples, such as clinical samples, including exudates, body fluids (e.g., serum, amniotic fluid, middle ear effusion, sputum, semen, urine, tears, mucus, bronchoalveolar lavage fluid) or even tissues, is absorbed or otherwise affixed to a selected matrix or surface. The fixed, single-stranded nucleic acid is then subjected to specific hybridization with selected probes comprising the nucleotide sequences encoding a PMP protein, or fragments or analogues thereof, under desired conditions. The selected conditions will depend on the particular criteria required and on, for example, the G+C content, type of target nucleic acid, source of nucleic acid, size of hybridization probe, etc. Following washing of the hybridization surface so as to remove non-specifically bound probe molecules, specific hybridization is detected, or even quantified, by means of the label. It is preferred to select nucleotide acid sequence portions that are conserved among species of Chlamydia. The selected probe may be at least 15 bp and may be in the range of about 30 to 90 bp.
The invention also relates to methods for identifying compounds which interact with and inhibit or activate an activity of the polypeptides or nucleic acid molecules of the invention comprising contacting a composition comprising the polypeptide or the nucleic acid molecule with the compound to be screened under conditions that permit interaction between the compound and the polypeptide or nucleic acid molecule to assess the interaction of a compound and to detect interaction of the compound with the polypeptide of nucleic acid. The interaction of the compound with the polypeptide or nucleic acid molecule is determined by the association of a second component (e.g., an antibody) capable of providing a detectable signal in response to the interaction of the polypeptide or nucleic acid molecule with the compound; and determining the presence or absence of a signal generated from the interaction of the compound with the polypeptide or nucleic acid molecule. Alternatively, the interaction of the compound with the polypeptide or nucleic acid molecule is determined by the ability of the compound to inhibit the activity of the polypeptide or the nucleic acid molecule. Thus, the invention also provides agonists and antagonists of the PMP polypeptides of the invention.
5.9. Applications
The proteins, polypeptides, peptides, antibodies, T-cells and nucleic acids of the invention are useful as reagents for clinical or medical diagnosis of Chlamydia infections and for scientific research on the properties of pathogenicity, virulence, and infectivity of Chlamydia, as well as host defense mechanisms. For example, DNA and RNA of the invention can be used as probes to identify the presence of Chlamydia in biological specimens by hybridization or PCR amplification. The DNA and RNA can also be used to identify other bacteria that might encode a polypeptide related to the Chlamydia PMP protein. The proteins of the invention may be used to prepare polyclonal and monoclonal antibodies that can be used to further purify compositions containing the proteins of the invention by affinity chromatography or for use as diagnostic or as prophylactic or therapeutic agents. The proteins can also be used in standard immunoassays to screen for the presence of antibodies or T-cells to Chlamydia in a biological sample.
5.10. Biological Deposits
Certain plasmids that contain portions of the gene having the open reading frame of the PMP genes encoding the PMP proteins of the present invention have been inserted into E. coli and deposited with the American Type Culture Collection (ATCC) located at 10801 University Boulevard, Manassas, Va. 20110-2209, U.S.A., pursuant to the Budapest Treaty and pursuant to 37 CFR 1.808 and prior to the filing of this application. All restrictions imposed on the availability of the deposited material will be irrevocably removed upon grant of a patent based upon this United States patent application. The invention described and claimed herein is not to be limited by the scope of the plasmids deposited, since the deposited embodiment is intended only as an illustration of the invention. Any equivalent or similar plasmids that encode similar or equivalent proteins or fragments or analogues thereof as described in this application are within the scope of the invention.












Plasmid
ATCC Accession No.
Date Deposited







M15 pREP (pQE-pmpE)#37
ATCC PTA-2462
Sep. 12, 2000


TOP10(pBAD-pmpI-Ct-Uni)#7
ATCC PTA-2461
Sep. 12, 2000









The above disclosure generally describes the present invention. A more complete understanding can be obtained by reference to the following specific examples. These examples are described solely for purposes of illustration and not intended to limit the scope of the invention. Changes in form and substitution of equivalents are contemplated as circumstances may suggest or render expedient. Although specific terms have been employed herein such terms are intended in a descriptive sense and not for purposes of limitation.
6. EXAMPLES
The above disclosure generally describes the present invention. The examples are described solely for the purpose of illustration and are not intended to limit the scope of the invention. Changes in form and substitution of equivalents are contemplated as circumstances suggest or render expedient. Although specific terms have been employed herein, such terms are intended in a descriptive sense and not for purposes of limitation.
Methods of molecular genetics, protein biochemistry and immunology used but not explicitly described in the disclosure and examples are amply reported in the scientific literature and are well within the ability of those skilled in the art.
6.1. Extraction of Envelope Proteins
McCoy cells are cultured either in standard 225 cm2 tissue culture flasks or in Bellco spinner flasks (Cytodex microcarrier, Pharmacia) at 37° C. in 5% CO2 using DMEM media supplemented with 10% Chlamydia-antibody-free fetal bovine serum, glucose and nonessential amino acids. C. trachomatis, including but not limited to the L2 serovar (ATCC VR-902B), elementary bodies (EBs) are prepared from lysates of infected McCoy cells. Basically, McCoy cells infected with C. trachomatis are sonicated and cellular debris is removed by centrifugation. The supernatant containing Chlamydial EBs is then centrifuged and the pellet containing the EBs is resuspended in Hanks' balanced salts solution (HBSS). RNAase/DNAase solution is added and incubated at 37° C. for 1 hour with occasional mixing. The EB containing solution is layered onto a discontinuous density gradient (40%, 44% and 54%) of Renogratin-60 (mixture of diatrizoate melgumine and diatrizoate sodium, Bracco Diagnostics, Princeton, N.J.) and ultracentrifuged for separation of the EBs on the gradient. After centrifugation, the EBs are harvested from the gradient between the interface of the 44% and 54% layers. The EBs are washed in phosphate buffered saline and resuspended in HBSS.
Purified EBs are sequentially extracted with 0.1% OGP [high ionic strength] in HBSS to remove peripheral surface proteins and held on ice. The same EB preparation is then extracted with 1.0% OGP, 10 mM DTT, 1 mM PMSF, and 10 mM EDTA, in a 50 mM Tris pH 7.4 buffer. The extracts are dialyzed (3500 molecular weight cut off) to remove detergent and other reagents and are concentrated by lyophilization. Eluents are dialyzed to remove excess detergent and then lyophilized. Envelope proteins are size fractionated by SDS-PAGE and visualized by silver staining or analyzed by Western blotting. Protein(s) of about 90-115 kDa present in moderate amounts are detected in the gel.
6.2. Amino Terminal Sequencing of PMP Polypeptide
To obtain the N-terminal amino acid sequence, sufficient quantities of the PMPE or PMPI protein (≧5 μg) are electroblotted onto a PVDF membrane (Applied Biosystems), and stained with Coomassie blue. Immobilized protein is released from the membrane and treated in situ with low levels of endopeptidase Lys-C, endopeptidase Arg-C and/or endopeptidase Glu-C to fragment the native protein. The resulting peptide fragments are purified by HPLC and their N-terminal amino acid sequences are determined using an ABI 430 Protein Sequenator and standard protein sequencing methodologies.
6.3. Determination of Post-Translational Modifications
Recently, several C. trachomatis membrane-associated proteins have been shown to be post-translationally modified. The 18 kDa and 32 kDa cysteine-rich EB proteins, which are lectin-binding proteins, have been shown to carry specific carbohydrate moieties (Swanson et al. 1990. Infect. Immun. 58:502-507). Incorporation of radiolabeled palmitic acid has been used to demonstrate that the about 27 kDa C. trachomatis Mip-like protein is lipidated (Lundemose et al. 1993. J. Bacteriol. 175:3669-3671). Swanson et al. have discovered that the MOMP from the L2 serovar contains N-acetylglucosamine and/or N-acetylgalactosamine and these carbohydrate moieties mediate binding of MOMP to Hela cell membranes.
To ascertain whether the PMPE or PMPI protein is glycosylated, EBs are grown on McCoy cells in the presence of tritiated galactose or glucosamine and analyzed by SDS-PAGE and autoradiography. Briefly, McCoy cells are grown in T225 flasks under standard conditions (DMEM+10% FCS, 35 ml per flask, 10% CO2) to about 90% confluency and inoculated with sufficient EBs to achieve 90%-100% infectivity. Following a 3 hour infection period at 37° C. cycloheximide is added (1 μg/ml) to inhibit host cell protein synthesis and the cultures reincubated for an additional 4-6 hours. Approximately 0.5 mCi of tritiated galactose (D-[4,5-3H(N)]galactose, NEN) or glucosamine (D-[1,6-3H(N)glucosamine, NEN) is then be added to each flask and the cultures allowed to incubate for an additional 30-40 hours. Cells are harvested by scraping, and EBs purified by gradient centrifugation. PMPE or PMPI protein is isolated from 1.0% OGP surface extracts, eluted with NaCl and analyzed by SDS-PAGE using 14C-labeled molecular weight markers (BRL). The resulting gel is dried and subjected to autoradiography by exposure for 1-4 weeks to Kodak X-AR film at −70° C.
To determine post synthesis lipid modification, C. trachomatis is cultivated on monolayers of McCoy cells according to standard procedures. Approximately 24 hours postinfection, conventional culture media (DMEM+10% FCS) is removed and replaced with a serum-free medium containing cycloheximide (1 μg/ml) and [U-14C]palmitic acid (0.5 mCi/T225 flask, NEN) and incubated for a further 16-24 hours to allow protein lipidation to occur. Surface EB extracts are prepared and analyzed by autoradiography as described above.
6.4. Anti-PMPE or Anti-PMPI Antiserum
Antisera to PMPE or PMPI polypeptides are prepared by injecting the PMPE or PMPI polypeptide into an animal, such as a rabbit, mouse or guinea pig, with or without an adjuvant by any method generally known to those skilled in the art. For instance, PMPE is injected with Freund's complete adjuvant followed by injections of PMPE with Freund's incomplete adjuvant. Normally, a semi-purified or purified form of the protein is injected. For instance, the PMPE polypeptide is resolved from other proteins using SDS-PAGE according to standard techniques well known to those skilled in the art, as previously described (Laemmli, 1970, Nature 227:680-685), and cutting the PMPE-containing band out of the gel. The excised band containing PMPE is macerated and injected into an animal to generate antiserum to the PMPE polypeptide. The antisera is examined using well known and generally accepted methods of ELISA to determine titer, Western blots to determine binding to proteins, and for immunofluorescent staining and for complement-mediated cytotoxic activity against Chlamydia. 
To aid in the characterization of the PMPE or PMPI protein, hyperimmune rabbit antisera is raised against whole EBs from C. trachomatis. Each animal is given a total of three immunizations of about 250 μg Chlamydia EBs per injection (beginning with the EBs mixed with complete Freund's adjuvant and followed with EBs mixed with incomplete Freund's adjuvant) at approximately 21 day intervals. At each immunization, approximately half of the material is administered intramuscularly (i.m.) and half is injected intranodally. Fourteen days after the third vaccination, a fourth booster of about 100 μg of EBs is given i.m. and the animals exsanguinated 7-10 days later.
6.5. ELISA
Anti-PMPE or anti-PMPI antibody titers are measured by ELISA using purified PMPE or PMPI protein ( ̃1 μg/well) or C. trachomatis EBs (whole or crude protein extracts) or cells infected with Chlamydia as capture ligands by any method known by those skilled in the art. Serial dilutions of antisera are made in PBS and tested by ELISA in duplicate. HRP-conjugated antibody is diluted and used as the second reporter antibody in these assays. Titers are expressed as the greatest dilution showing positive ELISA reaction, i.e., an O.D. 450 value>2SD above the mean negative control value (pre-bleed rabbit sera).
6.6. Western Blots
Chlamydia trachomatis is grown in McCoy cells and Chlamydia cell lysates are prepared as described in section 6.1, supra. The solubilized cells are resolved on 12% polyacrylamide gels and the separated proteins were electrophoretically transferred to PVDF membranes at 100 V for 1.5 hours as previously described (Thebaine et al. 1979, Proc. Natl. Acad. Sci. USA 76:4350-4354). The PVDF membranes are then pretreated with 25 ml of Dulbecco's phosphate buffered saline containing 0.5% sodium casein, 0.5% bovine serum albumin and 1% goat serum. All subsequent incubations are carried out using this pretreatment buffer.
PVDF membranes are incubated with 25 ml of a dilution of preimmune rabbit serum or serum from a rabbit immunized with PMPE or PMPI polypeptide (as described above) for 1 hour at room temperature or with monoclonal antibodies to PMPE or PMPI. PVDF membranes are then washed twice with wash buffer (20 mM Tris buffer [pH 7.5.] containing 150 mM sodium chloride and 0.05% Tween-20). PVDF membranes are incubated with 25 ml peroxidase-labeled goat anti-rabbit (or anti-mouse for monoclonals) IgG (Jackson ImmunoResearch Laboratories, West Grove, Pa.) for 30 minutes at room temperature. PVDF membranes are then washed 4 times with wash buffer, and are developed with 3,3′diaminobenzidine tetra-hydrochloride and urea peroxide as supplied by Sigma Chemical Co. (St. Louis, Mo.; catalog number D-4418) for 4 minutes each.
Hyperimmune antisera or monoclonal antibody is used to probe Western blots of crude EB or RB extracts as well as 1.0% OGP EB extract preparations to identify PMPE or PMPI polypeptides from other C. trachomatis serovars and Chlamydia species. Lysates from C. trachomatis A, B, Ba, C, D, Da, E, F, G, H, I, Ia, J, K, L1, L2, L3, or MoPn serovars or Chlamydia pneumoniae are electrophoresed to identify proteins reactive with antisera generated against PMPE or PMPI protein.
6.7. Cellular Envelope Location of PMPE and PMPI
Surface localization of the PMPE or PMPI protein on different Chlamydia strains and derivatives is examined by indirect fluorescence antibody (IFA). IFA is performed using the procedures generally known by those skilled in the art using hyperimmune anti-PMPE or PMPI protein as the primary antibody. Hak cells infected with whole EBs from C. trachomatis are achieved by the following method.
McCoy or Hak cells are grown to confluence in D-MEM media on 12 mm plain coverslips inside 24 well tissue culture plates then centrifugally inoculated with  ̃5×104 inclusion forming units (IFU) of the C. trachomatis. After  ̃24 hours incubation, the culture media is removed and infected cells fixed in methanol for 10 min. The fixed monolayer is then washed with PBS (1×) to remove fixative and overlayered with >300 l of anti-PMPE or PMPI rabbit antibody that has been diluted in PBS. After 1 hour incubation with the primary antibody, the cells are washed gently with PBS then incubated for  ̃30 minutes with mouse anti-rabbit IgG antibody conjugated with FITC. The second antibody is diluted using a PBS solution containing 0.0091% Evans Blue as a counter stain to visualize the monolayer. Cells are washed 2× in PBS to remove the secondary antibody, the coverslips are removed from the culture plates, and mounted onto microscope slides using a fluorescent mounting medium.
Identical cell samples are stained with pre-bleed rabbit antibody or FITC-conjugated second antibody alone are processed in parallel and served as antibody specificity (negative) controls. Counterstained samples are examined at a 1000-× magnification with a Zeiss Axioskop photomicroscope equipped with plan-neoflur objectives.
6.8. Properties of PMPE and PMPI Polypeptides
PMPE polypeptide exists as a protein of approximately 90-115 KDa in its native state as determined via Western blots of crude EB or RB extracts of Chlamydia, as described in Section 6.1. PMPI polypeptide exists as a protein of approximately 90-115 KDa in its native state as determined via Western blots of crude EB or RB extracts of Chlamydia. 
The isoelectric point of the PMPE protein is about 7.17. The isoelectric point of the PMPI protein is about 6.36.
6.9. Vaccine Efficacy
An in vitro neutralization model using methods generally known to those skilled in the art is used to show that protective antiserum inhibits Chlamydial infection (neutralization) of various tissue culture cell lines. Animal models are also essential for testing vaccine efficacy with both small animal (non-primate) and primate models necessary for preclinical evaluation. The guinea-pig is used for studying experimental ocular and genital infection by the Guinea-pig inclusion conjunctivitis agent (GPIC), C. psittaci. 
The mouse offers a consistent and reproducible model of genital tract infection using human genital tract isolates. This mouse model is a generally accepted pre-clinical assay and was used to evaluate MOMP as a subunit vaccine. Another model is known as the primate model of trachoma infection wherein the induction of secretory IgA was shown to be a prime component of protection. Vaccinogenic ability of new subunit antigen candidates is determined using the above-mentioned generally accepted in vitro neutralization and animal model systems.
6.9.1 In Vitro Neutralization Model
As a preliminary exercise to the animal protection studies, hyperimmune anti-PMPE or PMPI antibody is evaluated for its ability to block the infectivity of various C. trachomatis serovars (e.g., L2, B, F) in vitro. Although McCoy cells are used to propagate Chlamydia, these cells also allow antibody-mediated uptake via Fc receptors. Therefore, to evaluate anti-PMPE or anti-PMPI antibody inhibition of infectivity, Hak cells, which do not display Fe receptors, are used in these analyses.
Cells are grown on coverslips in 24-well plates to a subconfluent monolayer (about 90% confluency=1×105 cells/ml) at 37° C. in 5% CO2. Anti-PMPE or PMPI antibody is diluted to about 100 μg/ml (total protein) in sucrose-phosphate-glutamate (SPG) buffer and then serially diluted in SPG buffer. Frozen aliquots of pretitered Chlamydia EBs are diluted in SPG buffer to about 2×104 IFU (inclusion forming units)/ml. EBs are premixed with the diluted anti-PMPE or PMPI antibody and incubated 30 minutes at 37° C. on a rocking platform.
Prepared Hak cells are washed in HBSS and then incubated with the anti-PMPE or PMPI antibody/Chlamydia EB mixture in triplicate for each antibody using  ̃500 IFU/ml. Plates are centrifuged at  ̃500 rpm at room temperature for 1 hour then incubated for 2 hours at 37° C. or are incubated for 2 hours at 37° C. without prior centrifugation to allow EB infection of the monolayer. Then the inoculum is removed and plates washed 3 times with HBSS. Tissue culture media containing 1 μg/ml of cycloheximide is added and plates incubated for about 24-48 hours at 37° C. in 5% CO2 to allow inclusion bodies to develop. After incubation, the media is removed and cell monolayers washed 3× in PBS. Plates are fixed in methanol for 20 minutes and re-washed in PBS.
Cells are stained to visualize inclusions by incubating with anti-Chlamydia LPS antibody (diluted about 1:500), washed 3 times in PBS, followed by incubation with FITC-conjugated goat secondary antibody for 30 minutes at 37° C. Coverslips are washed, air dried, and mounted in glycerol on glass slides. Inclusions are counted in five fields through the midline of the coverslip on a Zeiss fluorescence photomicroscope. Results are reported as the percent reduction of inclusion-containing cells with respect to a heterogenous antibody control (rabbit pre-bleed sera).
6.9.2 Vaccine Efficacy (Mouse Model of Salpingitis and Fertility)
Immunization and Challenge
The Tuffrey murine infertility model is employed to evaluate the efficacy of rPMPE or rPMPI to protect animals against Chlamydia trachomatis-induced salpingitis and infertility. Three groups of female C3HeOuJ mice (6 weeks of age, Jackson Labs) are employed for this evaluation. The test group is immunized (e.g., intradermally, intraperitoneal, subcutaneously, intramuscularly, or mucosally) by administration of a vaccine formulation containing approximately 10-100 μg of purified rPMPE or rPMPI and adjuvant. For instance, mice that are immunized intranasally are sedated using an anesthesia cocktail consisting of 16% Ketaject and 16% Xlaject in 68% pyrogen-free PBS (100 μl) i.p./animal. Sedated animals are placed on their backs and using a standard laboratory pipette administered the vaccine formulations; approximately 10 μl of the vaccine solution per nostril with a 5-10 minute wait period between applications.
Two groups of female mice are immunized similarly but with a preparation containing adjuvant only, no antigen. One of these groups is subsequently challenged with C. trachomatis (sham immunized, infected) and serves as the negative fertility control while the other group is not challenged (sham immunized, sham infected) and serves as the positive fertility control.
At week 4, all animals are administered a single i.p. dose of progesterone (2.5 mg in pyrogen-free PBS, Depo-Provera, Upjohn) to stabilize the uterine epithelium. At week 5, animals immunized with rPMPE or rPMPI and animals in the negative control group are infected by bilateral intrauterine inoculation with approximately 5×105 IFU of C. trachomatis (including but not limited to, from serovar F, strain NI1) in 100 μl of sucrose phosphate glutamate buffer (SPG). To mimic the manipulations to the reproductive tract experienced by the other groups, animals in the positive control are bilaterally inoculated with 100 μl of a McCoy cell extract that contains no C. trachomatis. At week 7, animals from each group are sacrificed by CO2 asphyxiation and the complete genital tract (both upper and lower reproductive tracts) are removed for histopathological analysis. At week 9, the remaining females from each group are caged with 8-10 week old male C3H mice for a 2 month breeding period to assess fertility (1 male for every 2 females per cage with weekly rotation of the males within each group, animals from different experimental groups were not mixed). Palpation and periodic weighing are used to determine when animals in each pair become pregnant. The parameters used to estimate group fertility are: F, the number of mice which littered at least once during the mating period divided by the total number of mice in that study group; M, the number of newborn mice (born dead or alive) divided by the number of litters produced in that group during the mating period; and N, the number of newborn mice (born dead or alive) divided by the total number of mice in that group.
Histopathology
Genital tracts are treated for >24 hours in Bouin's fixative, progressively dehydrated in 50%, 70% and 100% methanol, soaked in toluol, and either paraffin embedded or directly embedded in OCT compound (Tissue-TEK, Miles) and subsequently snap frozen in liquid nitrogen. Tissue sections (approximately 6 μm) are stained with hematoxylin and eosin (after deparaffinization of the Bouin fixed samples). Inflammatory changes in the oviducts and ovaries are graded as follows: 0, no apparent inflammatory reaction; 1, a few mononuclear cells infiltrating the periovarial space or the submucosa of the oviduct; 2, same as 1 but to a greater extent; 3, same as 2 but with a thickened oviductal submucosa and the presence of inflammatory cells in the oviductal lumen; 4, same as 3 but to a greater extent. Inflammation in the cervix/vagina is scored based on the level of the intraepithelial infiltrate observed.
Determination of rPMPE or rPMPI Specific Humoral Responses
Blood samples are collected periodically during the immunization and challenge phases by retroorbital bleeding and serum prepared by centrifugation. Vaginal secretions are collected by repeated injection of 50-100 μl of sterile PBS into the vagina with a standard laboratory pipetter and immediately withdrawing the solution. Two to three injection/withdrawal cycles are performed.
Quantitation of antibody (Ab) responses by ELISA are performed as described in Section 6.5. Microwell ELISA plates (Maxisorb, NUNC) for determining antibody levels are coated overnight at 4° C. with  ̃0.5-1.0 μg of purified rPMPE or rPMPI per well in 10 mM carbonate/bicarbonate buffer (pH 9.6), washed with PBS containing 0.1% Tween-20 (washing buffer) and blocked for  ̃1 hr at 37° C. with a PBS solution containing 3% BSA. For the determination of antigen-specific serum IgG levels, test sera or vaginal secretions are serially diluted in washing buffer containing 0.5% BSA and aliquots (100 (l) incubated in the antigen-coated wells for  ̃2 hr at 37° C. The plates are then washed and incubated for  ̃1 hr at 37° C. with a horseradish peroxidase (HRP)-conjugated goat anti-mouse IgG second antibody (Sigma). A HRP-conjugated goat anti-mouse IgA secondary antibody is used to detect the presence of rPMPE or rPMPI specific IgA in serum or vaginal secretions. After incubation with the appropriate secondary Ab, the plates are washed and incubated for  ̃20-30 minutes at room temperature with TMB substrate (Sigma). Reactions are stopped by the addition of 2M H2SO4 and the absorbance determined at 450 nm on a Molecular Devices SpectroMax microplate reader. Titers are determined as the reciprocal of the sample dilution corresponding to an optical density of 1.0 at 450 nm.
Determination of rPMPE or rPMPI Specific Cellular Responses
Groups of mice are immunized with rPMPE or rPMPI plus adjuvant vaccine as described above. At week 5, animals from each group are sacrificed by CO2 asphyxiation, spleens removed and single cell suspensions prepared using conventional methodologies. For cellular assessment, animals are not treated with hormone. For both the positive control group (sham immunized and sham infected) and the negative control group (sham immunized, infected), spleen cells are pooled and tested for restimulation.
For the measurement of spleen cell proliferation, spleens are ground (5 to 10 rounds) in 5 ml RPMI 1640 Glutamax I supplemented with 10% fetal calf serum, 25 mM HEPES, 50 U/ml penicillin, 50 μg/ml streptomycin, 1 mM sodium pyruvate, nonessential amino acids, and 50 mM 2-mercaptoethanol (Gibco-BRL). Live cells are counted by Trypan Blue staining and diluted in the same media to reach a density of 1.0-2.0×106 cells/ml (Falcon 2063 polypropylene tubes). Triplicate cultures are set-up in round bottom 96-well culture plates (Nunclon, Nunc) using  ̃5×105 responder cells per well in 200 μl of media. Cells are stimulated with rPMPE or rPMPI (antigen-specific proliferation) or with concanavalin A (Boerhinger Mannheim) as a positive stimulation control; unstimulated cell cultures are used as a negative control of cellular activation. After 72-96 hours of incubation at 37° C. in 5% CO2, cells are pulsed labeled for  ̃18 hrs with 1.0 Ci 3H-thymidine (Amersham) per well. Pulsed cells are harvested onto glass-fiber sheets using a Tomtec Cell Harvester (Mk III) and counted for beta-emission in a 3-channel Wallac 1450 Trilux Liquid Scintillation Counter. The stimulation index (SI) for a sample (individual or pooled) is defined as the mean of the antigen or ConA-stimulated T-cell uptake of 3H-thymidine for triplicate wells divided by the mean of the unstimulated uptake for triplicate wells. SIs for both antigen-specific (rPMPE or rPMPI-specific) and ConA-specific proliferation are determined.
Results presented in FIG. 7 demonstrate that animals immunized with recombinant PMPE protein develop a strong and uniform antigen-specific T-cell proliferative response. These data also show that T-cells from animals immunized with recombinant PMPE recognize and are strongly stimulated by the infectious EB form of C. trachomatis. 
6.10. Isolation of C. Trachomatis Chromosomal DNA 
Chlamydia trachomatis were grown as described supra in Section 6.1. Gradient purified EBs were suspended in  ̃5.0 ml of sterile water. An equal volume of lysis buffer (200 mM NaCl, 20 mM EDTA, 40 mM Tris-HCl pH 8.0, 0.5% (w/v) SDS, 0.5% (v/v) 2-mercaptoethanol, and 250 μg/ml of proteinase K) was added and the cells suspended by gentle agitation and trituration. The cell suspension was then incubated  ̃12 hours at 50° C. to lyse the EBs and liberate chromosomal DNA. Proteinaceous material was precipitated by the addition of 5.0 ml of saturated NaCl ( ̃6.0 M, in sterile water) and centrifugation at  ̃5,500×g in a Sorval SS34 rotor at room temperature. Chromosomal DNA was precipitated from the cleared supernatant by the addition of two volumes of 100% ethanol. Aggregated DNA was collected and washed using gentle agitation in a small volume of a 70% ethanol solution. Purified chromosomal DNA was suspended in sterile water and allowed to dissolve/disburse overnight at 4° C. by gentle rocking. The concentration of dissolved DNA was determined spectrophotometrically at 260 nm using an extinction coefficient of 1.0 O.D. unit  ̃50 μg/ml.
6.11. PCR Cloning of the PMPE ORF
To produce high levels of recombinant PMPE protein for immunogenicity and protective efficacy studies, the PMPE ORF was PCR cloned into an E. coli high expression vector, pQE-30 (QiaGen). Genes cloned into the pQE-30 vector are expressed from a T5 promoter which is under the control of the lac operator. Genes cloned into pQE-30 are expressed as a fusion protein containing a Met-Arg-Gly-Ser-(His)6 (SEQ ID NO.:71) N terminus. An additional 15 amino acid segment encoded by vector sequences residing between the (His)6 domain and the SalI site are also part of the N terminus. Oligonucleotide PCR primers complementary to the DNA sequences encoding the first 10 amino acid residues of the N-terminus of the mature protein and the last 9 C-terminal amino acid residues of the C. trachomatis serovar L2 PMPE ORF present in the UC Berkeley genomic database (see Stephens et al., 1998, Science: 282: 754-759 and GenBank Accession No. NC000117) were synthesized. In addition to the PMPE specific sequences, these PCR primers were designed to contain flanking SalI restriction sites to allow cloning of the ORF into the pQE-30 expression vector. The oligonucleotides (SEQ ID NOs.:66 and 67) were used to amplify PMPE-specific PCR products from C. trachomatis L2 serovar, genomic DNA.
The sequence of the amplification primers for SEQ ID NO.:66 (forward primer) and SEQ ID NO.:67 (reverse primer) used for these PCR reactions are shown below.








Forward primer for PMPE









(SEQ ID NO.: 66.)









5′- ATC CAG CAG AG GGT CGA CGG GTT CCA GAT CCT ACG



AAA GAG TCG CTA TC- 3′


 


Reverse primer for PMPE








(SEQ ID NO.: 67)









5′- ATC CAG CAG AGG GTC GAC GGC C TTA GAA TCG CAG



AGC AAT TTC CCC ATT GA- 3′






In addition to the PMPE coding sequences, a TAA (TAA in reverse complement) stop codon was engineered into the reverse primer immediately after the last PMPE codon to end protein synthesis. A SalI restriction site was engineered into the reverse primer downstream and adjacent to the TAA stop codon to facilitate cloning into pQE-30.
Standard PCR amplification reactions (2 mM Mg2+, 200 μmol dNTPs, 0.75 units AmpliTaq, 50 l final volume) were programmed using  ̃0.1 μg of C. trachomatis L2 chromosomal DNA. Amplification of the PMPE target sequence was achieved using a standard 32-cycle, three-step thermal profile, i.e., 95° C., 30 sec; 55° C., 45 sec; 72° C., 3 min. Amplification was carried out in 0.2 ml polypropylene thin-walled PCR tubes (Perkin-Elmer) in a Perkin-Elmer model 2400 thermal cycler. PCR amplification reactions produced the expected PMPE-specific  ̃3.0 Kbp amplimer.
The  ̃3.0 Kbp PMPE amplimer was purified from unincorporated primers using hydroxyapatite spin columns (QiaGen) and digested to completion with an excess of SalI (BRL,  ̃10 units per 1 μg DNA) according to the manufacturers recommendations. The purified and digested PMPE ORF was then purified via QiaGen columns as described above and cloned into plasmid pQE-30 that had been previously digested to completion with SalI and treated with calf intestinal alkaline phosphatase (BRL,  ̃0.05 units/pmole of 5′ ends) to prevent vector religation ( ̃5:1, insert:vector ratio).
Digestion of the pQE-30 vector with SalI produces a single restriction fragment of  ̃3.4 Kbp.
Aliquots from the ligation reaction were then used to electrotransform a suitable E. coli host (e.g., M15 (pREP)). Transformed cells were plated on 2X-YT agar containing 100 μg/ml ampicillin (for pQE-30) and 40 μg/ml kanamycin (for pREP) grown at 37° C. for  ̃12-16 hours. Mini-prep DNA from ampicillin/kanamycin-resistant transformants picked at random were prepared using commercially available reagents (QiaGen Mini Prep Kit) and examined for the presence of recombinant plasmids larger than the pQE-30 plasmid (i.e., insert-carrying plasmids). Putative PMPE-insert carrying recombinant plasmids were then digested to completion with SalI and examined for the presence of the PMP-specific fragment by standard agarose gel electrophoresis (0.8% agarose, TAE buffer). All plasmids tested were found to contain the PMPE insert. Plasmid M15 pREP (pQE-pmpE-CT)#37 was one recombinant derivative isolated by these procedures.
6.12. PCR Cloning of the PMPI ORF
To produce high levels of recombinant PMPI protein for immunogenicity and protective efficacy studies, the PMPI ORF was PCR cloned into an E. coli high expression vector pBAD/Thio-E (Invitrogen) under the control of the araBAD promoter. Oligonucleotide PCR primers complementary to the DNA sequences encoding the first 10 amino acid residues of the N-terminus and the last 8 C-terminal amino acid residues of the C. trachomatis L2 PMPI ORF present in the UC Berkeley genomic database (see Stephens et al., 1998, Science: 282: 754-759 and GenBank Accession No. NC000117) were synthesized. In addition to the PMPI specific sequences, the 5′ forward PCR primer contained the sequence 5′ AGG CAG AGG CAT-3′ (SEQ ID NO.:68) immediately upstream of the PMPI ATG start codon while the 3′ reverse primer contained the sequence 5′-AGG CAG AGG GTC GAC′3′ (SEQ ID NO.:70) immediately downstream of the C-terminal GAA codon. The oligonucleotides (SEQ ID NO.:69 and 70) were used to amplify PMPI-specific PCR products from C. trachomatis L2 genomic DNA. The sequence of the amplification primers for SEQ ID NO.:69 (forward primer) and SEQ ID NO.:70 (reverse primer) used for these PCR reactions are shown below.








Forward primer PMPI









(SEQ ID NO.: 69)









5′- AGG CAG AGG CAT ATG CGA CCT GAT CAC ATG AAC



TTC TGT TG- 3′


 


Reverse primer PMPI








(SEQ ID NO.: 70)









5′-AGG CAG AGG GTC GAC GAA CCT GTA AGT GGT CCC CAG



ATC -3′






Standard PCR amplification reactions (2 mM Mg2+, 200 μmol dNTPs, 0.75 units AmpliTaq, 50 l final volume) were programmed using  ̃0.1 μg of C. trachomatis L2 chromosomal DNA. Amplification of the PMPI target sequence was achieved using a standard 32-cycle, three-step thermal profile, i.e., 95° C., 30 sec.; 55° C., 45 sec.; 72° C., 3 min. Amplification was carried out in 0.2 ml polypropylene thin-walled PCR tubes (Perkin-Elmer) in a Perkin-Elmer model 2400 thermal cycler. PCR amplification reactions produced the expected PMPI-specific  ̃3.0 Kbp amplimer.
The  ̃3.0 Kbp PMPI amplimer was purified from unincorporated primers using hydroxyapatite spin columns (QiaGen). The purified PMPI ORF was then cloned into the T/A PCR product cloning vector pUni/V5-HIS-TOPO plasmid (Invitrogen) using standard TOPO cloning methods described by the manufacturer. The plasmid pUni/V5-His-TOPO carries a loxP site upstream of the T/A cloning site that can be used to recombine insert carrying plasmids with other loxP-containing plasmids for subsequent controlled expression of recombinant protein.
Aliquots from the PMPI amplimer and pUni/V5-His-TOPO ligation reaction were then used to transform a suitable E. coli host (e.g., PIR1). Transformed cells were plated on 2X-YT agar containing 40 μg/ml kanamycin and grown at 37° C. for  ̃12-16 hours. Mini-prep DNA from kanamycin-resistant transformants picked at random were prepared using commercially available reagents (QiaGen Mini Prep Kit) and examined for the presence of recombinant plasmids larger than the  ̃2.2 Kbp vector plasmid Uni/V5-His-TOPO (i.e., insert-carrying plasmids). pUni/V5-His-TOPO plasmids carrying the cloned PMPI ORF were mixed ( ̃100 ng) with the plasmid pBAD/Thio-E ( ̃100 ng) in the presence of a recombination buffer supplied by the manufacturer and the two were recombined into a single molecule by homologous recombination at the lox sites on both the pUni/V5-His-TOPO-PMPI plasmid and pBAD/Thio-E vector catalyzed by the Cre recombinase. pBAD/Thio-E carries a segment of the E. coli thioredoxin protein ( ̃12 kD) that has been mutated to encode an N-terminal (His) affinity chromatography domain. A single loxP recombination site is also encoded by pBAD/Thio-E immediately downstream of the His-Thio redoxin coding sequence. The His-Thioredoxin coding sequence and the loxP site are themselves downstream of the araBAD promoter. Recombining pBAD/Thio-E with PMPI derivatives of pUni/V5-His-TOPO through the loxP sites using the loxP-specific Cre recombinase results in the formation of a chimeric protein with the His-thioredoxin domain at the N-terminus which is fused in frame to the PMPI ORF. Following recombination the chimeric plasmids were transformed into E. coli TOP10 cells. Transformed cells were selected on plates containing 40 μg/ml kanamycin. All  ̃9.5 kBp plasmids tested were found to contain the PMPI insert. Plasmid TOP10 (pBAD-PmpI-Ct-Uni)#7 was one recombinant derivative isolated by these procedures.
6.13. Expression of Recombinant PMPE
One milliliter of a frozen stock of E. coli strain M15 pREP containing plasmid (pQE-pmpE-CT)#37 was used to inoculate  ̃100 ml of 2X-YT broth containing 40 μg/ml kanamycin and 100 μg/ml ampicillin and grown overnight at 30° C. to prepare a fermentor seed culture. Approximately 20 ml of the overnight seed culture was then used to inoculate a New Brunswick Bioflow 3000 fermentor loaded with  ̃2.0 L of 2X-YT broth containing 40 μg/ml kanamycin and 100 μg/ml ampicillin. The culture was grown at 37° C. with vigorous aeration until an O.D.600 value of −1.0 was attained. Expression of rPMPE was induced by adding IPTG to a 1.0 mM final concentration and continuing fermentation. Incubation in the presence of IPTG was continued for approximately 4-5 hours.
At the end of the induction period, the E. coli culture, with some cells displaying classic recombinant protein inclusion bodies, was harvested by continuous flow centrifugation using an Heraeus Contifuge 28RS centrifuge. Following centrifugation, cell mass was scraped from the centrifuge bowl and stored at −70° C. until processed.
Approximately 15 gm of the M15 pREP (pQE-pmpE-CT)#37 frozen cell paste was resuspended by vortexing and trituration in  ̃40 ml of ice cold 10 mM sodium phosphate buffer, pH 7.3. Once suspended, lysozyme (Chicken egg white, Sigma) and DNase I (Bovine pancreas, Sigma) were added to final concentrations of 1.0 mg/ml and 0.01 mg/ml, respectively, and the mixture incubated on ice for 30-45 minutes. Cells were disrupted by 2 sequential passes through a pre-cooled ( ̃4° C.) SLM Aminco French Pressure Cell ( ̃14 Kpsi, 1′′-diameter bore). The cell lysate was then centrifuged for 5 min at  ̃500×g (4° C.) in a Sorvall SS34 rotor to remove unbroken cells. Insoluble material containing the rPMPE was isolated (pelleted) by centrifugation for 45 minutes at  ̃20,000×g (4° C.) in a Sorvall SS34 rotor. The supernatant from this centrifugation was discarded and the insoluble fraction stored at −20° C. in pellet form.
To selectively extract contaminating proteins and remove endotoxin, the rPMPE-containing insoluble pellet was thawed on ice and washed twice with 10 ml of PBS buffer containing 2.0% Triton X-100. Washing was performed at room temperature and suspension of the gelatinous rPMPE-containing pellet was accomplished by vortexing and homogenization in a conventional glass tissue grinder. Insoluble material containing the rPMPE was recovered after washing by centrifugation at  ̃10,000×g for 20 minutes (room temperature) in a Sorvall SS34 rotor. Insoluble material was then washed (again by vortexing and homogenization) 2 times with 10 ml of a 4.0 M urea solution containing 2.0 M NaCl. Washed rPMPE material was recovered by centrifugation as above. The insoluble rPMPE fraction was further washed 2 times with 10 ml of a PBS solution containing 1.0% Zwittergent 3-14 (Sigma).
The rPMPE pellet recovered after centrifugation of the final wash solution was then solubilized for 2 hours at room temperature in standard Laemelli SDS-PAGE sample buffer containing 4 M urea. Solubilized rPMPE was size fractionated into a single protein band of  ̃105 kDa by electrophoresis through a cylinderical  ̃37 mm× ̃12 cm 6% polyacrylamide (36:1, acrylamide:bis-acrylamide) Tris/glycine/SDS preparative gel. A 4% polyacrylamide stacking gel was formed on top of the resolving gel ( ̃37 mm× ̃3 cm). Electrophoresis was carried out on a BioRad model 491 PrepCell unit for  ̃12 hours at  ̃22° C. (12 watts constant wattage) using a conventional Tris/glycine/SDS running buffer (BioRad). As electrophoresis proceeded, size fractionated proteins eluting from the bottom of the PrepCell were pumped to an Amersham fraction collector where  ̃8.0 ml fractions were collected.
Aliquots ( ̃20 μl) from each fraction were mixed with an equal volume of 2× LSB heated to  ̃100° C. for 3 minutes and electrophoresed on a 4-20% SDS-PAG to identify fractions containing the PMPE protein. Prestained molecular weight standards were loaded into a parallel lane and were used as a size gauge. PMPE-containing factors were pooled and excess SDS detergent was removed by diluting the eluted sample with approximately 20 volumes of sterile, endotoxin-free 10 mM sodium phosphate buffer (pH 7.4) and concentrated to approximately 1.0 mg/ml by ultrafiltration in an Amicon stirred concentration cell using a YM30 ultrafiltration membrane.
Residual endotoxin was removed from the concentrated rPMPE solution by polymyxin B Affi-Prep Polymyxin Matrix (BioRad) treatment. Affi-Prep treatment was performed overnight at 4° C. in a batch mode according to the manufacturers recommendations.
The protein concentration of the concentrated, polymyxin B-treated rPMPE was determined using the Micro BCA method (Pierce Chem.) and BSA as a standard.
Purified rPMPE ( ̃0.9-1.2 mg/ml protein concentration) was evaluated for purity, identity, and residual endotoxin burden by SDS-PAGE, Western blot, and a colorimetric endotoxin assay (BioWhittaker), respectively. The gel-purified rPMPE material displayed a purity of >95% as a single band of the expected molecular size by gel analysis. Residual endotoxin is calculated to be ≦0.05 EU/g.
6.14. Expression of Recombinant PMPI
One milliliter of a frozen stock of E. coli strain TOP10 containing plasmid (pBAD-pmpI-Ct-Uni)#7 was used to inoculate  ̃100 ml of 2X-YT broth containing 40 μg/ml kanamycin and grown overnight at 37° C. to prepare a fermenter seed culture. Approximately 20 ml of the overnight seed culture was then used to inoculate a New Brunswick Bioflow 3000 fermenter loaded with  ̃2.0 L of 2X-YT broth containing 40 μg/ml kanamycin. The culture was grown at 37° C. with vigorous aeration until an O.D.600 value of C1.0 was attained. Expression of rPMPI was induced by addition of arabinose to a final concentration of 1.0 mM and continuing cultivation for approximately 4-5 hours.
At the end of the induction period, the E. coli culture, with some cells displaying classic recombinant protein inclusion bodies, was harvested by continuous flow centrifugation using an Heraeus Contifuge 28RS centrifuge. Following centrifugation, cell mass was scraped from the centrifuge bowl and stored at −70° C. until processed.
Approximately 15 gm of the TOP10 (pBAD-pmpI-Ct-Uni)#7 frozen cell paste was resuspended by vortexing and trituration in  ̃40 ml of ice cold 10 mM sodium phosphate buffer, pH 7.3. Once suspended, lysozyme (Chicken egg white, Sigma) and DNAase I (Bovine pancreas, Sigma) were added to final concentrations of 1.0 mg/ml and 0.01 mg/ml, respectively, and the mixture incubated on ice for 30-45 minutes. Cells were disrupted by 2 sequential passes through a pre-cooled ( ̃4° C.) SLM Aminco French Pressure Cell ( ̃14 Kpsi, 1′′ diameter bore). The cell lysate was then centrifuged for 5 min at  ̃500×g (4° C.) in a Sorvall SS34 rotor to remove unbroken cells. Insoluble material containing the rPMPI was isolated (pelleted) by centrifugation for 45 min at  ̃20,000×g (4° C.) in a Sorvall SS34 rotor. The supernatant from this centrifugation was discarded and the insoluble fraction stored at −20° C. in pellet form.
To selectively extract contaminating proteins and remove endotoxin, the rPMPI-containing insoluble pellet was thawed on ice and washed twice with 10 ml of PBS buffer containing 2.0% Triton X-100. Washing was performed at room temperature and suspension of the gelatinous rPMPI-containing pellet was accomplished by vortexing and homogenization in a conventional glass tissue grinder. Insoluble material containing the rPMPI was recovered after washing by centrifugation at  ̃10,000×g for 20 minutes (room temperature) in a Sorvall SS34 rotor. Insoluble material was then washed (again by vortexing and homogenization) 2 times with 10 ml of a 4.0 M urea solution containing 2.0 M NaCl. Washed rPMPI material was recovered by centrifugation as above. The insoluble rPMPI fraction was further washed 2 times with 10 ml of a PBS solution containing 1.0% Zwittergent 3-14 (Sigma).
The rPMPI pellet recovered after centrifugation of the final wash solution was then solubilized for 2 hours at room temperature in standard Laemelli SDS-PAGE sample buffer containing 4 M urea. Solubilized rPMPI-thiroredoxin-fusion protein was size fractionated into a single protein band of  ̃105 kDa using a model 491 PrepCell (BioRad) cylindrical gel as described above for PMPE above. PMPI was obtained from SDS PAG and residual endotoxin removed as described for PMPE above.
The protein concentration of the concentrated, polymyxin B-treated rPMPI-thioredoxin fusion protein was determined using the Micro BCA method (Pierce Chem.) and BSA as a standard.
Purified rPMPI ( ̃0.9-1.2 mg/ml protein concentration) was evaluated for purity, identity, and residual endotoxin burden by SDS-PAGE, Western blot, and a colorimetric endotoxin assay (BioWhittaker), respectively. The gel-purified rPMPI material displayed a purity of >95% as a single band of the expected molecular size by gel analysis. Residual endotoxin is calculated to be ≦0.05 EU/g
6.15. Affinity Chromatography Purification of Recombinant Protein
Recombinant PMPE or PMPI protein is purified to apparent homogeneity using standard preparative immobilized metal affinity chromatography (MAC) procedures. Briefly, an E. coli strain harboring an expression plasmid containing PMPE or PMPI protein gene is grown in Luria broth in a 5 L fermenter (New Brunswick) at 37° C. with moderate aeration until mid-log phase ( ̃0.5 O.D.600) and induced with IPTG or arabinose (1 mM final) for 4-5 hours. Cell paste is collected, washed in PBS and stored at −20° C. Aliquots of frozen cell paste ( ̃9-10 grams wet weight) are suspended in  ̃120 ml of D-PBS by mechanical agitation and lysed by passage through a French pressure cell (2×, 14,000 psi, 4° C.). Soluble protein is then removed from rPMPE or rPMPI protein inclusion bodies by high speed centrifugation ( ̃20,000×g, 4° C., 30 min).
The insoluble pellet containing rPMPE or rPMPI protein is suspended in  ̃20 ml of ice cold D-PBS by homogenization and centrifuged as above. Washed rPMPE or rPMPI protein inclusion bodies are then denatured by suspension in a sodium phosphate buffer (0.1 M, pH 7.0) containing 7.4 M guanidine hydrochloride, 5% 2-ME and 10% glycerol and loaded onto a Ni2+-affinity column (1.5 cm×25 cm, bed volume  ̃30 ml) prepared from Fast-Flow Chelating Sepharose (Pharmacia) and charged with Ni2+ or Zn2+ ions by standard procedures. Unbound material is removed by washing the column with  ̃5-10 column volumes of a sodium phosphate buffer (0.1 M, pH 7.0) containing  ̃7.4 M guanidine HCl.
Recombinant PMPE or PMPI protein bound to the affinity resin by virtue of the (His)6 affinity purification domain is eluted using sodium phosphate buffer (pH 7.4) containing 7.4 M guanidine HCl and 200 mM imidazole. Eluted material is dialyzed against TE buffer containing SDS (0.5%) to remove the guanidine. Dialyzed material is concentrated using a Amicon stirred cell concentrator using a YM30 membrane and mixed with a 1⁄5 volume of 5×SDS gel sample buffer containing 1 mM 2-mercaptoethanol and boiled at 100° C. for 5 minutes.
Samples are loaded onto Tris/glycine acrylamide gels (4% stacking gel, 4-20% resolving gel, 30:0.8 acrylamide:bis solution, 1 mm thickness). A prestained molecular weight standard (See Blue or Multimark, Novex) is run in parallel with the rPMPE or rPMPI protein samples to identify size fractions on the gel. The purity of rPMPE or rPMPI protein is determined using conventional SDS-PAGE and commercially available silver staining reagents (Silver Stain Plus, Novex).
6.16. Generation of a Radiolabeled Screening Probe
The sequence information shown above is used to design a pair of nondegenerate oligonucleotide primers. PCR amplification of DNA fragments is performed under the same conditions as described above with the exception that the annealing temperature is lowered to 50° C. The DNA fragment is isolated from an agarose gel as before and radiolabeled using [32P]-gamma-ATP and T4 polynucleotide kinase according to standard methods. Unincorporated radiolabel is separated from the probe on a G25 Sepharose spin column. Before use, the probe is denatured for 2 min. at 95° C. and subsequently chilled on ice (4° C.).
6.17. Hybridization of Plaque-Lift Filters and Southern Blots with Radiolabeled Probe
Phage plaques from library platings are immobilized on nylon filters using standard transfer protocols well known to those skilled in the art. Digested bacterial genomic DNA, phage or plasmid DNA is electrophoresed on 0.8% TAE-agarose gels and transferred onto nylon filters using a pressure blotter (Stratagene) according to the manufacturer's recommendations. Hybridizations with selected probes are performed at 37° C. (for example, to detect PMP homologs of other species). Hybridizations with specific probes are generally carried out at 50-60° C. (e.g., to detect the identical sequence or the analogous protein in another serovar). Washes of increasing stringency are done at the respective hybridization temperatures until nonspecific background is minimized.
6.18. Construction of a Chlamydia Genomic DNA Library
A genomic library was constructed in the λZAPII replacement vector obtained from Stratagene. The vector arms were digested with EcoR1. Digests of Chlamydia DNA by EcoR1 were performed to yield fragment sizes between 1 kb and 5 kb. Ligations of vector arms and insert DNA were carried out according to standard protocols. Ligation reactions were packaged in vitro using the Stratagene GigaPack Gold III extract. The packaged phage were plated on E. coli X1 Blue MRA (P2) (Stratagene). An initial library titer was determined and expressed as number of pfu.
The library is screened using 4×104 pfu that are plated at a density of 8×103 pfu/130 mm plate with a PMPE or PMPI specific, probe. Several putative positive phage plaques are located and the strongest hybridizing phage are eluted from cored agarose plugs, titered and replated for secondary screening. The selected phage are replated at low density (approximately 100 pfu/plate) and plaques are analyzed by PCR using primer pairs. Inserts carrying plasmids (phagemids) are rescued from the selected phage by co-infecting E. coli cells with an appropriate helper virus.
6.19. Determination of Insert Size and Mapping of DNA Fragments
In order to estimate the size of inserts, phagemid DNA is digested with appropriate restriction enzymes (e.g., NotI) and the digests are analyzed on a 0.5% TAE-agarose gel side by side with suitable DNA markers. In order to map restriction fragments that would hybridize to the probe, DNA from phagemid isolates is digested with a number of common restriction enzymes either alone or in combination with NotI. The rationale of this approach is to discriminate between fragments that span the insert/phagemid vector junction and those that map on the NotI insert. The series of single and double digests are run side-by-side for each phage isolate and analyzed by Southern analysis with radiolabeled probe.
6.20. Sequencing of the PMPE and PMPI Gene
Sequencing of the PMPE and PMPI gene is performed using the Dye Terminator Cycle Sequencing Kit from Perkin-Elmer according to the manufacturer's specifications. The sequencing reactions are read using an ABI Prism 310 Genetic Analyzer. The sequences are aligned using the AutoAssembler software (Perkin-Elmer) provided with the ABI Prism 310 sequencer.
The sequence of the nucleic acid encoding the PMPE protein and the deduced amino acid sequence of the PMPE expressed by Plasmid M15 pREP (pQE-pmpE-Ct-Uni)#37 are shown in FIG. 8 (SEQ ID Nos.:72 and 73).
6.21. In Vivo Efficacy of PMPE
The ability of PMPE to protect female C3HeOUJ mice using the procedure disclosed in Section 6.9.2, supra, is shown in Table 4. Groups of mice were immunized intranasally (i.n.) with 10 μg PMPE (with or without  ̃5 μg mLT as an adjuvant) prior to challenge with live C. trachomatis serovar F. Negative control mice were immunized with  ̃5 μg mLT intranasally prior to administration of live C. trachomatis. Positive control groups were immunized with adjuvant alone intranasally but were not administered live C. trachomatis. The fertility rate for mice vaccinated with PMPE or PMPE and mLT was 50% and 46% respectively. The fertility rate for negative control mice inunized with adjuvant alone (mLT) was 9% and the fertility of positive control mice not infected with C. trachomatis but administered mLT was 95%. These results demonstrate that PMPE is an effective vaccine for ameliorating infertility induced by infection with C. trachomatis. Thus, one with skill would in light of teaching of the specification be able to make the claimed PMPE polypeptides and determine if the PMPE polypeptides have the ability to ameliorate disease associated with infection with C. trachomatis. 







TABLE 4







FERTILITY ASSESSMENT FOR PMPE









Group
Vaccine and Route
% Fertility












I
PMPE + mLT/i.n.
50


II
PMPE/i.n.
46


III
mLT/i.n.(Neg. control)
9


IV
mLT/i.n. (Pos. control)
95









The present invention is not to be limited in scope by the microorganism deposited or the specific embodiments described herein. It will be understood that variations which are functionally equivalent are within the scope of this invention. Indeed, various modifications of the invention, in addition to those shown and described herein, will become apparent to those skilled in the art from the foregoing description and accompanying drawings. Such modifications are intended to fall within the scope of the appended claims.
Various publications are cited herein, the disclosures of which are incorporated by reference in their entireties.

## Claims

1. An isolated polynucleotide comprising the nucleic acid sequence which encodes a polypeptide comprising the amino acid sequence selected from the group consisting of:
(a) amino acids 32-965 of SEQ ID NO: 2;
(b) SEQ ID NO: 2;
(c) amino acids 590-625 of SEQ ID NO: 2;
(d) amino acids 1-500 of SEQ ID NO: 2;
(e) amino acids 625-700 of SEQ ID NO: 2;
(f) the amino acid sequence encoded by the Chlamydia insert in E. coli M15 assigned as ATCC PTA No. 2462; and
(g) a combination of two or more amino acid sequences of (a)-(f).

2. The polynucleotide of claim 1, wherein said polypeptide further comprises a heterologous polypeptide.

3. The polynucleotide of claim 2, wherein said heterologous polypeptide is selected from the group consisting of a pre- and/or pro-sequence, an affinity purification sequence, and an immunogenic sequence.

4. The polynucleotide of claim 2, wherein said heterologous polypeptide is selected from the group consisting of SEQ ID NO: 4; amino acids 13-40 of SEQ ID NO: 4; amino acids 70-110 of SEQ ID NO: 4; amino acids 150-225 of SEQ ID NO: 4; amino acids 250-290 of SEQ ID NO: 4; amino acids 370-455 of SEQ ID NO: 4; amino acids 400-455 of SEQ ID NO: 4; amino acids 470-520 of SEQ ID NO: 4; amino acids 615-670 of SEQ ID NO: 4; amino acids 710-775 of SEQ ID NO: 4; amino acids 765-825 of SEQ ID NO: 4; amino acids 830-860 of SEQ ID NO: 4; amino acids 1-500 of SEQ ID NO: 4; and the amino acid sequence encoded by the Chlamydia insert in E. coli TOP10 assigned as ATCC PTA No. 2461.

5. The polynucleotide of claim 1, wherein said nucleic acid sequence is selected from the group consisting of:
(a) nucleotides 94-2895 of SEQ ID NO: 1;
(b) SEQ ID NO: 1;
(c) the Chlamydia insert in E. coli M15 assigned as ATCC PTA No. 2462; and
(d) a combination of (a), (b), or (c), or the complement thereof.

6. A vector comprising the polynucleotide of claim 1.

7. A host cell comprising the vector of claim 6.

8. A composition comprising the polynucleotide of claim 1 and a carrier.

9. The composition of claim 8, further comprising an adjuvant.

10. An isolated polynucleotide comprising the nucleic acid sequence, which encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 4 or the amino acid sequence encoded by the Chlamydia insert in E. coli TOP10 assigned as ATCC PTA No. 2461.

11. The polynucleotide of claim 10, wherein said polypeptide further comprises a heterologous polypeptide.

12. The polynucleotide of claim 11, wherein said heterologous polypeptide is selected from the group consisting of a pre- and/or pro-sequence, an affinity purification sequence, and an immunogenic sequence.

13. The polynucleotide of claim 11, wherein said heterologous polypeptide is selected from the group consisting of SEQ ID NO: 2; amino acids 32-965 of SEQ ID NO: 2; amino acids 15-56 of SEQ ID NO: 2; amino acids 15-121 of SEQ ID NO: 2; amino acids 45-125 of SEQ ID NO: 2; amino acids 125-190 of SEQ ID NO: 2; amino acids 195-261 of SEQ ID NO: 2; amino acids 275-366 of SEQ ID NO: 2; amino acids 375-440 of SEQ ID NO: 2; amino acids 440-490 of SEQ ID NO: 2; amino acids 525-590 of SEQ ID NO: 2; amino acids 590-625 of SEQ ID NO: 2; amino acids 615-650 of SEQ ID NO: 2; amino acids 625-700 of SEQ ID NO: 2; amino acids 725-800 of SEQ ID NO: 2; amino acids 755-775 of SEQ ID NO: 2; amino acids 785-845 of SEQ ID NO: 2; amino acids 815-865 of SEQ ID NO: 2; amino acids 1-31 of SEQ ID NO: 2; amino acids 1-500 of SEQ ID NO: 2; and the amino acid sequence encoded by the Chlamydia insert in E. coli M15 assigned as ATCC PTA No. 2462.

14. The polynucleotide of claim 10, wherein said nucleic acid sequence is SEQ ID NO:3 or the Chlamydia insert in E. coli TOP10 assigned as ATCC PTA No. 2461.

15. A vector comprising the polynucleotide of claim 10.

16. A host cell comprising the vector of claim 15.

17. A composition comprising the polynucleotide of claim 10 and a carrier.

18. The composition of claim 17, further comprising an adjuvant.

19. An isolated polynucleotide encoding a polypeptide, which consists of the amino acid sequence selected from the group consisting of: amino acids 32-965 of SEQ ID NO: 2; SEQ ID NO: 2; the amino acid sequence encoded by the Chlamydia insert in E. coli M15 assigned as ATCC PTA No. 2462; amino acids 15-56 of SEQ ID NO: 2; amino acids 15-121 of SEQ ID NO: 2; amino acids 45-125 of SEQ ID NO: 2; amino acids 125-190 of SEQ ID NO: 2; amino acids 195-261 of SEQ ID NO: 2; amino acids 275-366 of SEQ ID NO: 2; amino acids 375-440 of SEQ ID NO: 2; amino acids 440-490 of SEQ ID NO: 2; amino acids 525-590 of SEQ ID NO: 2; amino acids 590-625 of SEQ ID NO: 2; amino acids 615-650 of SEQ ID NO: 2; amino acids 625-700 of SEQ ID NO: 2; amino acids 725-800 of SEQ ID NO: 2; amino acids 755-775 of SEQ ID NO: 2; amino acids 785-845 of SEQ ID NO: 2; amino acids 815-865 of SEQ ID NO: 2; amino acids 1-31 of SEQ ID NO: 2; and amino acids 1-500 of SEQ ID NO: 2.

20. A vector comprising the polynucleotide of claim 19.

21. A host cell comprising the vector of claim 20.

22. A composition comprising the polynucleotide of claim 19 and a cattier.

23. The composition of claim 22, further comprising an adjuvant.

24. The composition of claim 22, further comprising a heterologous polynucleotide.

25. The composition of claim 24, wherein said heterologous polynucleotide encodes the amino acid sequence, which is selected from the group consisting of SEQ ID NO: 4; amino acids 13-40 of SEQ ID NO: 4; amino acids 70-110 of SEQ ID NO: 4; amino acids 150-225 of SEQ ID NO: 4; amino acids 250-290 of SEQ ID NO: 4; amino acids 370-455 of SEQ ID NO: 4; amino acids 400-455 of SEQ ID NO: 4; amino acids 470-520 of SEQ ID NO: 4; amino acids 615-670 of SEQ ID NO: 4; amino acids 710-775 of SEQ ID NO: 4; amino acids 765-825 of SEQ ID NO: 4; amino acids 830-860 of SEQ ID NO: 4; amino acids 1-500 of SEQ ID NO: 4; and the amino acid sequence encoded by the Chlamydia insert in E. coli TOP10 assigned as ATCC PTA No. 2461.

26. An isolated polynucleotide encoding a polypeptide, which consists of the amino acid sequence selected from the group consisting of: SEQ ID NO: 4; amino acids 13-40 of SEQ ID NO: 4; amino acids 70-110 of SEQ ID NO: 4; amino acids 150-225 of SEQ ID NO: 4; amino acids 250-290 of SEQ ID NO: 4; amino acids 370-455 of SEQ ID NO: 4; amino acids 400-455 of SEQ ID NO: 4; amino acids 470-520 of SEQ ID NO: 4; amino acids 615-670 of SEQ ID NO: 4; amino acids 710-775 of SEQ ID NO: 4; amino acids 765-825 of SEQ ID NO: 4; amino acids 830-860 of SEQ ID NO: 4; and amino acids 1-500 of SEQ ID NO: 4.

27. A vector comprising the polynucleotide of claim 26.

28. A host cell comprising the vector of claim 27.

29. A composition comprising the polynucleotide of claim 26 and a carrier.

30. The composition of claim 29, further comprising an adjuvant.

31. The composition of claim 29, further comprising a heterologous polynucleotide.

32. The composition of claim 31, wherein said heterologous polynucleotide encodes the amino acid sequence, which is selected from the group consisting of SEQ ID NO: 2; amino acids 15-56 of SEQ ID NO: 2; amino acids 15-121 of SEQ ID NO: 2; amino acids 45-125 of SEQ ID NO: 2; amino acids 125-190 of SEQ ID NO: 2; amino acids 195-261 of SEQ ID NO: 2; amino acids 275-366 of SEQ ID NO: 2; amino acids 375-440 of SEQ ID NO: 2; amino acids 440-490 of SEQ ID NO: 2; amino acids 525-590 of SEQ ID NO: 2; amino acids 590-625 of SEQ ID NO: 2; amino acids 615-650 of SEQ ID NO: 2; amino acids 625-700 of SEQ ID NO: 2; amino acids 725-800 of SEQ ID NO: 2; amino acids 755-775 of SEQ ID NO: 2; amino acids 785-845 of SEQ ID NO: 2; amino acids 815-865 of SEQ ID NO: 2; amino acids 1-31 of SEQ ID NO: 2; amino acids 1-500 of SEQ ID NO: 2; and the amino acid sequence encoded by the Chlamydia insert in E. coli M15 assigned as ATCC PTA No. 2462.

33. An isolated polynucleotide comprising a nucleotide sequence, which encodes a polypeptide comprising the amino acid sequence selected from the group consisting of: amino acids 32-965 of SEQ ID NO: 2; SEQ ID NO: 2; the amino acid sequence encoded by the Chlamydia insert in E. coli M15 assigned as ATCC PTA No. 2462; amino acids 15-56 of SEQ ID NO: 2; amino acids 15-121 of SEQ ID NO: 2; amino acids 45-125 of SEQ ID NO: 2; amino acids 125-190 of SEQ ID NO: 2; amino acids 195-261 of SEQ ID NO: 2; amino acids 275-366 of SEQ ID NO: 2; amino acids 375-440 of SEQ ID NO: 2; amino acids 440-490 of SEQ ID NO: 2; amino acids 525-590 of SEQ ID NO: 2; amino acids 590-625 of SEQ ID NO: 2; amino acids 615-650 of SEQ ID NO: 2; amino acids 625-700 of SEQ ID NO: 2; amino acids 725-800 of SEQ ID NO: 2; amino acids 755-775 of SEQ ID NO: 2; amino acids 785-845 of SEQ ID NO: 2; amino acids 815-865 of SEQ ID NO: 2; amino acids 1-31 of SEQ ID NO: 2; and amino acids 1-500 of SEQ ID NO: 2, wherein said polypeptide further comprises a heterologous polypeptide.

34. The polynucleotide of claim 33, wherein said heterologous polypeptide is selected from the group consisting of a pre- and/or pro-sequence, an affinity purification sequence, and an immunogenic sequence.

35. The polynucleotide of claim 33, wherein said heterologous polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: 4; amino acids 13-40 of SEQ ID NO: 4; amino acids 70-110 of SEQ ID NO: 4; amino acids 150-225 of SEQ ID NO: 4; amino acids 250-290 of SEQ ID NO: 4; amino acids 370-455 of SEQ ID NO: 4; amino acids 400-455 of SEQ ID NO: 4; amino acids 470-520 of SEQ ID NO: 4; amino acids 615-670 of SEQ ID NO: 4; amino acids 710-775 of SEQ ID NO: 4; amino acids 765-825 of SEQ ID NO: 4; amino acids 830-860 of SEQ ID NO: 4; amino acids 1-500 of SEQ ID NO: 4; and the amino acid sequence encoded by the Chlamydia insert in E. coli TOP10 assigned as ATCC PTA No. 2461.

36. A vector comprising the polynucleotide of claim 33.

37. A host cell comprising the vector of claim 36.

38. A composition comprising the polynucleotide of claim 33 and a carrier.

39. An isolated polynucleotide comprising a nucleotide sequence, which encodes a polypeptide comprising the amino acid sequence selected from the group consisting of: amino acids 13-40 of SEQ ID NO: 4; amino acids 70-110 of SEQ ID NO: 4; amino acids 150-225 of SEQ ID NO: 4; amino acids 250-290 of SEQ ID NO: 4; amino acids 370-455 of SEQ ID NO: 4; amino acids 400-455 of SEQ ID NO: 4; amino acids 470-520 of SEQ ID NO: 4; amino acids 615-670 of SEQ ID NO: 4; amino acids 710-775 of SEQ ID NO: 4; amino acids 765-825 of SEQ ID NO: 4; amino acids 830-860 of SEQ ID NO: 4; and amino acids 1-500 of SEQ ID NO: 4, wherein said polypeptide further comprises a heterologous polypeptide.

40. The polynucleotide of claim 39, wherein said heterologous polypeptide is selected from the group consisting of a pre- and/or pro-sequence, an affinity purification sequence, and an immunogenic sequence.

41. The polynucleotide of claim 39, wherein said heterologous polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: 2; amino acids 15-56 of SEQ ID NO: 2; amino acids 15-121 of SEQ ID NO: 2; amino acids 45-125 of SEQ ID NO: 2; amino acids 125-190 of SEQ ID NO: 2; amino acids 195-261 of SEQ ID NO: 2; amino acids 275-366 of SEQ ID NO: 2; amino acids 375-440 of SEQ ID NO: 2; amino acids 440-490 of SEQ ID NO: 2; amino acids 525-590 of SEQ ID NO: 2; amino acids 590-625 of SEQ ID NO: 2; amino acids 615-650 of SEQ ID NO: 2; amino acids 625-700 of SEQ ID NO: 2; amino acids 725-800 of SEQ ID NO: 2; amino acids 755-775 of SEQ ID NO: 2; amino acids 785-845 of SEQ ID NO: 2; amino acids 815-865 of SEQ ID NO: 2; amino acids 1-31 of SEQ ID NO: 2; amino acids 1-500 of SEQ ID NO: 2; and the amino acid sequence encoded by the Chlamydia insert in E. coli M15 assigned as ATCC PTA No. 2462.

42. A vector comprising the polynucleotide of claim 39.

43. A host cell comprising the vector of claim 42.

44. A composition comprising the polynucleotide of claim 39 and a carrier.