EP1151097A1 - Äusseren membranproteine von haemophilus influenzae; deren verwendung als impfstoff - Google Patents

Äusseren membranproteine von haemophilus influenzae; deren verwendung als impfstoff

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Publication number
EP1151097A1
EP1151097A1 EP00906280A EP00906280A EP1151097A1 EP 1151097 A1 EP1151097 A1 EP 1151097A1 EP 00906280 A EP00906280 A EP 00906280A EP 00906280 A EP00906280 A EP 00906280A EP 1151097 A1 EP1151097 A1 EP 1151097A1
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EP
European Patent Office
Prior art keywords
polypeptide
seq
polynucleotide
sequence
amino acid
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP00906280A
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English (en)
French (fr)
Inventor
Jean-Louis SmithKline Beecham Biol. S.A. RUELLE
Joelle SmithKline Beecham Biol. S.A. THONNARD
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
GlaxoSmithKline Biologicals SA
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SmithKline Beecham Biologicals SA
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Application filed by SmithKline Beecham Biologicals SA filed Critical SmithKline Beecham Biologicals SA
Publication of EP1151097A1 publication Critical patent/EP1151097A1/de
Withdrawn legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/285—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Pasteurellaceae (F), e.g. Haemophilus influenza
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/02—Bacterial antigens
    • A61K39/102—Pasteurellales, e.g. Actinobacillus, Pasteurella; Haemophilus
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies

Definitions

  • This invention relates to methods for the production of polynucleotides, (herein referred to as "BASB067” polynucleotide(s)”), polypeptides encoded by them (referred to herein as “BASB067” or “BASB067” polypeptide(s)”), and recombinant materials.
  • the invention relates to methods for using such polypeptides and polynucleotides, including vaccines against bacterial infections.
  • the invention relates to diagnostic assays for detecting infection of certain pathogens.
  • Haemophilus influenza is a non-motile Gram negative bacterium. Man is its only natural host. H. influenzae isolates are usually classified according to their polysaccharide capsule. Six different capsular types designated a through f have been identified. Isolates that fail to agglutinate with antisera raised against one of these six serotypes are classified as nontypeable, and do not express a capsule.
  • H. influenzae type b is clearly different from the other types in that it is a major cause of bacterial meningitis and systemic diseases.
  • Nontypeable H. influenzae (NTHi) are only occasionally isolated from the blood of patients with systemic disease.
  • NTHi is a common cause of pneumonia, exacerbation of chronic bronchitis, sinusitis and otitis media.
  • Otitis media is an important childhood disease both by the number of cases and its potential sequelae. More than 3.5 millions cases are recorded every year in the United States, and it is estimated that 80 % of children have experienced at least one episode of otitis before reaching the age of 3 (1). Left untreated, or becoming chronic, this disease may lead to hearing loss that can be temporary (in the case of fluid accumulation in the middle ear) or permanent (if the auditive nerve is damaged). In infants, such hearing losses may be responsible for delayed speech learning.
  • Streptococcus pneumoniae Three bacterial species are primarily isolated from the middle ear of children with otitis media: Streptococcus pneumoniae, NTHi and M. catarrhalis. These are present in 60 to 90 % of cases. A review of recent studies shows that S. pneumoniae and NTHi together represent about 30 %, and M. catarrhalis about 15 % of otitis media cases (2). Other bacteria can be isolated from the middle ear (H. influenza type B, S pyogenes, ...) but at a much lower frequency (2 % of the cases or less).
  • Epidemiological data indicate that, for the pathogens found in the middle ear, the colonization of the upper respiratory tract is an absolute prerequisite for the development of an otitis; other factors are however also required to lead to the disease (3-9). These are important to trigger the migration of the bacteria into the middle ear via the Eustachian tubes, followed by the initiation of an inflammatory process. These other factors are unknown todate. It has been postulated that a transient anomaly of the immune system following a viral infection, for example, could cause an inability to control the colonization of the respiratory tract (5). An alternative explanation is that the exposure to environmental factors allows a more important colonization of some children, who subsequently become susceptible to the development of otitis media because of the sustained presence of middle ear pathogens (2).
  • H. influenzae Various proteins of H. influenzae have been shown to be involved in pathogenesis or have been shown to confer protection upon vaccination in animal models.
  • the NTHi 115 kDa Hia protein (17) is highly similar to the Hsf adhesin expressed by H. influenzae type b strains (18).
  • Another protein, the Hap protein shows similarity to IgAl serine proteases and has been shown to be involved in both adhesion and cell entry (19).
  • OMP outer membrane proteins
  • P6 is a conserved peptidoglycan-associated lipoprotein making up 1-5 % of the outer membrane (25). Later a lipoprotein of about the same mol. wt. was recognized, called PCP (P6 crossreactive protein) (26). A mixture of the conserved lipoproteins P4, P6 and PCP did not reveal protection as measured in a chinchilla otitis-media model (27). P6 alone appears to induce protection in the chinchilla model (28).
  • NTHi expresses a dual human transferrin receptor composed of TbpA and TbpB when grown under iron limitation. Anti-TbpB protected infant rats. (32). Hemoglobin / haptoglobin receptors have also been described for NTHi (33). A receptor for Haem: Hemopexin has also been identified (34). A lactoferrin receptor is also present in NTHi, but is not yet characterized (35). A protein resembling neisserial FrpB-protein has not been described in NTHi.
  • a 80kDa OMP the D15 surface antigen, provides protection against NTHi in a mouse challenge model. (36).
  • a 42kDa outer membrane lipoprotein, LPD is conserved amongst Haemophilus influenzae and induces bactericidal antibodies (37).
  • a minor 98kDa OMP (38) was found to be a protective antigen, this OMP may very well be one of the Fe- limitation inducible OMPs or high molecular weight adhesins that have been characterized thereafter.
  • H. Influenzae produces IgAl-protease activity (39). IgAl- proteases of NTHi reveals a high degree of antigenic variability (40).
  • NTHi, OMP26, a 26-kDa protein has been shown to enhance pulmonary clearance in a rat model (41).
  • the NTHi HtrA protein has also been shown to be a protective antigen. Indeed, this protein protected Chinchilla against otitis media and protected infant rats against H. influenzae type b bacteremia (42)
  • the frequency of NTHi infections has risen dramatically in the past few decades. This phenomenon has created an unmet medical need for new anti-microbial agents, vaccines, drug screening methods and diagnostic tests for this organism.
  • the present invention aims to meet that need. In particular the present invention aims to meet the need for a vaccine effective against NTHi.
  • the present invention relates to recombinant materials and methods for the production of BASB067, in particular BASB067 polypeptides and BASB067 polynucleotides, for use especially in therapeutic or prophylactic vaccines.
  • the invention relates to methods for using such polypeptides and polynucleotides, including prevention and treatment of microbial diseases, amongst others.
  • the invention relates to diagnostic assays for detecting diseases associated with microbial infections and conditions associated with such infections, such as assays for detecting expression or activity of BASB067 polynucleotides or polypeptides.
  • the BASB067 polynucleotide encodes a polypeptide that has the features of a surface-exposed molecule recognisable by the immune system.
  • the polypeptide encoded by BASB067 contains a signal peptide, indicating that it is exported at least to the periplasm between the inner and outer membranes of the bacterium.
  • the polypeptide has similarities to other known surface-exposed proteins and potential similarity to other known immunogenic and immunoprotective peptides.
  • BASB067 is 23% identical to the protective surface antigen D15 of Haemophilus influenzae.
  • BASB067 is similar to H. influenzae D15 over its entire length, with a similar secondary structure. As for H.
  • BASB067 has two domains.
  • the N-terminal domain (from amino acid 23 to 236) of BASB067 (SEQ ID NO:2) is predicted to contain a mixture of cc -helix and ⁇ -strands, as is the case for the N- terminal domain of D15.
  • D15 itself is known to contain immunodominant B-cell epitopes and a truncated expressed fragment thereof appears to be soluble (Y-P Yang at al. Infection and Immunity.1998, 66:3349-3354).
  • the N-terminal domain of BASB067 or fragments thereof could be used as vaccine antigens.
  • BASB067 has the characteristics of an integral outer membrane protein.
  • the external loops of the ⁇ -barrels of integral outer membrane proteins contain frequently immunodominant B-cell epitopes.
  • the C-terminal domain of BASB067 or fragments thereof provide strong candidate vaccine antigens.
  • the invention relates to the use of BASB067 polypeptides and polynucleotides as described in greater detail below.
  • the invention relates to the use of polypeptides and polynucleotides of a BASB067 of Haemophilus influenzae, which is related by amino acid sequence homology to Haemophilus influenzae surface antigen D15.
  • the invention relates especially to the use of BASB067 having the nucleotide and amino acid sequences set out in as SEQ ID NO: 1 ,3 and SEQ ID NO:2,4 respectively and fragments thereof.
  • the invention relates to the D15-like BASB067 polypeptides and polynucleotides of NTHi as set out in SEQ ID NO: 3 and 4, and fragments thereof, and to related or corresponding D15-like polypeptides and polynucleotides of non-laboratory strains of NTHi, and to vaccines comprising the polypeptides and polynucleotides.
  • the invention further relates to uses of polynucleotides and polypeptides which have at least 85% identity, preferably at least 90% identity, more preferably at least 95% identity, most preferably at least 97-99% or exact identity to the sequences identified in SEQ ID NO:l,3 and SEQ ID NO:2,4.
  • the invention also relates to novel NTHi polynucleotide and polypeptide sequences disclosed herein.
  • BASB067 uses for polypeptides of Haemophilus influenzae referred to herein as "BASB067”and “ “BASB067 polypeptides” as well as biologically, diagnostically, prophylactically, clinically or therapeutically useful variants thereof, and compositions comprising the same.
  • the present invention further provides uses for: (a) an isolated polypeptide which comprises an amino acid sequence which has at least 85%> identity, more preferably at least 90% identity, yet more preferably at least 95% identity, most preferably at least 91-99% or exact identity, to that of SEQ ID NO:2 or 4;
  • polypeptide encoded by an isolated polynucleotide comprising a polynucleotide sequence which has at least 85%) identity, more preferably at least 90% identity, yet more preferably at least 95%> identity, even more preferably at least 97-99%> or exact identity to SEQ ID NO:l or 3 over the entire length of SEQ ID NO:l or 3 respectively; or
  • polypeptide encoded by an isolated polynucleotide comprising a polynucleotide sequence encoding a polypeptide which has at least 85%> identity, more preferably at least 90%) identity, yet more preferably at least 95% identity, even more preferably at least 97- 99%o or exact identity, to the amino acid sequence of SEQ ID NO:2 or 4.
  • the BASB067 polypeptides provided in SEQ ID NO:2 and 4 are the BASB067 polypeptides from Haemophilus influenzae strains Rd KW20 and ntHi 289.
  • the invention also provides uses for immunogenic fragments of a BASB067 polypeptide, that is, a contiguous portion of the BASB067 polypeptide which has the same or substantially the same immunogenic activity as the polypeptide comprising the amino acid sequence of SEQ ID NO:2 or 4. That is to say, the fragment (if necessary when coupled to a carrier) is capable of raising an immune response which recognises the BASB067 polypeptide.
  • an immunogenic fragment may include, for example, the BASB067 polypeptide lacking an N-terminal leader sequence, and/or a transmembrane domain and.or a C-terminal anchor domain.
  • the immunogenic fragment of BASB067 comprises substantially all of the extracellular domain of a polypeptide which has at least 85%> identity, preferably at least 90% identity, more preferably at least 95% identity, most preferably at least 91-99% identity, more preferably at least more preferably at least 95% identity, most preferably at least 91-99% identity, to that of SEQ ID NO:2 or 4 over the entire length of SEQ ID NO:2 or 4.
  • a fragment is a polypeptide having an amino acid sequence that is entirely the same as part but not all of any amino acid sequence of any polypeptide of the invention.
  • fragments may be "free-standing,” or comprised within a larger polypeptide of which they form a part or region, most preferably as a single continuous region in a single larger polypeptide.
  • Preferred fragments include, for example, truncation polypeptides having a portion of an amino acid sequence of SEQ ID NO:2 or 4 or of a variant thereof, such as a continuous series of residues that includes an amino- and/or carboxyl-terminal amino acid sequence.
  • Degradation forms of the polypeptides of the invention produced by or in a host cell, are also preferred.
  • fragments characterized by structural or functional attributes such as fragments that comprise alpha-helix and alpha-helix forming regions, beta-sheet and beta-sheet-forming regions, turn and turn-forming regions, coil and coil- forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high antigenic index regions.
  • fragments include an isolated polypeptide comprising an amino acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous amino acids from the amino acid sequence of SEQ ID NO:2 or 4, or an isolated polypeptide comprising an amino acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous amino acids truncated or deleted from the amino acid sequence of SEQ ID NO:2 or 4.
  • Particularly preferred are variants in which several, 5-10, 1-5, 1-3, 1-2 or 1 amino acids are substituted, deleted, or added in any combination.
  • polypeptides, or immunogenic fragments, for use in the invention may be in the form of the "mature" protein or may be a part of a larger protein such as a precursor or a fusion protein. It is often advantageous to include an additional amino acid sequence which contains secretory or leader sequences, pro-sequences, sequences which aid in purification such as multiple histidine residues, or an additional sequence for stability during recombinant production. Furthermore, addition of exogenous polypeptide or lipid tail or polynucleotide sequences to increase the immunogenic potential of the final molecule is also considered.
  • the invention relates to the use of genetically engineered soluble fusion proteins comprising a polypeptide of the present invention, or a fragment thereof, and various portions of the constant regions of heavy or light chains of immunoglobulins of various subclasses (IgG, IgM, IgA, IgE).
  • immunoglobulin is the constant part of the heavy chain of human IgG, particularly IgGl, where fusion takes place at the hinge region.
  • the Fc part can be removed simply by incorporation of a cleavage sequence which can be cleaved with blood clotting factor Xa.
  • the proteins may be chemically conjugated, or expressed as recombinant fusion proteins allowing increased levels to be produced in an expression system as compared to non-fused protein.
  • the fusion partner may assist in providing T helper epitopes (immunological fusion partner), preferably T helper epitopes recognised by humans, or assist in expressing the protein (expression enhancer) at higher yields than the native recombinant protein.
  • the fusion partner will be both an immunological fusion partner and expression enhancing partner.
  • Fusion partners include protein D from Haemophilus influenzae and the non-structural protein from influenza virus, NS1 (hemagglutinin).
  • Another fusion partner is the protein known as LytA.
  • LytA Preferably the C terminal portion of the molecule is used.
  • Lyta is derived from Streptococcus pneumoniae which synthesize an N-acetyl-L-alanine amidase LytA, (coded by the lytA gene ⁇ Gene, 43 (1986) page 265-272 ⁇ ) an autolysin that specifically degrades certain bonds in the peptidoglycan backbone.
  • the C-terminal domain of the LytA protein is responsible for the affinity to the choline or to some choline analogues such as DEAE.
  • the present invention also includes variants of the aforementioned polypeptides, that is polypeptides that vary from the referents by conservative amino acid substitutions, whereby a residue is substituted by another with like characteristics. Typical such substitutions are among Ala, Val, Leu and He; among Ser and Thr; among the acidic residues Asp and Glu; among Asn and Gin; and among the basic residues Lys and Arg; or aromatic residues Phe and Tyr.
  • Polypeptides for use in the present invention can be prepared in any suitable manner.
  • Such polypeptides include isolated naturally occurring polypeptides, recombinantly produced polypeptides, synthetically produced polypeptides, or polypeptides produced by a combination of these methods. Means for preparing such polypeptides are well understood in the art.
  • a polypeptide for use in the invention is derived from Haemophilus influenzae, however, it may preferably be obtained from other organisms of the same taxonomic genus. A polypeptide for use in the invention may also be obtained, for example, from organisms of the same taxonomic family or order.
  • BASB067 polypeptides comprising a sequence set out in SEQ ID NO:l or 3 which includes a full length gene, or a variant thereof.
  • the BASB067 polynucleotides provided in SEQ ID NO: 1 or 3 are the BASB067 polynucleotides from Haemophilus influenzae strains Rd KW20 and ntHi 289.
  • a polynucleotide of the invention encoding BASB067 polypeptide may be obtained using standard cloning and screening methods, such as those for cloning and sequencing chromosomal DNA fragments from bacteria, followed by obtaining a full length clone.
  • a polynucleotide sequence for use in the invention such as a polynucleotide sequence given in SEQ ID NO:l or 3
  • a library of clones of chromosomal DNA of Haemophilus influenzae in E.coli or some other suitable host is probed with a radiolabeled oligonucleotide, preferably a 17-mer or longer, derived from a partial sequence.
  • Clones carrying DNA identical to that of the probe can then be distinguished using stringent hybridization conditions.
  • sequencing is performed, for example, using denatured double stranded DNA prepared from a plasmid clone. Suitable techniques are described by Maniatis, T., Fritsch, E.F. and Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, 2nd Ed.; Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1989). (see in particular Screening By Hybridization 1.90 and Sequencing Denatured Double-Stranded DNA Templates 13.70). Direct genomic DNA sequencing may also be performed to obtain a full length gene sequence.
  • DNA sequence set out in SEQ ID NO: 1 ,3 contains an open reading frame encoding a protein having about the number of amino acid residues set forth in SEQ ID NO:2,4 with a deduced molecular weight that can be calculated using amino acid residue molecular weight values well known to those skilled in the art.
  • the polynucleotide of SEQ ID NO: 1 between the start codon at nucleotide number 1 and the stop codon which begins at nucleotide number 1735 of SEQ ID NO:l, encodes the polypeptide of SEQ ID NO:2.
  • the present invention provides uses for an isolated polynucleotide comprising or consisting of: (a) a polynucleotide sequence which has at least 85%> identity, more preferably at least 90%> identity, yet more preferably at least 95% identity, even more preferably at least 97-99% or exact identity to SEQ ID NO:l or 3 over the entire length of SEQ ID NO:l or 3 respectively; or (b) a polynucleotide sequence encoding a polypeptide which has at least 85%) identity, more preferably at least 90%> identity, yet more preferably at least 95%> identity, even more preferably at least 97-99%o or 100%) exact, to the amino acid sequence of SEQ ID NO:2 or 4 over the entire length of SEQ ID NO:2 or 4 respectively.
  • a polynucleotide encoding a polypeptide for use in the present invention may be obtained by a process which comprises the steps of screening an appropriate library under stringent hybridization conditions (for example, using a temperature in the range of 45 - 65° C and an SDS concentration from 0.1 - 1%) with a labeled or detectable probe consisting of or comprising the sequence of SEQ ID NO: 1 or 3 or a fragment thereof; and isolating a full- length gene and/or genomic clones containing said polynucleotide sequence.
  • the invention provides uses for a polynucleotide sequence identical over its entire length to a coding sequence (open reading frame) in SEQ ID NO: 1 or 3. Also provided by the invention are uses for a coding sequence for a mature polypeptide or a fragment thereof, by itself as well as a coding sequence for a mature polypeptide or a fragment in reading frame with another coding sequence, such as a sequence encoding a leader or secretory sequence, a pre-, or pro- or prepro-protein sequence.
  • the polynucleotide may also contain at least one non-coding sequence, including for example, but not limited to at least one non-coding 5' and 3' sequence, such as the transcribed but non-translated sequences, termination signals (such as rho-dependent and rho-independent termination signals), ribosome binding sites, Kozak sequences, sequences that stabilize mRNA, introns, and polyadenylation signals.
  • the polynucleotide sequence may also comprise additional coding sequence encoding additional amino acids. For example, a marker sequence that facilitates purification of the fused polypeptide can be encoded.
  • the marker sequence is a hexa-histidine peptide, as provided in the pQE vector (Qiagen, Inc.) and described in Gentz et al., Proc. Natl. Acad. Sci., USA 86: 821-824 (1989), or an HA peptide tag (Wilson et al, Cell 37: 767 (1984), both of which may be useful in purifying polypeptide sequence fused to them.
  • Polynucleotides for use with the invention also include, but are not limited to, polynucleotides comprising a structural gene and its naturally associated sequences that control gene expression.
  • the nucleotide sequence encoding BASB067 polypeptide of SEQ ID NO:2 or 4 may be identical to the polypeptide encoding sequence contained in nucleotides 1 to 1734 of SEQ ID NO:l, or the polypeptide encoding sequence contained in nucleotides 1 to 1730 of SEQ ID NO:3, respectively. Alternatively it may be a sequence, which as a result of the redundancy (degeneracy) of the genetic code, also encodes the polypeptide of SEQ ID NO:2 or 4.
  • polynucleotide encoding a polypeptide encompasses polynucleotides that include a sequence encoding a polypeptide of the invention, particularly a bacterial polypeptide and more particularly a polypeptide of the Haemophilus influenzae BASB067 having an amino acid sequence set out in SEQ ID NO:2 or 4.
  • polynucleotides that include a single continuous region or discontinuous regions encoding the polypeptide (for example, polynucleotides interrupted by integrated phage, an integrated insertion sequence, an integrated vector sequence, an integrated transposon sequence, or due to RNA editing or genomic DNA reorganization) together with additional regions, that also may contain coding and/or non-coding sequences.
  • the invention further relates to variants of the polynucleotides described herein that encode variants of a polypeptide having a deduced amino acid sequence of SEQ ID NO:2 or 4. Fragments of polynucleotides of the invention may be used, for example, to synthesize full- length polynucleotides of the invention.
  • BASB067 variants that have the amino acid sequence of B ASB067 polypeptide of SEQ ID NO:2 or 4 in which several, a few, 5 to 10, 1 to 5, 1 to 3, 2, 1 or no amino acid residues are substituted, modified, deleted and/or added, in any combination.
  • silent substitutions, additions and deletions that do not alter the properties and activities of BASB067 polypeptide.
  • sue in the invention are polynucleotides that are at least 85%> identical over their entire length to a polynucleotide encoding BASB067 polypeptide having an amino acid sequence set out in SEQ ID NO:2 or 4, and polynucleotides that are complementary to such polynucleotides.
  • polynucleotides at least 95% identical over their entire length to the same are particularly preferred.
  • those with at least 97%) are highly preferred among those with at least 95%>, and among these those with at least 98%> and at least 99% are particularly highly preferred, with at least 99% being the more preferred.
  • Preferred embodiments are polynucleotides encoding polypeptides that retain substantially the same biological function or activity as the mature polypeptide encoded by a DNA of SEQ ID NO: l or 3.
  • polynucleotides that hybridize, particularly under stringent conditions, to BASB067 polynucleotide sequences, such as the polynucleotides in SEQ ID NO: 1,3.
  • the invention further relates to polynucleotides that hybridize to the polynucleotide sequences provided herein.
  • the invention especially relates to polynucleotides that hybridize under stringent conditions to the polynucleotides described herein.
  • stringent conditions and “stringent hybridization conditions” mean hybridization occurring only if there is at least 95%) and preferably at least 97% identity between the sequences.
  • a specific example of stringent hybridization conditions is overnight incubation at 42°C in a solution comprising: 50%> formamide, 5x SSC (150mM NaCI, 15mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5x Denhardt's solution, 10%) dextran sulfate, and 20 micrograms/ml of denatured, sheared salmon sperm DNA, followed by washing the hybridization support in 0. lx SSC at about 65°C.
  • Hybridization and wash conditions are well known and exemplified in Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y., (1989), particularly Chapter 11 therein. Solution hybridization may also be used with the polynucleotide sequences provided by the invention.
  • a coding region of a BASB067 gene may be isolated by screening using a DNA sequence provided in SEQ ID NO: 1,3 to synthesize an oligonucleotide probe.
  • a labeled oligonucleotide having a sequence complementary to that of a gene of the invention is then used to screen a library of cDNA, genomic DNA or mRNA to determine which members of the library the probe hybridizes to.
  • PCR Nucleic acid amplification
  • PCR Nucleic acid amplification
  • the PCR reaction is then repeated using "nested" primers, that is, primers designed to anneal within the amplified product (typically an adaptor specific primer that anneals further 3' in the adaptor sequence and a gene specific primer that anneals further 5' in the selected gene sequence).
  • the products of this reaction can then be analyzed by DNA sequencing and a full-length DNA constructed either by joining the product directly to the existing DNA to give a complete sequence, or carrying out a separate full-length PCR using the new sequence information for the design of the 5' primer.
  • the invention also provides uses for polynucleotides that encode a polypeptide that is the mature protein plus additional amino or carboxyl-terminal amino acids, or amino acids interior to the mature polypeptide (when the mature form has more than one polypeptide chain, for instance).
  • Such sequences may play a role in processing of a protein from precursor to a mature form, may allow protein transport, may lengthen or shorten protein half-life or may facilitate manipulation of a protein for assay or production, among other things.
  • the additional amino acids may be processed away from the mature protein by cellular enzymes.
  • a precursor protein, having a mature form of the polypeptide fused to one or more prosequences may be an inactive form of the polypeptide.
  • inactive precursors When prosequences are removed such inactive precursors generally are activated. Some or all of the prosequences may be removed before activation. Generally, such precursors are called proproteins.
  • a polynucleotide of the invention in genetic immunization will preferably employ a suitable delivery method such as direct injection of plasmid DNA into muscles (Wolff et al, Hum Mol Genet (1992) 1 : 363, Manthorpe et al, Hum. Gene Ther. (1983) 4: 419), delivery of DNA complexed with specific protein earners (Wu et al, J Biol Chem.
  • the invention relates to vectors that comprise a polynucleotide or polynucleotides of the invention, host cells that are genetically engineered with vectors of the invention and the production of polypeptides of the invention by recombinant techniques.
  • Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the invention.
  • Recombinant polypeptides for use in the present invention may be prepared using genetically engineered host cells comprising expression systems by processes well known in the art. Accordingly, in a further aspect, the present invention relates to expression systems that comprise a polynucleotide or polynucleotides of the present invention, to host cells which are genetically engineered with such expression systems, and to the production of polypeptides of the invention by recombinant techniques. For recombinant production of the polypeptides of the invention, host cells can be genetically engineered to incorporate expression systems or portions thereof or polynucleotides of the invention.
  • Introduction of a polynucleotide into the host cell can be effected by methods described in many standard laboratory manuals, such as Davis, et al. , BASIC METHODS IN MOLECULAR BIOLOGY, (1986) and Sambrook, et al. , MOLECULAR CLONING: A LABORATORY MANUAL, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), such as, calcium phosphate transfection, DEAE-dextran mediated transfection, transvection, microinjection, cationic lipid-mediated transfection, electroporation, transduction, scrape loading, ballistic introduction and infection.
  • bacterial cells such as cells of streptococci, staphylococci, enterococci, E coli, streptomyces, cyanobacteria, Bacillus subtilis, Neisseria, Moraxella and Haemophilus influenzae
  • fungal cells such as cells of a yeast, Kluveromyces, Saccharomyces, a basidiomycete, Candida albicans and Aspergillus
  • insect cells such as cells of Drosophila S2 and Spodoptera Sf9
  • animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, 293, CV-1 and Bowes melanoma cells
  • plant cells such as cells of a gymnosperm or angiosperm.
  • vectors include, among others, chromosomal-, episomal- and virus-derived vectors, for example, vectors derived from bacterial plasmids, from bacteriophage, from transposons, from yeast episomes, from insertion elements, from yeast chromosomal elements, from viruses such as baculoviruses, papova viruses, such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses, picornaviruses and retroviruses, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids.
  • the expression system constructs may contain control regions that regulate as well as engender expression.
  • any system or vector suitable to maintain, propagate or express polynucleotides and/or to express a polypeptide in a host may be used for expression in this regard.
  • the appropriate DNA sequence may be inserted into the expression system by any of a variety of well-known and routine techniques, such as, for example, those set forth in Sambrook et al, MOLECULAR CLONING, A LABORATORY MANUAL, (supra).
  • Polypeptides of the invention can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxyapatite chromatography, and lectin chromatography. Most preferably, high performance liquid chromatography is employed for purification. Well known techniques for refolding protein may be employed to regenerate active conformation when the polypeptide is denatured during isolation and or purification.
  • the expression system may also be a recombinant live microorganism, such as a virus or bacterium.
  • the gene of interest can be inserted into the genome of a live recombinant virus or bacterium. Inoculation and in vivo infection with this live vector will lead to in vivo expression of the antigen and induction of immune responses.
  • Viruses and bacteria used for this purpose are for instance: poxviruses (e.g; vaccinia, fowlpox, canarypox), alphaviruses (Sindbis virus, Semliki Forest Virus, Dialoguelian Equine Encephalitis Virus), adenoviruses, adeno-associated virus, picornaviruses (poliovirus, rhinovirus), herpesviruses (varicella zoster virus, etc), Listeria, Salmonella, Shigella, BCG. These viruses and bacteria can be virulent, or attenuated in various ways in order to obtain live vaccines. Such live vaccines also form part of the invention.
  • poxviruses e.g; vaccinia, fowlpox, canarypox
  • alphaviruses Semliki Forest Virus, Kunststoffuelian Equine Encephalitis Virus
  • adenoviruses adeno-associated virus
  • picornaviruses
  • This invention is also related to the use of BASB067 polynucleotides and polypeptides of the invention for use as diagnostic reagents. Detection of BASB067 polynucleotides and/or polypeptides in a eukaryote, particularly a mammal, and especially a human, will provide a diagnostic method for diagnosis of disease, staging of disease or response of an infectious organism to drugs.
  • Eukaryotes particularly mammals, and especially humans, particularly those infected or suspected to be infected with an organism comprising the BASB067 gene or protein, may be detected at the nucleic acid or amino acid level by a variety of well known techniques as well as by methods provided herein.
  • Polypeptides and polynucleotides for prognosis, diagnosis or other analysis may be obtained from a putatively infected and/or infected individual's bodily materials.
  • Polynucleotides from any of these sources may be used directly for detection or may be amplified enzymatically by using PCR or any other amplification technique prior to analysis.
  • RNA, particularly mRNA, cDNA and genomic DNA may also be used in the same ways.
  • amplification, characterization of the species and strain of infectious or resident organism present in an individual may be made by an analysis of the genotype of a selected polynucleotide of the organism.
  • Deletions and insertions can be detected by a change in size of the amplified product in comparison to a genotype of a reference sequence selected from a related organism, preferably a different species of the same genus or a different strain of the same species.
  • Point mutations can be identified by hybridizing amplified DNA to labeled BASB067 polynucleotide sequences. Perfectly or significantly matched sequences can be distinguished from imperfectly or more significantly mismatched duplexes by DNase or RNase digestion, for DNA or RNA respectively, or by detecting differences in melting temperatures or renaturation kinetics.
  • Polynucleotide sequence differences may also be detected by alterations in the electrophoretic mobility of polynucleotide fragments in gels as compared to a reference sequence. This may be carried out with or without denaturing agents. Polynucleotide differences may also be detected by direct DNA or RNA sequencing. See, for example; Myers et al, Science, 230: 1242 (1985). Sequence changes at specific locations also may be revealed by nuclease protection assays, such as RNase, VI and SI protection assay or a chemical cleavage method. See, for example, Cotton et al, Proc. Natl. Acad. Sci, USA, 85: 4397-4401 (1985).
  • an array of oligonucleotides probes comprising BASB067 nucleotide sequence or fragments thereof can be constructed to conduct efficient screening of, for example, genetic mutations, serotype, taxonomic classification or identification.
  • Array technology methods are well known and have general applicability and can be used to address a variety of questions in molecular genetics including gene expression, genetic linkage, and genetic variability (see, for example, Chee et al., Science, 274: 610 (1996)).
  • the present invention relates to a diagnostic kit which comprises: (a) a polynucleotide of the present invention, preferably the nucleotide sequence of SEQ ID NO: 1,3, or a fragment thereof ; (b) a nucleotide sequence complementary to that of (a); (c) a polypeptide of the present invention, preferably the polypeptide of SEQ ID NO:2,4 or a fragment thereof; or (d) an antibody to a polypeptide of the present invention, preferably to the polypeptide of SEQ ID NO:2,4.
  • kits may comprise a substantial component.
  • Such a kit will be of use in diagnosing a disease or susceptibility to a Disease, among others.
  • This invention also relates to the use of polynucleotides of the present invention as diagnostic reagents.
  • Detection of a mutated form of a polynucleotide of the invention, preferably SEQ ID NO: 1 ,3, which is associated with a disease or pathogenicity will provide a diagnostic tool that can add to, or define, a diagnosis of a disease, a prognosis of a course of disease, a determination of a stage of disease, or a susceptibility to a disease, which results from under-expression, over-expression or altered expression of the polynucleotide.
  • Organisms, particularly infectious organisms, carrying mutations in such polynucleotide may be detected at the polynucleotide or polypeptide level by a variety of techniques, such as those described elsewhere herein.
  • the nucleotide sequences of the present invention are also valuable for organism chromosome identification.
  • the sequence is specifically targeted to, and can hybridize with, a particular location on an organism's chromosome, particularly to a Haemophilus influenzae chromosome.
  • the mapping of relevant sequences to chromosomes according to the present invention may be an important step in correlating those sequences with pathogenic potential and/or an ecological niche of an organism and/or drug resistance of an organism, as well as the essentiality of the gene to the organism.
  • the physical position of the sequence on the chromosome can be correlated with genetic map data. Such data may be found on-line in a sequence database.
  • the relationship between genes and diseases that have been mapped to the same chromosomal region are then identified through known genetic methods, for example, through linkage analysis (coinheritance of physically adjacent genes) or mating studies, such as by conjugation.
  • the differences in a polynucleotide and/or polypeptide sequence between organisms possessing a first phenotype and organisms possessing a different, second different phenotype can also be determined. If a mutation is observed in some or all organisms possessing the first phenotype but not in any organisms possessing the second phenotype, then the mutation is likely to be the causative agent of the first phenotype.
  • Cells from an organism carrying mutations or polymorphisms (allelic variations) in a polynucleotide and/or polypeptide of the invention may also be detected at the polynucleotide or polypeptide level by a variety of techniques, to allow for serotyping, for example.
  • RT-PCR can be used to detect mutations in the RNA. It is particularly preferred to use RT-PCR in conjunction with automated detection systems, such as, for example, GeneScan.
  • RNA, cDNA or genomic DNA may also be used for the same purpose, PCR.
  • PCR primers complementary to a polynucleotide encoding BASB067 polypeptide can be used to identify and analyze mutations.
  • the invention further provides primers for, among other things, amplifying BASB067 DNA and/or RNA isolated from a sample derived from an individual, such as a bodily material.
  • the primers may be used to amplify a polynucleotide isolated from an infected individual, such that the polynucleotide may then be subject to various techniques for elucidation of the polynucleotide sequence. In this way, mutations in the polynucleotide sequence may be detected and used to diagnose and/or give a prognosis for the infection or its stage or course, or to serotype and/or classify the infectious agent.
  • the invention further provides a process for diagnosing, disease, preferably bacterial infections, more preferably infections caused by Haemophilus influenzae, comprising determining from a sample derived from an individual, such as a bodily material, an increased level of expression of polynucleotide having a sequence of Table 1 [SEQ ID NO: 1,3].
  • Increased or decreased expression of a BASB067 polynucleotide can be measured using any on of the methods well known in the art for the quantitation of polynucleotides, such as, for example, amplification, PCR, RT-PCR, RNase protection, Northern blotting, spectrometry and other hybridization methods.
  • a diagnostic assay in accordance with the invention for detecting over- or under- expression of BASB067 polypeptide compared to normal control tissue samples may be used to detect the presence of an infection, for example.
  • Assay techniques that can be used to determine levels of a BASB067 polypeptide, in a sample derived from a host, such as a bodily material, are well known to those of skill in the art. Such assay methods include radioimmunoassays, competitive-binding assays, Western Blot analysis, antibody sandwich assays, antibody detection and ELISA assays.
  • the polynucleotides of the invention may be used as components of polynucleotide arcays, preferably high-density anays or grids. These high-density anays are particularly useful for diagnostic and prognostic purposes.
  • a set of spots each comprising a different gene, and further comprising a polynucleotide or polynucleotides of the invention may be used for probing, such as using hybridization or nucleic acid amplification, using probes obtained or derived from a bodily sample, to determine the presence of a particular polynucleotide sequence or related sequence in an individual.
  • Such a presence may indicate the presence of a pathogen, particularly Haemophilus influenzae, and may be useful in diagnosing and/or giving a prognosis for disease or a course of disease.
  • a grid comprising a number of variants of the polynucleotide sequence of SEQ ID NO: 1 is preferred. Also preferred is a gridcomprising a number of variants of a polynucleotide sequence encoding the polypeptide sequence of SEQ ID NO: 2.
  • polypeptides and polynucleotides of the invention or variants thereof, or cells expressing the same can be used as immunogens to produce antibodies immunospecific for such polypeptides or polynucleotides respectively.
  • antibodies against BASB067 polypeptides or polynucleotides there are provided antibodies against BASB067 polypeptides or polynucleotides.
  • Antibodies generated against the polypeptides or polynucleotides of the invention can be obtained by administering the polypeptides and/or polynucleotides of the invention, or epitope-bearing fragments of either or both, analogues of either or both, or cells expressing either or both, to an animal, preferably a nonhuman, using routine protocols.
  • any technique known in the art that provides antibodies produced by continuous cell line cultures can be used. Examples include various techniques, such as those in Kohler, G. and Milstein, C, Nature 256: 495-497 (1975); Kozbor et al, Immunology Today 4: 72 (1983); Cole et al, pg. 77-96 in MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc. (1985).
  • phage display technology may be utilized to select genes for antibodies with binding activities towards a polypeptide of the invention either from repertoires of PCR amplified v-genes of lymphocytes from humans screened for possessing anti- BASB067 or from naive libraries (McCafferty, et al, (1990), Nature 348, 552-554; Marks, et al, (1992) Biotechnology 10, 779-783).
  • the affinity of these antibodies can also be improved by, for example, chain shuffling (Clackson et al, (1991) Nature 352: 628).
  • the above-described antibodies may be employed to isolate or to identify clones expressing the polypeptides or polynucleotides of the invention to purify the polypeptides or polynucleotides by, for example, affinity chromatography.
  • antibodies against BASB067-polypeptide or BASB067-polynucleotide may be employed to treat infections, particularly bacterial infections.
  • Polypeptide variants include antigenically, epitopically or immunologically equivalent variants form a particular aspect of this invention.
  • the antibody or variant thereof is modified to make it less immunogenic in the individual.
  • the antibody may most preferably be "humanized," where the complementarity determining region or regions of the hybridoma-derived antibody has been transplanted into a human monoclonal antibody, for example as described in Jones et al. (1986), Nature 321, 522-525 or Tempest et al, (1991) Biotechnology 9, 266-273.
  • the present invention relates to genetically engineered soluble fusion proteins comprising a polypeptide of the present invention, or a fragment thereof, and various portions of the constant regions of heavy or light chains of immunoglobulins of various subclasses (IgG, IgM, IgA, IgE).
  • immunoglobulins Prefened as an immunoglobulin is the constant part of the heavy chain of human IgG, particularly IgGl, where fusion takes place at the hinge region.
  • the Fc part can be removed simply by incorporation of a cleavage sequence which can be cleaved with blood clotting factor Xa.
  • this invention relates to processes for the preparation of these fusion proteins by genetic engineering, and to the use thereof for drug screening, diagnosis and therapy.
  • a further aspect of the invention also relates to polynucleotides encoding such fusion proteins. Examples of fusion protein technology can be found in International Patent Application Nos. WO94/29458 and WO94/22914.
  • a mimotope is generally a peptide sequence, sufficiently similar to the native peptide (sequentially or structurally), which is capable of binding to the binding site of the native peptide.
  • a mimotope is capable of being recognised by antibodies which recognise the native peptide; or is capable of raising antibodies which recognise the native peptide, optionally when coupled to a suitable canier.
  • T cell recognition a mimotope is capable of being recognised by the same T cells that recognise the native peptide; or is capable of generating a T cell response which recognises the native peptide.
  • Peptide mimotopes may be designed for a particular purpose by addition, deletion or substitution of elected amino acids.
  • the peptides may be modified for the purposes of ease of conjugation to a protein carrier.
  • the peptides may be altered to have an N-terminal cysteine and a C-terminal hydrophobic amidated tail.
  • the addition or substitution of a D-stereoisomer form of one or more of the amino acids may be performed to create a beneficial derivative, for example to enhance stability of the peptide and/or to increase the affinity of the peptide for a particular ligand.
  • Mimotopes may also be retro sequences of the natural peptide sequences, in that the sequence orientation is reversed; or alternatively the sequences may be entirely or at least in part comprised of D-stereoisomer amino acids (inverso sequences). Also, the peptide sequences may be retro-inverso in character, in that the sequence orientation is reversed and the amino acids are of the D-stereoisomer form. Retro, inverso and retro- inverso peptides are described in WO95/24916 and WO94/05311.
  • peptide mimotopes may be identified using antibodies which are capable themselves of binding to the polypeptides of the present invention using techniques such as phage display technology (EP 0 552 267 BI). This technique, generates a large number of peptide sequences which mimic the structure of the native peptides and are, therefore, capable of binding to anti-native peptide antibodies, but may not necessarily themselves share significant sequence homology to the native polypeptide.
  • One particularly important aspect of the invention relates to a method for inducing an immunological response in an individual, particularly a mammal, preferably humans, which comprises inoculating the individual with BASB067 polynucleotide and/or polypeptide, or a fragment, or a mimotope, or variant thereof, adequate to produce antibody and/or T cell immune response to protect said individual from infection, particularly bacterial infection and most particularly Haemophilus influenzae infection. Also provided are methods whereby such immunological response slows bacterial replication.
  • Yet another aspect of the invention relates to a method of inducing an immunological response in an individual which comprises delivering to such individual a nucleic acid vector, sequence or ribozyme to direct expression of BASB067 polynucleotide and/or polypeptide, or a fragment, or a mimotope, or a variant thereof, for expressing BASB067 polynucleotide and/or polypeptide, or a fragment, or a mimotope, or a variant thereof in vivo in order to induce an immunological response, such as, to produce antibody and/or T cell immune response, including, for example, cytokine-producing T cells or cytotoxic T cells, to protect said individual,, preferably a human, from disease, whether that disease is already established within the individual or not.
  • an immunological response such as, to produce antibody and/or T cell immune response, including, for example, cytokine-producing T cells or cytotoxic T cells, to protect said individual,, preferably a human, from disease,
  • nucleic acid vectors may comprise DNA, RNA, a ribozyme, a modified nucleic acid, a DNA/RNA hybrid, a DNA-protein complex or an RNA-protein complex.
  • a further aspect of the invention relates to an immunological composition that when introduced into an individual, preferably a human, capable of having induced within it an immunological response, induces an immunological response in such individual to a BASB067 polynucleotide and/or polypeptide encoded therefrom, wherein the composition comprises a recombinant BASB067 polynucleotide and/or polypeptide encoded therefrom, or a fragment, or a mimotope, or a variant thereof, and/or comprises DNA and/or RNA which encodes and expresses an antigen of said BASB067 polynucleotide, polypeptide encoded therefrom, or other polypeptide of the invention, such as a fragment or a mimotope or a variant.
  • the immunological response may be used therapeutically or prophylactically and may take the form of antibody immunity and/or cellular immunity, such as cellular immunity arising from CTL or CD4+ T cells.
  • a BASB067 polypeptide or a fragment thereof may be fused with co-protein or chemical moiety which may or may not by itself produce antibodies or induce a T cell response, but which is capable of stabilizing the first protein and producing a fused or modified protein which will have antigenic and/or immunogenic properties, and preferably protective properties.
  • fused recombinant protein preferably further comprises an antigenic co- protein, such as lipoprotein D from Haemophilus influenzae, Glutathione-S-transferase (GST) or beta-galactosidase, or any other relatively large co-protein which solubilizes the protein and facilitates production and purification thereof.
  • the co-protein may act as an adjuvant in the sense of providing a generalized stimulation of the immune system of the organism receiving the protein.
  • the co-protein may be attached to either the amino- or carboxy-terminus of the first protein.
  • a BASB067 polypeptide and/or polynucleotide, or a fragment, or a mimotope, or a variant thereof may be present in a vector, such as the live recombinant vectors described above for example live bacterial vectors.
  • non-live vectors for the BASB067 polypeptide for example bacterial outer-membrane vesicles or "blebs".
  • OM blebs are derived from the outer membrane of the two-layer membrane of Gram-negative bacteria and have been documented in many Gram-negative bacteria (Zhou, L et al. 1998. FEMS Microbiol. Lett. 163:223-228) including C. trachomatis and C. psittaci.
  • a non-exhaustive list of bacterial pathogens reported to produce blebs also includes: Bordetella pertussis, Borrelia burgdorferi, Brucella melitensis, Brucella ovis, Esherichia coli, Haemophilus influenza, Legionella pneumophila, Neisseria gonorrhoeae, Neisseria meningitidis, Pseudomonas aeruginosa and Yersinia enterocolitica.
  • Blebs have the advantage of providing outer-membrane proteins in their native conformation and are thus particularly useful for vaccines. Blebs can also be improved for vaccine use by engineering the bacterium so as to modify the expression of one or more molecules at the outer membrane.
  • a desired immunogenic protein at the outer membrane such as the BASB067 polypeptide
  • the expression of outer-membrane molecules which are either not relevant (e.g. unprotective antigens or immunodominant but variable proteins) or detrimental (e.g. toxic molecules such as LPS, or potential inducers of an autoimmune response) can be downregulated.
  • the non-coding flanking regions of the BASB067 gene contain regulatory elements important in the expression of the gene. This regulation takes place both at the transcriptional and translational level.
  • the sequence of these regions can be obtained by DNA sequencing. This sequence information allows the determination of potential regulatory motifs such as the different promoter elements, terminator sequences, inducible sequence elements, repressors, elements responsible for phase variation, the shine-dalgarno sequence, regions with potential secondary structure involved in regulation, as well as other types of regulatory motifs or sequences.
  • This sequence information allows the modulation of the natural expression of the BASB067 gene.
  • the upregulation of the gene expression may be accomplished by altering the promoter, the shine-dalgarno sequence, potential repressor or operator elements, or any other elements involved.
  • downregulation of expression can be achieved by similar types of modification.
  • the expression of the gene can be put under phase variation control, or it may be uncoupled from this regulation.
  • the expression of the gene can be put under the control of one or more inducible elements allowing regulated expression. Examples of such regulation include, but are not limited to, induction by temperature shift, addition of inductor substrates like selected carbohydrates or their derivatives, trace elements, vitamins, co-factors, metal ions, etc.
  • modifications as described above can be introduced by several different means.
  • the modification of sequences involved in gene expression can be earned out in vivo by random mutagenesis followed by selection for the desired phenotype.
  • Another approach consists in isolating the region of interest and modifying it by random mutagenesis, or site-directed replacement, insertion or deletion mutagenesis.
  • the modified region can then be reintroduced into the bacterial genome by homologous recombination, and the effect on gene expression can be assessed.
  • the sequence knowledge of the region of interest can be used to replace or delete all or part of the natural regulatory sequences.
  • the regulatory region targeted is isolated and modified so as to contain the regulatory elements from another gene, a combination of regulatory elements from different genes, a synthetic regulatory region, or any other regulatory region, or to delete selected parts of the wild-type regulatory sequences.
  • These modified sequences can then be reintroduced into the bacterium via homologous recombination into the genome.
  • a non-exhaustive list of prefened promoters that could be used for up-regulation of gene expression includes the promoters porA, porB, lbpB, tbpB, pi 10, 1st, hpuAB from N. meningitidis or N.
  • gonorrohea ompCD, copB, lbpB, ompE, UspAl, UspA2, TbpB from M. Catarrhalis; pi, p2, p4, p5, p6, lpD, tbpB, D15, Hia, Hmwl, Hmw2 from H. influenzae.
  • the expression of the gene can be modulated by exchanging its promoter with a stronger promoter (through isolating the upstream sequence of the gene, in vitro modification of this sequence, and reintroduction into the genome by homologous recombination).
  • Upregulated expression can be obtained in both the bacterium as well as in the outer membrane vesicles shed (or made) from the bacterium.
  • the described approaches can be used to generate recombinant bacterial strains with improved characteristics for vaccine applications. These can be, but are not limited to, attenuated strains, strains with increased expression of selected antigens, strains with knock-outs (or decreased expression) of genes interfering with the immune response, strains with modulated expression of immunodominant proteins, strains with modulated shedding of outer-membrane vesicles.
  • a modified upstream region of the BASB067 gene which modified upstream region contains a heterologous regulatory element which alters the expression level of the BASB067 protein located at the outer membrane.
  • the upstream region according to this aspect of the invention includes the sequence upstream of the BASB067 gene.
  • the upstream region starts immediately upstream of the BASB067 gene and continues usually to a position no more than about 1000 bp upstream of the gene from the ATG start codon.
  • the upstream region can start immediately preceding the gene of interest, or preceding the first gene in the operon.
  • a modified upstream region according to this aspect of the invention contains a heterologous promotor at a position between 500 and 700 bp upstream of the ATG.
  • the invention provides the BASB067 gene polypeptide, in a modified bacterial Bleb.
  • the invention further provides modified host cells capable of producing the non-live membrane-based bleb vectors.
  • the invention further provides vectors comprising the BASB067 gene having a modified upstream region containing a heterologous regulatory element.
  • Vaccine antigens may be provided in a variety of other forms known in the art, depending on the properties of the protein.
  • Lipoproteins for example, because of the hydrophobicity of the lipids added to their N-terminus, are able to aggregate and to form micelles. The particulate nature of these structures can enhance the immunogenicity of the lipoprotein, as compared to the unlipidated version of the protein.
  • the size of the micelles may also have an impact on the immunogneicity of the lipoprotein and this can be modified for example by adjusting the extraction procedure.
  • compositions particularly vaccine compositions, and methods comprising the polypeptides and/or polynucleotides of the invention and immunostimulatory DNA sequences, such as those described in Sato, Y. et al. Science 273: 352 (1996).
  • polynucleotide or particular fragments thereof which have been shown to encode non-variable regions of bacterial cell surface proteins, in polynucleotide constructs used in such genetic immunization experiments in animal models of infection with Haemophilus influenzae.
  • Such experiments will be particularly useful for identifying protein epitopes able to provoke a prophylactic or therapeutic immune response. It is believed that this approach will allow for the subsequent preparation of monoclonal antibodies of particular value, derived from the requisite organ of the animal successfully resisting or clearing infection, for the development of prophylactic agents or therapeutic treatments of bacterial infection, particularly Haemophilus influenzae infection, in mammals, particularly humans.
  • the invention also includes a vaccine formulation which comprises an immunogenic recombinant polypeptide and/or polynucleotide of the invention together with a suitable carrier, such as any pharmaceutically acceptable carrier.
  • a suitable carrier such as any pharmaceutically acceptable carrier. Since the polypeptides and polynucleotides may be broken down in the stomach, each could be administered via a mucosal surface such as intranasally, or administered parenterally, including, for example, administration that is subcutaneous, intramuscular, intravenous, or intradermal.
  • Formulations suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostatic compounds and solutes which render the formulation isotonic with the bodily fluid, preferably the blood, of the individual; and aqueous and non-aqueous sterile suspensions which may include suspending agents or thickening agents.
  • the formulations may be presented in unit-dose or multi-dose containers, for example, sealed ampoules and vials and may be stored in a freeze-dried condition requiring only the addition of the sterile liquid carrier immediately prior to use.
  • the vaccine formulation of the invention may also include adjuvant systems for enhancing the immunogenicity of the formulation.
  • An immune response may be broadly distinguished into two extreme catagories, being a humoral or cell mediated immune responses (traditionally characterised by antibody and cellular effector mechanisms of protection respectively). These categories of response have been termed TH l-type responses (cell-mediated response), and TH2-type immune responses (humoral response).
  • Extreme TH l-type immune responses may be characterised by the generation of antigen specific, haplotype restricted cytotoxic T lymphocytes, and natural killer cell responses.
  • mice TH l-type responses are often characterised by the generation of antibodies of the IgG2a subtype, whilst in the human these conespond to IgGl type antibodies.
  • TH2- type immune responses are characterised by the generation of a broad range of immunoglobulin isotypes including in mice IgGl, IgA, and IgM.
  • cytokines the driving force behind the development of these two types of immune responses.
  • High levels of TH l-type cytokines tend to favour the induction of cell mediated immune responses to the given antigen, whilst high levels of TH2-type cytokines tend to favour the induction of humoral immune responses to the antigen.
  • TH1 and TH2-type immune responses are not absolute. In reality an individual will support an immune response which is described as being predominantly TH1 or predominantly TH2. However, it is often convenient to consider the families of cytokines in terms of that described in murine CD4 T cell clones by Mosmann and Coffman (Mosmann, T.R. and Coffman, R.L. (1989) TH1 and TH2 cells: different patterns oflymphokine secretion lead to different functional properties. Annual Review of Immunology, 7, pi 45-173). Traditionally, TH l-type responses are associated with the production of the IFN- ⁇ and IL-2 cytokines by T-lymphocytes.
  • cytokines often directly associated with the induction of TH l-type immune responses are not produced by T-cells, such as IL-12.
  • TH2- type responses are associated with the secretion of IL-4, IL-5, IL-6 and IL-13.
  • the best indicators of the TH1 :TH2 balance of the immune response after a vaccination or infection includes direct measurement of the production of TH1 or TH2 cytokines by T lymphocytes in vitro after restimulation with antigen, and/or (in the murine system) the measurement of the IgGl :IgG2a ratio of antigen specific antibody responses.
  • a TH l-type adjuvant is one which preferentially stimulates isolated T-cell populations to produce a high ratio of TH l-type cytokines when re-stimulated with antigen in vitro, and promotes development of both CD8+ cytotoxic T lymphocytes and antigen specific immunoglobulin responses associated with TH l-type isotype.
  • Adjuvants which are capable of preferential stimulation of the TH1 cell response are described in International Patent Application No. WO 94/00153 and WO 95/17209.
  • 3 De-O-acylated monophosphoryl lipid A is one such adjuvant. This is known from GB 2220211 (Ribi). Chemically it is a mixture of 3 De-O-acylated monophosphoryl lipid A with 4, 5 or 6 acylated chains and is manufactured by Ribi Immunochem, Montana. A prefened form of 3 De-O-acylated monophosphoryl lipid A is disclosed in European Patent 0 689 454 BI (SmithKline Beecham Biologicals SA).
  • the particles of 3D-MPL are small enough to be sterile filtered through a 0.22micron membrane (European Patent number 0 689 454).
  • 3D-MPL will be present in the range of lO ⁇ g - lOO ⁇ g preferably 25-50 ⁇ g per dose wherein the antigen will typically be present in a range 2-50 ⁇ g per dose.
  • Another prefened adjuvant comprises QS21, an HPLC purified non-toxic fraction derived from the bark of Quillaja Saponaria Molina. Optionally this may be admixed with 3 De-O-acylated monophosphoryl lipid A (3D-MPL), optionally together with a canier.
  • QS21 an HPLC purified non-toxic fraction derived from the bark of Quillaja Saponaria Molina.
  • this may be admixed with 3 De-O-acylated monophosphoryl lipid A (3D-MPL), optionally together with a canier.
  • 3D-MPL 3 De-O-acylated monophosphoryl lipid A
  • Non-reactogenic adjuvant formulations containing QS21 have been described previously (WO 96/33739). Such formulations comprising QS21 and cholesterol have been shown to be successful THl stimulating adjuvants when formulated together with an antigen.
  • Further adjuvants which are preferential stimulators of THl cell responses include immunomodulatory oligonucleotides, for example unmethylated CpG sequences as disclosed in WO 96/02555.
  • THl stimulating adjuvants such as those mentioned hereinabove, are also contemplated as providing an adjuvant which is a preferential stimulator of THl cell response.
  • QS21 can be formulated together with 3D-MPL.
  • the ratio of QS21 : 3D-MPL will typically be in the order of 1 : 10 to 10 : 1 ; preferably 1 :5 to 5 : 1 and often substantially 1 : 1.
  • the prefened range for optimal synergy is 2.5 : 1 to 1 : 1 3D-MPL: QS21.
  • a carrier which enhances immunogenicity is also present in the vaccine composition according to the invention.
  • a canier may be an oil in water emulsion, or an aluminium salt, such as aluminium phosphate or aluminium hydroxide.
  • a prefened oil-in-water emulsion comprises a metabolisible oil, such as squalene, alpha tocopherol and Tween 80.
  • a metabolisible oil such as squalene, alpha tocopherol and Tween 80.
  • the antigens in the vaccine composition according to the invention are combined with QS21 and 3D-MPL in such an emulsion.
  • the oil in water emulsion may contain span 85 and/or lecithin and/or tricaprylin.
  • QS21 and 3D-MPL will be present in a vaccine in the range of l ⁇ g - 200 ⁇ g, such as 10-100 ⁇ g, preferably lO ⁇ g - 50 ⁇ g per dose.
  • the oil in water will comprise from 2 to 10%> squalene, from 2 to 10%> alpha tocopherol and from 0.3 to 3%> tween 80.
  • the ratio of squalene: alpha tocopherol is equal to or less than 1 as this provides a more stable emulsion.
  • Span 85 may also be present at a level of 1%. In some cases it may be advantageous that the vaccines of the present invention will further contain a stabiliser.
  • Non-toxic oil in water emulsions preferably contain a non-toxic oil, e.g. squalane or squalene, an emulsifier, e.g. Tween 80, in an aqueous canier.
  • a non-toxic oil e.g. squalane or squalene
  • an emulsifier e.g. Tween 80
  • the aqueous canier may be, for example, phosphate buffered saline.
  • a particularly potent adjuvant formulation involving QS21, 3D-MPL and tocopherol in an oil in water emulsion is described in WO 95/17210.
  • the present invention also provides a polyvalent vaccine composition comprising a vaccine formulation of the invention in combination with other antigens, in particular antigens useful for treating other bacterial or viral diseases, cancers, autoimmune diseases and related conditions.
  • a polyvalent vaccine composition may include a TH-1 inducing adjuvant as hereinbefore described.
  • compositions for purposes of compositions, kits and administration
  • compositions comprising a BASB067 polynucleotide and/or BASB067 polypeptide for administration to a cell or to a multicellular organism.
  • the invention also relates to compositions comprising a polynucleotide and/or a polypeptides discussed herein or their agonists or antagonists.
  • the polypeptides and polynucleotides of the invention may be employed in combination with a non-sterile or sterile carrier or carriers for use with cells, tissues or organisms, such as a pharmaceutical carrier suitable for administration to an individual.
  • Such compositions comprise, for instance, a media additive or a therapeutically effective amount of a polypeptide and/or polynucleotide of the invention and a pharmaceutically acceptable carrier or excipient.
  • Such carriers may include, but are not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol and combinations thereof.
  • the formulation should suit the mode of administration.
  • the invention further relates to diagnostic and pharmaceutical packs and kits comprising one or more containers filled with one or more of the ingredients of the aforementioned compositions of the invention.
  • Polypeptides, polynucleotides and other compounds of the invention may be employed alone or in conjunction with other compounds, such as therapeutic compounds.
  • compositions may be administered in any effective, convenient manner including, for instance, administration by topical, oral, anal, vaginal, intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal intradermalor transdermal routes among others.
  • the active agent may be administered to an individual as an injectable composition, for example as a sterile aqueous dispersion, preferably isotonic.
  • the present invention provides for pharmaceutical compositions comprising a therapeutically effective amount of a polypeptide and/or polynucleotide, such as the soluble form of a polypeptide and/or polynucleotide of the present invention, agonist or antagonist peptide or small molecule compound, in combination with a pharmaceutically acceptable carrier or excipient.
  • a pharmaceutically acceptable carrier or excipient include, but are not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol, and combinations thereof.
  • the invention further relates to pharmaceutical packs and kits comprising one or more containers filled with one or more of the ingredients of the aforementioned compositions of the invention.
  • Polypeptides, polynucleotides and other compounds of the present invention may be employed alone or in conjunction with other compounds, such as therapeutic compounds.
  • composition will be adapted to the route of administration, for instance by a systemic or an oral route.
  • Prefened forms of systemic administration include injection, typically by intramuscular or subcutaneous injection. Other injection routes, such as intradermal, intraperitoneal, or intravenous can be used.
  • Alternative means for systemic administration include transmucosal and transdermal administration using penetrants such as bile salts or fusidic acids or other detergents.
  • oral administration may also be possible. Administration of these compounds may also be topical and/or localized, in the form of salves, pastes, gels, solutions, powders and the like.
  • the dosage level of the active agent will be from 0.01 ⁇ g/kg to 10 ⁇ g/kg, typically around 1 ⁇ g/kg.
  • the physician in any event will determine the actual dosage which will be most suitable for an individual and will vary with the age, weight and response of the particular individual.
  • the above dosages are exemplary of the average case. There can, of course, be individual instances where higher or lower dosage ranges are merited, and such are within the scope of this invention.
  • Suitable dosages are in the range of 0.1-100 ⁇ g/kg of subject.
  • a vaccine composition is conveniently in injectable form. Conventional adjuvants may be employed to enhance the immune response.
  • a suitable unit dose for vaccination is 0.5-5 microgram/kg of antigen, and such dose is preferably administered 1-3 times and with an interval of 1-3 weeks. With the indicated dose range, no adverse toxicological effects will be observed with the compounds of the invention which would preclude their administration to suitable individuals. Wide variations in the required dosage, however, are to be expected in view of the variety of compounds available and the differing efficiencies of various routes of administration. For example, oral administration would be expected to require higher dosages than administration by injection. Variations in these dosage levels can be adjusted using standard empirical routines for optimization, as is well understood in the art.
  • Polynucleotide and polypeptide sequences form a valuable information resource with which to determine their 2- and 3-dimensional structures as well as to identify further sequences of similar homology. These approaches are most easily facilitated by storing the sequence in a computer readable medium and then using the stored data in a known macromolecular structure program or to search a sequence database using well known searching tools, such as the GCG program package.
  • sequence analysis includes, for example, methods of sequence homology analysis, such as identity and similarity analysis, DNA, RNA and protein structure analysis, sequence assembly, cladistic analysis, sequence motif analysis, open reading frame determination, nucleic acid base calling, codon usage analysis, nucleic acid base trimming, and sequencing chromatogram peak analysis.
  • a computer based method for performing homology identification. This method comprises the steps of: providing a first polynucleotide sequence comprising the sequence of a polynucleotide of the invention in a computer readable medium; and comparing said first polynucleotide sequence to at least one second polynucleotide or polypeptide sequence to identify homology.
  • a computer based method is also provided for performing homology identification, said method comprising the steps of: providing a first polypeptide sequence comprising the sequence of a polypeptide of the invention in a computer readable medium; and comparing said first polypeptide sequence to at least one second polynucleotide or polypeptide sequence to identify homology.
  • Identity is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as the case may be, as determined by comparing the sequences.
  • identity also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences.
  • Identity can be readily calculated by known methods, including but not limited to those described in (Computational Molecular Biology, Lesk, A.M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D.W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A.M., and Griffin, H.G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heine, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M.
  • Methods to determine identity are designed to give the largest match between the sequences tested. Moreover, methods to determine identity are codified in publicly available computer programs. Computer program methods to determine identity between two sequences include, but are not limited to, the GAP program in the GCG program package (Devereux, J., et al., Nucleic Acids Research 12(1): 387 (1984)), BLASTP, BLASTN (Altschul, S.F. et al., J. Molec. Biol.
  • BLAST Pearson and Lipman Proc. Natl. Acad. Sci. USA 85; 2444-2448 (1988).
  • the BLAST family of programs is publicly available from NCBI and other sources (BLAST Manual, Altschul, S., et al, NCBI NLM NIH Bethesda, MD 20894; Altschul, S., et al, J. Mol. Biol. 215: 403-410 (1990).
  • the well known Smith Waterman algorithm may also be used to determine identity.
  • Parameters for polynucleotide comparison include the following:
  • Polynucleotide embodiments further include an isolated polynucleotide comprising a polynucleotide sequence having at least a 50, 60, 70, 80, 85, 90, 95, 97 or 100% identity to the reference sequence of SEQ ID NO: 1 ,3, wherein said polynucleotide sequence may be identical to the reference sequence of SEQ ID NO: 1,3 or may include up to a certain integer number of nucleotide alterations as compared to the reference sequence, wherein said alterations are selected from the group consisting of at least one nucleotide deletion, substitution, including transition and transversion, or insertion, and wherein said alterations may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among the nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence, and wherein said number of nucleotide alterations is determined by multiplying the total number of nucleotides in SEQ ID NO: 1
  • n n is the number of nucleotide alterations
  • x n is the total number of nucleotides in SEQ ID NO: 1,3
  • y is 0.50 for 50%, 0.60 for 60%, 0.70 for 70%, 0.80 for 80%, 0.85 for 85%, 0.90 for 90%, 0.95 for 95%, 0.97 for 97% or 1.00 for 100%
  • • is the symbol for the multiplication operator, and wherein any non-integer product of x n and y is rounded down to the nearest integer prior to subtracting it from x n .
  • Alterations of a polynucleotide sequence encoding the polypeptide of SEQ ID NO:2,4 may create nonsense, missense or frameshift mutations in this coding sequence and thereby alter the polypeptide encoded by the polynucleotide following such alterations.
  • a polynucleotide sequence of the present invention may be identical to the reference sequence of SEQ ID NO:l,3, that is it may be 100% identical, or it may include up to a certain integer number of nucleic acid alterations as compared to the reference sequence such that the percent identity is less than 100% identity.
  • Such alterations are selected from the group consisting of at least one nucleic acid deletion, substitution, including transition and transversion, or insertion, and wherein said alterations may occur at the 5' or 3' terminal positions of the reference polynucleotide sequence or anywhere between those terminal positions, interspersed either individually among the nucleic acids in the reference sequence or in one or more contiguous groups within the reference sequence.
  • the number of nucleic acid alterations for a given percent identity is determined by multiplying the total number of nucleic acids in SEQ ID NO: 1,3 by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of nucleic acids in SEQ ID NO: 1,3, or:
  • n n is the number of nucleic acid alterations
  • x n is the total number of nucleic acids in SEQ ID NO: 1,3
  • y is, for instance 0.70 for 70%, 0.80 for 80%, 0.85 for 85% etc.
  • • is the symbol for the multiplication operator, and wherein any non-integer product of x n and y is rounded down to the nearest integer prior to subtracting it from x n .
  • Polypeptide embodiments further include an isolated polypeptide comprising a polypeptide having at least a 50,60, 70, 80, 85, 90, 95, 97 or 100% identity to a polypeptide reference sequence of SEQ ID NO:2,4, wherein said polypeptide sequence may be identical to the reference sequence of SEQ ID NO:2,4 or may include up to a certain integer number of amino acid alterations as compared to the reference sequence, wherein said alterations are selected from the group consisting of at least one amino acid deletion, substitution, including conservative and non-conservative substitution, or insertion, and wherein said alterations may occur at the amino- or carboxy -terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, interspersed either individually among the amino acids in the reference sequence or in one or more contiguous groups within the reference sequence, and wherein said number of amino acid alterations is determined by multiplying the total number of amino acids in SEQ ID NO:2,4 by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of amino acids
  • n a is the number of amino acid alterations
  • x a is the total number of amino acids in SEQ ID NO:2,4
  • y is 0.50 for 50%, 0.60 for 60%, 0.70 for 70%, 0.80 for 80%, 0.85 for 85%, 0.90 for 90%, 0.95 for 95%, 0.97 for 97% or 1.00 for 100%
  • • is the symbol for the multiplication operator, and wherein any non-integer product of x a and y is rounded down to the nearest integer prior to subtracting it from x a .
  • a polypeptide sequence of the present invention may be identical to the reference sequence of SEQ ID NO:2,4, that is it may be 100%> identical, or it may include up to a certain integer number of amino acid alterations as compared to the reference sequence such that the percent identity is less than 100%) identity.
  • Such alterations are selected from the group consisting of at least one amino acid deletion, substitution, including conservative and non-conservative substitution, or insertion, and wherein said alterations may occur at the amino- or carboxy-terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, interspersed either individually among the amino acids in the reference sequence or in one or more contiguous groups within the reference sequence.
  • the number of amino acid alterations for a given %> identity is determined by multiplying the total number of amino acids in SEQ ID NO:2,4 by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of amino acids in SEQ ID NO:2,4, or:
  • n a is the number of amino acid alterations
  • x a is the total number of amino acids in SEQ ID NO:2,4
  • y is, for instance 0.70 for 70%, 0.80 for 80%, 0.85 for 85% etc.
  • • is the symbol for the multiplication operator, and wherein any non-integer product of x a and y is rounded down to the nearest integer prior to subtracting it from x a .
  • Isolated means altered “by the hand of man” from its natural state, i.e., if it occurs in nature, it has been changed or removed from its original environment, or both.
  • a polynucleotide or a polypeptide naturally present in a living organism is not “isolated,” but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is “isolated”, as the term is employed herein.
  • a polynucleotide or polypeptide that is introduced into an organism by transformation, genetic manipulation or by any other recombinant method is "isolated” even if it is still present in said organism, which organism may be living or non-living.
  • a polynucleotide or polypeptide whose expression is specifically altered by genetic manipulation is “isolated” even though the polynucleotide or polypeptide may be present in the organism in which it is naturally present.
  • Polynucleotide(s) generally refers to any polyribonucleotide or polydeoxyribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA including single and double-stranded regions.
  • Variant refers to a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide, but retains essential properties.
  • a typical variant of a polynucleotide differs in nucleotide sequence from another, reference polynucleotide. Changes in the nucleotide sequence of the variant may or may not alter the amino acid sequence of a polypeptide encoded by the reference polynucleotide. Nucleotide changes may result in amino acid substitutions, additions, deletions, fusions and truncations in the polypeptide encoded by the reference sequence, as discussed below.
  • a typical variant of a polypeptide differs in amino acid sequence from another, reference polypeptide.
  • a variant and reference polypeptide may differ in amino acid sequence by one or more substitutions, additions, deletions in any combination.
  • a substituted or inserted amino acid residue may or may not be one encoded by the genetic code.
  • a variant of a polynucleotide or polypeptide may be a naturally occurring such as an allelic variant, or it may be a variant that is not known to occur naturally. Non-naturally occurring variants of polynucleotides and polypeptides may be made by mutagenesis techniques or by direct synthesis.
  • Disease(s) means any disease caused by or related to infection by bacteria, including, for example, otitis media, acute otitis media, recunent otitis media, otitis media with effusion, sinusitis, conjuctivitis, rhinopharyngitis, laryngitis, obstructive laryngitis, alveolitis, bronchitis, chronic bronchitis, enhancement of chronic obstructive pulmonary disease, complications of cystic fibrosis, pericarditis, endocarditis, osteomyelitis, arthritis, genitouinary tract colonization and neonatal infection, bacteremia, septicemia, meningitis.
  • Example 1 Discovery and confirmatory DNA sequencing of the BASB067 gene from one non-typeable Haemophilus influenzae strain (NTHi).
  • the BASB067 gene of SEQ ID NO:l comes from Heamophilus influenzae strain Rd KW20.
  • the translation of the BASB067 polynucleotide sequence is shown in SEQ ID NO:2.
  • the sequence of the BASB067 gene was also determined in NTHi strain 289.
  • plasmid D ⁇ A (see example 2A) containing the gene region encoding the mature BASB067 from NTHi. strain 289 was used as a PCR template.
  • polynucleotide and deduced polypeptide sequences refened to as SEQ ID NO:3 and SEQ ID NO:4 respectively, were obtained.
  • the signal sequence is from plamid pBAD/glll (A).
  • the mature BASB067 polynucleotide sequence begins at nucleotide (nt) 61 of SEQ ID NO:3.
  • the mature BASB067 polypeptide sequence begins at amino acid (aa) 21 of SEQ ID NO:4.
  • This plasmid provides the signal peptide from the bacteriophage fd pill protein such that a mature BASB067 protein could be targeted to the periplasm of E. coli.
  • the BASB067 PCR product was purified from the amplification reaction using Wizard PCR prepTM (Promega) according to the manufacturers instructions. To produce the required Ncol and Asp 718 termini necessary for cloning, purified PCR product was sequentially digested to completion with Ncol and Asp 718 restriction enzymes as recommended by the manufacturer (Boehringer Mannheim). Digested BASB067 PCR products and pBAD were gel- purified and ligated together using an approximately 5-fold molar excess of the digested fragment to the vector.
  • the following strains of Haemophilus influenzae are provided as a useful reference for the present invention.
  • the BASB067 gene utilised in accordance with the invention is not limited with regard to the strain, but it may correspond to theBASB067 gene as found in any of the strains listed below or any related strain. This information is provided merely for convenience to those of skill in the art and is not an admission that any provision of a deposit is required for enablement.
  • strain 3219C (ET7) strain 3241 A (ET30) strain 840645 (ET51) strain 901905U (ET60) strain A840177 (ET40) strain A840177 (ET69)
  • HiRd strain An example of a HiRd strain is described in R.D. Fleischmann et al., Science . Vol 269: 496-512 (1995) and K. W. Wilcox et al., J. Bact. Vol 122: 443 (1975) with the strain name KW20. This strain was deposited by the authors with the American Type Culture Collection under deposit number ATCC 51907.
  • the signal sequence is from plasmid pBAD/glll 5(A); mature BASB067 begins at nucleotide 61.
  • SeqlD No: 2 Identity to SeqlD No: 2 is indicated by a dot and Gap is indicated by a dash.
  • the signal sequence is from plamid pBAD/glll (A); mature BASB067 begins at amino acid 21.

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