AU709537B2 - Protein allergens of the species Cynodon dactylon - Google Patents

Description

1A Protein Allergens of the Sn~eis CXnodon Dactylon Background of the Invention: Bermuda grass (C7vnodon dacrylon) is an important source of pollen allergens in many areas of the world, especially in tropical and sub-tropical climates, These allergens have been studied by a number of means including IgE immunoblotting (Ford and Baldo, B.A. I Allergy Clin. ImnmunoL 79: 711-720 (1987); Shen et al., Clin. Allergy 18: 401-409 (1988), column chromatography (On-en, and Dowdie, S. Afr. Med. J 51: 586 (1977); Matthiesen et al., J. Allergy Glin. lImmunol. 81:.266 (Ab) (1988)), and immunoelectrophoresis (Mattbiesen et al., supra, 1988).

The major allergen of Bermuda grass pollen allergen has been identified as a protein with a molecular weight (MfW) in the range of 30-34 lcD, binding IgE from sera of more than 76% of individuals allergic to Bermuda grass (Ford and Baldo, (1987) Supra; Shen et al, (1988) Supra, and has been designated Cyn d I (Kahn and Marsh, (1986) Mol. Immunol., 23:1281-1288; Marsh et al., (1988) Ann. Allergy, 60:499-504, Marthiesen et al, 1988, Supra). Cyn d I is a member of the Group I family of allergens (Kahn and Marsh, (1986) Supra, found in many taxonomically related grasses including ryegrass (Loip Kentucky bluegrass (Poa p 1) and Timothy grass (Phi p 1) (S tandring et al, 1987 In Archs Allergy Appi. Immun.,83, 96-103; Esch and Klapper, (1987.) J. Allergy Cli,,.

Immunol., 79:489-495; Matthiesen and Lowenstein (1991) Guin. Exp. Allergy,21, 309-320. However, the allergens of Bermuda grass show limited antibody crossreactivity with those of other grasses (March et al. Supra, Berstein et al. (1976) Allergy Clin. nunol..57: 141-152 A number of studies have shown that Cyn d I differs from the Group I homologues of closely related grasses (Matthiesen and Lowenstein, (1991) Supra. The sequence of the first 27 amino acids at the Nterminus of Cyn d I has been determined. (Matthiesen et al, 1988, Supra; Matthiesen et al, (1990) Epitopes of Atopic Allergens, Brussels, UCB Institute of Allergy, 9-13; Singh et al, Monographs in Allergy, (1990), 28:101-120; Matthiesen and Lowenstein, (1991), supra).

The presence of Bermuda grass pollen allergens in the environment causes hayfever and seasonal asthma in many individuals and continues to have significant socio-economic impact on Western communities.

While the available spectrum of drugs, including anti-histamines and steroids, have resulted in improvement in the treatment of allergic disease, they do have unfortunate side-effects associated with long term usage. Because of these problems, renewed interest has been shown in the immunotherapy of allergic disease. Immunotherapy involves the injection of potent allergen extracts to desensitize patients against allergic reactions (Bousquet, J. and Michel, F.B., (1989) Allergy and Clin Immol. News 1: 7-10. Unfortunately, the pollen preparations used as allergens are polyvalent and of poor quality. Consequently, crude extracts are frequently used at high concentrations and may trigger potentially lethal systemic reactions, including anaphylaxis. The product 20 expressed from the cloned gene, fragments thereof, or synthetic peptides based on the sequence of the allergens provide a safer medium for therapy since they can be quality controlled, characterized and standardized, and they optimally do not bind IgE.

25 Summary of the Invention The present invention provides nucleic acid sequences coding for the major protein allergen of the species Cynodon dactylon (Cyn d or at least one fragment thereof or the functional equivalent of such nucleic acid sequences. The present invention also provides expression vectors comprising such nucleic acid sequences and host cells transformed therewith. The present invention further provides isolated recombinantly, chemically or synthetically produced Cyn d I or fragments thereof. Isolated Cyn d I or antigenic fragments thereof are useful for diagnosing and treating sensitivity in an individual to Bermuda grass pollen allergens.

Brief Description of the Figures Fig. 1 shows the nucleotide sequence coding for and deduced partial amino acid sequence of Cyn d derived from a cDNA clone designated clone 2 (C2).

Fig. 2 shows a partial nucleotide sequence coding for and deduced partial amino acid sequence of Cyn d I, derived from a cDNA clone designated clone 18 (C18).

Fig. 3 shows a comparison of the nucleic acid sequences of clones 2 and 18.

20 Fig. 4 shows a comparison of the deduced amino acid sequences of clones 2 and 18.

Fig. 5 shows a comparison of the deduced amino acid sequences of 7 clones coding for Cyn d I; clone 18, (C18), clone 22 (C22), clone 23 (C23) clone 2 (C2), clone 3 clone 21 (C21), and clone 33 (C33); Fig. 6 shows a partial nucleotide sequence coding for and deduced partial amino acid sequence of Cyn d I derived from a cDNA clone designated clone 14al.

o Fig. 7 shows the partial nucleotide sequence coding for partial and deduced partial amino acid sequence of Cyn dI derived from a cDNA clone designated clone 14cl.

Fig. 8 shows a partial amino acid sequence of Cyn dI designated Cyn d 1.14 predicted from a composite of clones 14al and 14cl.

Fig. 9 shows a predicted full-length amino acid sequence of Cyn d I designated Cyn dI.18.

Fig. 10 shows a predicted partial amino acid sequence of Cyn dI designated Cyn d 1.2/3.

Fig. 11a shows separation by SDS-PAGE of protein fractions obtained by the primary preparative isoelectric focusing (IEF) of these proteins on the Rotofor.

Fig. 11b shows a Western blot of separated proteins screened with MAb3.2.

20 Fig. 12a shows a separation by SDS-PAGE of protein fractions obtained by *refractionation on the Rotofor of pooled fractions, 10-13, from a primary separation of crude pollen extract.

Fig. 12b shows separation by SDS-PAGE of protein fractions obtained by refractionation on the Rotofor of pooled fractions, 15-20, from a primary separation crude pollen extract.

Fig. 13 shows Western blots of native Cyn d la and Cyn d Ib separated by 'SDS-PAGE and probed with IgE from sera of individuals allergic to Bermuda grass.

Fig. 14 shows binding of MAbs 1D1, 3A2, 3C2 and 4D2 to cDNA clones from a Cyn d I AgtII library. The number on the overlay corresponds to the cDNA clone number.

Fig. 15 shows a partial nucleotide sequence coding for and deduced partial amino acid sequence of Cyn d I derived from a cDNA clone designated clone 3.

Fig. 16 shows a partial nucleotide sequence coding for and deduced partial amino acid sequence of Cyn d I derived from a cDNA clone designated clone 22.

Fig. 17 shows a partial nucleotide sequence coding for and deduced partial amino acid sequence of Cyn dI derived from a cDNA clone designated clone 23.

Fig. 18 shows a nucleotide sequence and deduced amino acid sequence of Cyn d I derived from a full-length cDNA clone designated CD1.

Fig. 19 shows a partial nucleotide and deduced amino acid sequence of Cyn d I derived from a cDNA clone designated KAT-39-1.

Fig. 20 shows the comparison of predicted full-length amino acid sequences of the Cyn dl mature proteins designated Cyn dI.18, Cyn dI.CD1 and Cyn d 1.2/3 .(full-length).

i* Detailed Description of the Invention The present invention provides nucleic acid sequences, or the functional equivalents thereof, coding for Cyn d I, the major allergen found in Bermuda grass pollen. Cyn d I appears to be a family of closely related allergens. As defined herein, a "family of allergens" are proteins related in function and amino acid sequence but encoded by genes at separate genetic loci. Each family member can have polymorphism in which nucleotide variation may occur at a given genetic loci.

Polymorphism in the nucleic acid sequence may result in amino acid polymorphism, but this is not always the case as the nucleotide code which encodes for the amino acids is degenerate. The nucleic acid sequence coding for Cyn d I, may vary among individual Bermuda grass plants due to natural allelic variation. Any and all such nucleotide variations and resulting amino acid polymorphisms are within the scope of the invention.

A partial nucleic acid sequence coding for Cyn d I, derived from a cDNA clone designated clone 2. has the sequence shown in Fig. 1. The partial nucleic acid sequence coding for Cyn d I shown in Fig. 1 comprises 435 bases. The 3' untranslated region starts at base 436 and extends to base 662. The deduced partial amino acid sequence of Cyn d I encoded for by clone 2 (C2) is also shown in Fig. 1.

Fig. 2 shows the partial nucleic acid and deduced amino acid sequences for a second cDNA clone designated clone 18 (C18). The nucleic acid sequence coding for Cyn d I shown in Fig. 2 comprises 600 nucleotides encoding 200 deduced amino acids. The 3' untranslated region starts at base 601 and extends to base 775.

As shown in Fig. 3, although the coding sequences for clone 2 and clone 18 are clearly homologous, the 3' untranslated regions are much more divergent.

This suggests that clones 2 and 18 may encode separate members of a Cyn dI gene family.

As shown in Fig. 4, the deduced amino acid sequences encoded by clone 2 and clone 18 have 88.2% homology (84.1% identity). There are 22 amino acid 20 differences in the 143 amino acid overlap deduced from the two clones of which 6 are conservative substitutions and 16 are non-conservative substitutions. The partial protein encoded by clone 18 is two amino acids longer at the carboxy terminus than the partial protein encoded by clone 2 (Fig. Amino acid homology was demonstrated using software contained in PCGENE 25 (Intelligenetics, Mountain View, CA).

A comparison of the deduced amino acid sequences encoded by seven A comparison of the deduced amino acid sequences encoded by seven cDNA clones derived from the Cyn d I library as described in Example 1 are shown in Fig. 5. The amino acid sequences encoded by these cDNA clones designated C2, C3, C21, C22, C23 and C33 are shown aligned with the deduced amino acid sequence encoded by clone 18 (C18). which is the longest clone derived from the Cyn d I cDNA library. As is shown in Fig. 5 and Fig. 6, the overlapping portion of the amino acid sequences encoded by clones 18, 22, 23, 21 and 33 are identical. This suggests that clones 18, 22, 23, 21 and 33 are examples of the same Cyn d I gene family member. However, clones 22 and 23 are two amino acids shorter than clone 18 and have different 3' untranslated regions (Figs. 2, 16 and 17). This may suggest that clones 22 and 23 represent a separate member of the Cyn d I gene family. Alternatively, they could represent differentially spliced forms of the same family member.

As is shown in Fig. 5, there are only five amino acid differences between the deduced amino acid sequences encoded by clones 2 and 3. Accordingly, clones 2 and 3 may represent polymorphisms of a Cyn d I gene family member, which Cyn d I gene family member is different from the Cyn d I gene family member(s) to which clones 18, 21, and 33 belong. Assuming that clones 2 and 3 do represent polymorphisms of a Cyn d I gene family member, a predicted partial amino acid sequence of Cyn d I designated Cyn d 1.2/3 as shown in Fig. 10 may 20 be generated from the amino acid sequences encoded by clones 2 and 3.

Fig. 6 shows the nucleotide sequence of cDNA clone 14al and its deduced -amino acid sequence. This clone was isolated from a PCR as described in Example 2 and the amino acid sequence it encodes corresponds to the amino portion of the Cyn d I family member partially encoded by clone 18. There is a 25 19 nucleotide overlap between the 3' end of clone 14al and the 5' end of clone 18.

Clone 14al was amplified in the PCR using oligonucleotide primers based on non-coding strand sequence of clone 18, as described in Example 2. The methionine encoded by nucleotides 41-43 of clone 14al presumably represents the first amino acid of the translated protein. This is the first methionine encoded after the in-frame stop codon at nucleotides 11-13 of clone 14al indicating that the initiation of protein translation does not occur 5' of the methionine encoded by nucleotides 41-43 of clone 14al. The nucleotide sequence surrounding the presumptive initiator methionine has a 78% match with the consensus sequence, AACAATGGC-3' (Lutcke et al. 1987. EMBO J. 6:43-48), for protein initiation in plants. There is a leader sequence of 22 amino acids before the start of the Nterminus of the mature Cyn d I protein (indicated by amino acid 1 in Fig. the N-terminus of the mature Cyn d I protein (the first 27 amino acids) having previously been identified (Matthiesen et al., 1988, J. Allergy Clin. Immuno 81:226; Singh et al., 1990, Monogr. Allergy, 28:101-120; Matthiesen et al., 1991, J. Allergy Clin. Immunol., 88:763-774).

Fig. 7 shows the nucleotide sequence of cDNA clone 14c1 and its deduced amino acid sequence. This clone was also isolated from a PCR as described in Example 2 and the amino acid sequence it encodes corresponds to the amino 0: portion of the Cyn d I family member partially encoded by clone 18. This clone is homologous with clone 14al, but has one amino acid difference with clone 14al in the sequence of the mature protein (the N-terminus of the mature Cyn d I protein being indicated by amino acid 1 in Fig. Clone 14cl has nucleotide differences in the leader sequence encoding seven amino acid differences with clone 14al, including a 12 nucleotide insert that would encode an additional 4 0000 amino acids. A composite sequence of 14al and 14cl including the potential polymorphisms of these clones is designated Cyn d 1.14 shown in Fig. 8.

The sequences of clones 1al and 14cl ar useful in generating a The sequences of clones 14al and 14cl are useful in generating a predicted full-length nucleic acid sequence encoding Cyn d I. Predicted fulllength nucleotide sequences encoding Cyn d I may be derived from the formula:

LINYX

wherein

L

1 is a nucleic acid sequence of 0-300 nucleotides which includes nucleotides which encode a leader sequence of the Cyn d I protein and which may also include nucleotides of a 5' untranslated region, N is a nucleic acid sequence comprising up to 600 nucleotides and includes nucleotides which encode the amino terminus portion of mature Cyn d I, Y is that portion of the nucleic acid sequence of clone 2, clone 18, clone 3, clone 22, or clone 23 or any polymorphic form of those clones which encodes the mature Cyn d I protein and X is a nucleic acid sequence of 0-600 nucleotides which includes nucleotides of the 3' untranslated portion of Cyn d L For example, LI may include the nucleic acid sequence represented by nucleotides 1-106 of clone 14al as shown in Fig. 6 which includes the 5' untranslated region of clone 14al as well as those 15 nucleotides (nucleotides 41-106 as shown in Fig. 6) of clone 14al which encode a Cyn d I leader sequence.

L

1 may also include the nucleic acid sequence represented by nucleotides 1-103 of clone 14cl as shown in Fig 7 which includes the 5' untranslated region of clone 14cl as well as those nucleotides (nucleotides 28-103 as shown in Fig. 7) of clone 14cl which encode a Cyn d I leader 20 sequence. L 1 may also be a nucleic acid sequence which includes nucleotides of clone 14al which encode only the leader sequence portion of Cyn d I (nucleotides 41-106 as shown in Fig. 6) or the nucleotides of clone 14c1 which encode only the leader sequence portion of Cyn d I (nucleotides 28-103 as shown in Fig. 7) or any polymorphic form thereof. When one is generating a nucleic acid sequence encoding mature Cyn d I, then L is 0 and X is 0 and the formula then simply is NY. N is preferably the nucleic acid sequence represented by encodes the full-length or mature Cyn d I protein.

A predicted full-length amino acid sequence for Cyn d I designated Cyn d I.18 shown in Fig. 9 can be generated by merging the amino acid sequence shown in Fig. 8 designated Cyn d I.14 with amino acid residues 53-246 of clone 18 as shown in Fig. 5. The predicted composite of the mature protein in this case, which comprises amino acid 1-246 of Cyn d 1.18 shown in Fig. 9 would have a predicted molecular weight of approximately 26.7 kDa without any posttranslational modifications. As used herein, the "mature" Cyn d I protein does not include the amino acid sequence of the leader portion of the Cyn d I protein. In all applicable figures discussed herein, polymorphism or potential polymorphism is shown in superscript and subscript.

A full-length clone was generated using PCR as discussed in Example 3 and as shown in Figs. 18 and 20. The full-length clone shown in Fig. 18 and designated clone CD1 was generated from a PCR using oligonucleotide primers based on nucleorides 107-125 of clone 14al (Fig 6) and nucleotides 604-621 of clone 18 (Fig.

The deduced amino acid sequence of clone CD1 corresponds to the predicted composite full-length amino acid sequence of the Cyn d I protein family member designated Cyn d 1.18, as discussed above and as shown in Fig. 9. with the exception of two amino acids. The deduced amino acid sequence of clone CD1 as shown in Figs. 18 and 20 is designated Cyn d I.CD1. Cyn d I.CD1 is substantially the same Cyn d I protein as the predicted composite sequence represented by Cyn d 1.18 shown in Fig. 9.

Another predicted composite full-length amino acid' sequence designated Cyn d 1.2/3 (full-length) is shown in Fig. 20. Part of this sequence is deduced from a Cyn d I clone which was generated from a PCR using oligonucleotide primers based on nucleotides 178-206 of clone 2 (Fig. 1) (which is identical to the corresponding nucleotide sequence of clone 3 (Fig. 15)) and nucleotides essentially identical to nucleotides 107-130 of clone 14al (Fig. This clone was designated clone KAT- 39-1. The nucleotide and deduced amino acid sequences of clone KAT-39-1 are shown in Fig 19. The deduced amino acid sequence of clone KAT-39-1 represents a partial amino acid sequence of Cyn d I that overlaps with part of the predicted amino acid sequence of Cyn d 1.2/3 as shown in Fig. 10. Therefore, the composite sequence formed by combining the nucleic and deduced amino acid sequences of clone KAT-39-1 in conjunction with the nucleic and deduced amino acid sequences of Cyn d 1.2/3 represent the nucleic and deduced amino acid sequences of the predicted Cyn d I protein family member composite designated Cyn d 1.2/3 (fulllength) as shown in Fig. 20. Fig. 20 shows a comparison of the amino acid sequences of composite sequences designated Cyn d 1.18 and Cyn d 1.2/3 (fulllength), and the full-length amino acid sequence deduced from the full-length cDNA 15 clone, CD1, designated Cyn d I.CD1.

Nucleic acids encoding Cyn d I protein allergens as described above may be obtained from any part of Cynodon dacrylon plants. Nucleic acids encoding Cyn d I may be obtained from genomic DNA. The nucleic acids coding for Cyn d I may be obtained using the methods disclosed herein or any other suitable technique for isolation and cloning of genes.

Fragments of the nucleic acid sequence coding for fragments of Cyn d I are also within the scope of the invention. Fragments within the scope of the invention include those coding for parts of Cyn d I which induce an immune response in mammals, preferably humans, such as stimulation of minimal amounts of IgE; binding of IgE; eliciting the production of IgG and IgM antibodies; or the eliciting of a T cell response such as proliferation and/or lymphokine secretion and/or the induction of T cell anergy. The foregoing fragments of Cyn d I are referred to herein as antigenic fragments. Fragments within the scope of the invention also include those capable of hybridizing with nucleic acid from other plant species for use in screening protocols to detect allergens that are cross-reactive with Cyn d I. As used herein, a fragment of the nucleic acid sequence coding for Cyn d I refers to a nucleotide sequence having fewer bases than the nucleotide sequence coding for the entire amino acid sequence of Cyn d I and/or mature Cyn d I. Generally, the nucleic acid sequence coding for the fragment or fragments of Cyn d I will be selected from the bases coding for the mature protein, however, in some instances it may be desirable to select all or a part of a fragment or fragments from the leader sequence portion of the nucleic acid sequence of the invention. The nucleic acid sequence of the invention may also contain linker sequences, modified restriction endonuclease sites and other sequences useful for cloning, expression or purification of Cyn d I 0o96.: 15 or fragments thereof.

The present invention provides expression vectors and host cells 9* transformed to express the nucleic acid sequences of the invention. Nucleic acid coding for Cyn d I, or at least one fragment thereof may be expressed in bacterial cells such as E. coli, insect cells (baculovirus), yeast, or mammalian cells such as 20 Chinese hamster ovary cells (CHO). Suitable expression vectors, promoters, enhancers, and other expression control elements may be found in Sambrook et al. Molecular Cloning: A Laboratory Manual, second edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1989). Other suitable expression vectors, promoters, enhancers, and other expression elements are known to those skilled in the art. Expression in mammalian, yeast or insect cells leads to partial or complete glycosylation of the recombinant material and formation of any inter- or intra-chain disulfide bonds. Suitable vectors for expression in yeast include YepSecl (Baldari et al. (1987) Embo J. 6: 229-234); pMFa (Kurjan and Herskowitz (1982) Cell 30: 933-943); JRY88 (Schultz et al.

(1987) Gene 54: 113-123) and pYES2 (Invitrogen Corporation, San Diego, CA).

These vectors are freely available. Baculovirus and mammalian expression systems are also available. For example, a baculovirus system is commercially available (PharMingen, San Diego, CA) for expression in insect cells while the pMSG vector is commercially available (Pharmacia, Piscataway, NJ) for expression in mammalian cells.

For expression in E. coli, suitable expression vectors include, among others, pTRC (Amann et al. (1988) Gene 69: 301-315); pGEX (Amrad Corp., Melbourne, Australia); pMAL Biolabs, Beverly, MA); pRIT5 (Pharmacia, Piscataway, NJ); pET- lId (Novagen, Madison, WI) Jameel et al., (1990) J.

Virol. 64:3963-3966; and pSEM (Knapp et al. (1990) BioTechniques 8: 280-281).

15 The use of pTRC, and pET-I ld, for example, will lead to the expression of unfused protein. The use of pMAL, pRIT5 pSEM and pGEX will lead to the expression of allergen fused to maltose E binding protein (pMAL), protein A truncated B-galactosidase (PSEM), or glutathione S-transferase (pGEX).

When Cyn d I, fragment, or fragments thereof is expressed as a fusion protein, it is particularly advantageous to introduce an enzymatic cleavage site at the fusion junction between the carrier protein and Cyn d I or fragment thereof. Cyn d I or a fragment thereof may then be recovered from the fusion protein through enzymatic cleavage at the enzymatic site and biochemical purification using 'i convendonal techniques for purification of proteins and peptides. Suitable enzymatic cleavage sites include those for blood clotting Factor Xa or thrombin for which the appropriate enzymes and protocols for cleavage are commercially available from, for example, Sigma Chemical Company, St. Louis, MO and N.E.

Biolabs, Beverly, MA. The different vectors also have different promoter regions allowing constitutive or inducible expression with, for example, IPTG induction (PRTC, Amann et al., (1988) supra; pET-1 d, Novagen, Madison, WI) or temperature induction (pRIT5, Pharmacia, Piscataway, NJ). It may also be appropriate to express recombinant Cyn d I in different E. coli hosts that have an altered capacity to degrade recombinantly expressed proteins U.S. patent 4,758,512). Alternatively, it may be advantageous to alter the nucleic acid sequence to use codons preferentially utilized by E. coli, where such nucleic acid alteration would not affect the amino acid sequence of the expressed protein.

Host cells can be transformed to express the nucleic acid sequences of the invention using conventional techniques such as calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, or electroporation. Suitable methods for transforming the host cells may be found in Sambrook et al. supra, and other laboratory textbooks. The nucleic acid sequences of the invention may also be synthesized using standard techniques.

The present invention also provides a method of producing purified Cyn d I or at least one fragment thereof comprising the steps of culturing a host cell transformed with a DNA sequence encoding Cyn d I or at least one fragment thereof in an appropriate medium to produce a mixture of cells and medium containing Cyn d I or at least one fragment thereof; and purifying the mixture to produce substantially pure Cyn d I or at least one fragment thereof. Host cells transformed with an expression vector containing DNA coding for Cyn d I or at .least one fragment thereof are cultured in a suitable medium for the host cell.

Cyn d I protein and peptides can be purified from cell culture medium, host cells, or both using techniques known in the art for purifying peptides and proteins including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis and immunopurification with antibodies specific for Cyn d I or fragments thereof. The terms isolated and purified are used interchangeably herein and refer to peptides, protein, protein fragments, and nucleic acid sequences substantially free of cellular material or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when synthesized chemically. Accordingly, an isolated peptide of the invention is produced by recombinant DNA techniques or synthesized chemically and is substantially free of cellular material, culture medium, chemical precursors or other chemicals.

Another aspect of the invention provides preparations comprising Cyn d I or at least one fragment thereof synthesized in a host cell transformed with a DNA sequence encoding all or a portion of Cyn d I, or chemically synthesized, and purified Cyn d I protein, or at least one antigenic fragment 15 thereof produced in a host cell transformed with a nucleic acid sequence of the invention, or chemically synthesized. In preferred embodimients of the invention, the Cyn d I protein is produced in a host cell transformed with the nucleic acid sequence coding for at least the mature Cyn d I protein.

Fragments of Cyn d I can be obtained, for example, by screening peptides synthesized from the corresponding fragment of a nucleic acid sequence of the invention coding for such peptides or synthesized chemically using techniques known in the art. Peptide fragments of the allergen may be obtained by selection of fragments of a desired length with no overlap of the peptides, or selection of overlapping fragments of a desired length, which can be produced recombinantly or synthetically. The fragments can be tested to determine antigenicity the ability of the fragment to induce an immune response). Such fragments are 16 referred to herein as antigenic fragments. Fragments of Cyn d I protein allergen which are capable of eliciting a T cell response such as stimulation proliferation or lymphokine secretion) and/or are capable of inducing T cell anergy are particularly desirable. Fragments of Cyn d I which do not bind immunoglobulin E (IgE) or bind IgE to a substantially lesser extent than the protein allergen from which the fragments are derived are also particularly desirable. The major complications of standard immunotherapy are systemic responses such as anaphylaxis. Immunoglobulin.E is a mediator of anaphylactic reactions which result from the binding and cross-linking of antigen to IgE on mast cells or basophils and the release of mediators histamine, scrotonin, eosinophil, chemotactic factors). Thus, anaphylaxis could be avoided by the use of a fragment which does not bind IgE, or if the fragment binds IgE, such binding does not result in the release of mediators histamine etc.) from mast cells or basophils. In addition, fragments which have minimal IgE stimulating activity 15 are particularly desirable for therapeutic effectiveness. Minimal IgE stimulating activity refers to IgE stimulating activity which is less than the amount of IgE ~production stimulated by the whole Bermuda grass protein allergen. Preferred fragments of the invention include but are not limited to fragments derived from amino acids 5-246, 10-246, 20-246 and 25-246 of Cyn d 1.18 as shown in Fig. fragments derived from amino acids 5-246, 10-246, 20-246 and 25-246 of Cyn d I.CD1 as shown in Fig. 20; and fragments derived from amino acids 5-244, 244, 20-244 and 25-244 of Cyn d 1.2/3 (full-length) as shown in Fig. Cyn d I and preferred antigenic fragments thereof, when administered to a Bermuda grass pollen-sensitive individual, are capable of modifying the allergic response of the individual to the allergen, and preferably are capable of modifying the B cell. the T cell response or both the B cell and the T cell 17 response of the individual to the allergen. As used herein, modification of the allergic response of an individual sensitive to a Bermuda grass pollen allergen such as Cyn d I can be defined as non-responsiveness or diminution in symptoms to the allergen, as determined by standard clinical procedures (See Varney et al., British Medical Journal 302: 265-269 (1990)) including dimunition in Bermuda grass pollen induced asthmatic symptoms. As referred to herein, a dimunition in symptoms includes any reduction in symptoms in the allergic response of an individual to the allergen following a treatment regimen with a protein or peptide of the invention. This dimunition in symptoms may be determined subjectively the patient feels more comfortable upon exposure to the allergen), or clinically, such as with a standard test. Initial screening for IgE binding to Cyn d I or fragments thereof may be performed by scratch tests or intradermal skin tests on laboratory animals or human volunteers, or in in vitro systems such as RAST (radioallergosorbent test), RAST inhibition, ELISA assay, 15 radioimmunoassay (RIA), or histamine release.

Antigenic fragments of the present invention which have T cell stimulating activity, and comprise at least one T cell epitope are particularly desirable. T cell epitopes are believed to be involved in initiation and perpetuation of the immune response to a protein allergen which is responsible for the clinical symptoms of allergy. These T cell epitopes are thought to trigger :early events at the level of the T helper cell by binding to an appropriate HLA molecule on the surface of an antigen presenting cell and stimulating the relevant T cell subpopulation. These events lead to T cell proliferation, lymphokine secretion, local inflammatory reactions, recruitment of additional immune cells to the site, and activation of the B cell cascade leading to production of antibodies.

One isotype of these antibodies. IgE, is fundamentally important to the 18 development of allergic symptoms and its production is influenced early in the cascade of events, at the level of the T helper cell, by the nature of the lymphokines secreted. A T cell epitope is the basic element or smallest unit of recognition by a T cell receptor, where the epitope comprises amino acids essential to receptor recognition and may be contiguous and/or non-contiguous in the amino acid sequence of the protein. Amino acid sequences which mimic those of the T cell epitopes and which modify the allergic response to protein allergens are within the scope of this invention.

Exposure of patients to Cyn d I or to the antigenic fragments of the present invention which comprise at least one T cell epitope may tolerize or anergize appropriate T cell subpopulations such that they become unresponsive to the protein allergen and do not participate in stimulating an immune response upon such exposure. In addition, administration of Cyn d I or an antigenic fragment of the present invention which comprises at least one T cell epitope may modify the lymphokine secretion profile as compared with exposure to the naturally-occurring protein allergen or portion thereof result in a decrease of IL-4 and/or an increase in IL-2). Furthermore, exposure to Cyn d I or such antigenic fragment may influence T cell subpopulations which normally participate in the response to the allergen such that these T cells are drawn away from the site(s) of normal exposure to the allergen nasal mucosa, skin, and lung) towards the site(s) of therapeutic administration of the fragment. This redistribution of T cell subpopulations may ameliorate or reduce the ability of an individual's immune system to stimulate the usual immune response at the site of normal exposure to the allergen, resulting in a dimunution in allergic symptoms.

Cyn d I and fragments or portions derived therefrom (peptides) can be used in methods of diagnosing, treating and preventing allergic reactions to Bermuda grass pollen. Thus, the present invention provides therapeutic compositions comprising isolated Cyn d I or at least one fragment thereof and a pharmaceutically acceptable carrier or diluent. Cyn d I or at least one fragment thereof is preferably produced in a cell transformed to express the protein allergen or the fragment thereof or is synthetically prepared. Administration of the therapeutic compositions of the present invention to an individual to be desensitized can be carried out using known techniques. Cyn d I or a fragment thereof can be administered to an individual in combination with, for example, an appropriate diluent, a carrier and/or an adjuvant Pharmaceutically acceptable diluents include saline and aqueous buffer solutions. Pharmaceutically acceptable carriers include polyethylene glycol (Wie et al. (1981) Int. Arch. Allergy AppL Immunol. 64:84-99) and liposomes (Strejan et al. (1984) J. NeuroimmunoL7: 27).

For purposes of inducing T cell anergy, the therapeutic composition is preferably administered in non-immunogenic form, it does not contain adjuvant. Such 15 compositions will generally be administered by injection (subcutaneous, intravenous etc.), oral administration, inhalation, transdermal application or rectal S..administration. The therapeutic compositions of the invention are administered to Bermuda grass pollen-sensitive individuals in a treatment regimen at dosages and for lengths of time effective to reduce sensitivity reduce the allergic response) of the individual to Bermuda grass pollen. Effective amounts of the therapeutic compositions will vary according to factors such as the degree of sensitivity of the individual to Bermuda grass pollen, the age, sex, and weight of the individual, and the ability of the Bermuda grass pollen allergen or fragment thereof to elicit an antigenic respons :n the individual.

cDNA coding for a Cyn d I (or the mRNA from which it was transcribed) or a portion thereof can be used to identify similar sequences in any variety or type of plant and thus, to identify or "pull out" sequences which have sufficient homology to hybridize to the cDNA of the protein allergen or mRNA or portion thereof. For example, cDNA of the present invention may hybridize to DNA from temperate grasses such as rye-grass, Kentucky Blue grass, Timothy grass and orchard grass, and from other grasses such as Bahia grass and sorghum, under conditions of low stringency. Those sequences which have sufficient homology (generally greater than 40%) can be selected for further assessment using the method described herein. Alternatively, high stringency conditions can be used. In this manner, DNA of the present invention can be used to identify, in other types of plants, preferably related families, genera, or species, sequences encoding polypeptides having amino acid sequences similar to that of a Cyn d I, *and thus to identify allergens in other species. Thus, the present invention includes not only the Bermuda grass allergen Cyn d I, but also other allergens :i encoded by DNA which hybridizes to DNA of the present invention. The 15 invention further includes isolated protein allergens or fragments thereof, excluding those protein allergens or fragments from the genus Lolium, which are immunologically related to Cyn d I or fragments thereof, such as by antibody cross-reactivity, or other immunological assay wherein the protein allergens or fragments thereof are capable of binding to antibodies specific for Cyn d I or fragments of the invention or by T cell cross-reactivity wherein the isolated allergenic proteins or fragments thereof are capable of stimulating T cells specific for the proteins and peptides of the invention. The invention also includes protein allergens or fragments thereof which have greater than 73% homology with Cyn d I or have greater than 90% homology with Cyn d I.

Proteins or peptides encoded by the cDNA of the present invention can be used, for example as "purified" allergens. Such purified allergens are useful in the standardization of allergen extracts which are key reagents for the diagnosis and treatment of sensitivity to Bermuda grass pollen. Furthermore, by using proteins or fragments thereof based on the nucleic acid sequences of Cyn d I, anti-peptide antisera, polyclonal antibodies or monoclonal antibodies can be made using standard methods. These sera or polyclonal or monoclonal antibodies can be used to standardize allergen extracts and/or used in purification of native or recombinant protein allergens.

Through use of Cyn d I and synthetically or recombinantly produced isolated antigenic fragments thereof, preparations of consistent, well-defined composition and biological activity can be made and administered for therapeutic purposes to modify the allergic response of a Bermuda grass pollen-sensitive individual. Administration of such peptides or protein may, for example, modify .B-cell response to Cyn d I, T cell response to Cyn d I or both responses. Isolated o peptides can also be used to study the mechanism of immunotherapy of Bermuda 15 grass pollen allergy and to design modified derivatives or analogues useful in immunotherapy.

It is possible to modify the structure of Cyn d I or fragments thereof of the invention, for such purposes as increasing solubility, enhancing therapeutic or preventive efficacy, or stability shelf life ex vivo, and resistance to proteolytic degradation in vivo). Modified Cyn d I or a modified fragment thereof can be produced in which the amino acid sequence has been altered, such as by amino acid substitution, deletion, or addition, to modify immunogenicity and/or reduce allergenicity, or to which a component has been added for the same purpose. For example, the amino acid residues essential to T cell epitope function can be determined using known techniques substitution of each residue and determination of presence or absence of T cell reactivity). Those residues shown to be essential can be modified replaced by another amino acid whose presence is shown to enhance T cell reactivity), as can those which are not required for T cell reactivity by being replaced by another amino acid whose incorporation enhances T cell reactivity but does not diminish binding to relevant MHC). In order to enhance stability and/or reactivity, Cyn dI or a fragment thereof can also be modified to incorporate one or more polymorphisms in the amino acid sequence of the protein allergen resulting from natural allelic variation.

Additionally, D-amino acids, non-natural amino acids or non-amino acid analogues can be substituted or added to produce a modified protein or fragment within the scope of this invention. Furthermore, Cyn dI or fragments thereof can be modified using the polyethylene glycol (PEG) method of A. Sehon and co-workers (Wie et al.

supra) to produce a peptide conjugated with PEG. Modifications of Cyn d I or fragments thereof can also include reduction/alkylation (Tarr in: Methods of Protein 15 Microcharac-terization, J.E. Silver ed. Humana Press, Clifton, NJ, pp 155-194 (1986)); acylation (Tarr, supra); esterification (Tarr, supra); chemical coupling to an appropriate carrier (Mishell and Shiigi, eds, Selected Methods in Cellular Immunology WH Freeman, San Francisco, CA (1980); U.S. Patent 4,939,239); or mild formalin treatment (Marsh International Archives of Allergy and Applied Immunology 41: 20 199-215 (1971)).

Site-directed mutagenesis of DNA encoding Cyn d I or fragment thereof can be used to modify the structure. Such methods may involve PCR (Ho et al., Gene 77:51-59 (1989)) or total synthesis of mutated genes (Hostomsky, et al., Biochem.

Biophys. Res. Comm 161:1056-1063 (1989)). To enhance bacterial expression, the aforementioned methods can be used in conjunction with other procedures to change the plant codons in DNA constructs encoding the peptides to ones preferentially used in E. coli.

Using the structural information now available, it is possible to design Cyn d I peptides which, when administered to a Bermuda grass pollen sensitive individual in sufficient quantities, will modify the individual's allergic response to Bermuda grass pollen. This can be done, for example, by examining the structure of Cyn d I and producing peptides (via an expression system or synthetically) to be examined for their ability to influence B cell and/or T cell responses in Bermuda grass pollen sensitive individuals and selecting appropriate B or T cell epitopes recognized by the cells. Protein, peptides or antibodies of the present invention can also be used for detecting and diagnosing sensitivity to Bermuda grass pollen allergens. For example, this could be done by combining blood or blood products obtained from an individual to be assessed for sensitivity to Bermuda grass pollen with an isolated antigenic fragment of Cyn d I, or isolated Cyn d I, under conditions appropriate for binding of components antibodies, T cells, B cells) in the blood with the fragment(s) or protein and determining the extent to which such binding occurs.

It is now also possible to design an agent or a drug capable of blocking or inhibiting the ability of Cyn d I to induce an allergic reaction in Bermuda grass pollen sensitive individuals. Such agents could be designed, for example, in such 20 a manner that they would bind to relevant anti-Cyn d I-IgE's, thus preventing IgE-allergen binding and subsequent mast cell degranulation. Alternatively, such agents could bind to cellular components of the immune system, resulting in suppression or desensitization of the allergic response to Bermuda grass pollen.

A non-restrictive example of this is the use of appropriate B and T cell epitope peptides, or modifications thereof, based on the cDNA/protein structures of the present invention to suppress the allergic response to Bermuda grass pollen. This can be carried out by defining the structures of B and T cell epitope peptides which affect B and T cell function in in vitro studies with blood components from Bermuda grass pollen sensitive individuals.

The DNA used in any embodiment of this invention can be cDNA obtained as described herein, or alternatively, can be any oligodeoxynucleotide sequence having all or a portion of a sequence represented herein, or their functional equivalents. Such oligodeoxynucleotide sequences can be produced chemically or mechanically, using known techniques. A functional equivalent of an oligonucleotide sequence is one which is capable of hybiidizing to a complementary oligonucleotide to which the sequence (or corresponding sequence portions) thereof hybridizes, or the sequence (or corresponding sequence portion) complementary to the nucleic acid sequences, and/or which encodes a product a polypeptide or peptide) having the same functional characteristics of the product encoded by the sequence (or corresponding 15 sequence portion). Whether a functional equivalent must meet one or both criteria will depend on its use if it is to be used only as an oligoprobe, it need meet only the first criterion and if it is to be used to produce Cyn d I, it need only meet the second criterion).

This invention is further illustrated by the following non-limiting examples.

SO

Example 1 Isolation of Cyn d I for protein sequencing and MAb production.

Preparation of pollen extract Bermuda grass pollen was purchased from Greer Laboratories, Lenoir, NC, USA. To prepare the pollen extract of soluble proteins which was loaded on the Rotofor, 5 grams of Bermuda grass pollen was extracted three times by shaking with 10ml of 10mM phosphate buffered saline (PBS) for one hour at 4 After each extraction, the mixture was centrifuged (2500 rpm, 10 minutes) and the supernatant collected. After three extractions the supernatants were pooled and filtered through a 3mm Whatman filter.

Preparative isoelectric focusing (IEF) Preparative IEF in the Rotofor (Biorad, Richmond, CA) has been described in detail by Egan et al. (1988) Analy. Biochem, 172, 488-494. Briefly, 5ml of ampholyte solution (Bio-lyte, pH range 3-10; 40%) was added to the pollen extract and the volume adjusted to 50ml with distilled water. This mixture was loaded into i the Rotofor cell and focussed at 4oC and 12W constant power. After four hours, 15 fractions were collected and their pH determined. Fractions containing the proteins of interest were identified with MAb 3.2 on immunoblots after SDS-PAGE. This MAb was raised against purified Lol p I but was found to be cross-reactive with Group I homologues from nine other grasses including Bermuda grass (Kahn and Marsh, 1986, Mol. Immunol., 23, 1281-1288). Fractions containing the proteins of 20 interest were pooled and refractionated in the Rotofor using the same conditions as above except that samples were focussed for 2.5 hours. ThepH of each fraction was determined.

SDS-PAGE and Western blotting Proteins in Rotofor fractions were separated under reducing conditions by electrophoresis on 10-15% gradient SDS-polyacrylamide gels. Conditions for electrophoresis were essentially as described by Singh and Knox, Int. Archs Appl.

Imniun., 78, 300-304 (1985). Molecular weights (MW) were determined using low MW standards from Pharmacia. Proteins on polyacrylamide gels were visualized by staining with Coomassie Brilliant Blue R250.

Proteins were transferred to nitrocellulose (Schleicher and Schuell, 0.45pm) according to Towbin et al. (1979); Proc. Natl. Acad. Sci. 76, 4350-4354; at 120 mA overnight at 40C. After protein transfer, non-specific binding sites were blocked by incubation of the Western blots in powdered milk [10% in 10mM TBS (Tris-buffered saline: 150mM NaC/1lOmM Tris.HC1, pH Separation by SDS-PAGE of fractions obtained by preparative IEF, revealed that Cyn d I focussed in fractions 10-20 with a pH range of 6-10. These fractions contained 31-32kD proteins which bound MAb 3.2. The proteins in fractions 10-13 (32kD) which bound MAb 3.2 had a slightly higher MW than those in fractions 20 (31kD) (Fig. 1 la-b). The intermediate fraction 14 contained both proteins that bound MAb 3.2. These proteins have been designated Cyn d Ia (32 kD) and Cyn d 15 Ib (31 kD).

Fractions 10-13 of Fig. 1 la containing Cyn d Ia were pooled and refractionated. Cyn d Ia was found in all fractions of Fig. 12a, but dominated the protein component of fractions 13-20 (Fig. 12a). These fractions had a pH of 6.5; an indication of the pi of Cyn d Ia.

20 Fractions 15-20 of Fig. 1 la were pooled and refractionated in order to purify Cyn d Ib. Cyn d Ib was found in all fractions of Fig. 12b but dominated the protein profile of fractions 1-12 (Fig. 12b). These fractions had a pH of 7.4; an indication of the pi of Cyn d Ib.

Immunoblot analysis Western blots were incubated in MAb 3.2 or in sera of allergic individuals.

MAb 3.2 was diluted 1:1000 in PBS containing 0.5% BSA. MAb binding was visualized by incubation in a solution of peroxidase-labelled, anti-mouse Ig antibody (Dakopatts Corporation. Carpinteria, CA, USA) followed by addition of the enzyme substrate as described by Singh and Knox (1985) supra. Human serum was diluted 1:4 in 150 mM PBS containing 0.5% BSA. IgE binding was visualized by incubation of the blot in 125 I-labelled anti-human IgE (Kallestad) (diluted 1:6 in PBS/BSA) followed by autoradiography. Purified Cyn d la and Ib were assessed for their ability to bind to IgE from the serum of allergic individuals (Fig. 13). Both fractions bound IgE from the sera of a Bermuda grass allergic individual.

NH2-terminal amino acid sequencing Cyn d I proteins Cyn d la and Cyn d Ib, isolated, as described above, and electrotransfered onto polyvinylidene difluoride (PVDF) membrane (Millipore, Bedford, MA, USA) using 10mM CAPS 10% methanol (pH 11.0) as the transfer .15 buffer (Ward et al., 1990) (3 [cyclohexylamino]--propane'sulfonic acid), were then visualized by staining with Coomassie Brilliant Blue R250, destained in methanol acetic acid water (50:10:40, v/v/v) and washed extensively with deionized water.

The NH 2 -terminal amino acid sequence of both Cyn d la and Cyn d Ib proteins was determined as described by Ward et al. (1990); 20 Cyn d I proteins, isolated by Rotofor, were also purified using reverse-phase HPLC and the NH 2 -terminal amino acid sequence of the 31 kD protein determined.

The two Cyn d I components show minor amino acid sequence variations in their NH 2 -terminal regions and there is homology between Cyn d I and Lol p I from ryegrass (Table 1).

TABLE 1: NH-,-termrinal sequences of Cyn d I isoallergens and Lol p I.

Allergen -NH2.terminal amino-acid sequence Cyn d la AMG KPGPXITATYGDKXLDA(K

AFD

Cyn d Ib AIGXKPGPX1TAXY(G)X(K)XLXA I_

(T)

Cyn d Ib* AIGDKPGPXITATYXXKW

LDAKATFYGS

NP(R) GAA Cyn d I AMGDKPGPXITATYGDKWLDAKAT

FYG

Cy-n d Ialb 2

AIGDKPGPXITATYGSKXLEAKATFY

Cyn d Ic 2

AMGDKPGPXITAVY

LpIL IAKVPPGPNITAEYGDKWLDAKSTWYGP determ-ined after transfer to PVDF membrane; *determined after HIPLC purification :5 Matthiesen et al, 1991, supra 2 Matthiesen, 1992, et al., European Congress Allergy Clin. Ixnmunol. Conference Paris, France, May 1992, Abstract.

3 Cottam et al., 1986. Biochem. 234, 305-310, I.Griffitb etal., 1991, FEBS Letters. 279. 210-2 15; Perez et al., (1990), J.BioL Chem. 265:16210-16215.

(tentative desi2natbon: X-uniaiown amino acid.

Production and screening of MAbs Anti-Cyn d I MAbs were obtained by intraperitoneal immunization of a Balb/c mouse with 50gjg of Cyn d I (isolated on the Rotofor, Biorad, Richmond, CA). RIBI (RIBI Immunochem, Hamilton, MIT, USA) was used as an adjuvant in the first of four immunizations. The remaining intraperitoneal immunizations were in saline. Fusion and growth of hybridomas was essentially as described by Harlow and Lane 1988, Antibodies: A Laboratry Manual, Cold Spring Harbor Laboratory. Single cell cloning was by limited dilution. Hybridomas producing anti-Cyn d I antibodies were identified using an ELISA assay. ELISA plates were coated overnight with 6Ojig of Bermnuda grass pollen extract diluted in CAPS buffer (6.67 mM NaCO 3 35mM NaHCO 3 pH The wells were then washed three times with TPBS (PBS containing 0.1% Tween 20) and blocked for 30 minutes with PBS containing 1% BSA (PBS/BSA). 100pL of primary antibody was added to each well and incubated for 60 minutes, followed by washing (as above) and incubation in p-gal labelled anti-mouse Ig (1/250 dilution in PBS/BSA, 60 minutes).

After washing 200 pL of the fluorescent substrate 4 -methylumbelliferyl-B-D-galactoside (MUG) was added to each well and incubated at 37 C for 30 minutes. The plates were then read on the fluoroCount 96 flurometer (Pharmacia).

Antibodies which were positive by this method were designated 3A2, 4D2.

1D1 and 3C2 and tested for binding to Cyn d I on a Western blot of Bermuda grass 'ooo' pollen proteins separated by SDS-PAGE.

15 cDNA library and immunological screening Poly mRNA was isolated from Bermuda grass pollen purchased from Greer Laboratories, Lenoir, NC, USA essentially as described by Herrin and Michaels (1984). cDNA was synthesized using the Pharmacia cDNA synthesis k:t and cloned into the Eco R I site of the vector lambda-gt 11. Recombinant proteins 20 from phage plaques were transferred to nitrocellulose filters by overlaying the plated cDNA library with nitrocellulose filters impregnated with IPTG. These filters were then incubated in mixed anti-Cyn d I MAbs. Binding of MAbs to recombinant o. proteins was visualized as described above. Plaques producing proteins which bound to anti- Cyn d I MAbs were isolated and purified.

Isolation of cDNA clones The Bermuda grass pollen cDNA library, as described above, was initially screened with a mixture of anti-Cyn d I hybridoma supernatants containing mainly MAb 3.2 and 30 positive cDNA clones were plaque purified. These clones were then tested for binding to anti-Cyn d I MAbs 3A2, 4D2, 3C2 and 1DI. All clones selected after the first round of screening produced recombinant fusion proteins specific for MAb 3A2. Binding of the clones to MAbs is shown in Fig. 14 and is summarized in Table 2. It is concluded that the cDNA clones isolated here encode Cyn d I based on the MAb binding shown to the recombinant fusion proteins.

MAb 1D1 had a much higher background binding than the other MAbs, making its binding much more subjective.

TAkBLE 2 Monoclolial Antbody Bindling I 3A-2 V17 I Ini I I a a a a.

a a a a.

1 2 I E 700 3 1+ 11 650 28 26 218 goo____ 31 32 1+ 400____ 33 00 3 900____ 26 3 7 Nucleotide and amino acid sequences of cDNA clones Clones 2, 3, 18, 21, 22, 23 and 33 (see Table 2) were chosen for further study on the basis of their antibody affinity. cDNA inserts from clones 2, 3, 18, 21, 22, 23 and 33 were isolated from the phage and subcloned into pGEM-4Z (Promega) or Bluescript (Stratagene) vectors. DNA sequence was determined by double stranded sequencing carried out by the chain termination method (Sanger et al., Proc. Nat7Acad. Sci., (1977), 74:5460-5463) using T7 polymerase (Pharmacia). The nucleotide and deduced amino acid sequences of these clones are shown in Fig. 1 (clone Fig. 2 (clone 18), Fig. 15 (clone Fig. 16 (clone 22) and Fig. 17 (clone 23).

All clones sequenced show homology with each other, particularly in the open reading frame (ORF). In addition, there is significant nucleotide sequence homology between all clones sequenced and Lol p I, a major allergen of ryegrass.

15 However, the sequenced clones can be separated into three groups on the basis of nucleotide and deduced amino acid sequence homology, those with sequence most similar to clone 2 clone those with sequence most similar to clone 18 clones 21 and 33), and those most similar to clone 22 clone 23). The deduced amino acid sequences encoded by the ORFs of clones 18 and 2 were 20 compared to the deduced amino acid sequence of Lol p I (Perez et al, 1991 supra; Griffith et al, 1991, supra)(Fig. There is 67% amino acid homology between Lolp I and clone 18 and 72% between Lolp I and clone 2. The deduced amino acid sequences of clones 2 and 18 have 83% identity (87% homology) with each other.

33 Example 2 Cloning the 5' end of Cyn d I Double-stranded cDNA was synthesized from approximately 4 plg of pollen RNA (Greer Labs, Lenoir, NC, USA) using the cDNA Synthesis System Plus kit (BRL, Bethesda, MD, USA). After a phenol extraction and ethanol precipitation, the cDNA was blunted with T4 DNA polymerase (Promega, Madison, WI, USA), and ligated to ethanol precipitated, self-annealed, AT, GGGTCTAGAGGTACCGTCCGATC-GATCATT-3', and AL, AATGATCGATGCT-3', oligonucleotides for use in a modified Anchored PCR (Marsh et al, 1986: Roux and Dhanarajan, 1990; Rafnar et al, 1991) reaction.

cDNA encoding the amino terminus of Cyn d I was amplified from the linkered .i cDNA (5 pl from a 20 gl reaction) with 1 tg each of oligonucleotides AP, .GGGTCTAGAGGTACCGTCCG-3', and CD-5, an oligonucleotide primer based on non-coding strand sequence of Cyn d I 15 corresponding to the amino acid sequence KNYEHI. The primary polymerase chain reactions (PCR) were carried out in a programmable thermal controller from MJ Research, Inc. (Cambridge, MA, USA) using the GeneAmp DNA Amplification kit (Perkin Elmer Cetus, Norwalk, CT, USA) in a reaction containing 10 tl 10x buffer containing dNTPs, 1 Vg of each primer, cDNA, 0.5 pl 20 Amplitaq DNA polymerase, and distilled water to 100 hl. Twenty-five rounds of amplification consisted of denaturation at 94 0 C for 1 minute, annealing of primers to the template at 65 0 C for 1.5 minutes, and chain elongation at 720C for 2 minutes. Five percent (5l) of this primary amplification was then used in a secondary amplification with 1 tg each of CD-4, CCTTGAAG-3', a Cyn d I oligonucleotide primer nested relative to CD-5 based on non-coding strand sequence corresponding to amino acids IFKDGL, and AP, as above. All oligonucleotides were synthesized by Research Genetics, Inc (Huntsville, AL). Oligonucleotide primers AP, AT and AL have been previously described (Rafnar et al, 1991; Morgenstern et al, 1991; Griffith et al, 1991; Rogers et al, 1991).

The first eight nucleotides of CD-4 were added to create a Bar HI restriction site for cloning purposes.

Amplified DNA was recovered by sequential chloroform, phenol, and chloroform extractions, followed by precipitation at -20 C with 0.5 volumes of ammonium acetate and 1.5 volumes of isopropanol. After precipitation and washing with 70% ethanol, the DNA was simultaneously digested with Xba I and Bam HI in a 15 N1 reaction and electrophoresed through a preparative 3% SeaPlaque low melt agarose gel (FMC Corp., Rockland ME, USA). The appropriate sized DNA band was visualized by ethidium bromide (EtBr) staining, excised, and ligated into appropriately digested M13mpl9 for dideoxy DNA sequencing (Sanger et al, (1977), 15 Proc. Nat'l. Acad. Sci USA 74:5460-5463) with the Sequenase kit Biochemicals, Cleveland, OH, USA). Two clones, 14al and 14cl, were obtained from this ligation, completely sequenced and found to contain in-frame initiator methionines. The methionine encoded by nucleotides 28-30 of the 14al sequence (Fig. 6) most preferably represents the initiating codon since the surrounding sequence closely S 20 matches the common plant sequence, 5'-AACAATGGC-3' (Lutcke at al, (1987) ~Embo. 6:43-48), and there is an in-frame stop codon just upstream. Although 14cl (Fig. 7) contained two potential in-frame methionines, the methionine encoded by nucleotides 27-29 is most probably the initiator methionine since the surrounding sequence more closely matches the consensus plant sequence, 5'-AACAATGGC-3' (Lutcke at al, supra), than does the methionine encoded by nucleotides 42-45 (78% vs. 56% match). Furthermore, the sequence surrounding nucleotides 27-29 is identical to that of clone 14al. Both clone 14al and clone 14cl sequences had 17 nucleotide overlaps with the longest Cyn dI clone, clone 18. The amino terminus of the mature Cyn d I NH2-AIGDKPGPNITATGNKWLEAKATFYG encoded by clone 14al and NH2-AIGDKPGPNITATGSKWLEAKATFYG- encoded by clone 14cl could be identified by comparison with two previously published protein sequences for Cyn d I: NH2-AMGDKPGP?ITATYGDKWLDAKATFYG (Matthiesen et al, 1988, supra; Matthiesen et al, 1990, supra; Matthiesen et al, 1991, supra) and NH2-AIGDKPGPKITATY??KWLEAKAT (Singh et al, 1990, supra). This indicated that clones 14al and 14cl had leader sequences of 22 and 26 amino acids, respectively. These leader sequences would be cleaved to create the mature form of the Cyn d I protein. The potential full-length amino acid sequence of Cyn d I designated Cyn d 1.18 (Fig. 9) was created by attaching the sequence of Cyn d 1.14 to clone 18 at their overlap as shown in Fig. 9. In both cases, the mature form of Cyn dI is predicted to be 246 amino acids with a calculated molecular weight of 26.7 kDa.

Example 3 RNA was isolated from the pollen of Cynodon dactylon using a modification 20 of the guanidinium thiocyanate method of Chomczynski and Sacchi (1987) Analytical Biochem 162: 156-159. Pollen was ground in liquid nitrogen with 9 mis of guanidinium thiocyanate buffer (5M guanidinium thiocyanate in 0.05% Tris-HCI [pH 0.05 vol. P-mercaptoethanol, 0.1 vol. 5% sodium lauroyl sarkosine). The pollen solution was then shaken with phenol (10 ml) for 10 min, after which 10 ml of 25 chloroform:isoamyl alcohol 24:1 was added and the mixture shaken for a further min. The mixture was centrifuged at 7,000xg for 25 min and the aqueous phase *o collected.

The aqueous phase was re-extracted wvith p henol: chlorofom:isOamYl alcohol 25:24:1 followed by centrifugation at 2.OO0xg until the interface was clear. The aqueous phase was then decanted into a quickseal ultracentrifuge tube, underlain with a 3 ml CsCl cushion (5.7 M CsCl in 0. 1 M EDTA; density =1.71 g/ml) and centrifuged (20 hrs, 40,000 rpm, 200C) in a Beckman Ti 70.1 rotor (Beckman L8-70 ultracentrifuge; Beckman Instruments, Fullerton. CA). After centrifugation, RNA in the pellet was resuspended in 0.05% SDS, phenol/chloroform extracted and ethanol precipitated overnight at -200C.

Poly A+ RNA was isolated using a Pharmacia rnRNA Purification kit (Pharmacia, Piscataway, following the manufacturers instructions.

First strand cDNA was prepared by heating 0.8 pg mRNA to 700'C with pg of oligo-dT primer (Pharrnacia, Piscataway, NJ). After the m.RNA solution was cooled on ice, 5X first strand buffer and 25U R.NAsin ribonuclease inhibitor were added. The mixture was then heated at 420C for 1 hr. final :15 reaction conditions were 50 mM Tris-HC1, pH 8.3, 50 mM KCI, 10 mM Mg902, mM spermidine, 10 mM DTT. 4 mM sodium pyrophosphate, 1 mM each of dATP, dCTP, dGTP, and 'fTP. 25U RNAsin ribonuclease inhibitor and :::AMV reverse transcriptase/pg PUNA (Promega cDNA synthesis kIt, Proniega, Madison, WI) in a final volume of 25 pl. cDNA sequences encoding Cyn d I 20 were amplified using the Perkin-Elmer Cetus gene amnplification kit (U.S.

Biochemicals, Cleveland, OH). 5 pl. of the first strand cDNA synthesis product was mixed with lox buffer to a final buffer concentration of 2 mM M902, 50 mM KCl, 10 mM Tris-HCI, 1 gg of oligonucleotide primer ((jGcjATCGGCGG..ACAAG-CCAG- 3 Y 1 pg of oligonucleotide primer CDLYB 18,5S-CCCTGCAGATGGAGGATCATCGTTC 3 0.2 mM, dNTP and 2.5 units of Taq DNA polymnerase (Pharmacia, Piscataway,

NJ).

Nucleotides 1-8 of CDI5'N were added to create an Eco RI endonuclease restriction site for cloning purposes, while nucleotides 9-27 correspond to nucleotides 107 to 125 of clone 14al in Figure 6 that encode amino acids 1-6 (AIGDKP) of Cyn d I (Table I, Figs. 8 and Nucleotides 1-8 ofCDI3'B18 were added to create a Pst I endonuclease restriction site for cloning purposes, while nucleotides 9-26 correspond to non-coding strand sequence complementary to nucleotides 604 to 621 of clone 18 (Figure 2).

The PCR was performed in a Perkin-Elmer Cetus Thermal Cycler (Perkin-Elmer, Norwalk, CT) and consisted of 5 cycles of denaturation (94 0 C, 1 min), annealing (450C, 1.5 min), and elongation (720C, 3 min) followed by cycles of denaturation (940C, 1 min), annealing (550C, 1.5 min), and elongation (72oC, 3 min). The final elongation reaction was performed at 72 0 C for 10 min.

Amplified product was recovered by phenol extraction, chloroform extraction, and then precipitation at -200C with 0.5 vol 7.5 M ammonium acetate and 15 volumes isopropanol. Reaction product was blunted with Klenow fragment of DNA polymerase then cut with Eco RI and cloned into Bluescript vector digested with Eco RI and Hin cil. The clone CD was sequenced by the dideoxy chain termination method (Sanger, supra.), as described in Example 1, and found to contain the nucleotide and deduced amino acid sequences of Cyn d I shown in Figure 18.

o Example 4 Double stranded cDNA was prepared and amplified using oligonucleotide primers CD-13 and CD-15 in a primary PCR reaction as described in Example 2.

CD-13 has the sequence CCC-3', whereas nucletoide 14 could be C or G. Nucleotides 1 through 8 of CD- 13 (5'-TTTCTAGA-3') were added to create a Xba I restriction site for cloning purposes. The remaining nucleotides encoded amino acids Ala(Ile/Met)-GlyAspLysProGlyPro, where amino acid 2 could be either Ile or Met (amino acids 1 through 8 of Cyn d Ia and Cyn d Ib (Table CD-15 has the sequence5'-GCGTACTTCACGAGCAGCGCCAG-GTAATT-3',which corresponds to non-coding strand sequence complementary to coding strand sequence that encodes amino acids AsnTyrLeuAlaLeuLeuValLysTyrAla (numbered amino acids 159 through 168 of clone 2 (C2) and clone 3 (C3) in Fig. Five percent of the primary reaction was amplified in a secondary PCR, as described in Example 2, using oligonucleotide primers CD-13 and CD-16. CD-16 has the sequence 5'-TTGAATTCGACACGGCGGAACTGCAGCAT-3', where nucleotide 12 could be G or A. Nucleotides 1 through 8 of CD-16 were added to create an Eco RI restriction site for cloning purposes. Nucleotides 9 through 29 corresponded to non-coding strand sequence complementary to coding strand sequence that encode amino acids MetLeuGlnPheArgArgVal (numbered amino acids 132 through 138 of C2 and C3 in Fig. The PCR amplifications were performed as described in Example 2.

Amplified product was recovered, appropriately digested and ligated into pUC for 20 sequencing as described in Example 2. A clone, designated KAT-39-1, was isolated that had sequence identifying it as a Cyn d I clone. The nucleotide and deduced amino acid sequences of clone KAT-39-1 are shown in Fig. 19. This clone is an extension of the Cyn dI clones C2 and C3. Oligonucleotides CD-15 and CD-16 have single nucleotide mismatches at their 3' ends with the corresponding sequence in 25 Cyn d I clone C18 and its homologues. Therefore, only clone C2 or C3, or a close family member would be amplified. A composite sequence of KAT-39-1 and Cyn d 1.2/3 designated Cyn d 1.2/3 (full-length), is shown in Fig. 20 in comparison to Cyn d I.CD1 and Cyn d I.18.

Although the invention has been described with reference to its preferred embodiments, other embodiments can achieve the same results. Variation and modifications to the present invention will be obvious to those skilled in the art and it is intended to cover in the appended claims all such modifications and equivalents that follow in the true spirit and scope of this invention.

Throughout this specification and the claims which follow, unless the context requires otherwise, the word "comprise", and variations such as "comprises" and "comprising", will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integers or steps.

P:\OPER\MRO\6425196.SPE 16/6/99 THE CLAIMS DEFINING THE INVENTION ARE AS FOLLOWS: 1. An isolated nucleic acid molecule comprising a nucleotide sequence that encodes the Bermuda grass pollen protein allergen Cyn d that comprises the amino acid sequence set forth in Figure 20 or at least one antigenic fragment thereof or the functional equivalent of said nucleic acid sequence.

2. The isolated nucleic acid molecule of claim 1 having the formula: L NYX wherein L, is a nucleotide sequence of 0-300 nucleotides in length and including nucleotides encoding a leader sequence of Cyn d I; N is a nucleotide sequence comprising up to 600 nucleotides in length and including nucleotides encoding the amino terminus portion of mature Cyn d I; Y is the portion of the nucleotide sequence of any one of clone 2, clone 18, clone 3, clone 22, clone 23 or any polymorphic form thereof that codes for mature Cyn d I; and X is a nucleotide sequence of 0-600 nucleotides comprising the 3' untranslated portion of Cyn d I, and wherein L, and X can be 0.

3. The isolated nucleic acid molecule of claim 2 wherein Y comprises a nucleotide sequence set forth in any one of Figures 1, 2, 15, 16 or 17 or a substantially identical homologue thereof encoding the mature Cyn d Ipolypeptide.

4. The isolated nucleic acid molecule of claims 2 or 3 wherein the nucleotide sequence of N does not overlap the 5' end of the nucleotide sequence of Y.

The isolated nucleic acid molecule of claims 3 or 4 wherein L, comprises nucleotides 1-106 of clone 14al as shown in Fig. 6, or nucleotides 1-103 of clone 14cl as shown in Fig. 7, or a functional equivalent thereof.

6. The isolated nucleic acid molecule of claim 5, wherein N comprises nucleotides 107-

Claims (2)

104-243 of clone 14cl as shown in Fig. 7 or a functional equivalent thereof; Y comprises nucleotides 1-603 of clone 18 as shown in Fig. 2 or a functional equivalent thereof; and X comprises nucleotides

604-775 of clone 18 as shown in Fig. 2 or a functional equivalent thereof. 7. The isolated nucleic acid molecule according to claim 5, wherein N comprises nucleotides 107-247 of clone 14al as shown in Fig. 6, or nucleotides 104-246 of clone 14cl as shown in Fig. 7 or a functional equivalent thereof; Y comprises nucleotides 1-594 of clone 22 as shown in Fig. 16 or a functional equivalent thereof; and X comprises nucleotides 595-802 of clone 22 as shown in Fig. 16 or a functional equivalent thereof. 8. The isolated nucleic acid molecule of claim 5, wherein N comprises nucleotides 107- 246 of clone 14al as shown in Fig. 6 or the nucleic acid sequence represented by nucleotides 104-245 of clone 14c1 as shown in Fig. 7 or a functional equivalent thereof; Y comprises nucleotides 1-595 of clone 23 as shown in Fig. 17 or a functional equivalent thereof; and X comprises nucleotides 596-832 of clone 23 as shown in Fig. 17 or a functional equivalent thereof. 9. The isolated nucleic acid molecule according to claims 3 or 4, wherein L 1 comprises nucleotides 41-106 of clone 14al as shown in Fig. 6, or nucleotides 28-103 of clone 14cl as shown in Fig. 7 or a functional equivalent thereof. The isolated nucleic acid molecule of claim 9, wherein N comprises nucleotides 107- 244 of clone 14al as shown in Fig. 6 or the nucleic acid sequence represented by nucleotides 104-243 of clone 14cl as shown in Fig. 7 or a functional equivalent thereof; Y comprises nucleotides 1-603 of clone 18 as shown in Fig. 2 or a functional equivalent thereof; and X is 0. 11. The isolated nucleic acid molecule of claim 9, wherein N comprises nucleotides 107- P:\OPER\MRO\64251-96.SPE- 16/6/99 -42- 247 of clone 14a1 as shown in Fig. 6 or the nucleic acid sequence represented by nucleotides 104-246 of clone 14cl as shown in Fig. 7 or a functional equivalent thereof; Y comprises nucleotides 1-594 of clone 22 as shown in Fig. 16 or a functional equivalent thereof; and X is 0. 12. The isolated nucleic acid molecule of claim 9, wherein N comprises nucleotides 107- 246 of clone 14al as shown in Fig. 6 or the nucleic acid sequence represented by nucleotides 104-245 of clone 14c1 as shown in Fig. 7 or a functional equivalent thereof; Y comprises nucleotides 1-595 of clone 23 as shown in Fig. 17 or a functional equivalent thereof; and X is 0. 13. The isolated nucleic acid molecule of claims 3 or 4, wherein L 1 is 0; N comprises nucleotides 107-244 of clone 14a1 as shown in Fig. 6 or the nucleic acid sequence represented by nucleotides 104-243 of clone 14c1 as shown in Fig. 7 or a functional equivalent thereof; Y comprises nucleotides 1-603 of clone 18 as shown in Fig. 2 or a functional equivalent thereof; and X is 0. 14. The isolated nucleic acid molecule of claims 3 or 4, wherein L 1 is 0; N comprises nucleotides 107-247 of clone 14a1 as shown in Fig. 6 or the nucleic acid sequence represented by nucleotides 104-246 of clone 14c1 as shown in Fig. 7 or a functional equivalent thereof; Y comprises nucleotides 1-594 of clone 22 as shown in Fig. 16 or a functional equivalent thereof; and X is 0. The isolated nucleic acid molecule of claims 3 or 4, wherein L 1 is 0; N comprises nucleotides 107-246 of clone 14al as shown in Fig. 6 or the nucleic acid sequence represented by nucleotides 104-245 of clone 14c1 as shown in Fig. 7 or a functional equivalent thereof; Y comprises nucleotides 1-595 of clone 23 as shown in Fig. 17 or a functional equivalent thereof; and X is 0. 16. The isolated nucleic acid molecule according to any one of claims 1 to 4, wherein Y P:\OPER\MRO\64251-96.SP 16/6/99 -43- comprises nucleotides 1-438 of clone 2 as shown in Fig. 1 or a functional equivalent thereof. 17. The isolated nucleic acid molecule according to claims 3 or 4, wherein Y comprises nucleotides 1-417 of clone 3 as shown in Fig. 15 or a functional equivalent thereof; and X comprises nucleotides 418-594 of clone 3 as shown in Fig. 15 or a functional equivalent thereof. 18. The isolated nucleic acid molecule of claims 3 or 4, wherein L 1 is 0; Y comprises nucleotides 1-438 of clone 2 as shown in Fig. 1 or a functional equivalent thereof; and Xis 0. 19. The isolated nucleic acid molecule of claims 3 or 4, wherein L 1 is 0; Y comprises nucleotides 1-417 of clone 3 as shown in Fig. 15 or a functional equivalent thereof; and X is O. An isolated nucleic acid molecule that encodes the Bermuda grass pollen protein allergen, Cyn d I, comprising the nucleotide sequence set forth in Fig. 18 or the nucleotide sequence of clone CD1 or a functional equivalent thereof. 21. An isolated nucleic acid molecule which encodes the amino acid sequence of mature Cyn d I.CD1 as shown in Fig. 22. An isolated nucleic acid molecule that encodes Bermuda grass pollen allergen, Cyn d I or the functional equivalent of said nucleic acid molecule comprising a nucleotide sequence which encodes the amino acid sequence of Cyn d 1.2/3 (full-length) as shown in Fig. 23. An expression vector comprising the nucleic acid molecule according to any one of claims 1 to 22. P:\OPER\MRO\64251-96.SPE 16/6/99 -44- 24. A non-naturally occurring transformed host cell that is capable of expressing a Cyn d I protein or peptide encoded by the nucleic acid molecule according to any one of claims 1 to 22. An isolated Bermuda grass pollen protein allergen Cyn d I, or an isolated antigenic fragment thereof encoded by the isolated nucleic acid molecule according to any one of claims 1 to 22. 26. An isolated Bermuda grass pollen protein allergen Cyn d I comprising the amino acid sequence represented by amino acids 1-246 of Cyn d I. 18 as shown in Fig. 27. An isolated antigenic fragment of the Bermuda grass pollen protein allergen of claim 26. 28. An isolated Bermuda grass pollen protein allergen Cyn d I comprising the amino acid sequence represented by amino acids 1-246 of Cyn d I.CD1 as shown in Fig. 29. An isolated antigenic fragment of the Bermuda grass pollen protein allergen of claim 28. An isolated Bermuda grass pollen protein allergen Cyn d I comprising the amino acid sequence represented by amino acids 1-244 of Cyn d 1.2/3 (full-length) as shown in Fig. 31. An isolated antigenic fragment of the Bermuda grass pollen protein allergen of claim 32. The isolated antigenic fragment according to any one of claims 25, 27, 29 or 31 wherein said fragment has T cell stimulating activity. P:\OPER\MRO\64251-96.SPE 16/6/99 33. An isolated peptide of Cyn d having an amino acid sequence derived from the Cyn d 1.18 polypeptide set forth in Fig. 20 and selected from the group consisting of: amino acids 2-246; amino acids 5-246; amino acids 10-246; amino acids 20-246; and amino acids 25-246 or an antigenic fragment of any one of said amino acid sequences. 34. An isolated peptide of Cyn d I having an amino acid sequence derived from the Cyn d I.CD1 polypeptide set forth in Fig. 20 and selected from the group consisting of: amino acids 5-246; amino acids 10-246; amino acids 20-246; and amino acids 25-246; or an antigenic fragment of any one of said amino acid sequences. An isolated peptide of Cyn d having an amino acid sequence derived from the Cyn d 1.2/3 polypeptide of Fig. 20 and selected from the group consisting of: amino acids 1-244; amino acids 2-244; amino acids 5-244; amino acids 10-244; amino acids 244; and amino acids 25-244 or an antigenic fragment of any one of said amino acid sequences. 36. The isolated antigenic fragment of claim 29 wherein said fragment has minimal immunoglobulin E stimulating activity. 37. The isolated antigenic fragment according to any one of claims 25, 27, 29 or 31 wherein: said fragment does not bind immunoglobulin E specific for a protein allergen of the species Cynodon dactylon in a substantial percentage of individuals sensitive to said protein allergen; or (ii) if binding of said fragment to immunoglobulin E specific for a protein allergen of the species C. dactylon occurs, such binding does not result in histamine release from mast cells or basophils in a substantial percentage of individuals sensitive to said protein allergen. 38. The isolated peptide or isolated antigenic fragment according to any one of claims 29, 33, 34 or 35 which binds immunoglobulin E to a substantially lesser extent than the P:\OPER\MRO\64251-96.SPE 16/6/99 -46- protein allergen from which the fragment is derived binds said immunoglobulin E. 39. The isolated protein allergen or isolated antigenic fragment of claim 25 which modifies, in a Bermuda grass pollen-sensitive individual to which it is administered, the allergic response of the individual to Bermuda grass pollen allergen. The isolated protein allergen of claim 28 which modifies, in a Bermuda grass pollen- sensitive individual to which it is administered, the allergic response of the individual to Bermuda grass pollen allergen. 41. The isolated antigenic fragment of claim 29 which modifies, in a Bermuda grass pollen-sensitive individual to which it is administered, the allergic response of the individual to a Bermuda grass pollen allergen. 42. The isolated protein allergen or isolated antigenic fragment of claim 25 which modifies the B cell response of the individual to a Bermuda grass pollen allergen; or the T cell response of the individual to a Bermuda grass pollen allergen; or both the B cell response and the T cell response of the individual to a Bermuda grass pollen allergen. 43. The isolated protein allergen of claim 28 which modifies the B cell response of the individual to a Bermuda grass pollen allergen; or the T cell response of the individual to a Bermuda grass pollen allergen; or both the B cell response and the T cell response of the individual to a Bermuda grass pollen allergen. 44. The isolated peptide or isolated antigenic fragment of claim 34 which modifies the B cell response of the individual to a Bermuda grass pollen allergen; or the T cell response of the individual to a Bermuda grass pollen allergen; or both the B cell response and the T cell response of the individual to a Bermuda grass pollen allergen. P:\OPER\MRO\64251-96.SPE- 16/6/99 -47- A non-naturally occurring modified Cyn d I protein allergen or non-naturally occurring or modified antigenic fragment of the Cyn d I protein allergen which when administered to a Bermuda grass pollen sensitive individual, reduces the allergic response of the individual to a Bermuda grass pollen allergen, wherein said modified protein allergen or modified antigenic fragment is encoded by a nucleotide sequence set forth in Fig. 20 or a fragment thereof. 46. An isolated protein allergen which has greater than 73 homology with Cyn d I or an isolated antigenic fragment thereof, wherein said protein allergen or antigenic fragment is encoded by a nucleotide sequence set forth in Fig. 20 or a fragment thereof. 47. An isolated protein allergen which has greater than 73 homology with Cyn d I and which is immunologically cross reactive with antibodies specific for Cyn d I or an isolated antigenic fragment of said protein allergen, wherein said protein allergen or antigenic fragment is encoded by a nucleotide sequence set forth in Fig. 20 or a part thereof. 48. An isolated protein allergen which is capable of stimulating T cells specific for Cyn d I or an isolated fragment thereof, wherein said protein allergen or antigenic fragment is encoded by a nucleotide sequence set forth in Fig. 20 or a part thereof. 49. A therapeutic composition comprising isolated Bermuda grass Cyn d I protein allergen, or at least one isolated antigenic fragment thereof in combination with a pharmaceutically acceptable carrier or diluent, wherein said protein allergen or antigenic fragment is encoded by a nucleotide sequence set forth in Fig. 20 or a part thereof. The therapeutic composition of claim 49, wherein said protein allergen or antigenic fragment comprises the amino acid sequence represented by amino acids 1-246 of Cyn P:\OPER\MRO\64251-96.SPE- 16/6/99 -48- d I.CD1 as shown in Fig. 51. The therapeutic composition of claim 49, wherein said protein allergen or antigenic fragment has the amino acid sequence represented by amino acids 1-246 of Cyn d 1. 18 as shown in Fig. 52. The therapeutic composition of claim 49 wherein said protein allergen or antigenic fragment comprises the amino acid sequence represented by amino acids 1-244 of Cyn d 1.2/3 (full-length) as shown in Fig. 53. A method of treating sensitivity in an individual to a protein allergen of Bermuda grass pollen, or an allergen which is immunologically cross-reactive with Bermuda grass pollen allergen, comprising administering to said individual a therapeutically effective amount of a therapeutic composition of claim 49. 54. A method of treating sensitivity in an individual to a protein allergen of Bermuda grass pollen, or an allergen which is immunologically cross-reactive with Bermuda grass pollen allergen, comprising administering to said individual a therapeutically effective amount of a therapeutic composition according to any one of claims 50, 51 or 52. A method of detecting in an individual sensitivity to a Cyn d I protein allergen, comprising: combining a blood sample obtained from said individual with an isolated protein allergen of Bermuda grass pollen or antigenic fragment thereof selected from the group consisting of: a recombinant polypeptide, peptide or antigenic fragment produced in a host cell transformed with the nucleic acid according to any one of claims 1 to 22 or the expression vector of claim 23; and (ii) an isolated protein allergen or antigenic fragment or peptide according P:\OPER\MRO\64251-96.SPE- 16/6/99 -49- to any one of claims 25 to 48 or a chemically synthesized form thereof, under conditions appropriate for binding of blood components with the protein allergen or fragment thereof; determining the extent to which such binding occurs. 56. The method of claim 55 wherein the extent to which binding occurs is determined by assessing T cell function, binding of the protein or fragment thereof to antibodies present in the blood or a combination thereof. 57. A method of detecting sensitivity of an individual to Bermuda grass pollen allergen comprising administering to said individual a sufficient quantity of the Bermuda grass pollen allergen Cyn dl I encoded by a nucleotide sequence set forth in Fig. or at least one antigenic fragment thereof produced in a host cell transformed with the nucleic acid sequence according to any one of claims 1 to 22 or the expression vector of claim 23 or an isolated protein allergen, antigenic fragment or peptide according to any one of claims 25 to 48 or a chemically synthesized form thereof, to produce an allergic response in said individual, and (ii) determining the occurrence of an allergic response in the individual to said Bermuda grass pollen allergen or antigenic fragment thereof. 58. A monoclonal antibody specifically reactive with the Cyn dl I protein allergen encoded by a nucleotide sequence set forth in Fig. 20 or at least one antigenic fragment thereof. 59. A method of producing Cyn d I or at least one fragment thereof comprising the steps of: culturing a host cell transformed with the DNA sequence according to any one of claims 1 to 22 in an appropriate medium for a time and under conditions sufficient to produce a mixture of cells and medium containing said Japanese cedar pollen allergen Cyn d I or at least one fragment thereof; and P: \OPER\MRO\64251-96. SPE 16/6/99 purifying said mixture to produce substantially pure Cyn d I, or at least one fragment thereof. A method of designing antigenic fragments of Cyn d I which when administered to Bermuda grass pollen allergen sensitive individuals in a therapeutic regimen will modify the individual's allergic symptoms to Bermuda grass pollen comprising the steps of: recombinantly or synthetically producing fragments of a Cyn d I protein allergen having the amino acid sequence set forth in Fig. examining said fragments for their ability to influence B cell and/or T cell responses in Bermuda grass pollen sensitive individuals; selecting appropriate fragments which contain epitopes recognized by the cells. 61. An isolated peptide of Cyn d I or an isolated fragment thereof, said peptide or fragment thereof comprising at least one T cell epitope of Cyn d I, said peptide having an amino acid sequence comprising amino acids 25-246 of Cyn d 1. 18, as shown in Fig. 62. An isolated peptide of Cyn d I or an isolated fragment thereof, said peptide or fragment thereof comprising at least one T cell epitope of Cyn d I, said peptide having an amino acid sequence comprising amino acids 25-246 of Cyn d I.CD 1, as shown in Fig. 63. An isolated peptide of Cyn d I or an isolated fragment thereof, said peptide or fragment thereof comprising at least one T cell epitope of Cyn d I, said peptide having an amino acid sequence comprising amino acids 25-244 of Cyn d 1.2/3 (full-length), as shown in Fig. 64. Use of the isolated protein allergen, antigenic fragment or peptide according to any one of claims 25 to 48 in the manufacture of a medicament for treating the sensitivity P:\OPER\MRO\64251-96.SPE- 16/6/99 -51 of an individual to a protein allergen of Bermuda grass pollen or an allergen that is immunologically cross-reactive with Bermuda grass pollen allergen. Use of the isolated nucleic acid molecule according to any one of claims 1 to 22 or the expression vector of claim 23 in the manufacture of a medicament for treating sensitivity of an individual to a protein allergen of Bermuda grass pollen or an allergen that is immunologically cross-reactive with Bermuda grass pollen allergen. 66. The isolated nucleic acid molecule according to any one of claims 1 to 22 substantially as hereinbefore described with reference to the Figures and/or Examples. 67. The isolated protein allergen, antigenic fragment or peptide according to any one of claims 25 to 48 or 61 to 63 substantially as hereinbefore described with reference to the Figures and/or Examples. 68. The monoclonal antibody of claim 58 substantially as hereinbefore described with reference to the Figures and/or Examples. 69. The method of claims 59 or 60 substantially as hereinbefore described with reference to the Figures and/or Examples. DATED this 16th day of June, 1999. The University of Melbourne DAVIES COLLISON CAVE Patent Attorneys for the Applicant Q:\OPER\MRO\MELBUNI.239 26/8/96 ABSTRACT The present invention provides nucleic acid sequences coding Cyn dl or at least one fragment thereof or the functional equivalent of such nucleic acid sequences. The present invention also provides expression vectors comprising such nucleic acid sequences and host cells transformed therewith. The present invention further provides isolated Bermuda grass pollen protein allergen Cyn dl or fragments thereof. Isolated Bermuda grass pollen protein allergens or antigenic or allergenic fragments thereof are useful for diagnosing and treating sensitivity in an individual to Bermuda grass pollen allergens. C 9*