Definitions

• the present invention relates to factor H-binding proteins and peptides, nucleic acid sequences encoding these proteins and peptides, antibodies specifically binding them and pharmaceutical compositions, especially vaccine compositions, containing them.
• Streptococcus pneumoniae remains a significant cause of morbidity and mortality, causing conditions such as otitis media, community- acquired pneumoniae, septicemia and meningitis. Infants, the elderly and immunocompromised patients are particularly susceptible to pneumococcal infection.
• the polysaccharide capsule of the pneumococcus has long been recognized as the major virulence determinant (1). Virulence varies with capsular serotype, but experiments with conversion of serotypes clearly demonstrate that other factors than the capsule play a significant role (2). A number of non-capsular virulence factors have also been extensively examined. Although their relative contribution to pneumococcal virulence remains unclear, it is apparent that proteins such as PspA, pneumolysin and PsaA play a role in pneumococcal virulence (3-5).
• fH is a 150 kDa plasma protein composed of 20 short consensus repeats, and is the best characterised member of the factor H protein family (10).
• fH is a crucial protein in the regulation of complement.
• the critical step in the amplification loop of the alternative pathway is the formation of C3 convertase (C3bBb) from surface-deposited C3b and factor B.
• fH inhibits complement activation by preventing association of factor B with C3b, acting as a cofactor in C3b degradation by factor I, and promoting the dissociation of Bb from both C3 and C5 convertase.
• Examples of bacterial surface structures interacting with fH include M and
• Vaccines against Streptococcus pneumoniae that are currently in use are all based upon capsule structures (carbohydrate antigens) Each serotype has a unique capsule structure. Therefore, vaccine compositions against Streptococcus pneumoniae contain numerous different capsular antigens in order to protect against the most common serotypes. Still, these compositions fail to provide an adequate protection in all individuals.
• the present invention provides a polypeptide having the ability to bind factor H comprising: (a) the amino acid sequence of Thr38 to Lysl49 of SEQ ID NO: 1 (b) a variant of (a) which is capable of binding factor H, or (c) a fragment of (a) or (b) of at least 20 amino acids in length which is capable of binding factor H, for use in prophylaxis or therapy.
• the present invention also provides a vaccine composition
• a vaccine composition comprising a polypeptide having an amino acid sequence selected from: (a) the amino acid sequence of Thr38 to Lysl49 of SEQ ID NO: 1, (b) a variant of (a) which is capable of generating an immune response to Streptococcus pneumoniae or binding to an anti-protein Hie antibody, or (c) a fragment of (a) or (b) of at least 6 amino acids in length which is capable of generating an immune response against Streptococcus pneumoniae, or of binding to an anti protein Hie antibody.
• the invention provides a polypeptide of 15 to 800 amino acids in length comprising: (a) the amino acid sequence of SEQ ID NO: 1, or (b) a polypeptide showing sequence identity of at least 85%, preferably at least 95%), and most preferably at least 99%) sequence identity with (a).
• the polypeptide has the ability to bind factor H.
• the invention also provides a polynucleotide encoding a polypeptide, the polynculeotide comprising: (i) the nucleotide coding sequence of SEQ ID NO: 4 or a sequence complementary thereto, (ii) a nucleotide sequence which selectively hybridizes to said sequence (i) or a fragment thereof, or (iii) a nucleotide sequence which codes for a polypeptide having the same amino acid sequence as that encoded by a said sequence of (i) or (ii).
• the present invention provides proteins and peptides derived from Streptococcus pneumoniae, type 3, which bind the complement factor H (fH). These proteins and peptides show a homology of at least 50 %, preferably at least 60 %, and most preferably at least 70 %> with the subsequence from Thr38 to Lysl49 of the sequence disclosed herein as SEQ ID NO: 1.
• the above subsequence which is located in the amino-terminal of a surface protein isolated from Streptococcus pneumoniae, type 3, is highly associated with binding of fH.
• the invention in another aspect, relates to proteins and peptides showing a homology of at least 85 %>, preferably at least 95 %>, and most preferably at least 99 %> with the Hie protein, the amino acid sequence of which is disclosed as SEQ ID NO: 1.
• the inventions also provides vaccine compositions comprising the above proteins and peptides. Description of the Figures
• Fig. 1 discloses a comparison of Hie and PspC. Schematic representation of
• Hie and PspC The signal peptide (SP) and the wall spanning region (W) are indicated;
• Fig. 2 shows a sequence comparison of Hie and allelic variants of PspC, namely PspC6A (SEQ ID NO: 5), PspC2 (SEQ ID NO: 7), PspC19 (SEQ ID NO: 9),
• PspC19TIGR (SEQ ID NO: 10) and SpsAl (SEQ ID NO: 11). ClustalW alignment of the NH2 -terminal region from Hie (serotype 3) and allelic variants of PspC, including SpsA. Identical and similar residues are shaded in dark and light, respectively. Numbers in the protein names indicate the serotype of the strain from which the sequence was obtained. PspC.TIGR is from a serotype 4 strain.
• GenBank/EMBL accession numbers are as follows: PspC2, AF068645;
• Fig. 3 relates to binding of radiolabelled factor H to a Hic-deficient mutant.
• Serial dilutions of PR218 (D) and the Hic-deficient mutant FP 13 ( ⁇ ) were incubated with radiolabelled fH. Binding is expressed as the percentage of added radioactivity.
• the data points are averages of three experiments with duplicate samples. Standard deviation is indicated by error bars;
• Fig. 4 discloses binding of factor H to Hie.
• a competitive binding assay was performed by incubating PR218 bacteria (10 9 CFU/ml) with radiolabelled fH in the presence of increasing concentrations of unlabelled fH (O), GST (D), and
• Fig. 5 presents kinetic analysis of the interaction between Hie and factor H by surface plasmon resonance.
• concentration of the analyte (fH) was 2000, 667, 333, 167 and 83 nM, and the time scale has been adjusted so that 0 s represents the injection starting point.
• Fig. 6 shows that Hie and factor H inhibit alternative pathway hemolysis.
• SED ID NO: 1 is the amino acid sequence of protein Hie.
• SED ID Nos: 2 and 3 are the primers used to amplify a portion of Hie.
• SED ID NO: 4 is the DNA sequence encoding protein Hie.
• SED ID Nos: 5 and 6 are the amino acid and encoding DNA sequence respectively for PspC6A.
• SED ID NO: 7 and 8 are the amino acid and encoding DNA sequence respectively for PspC2.
• SED ID NO: 9 is the amino acid sequence of PspC19.
• SED ID NO: 10 is the amino acid sequence of PspC 19 TIGR.
• SED ID NO: 11 is the amino acid sequence of SpsAl .
• fH complement factor H
• PspA pneumococcal surface protein A
• PsaA pneumococcal surface antigen A
• PspC pneumococcal surface protein C
• CbpA choline-binding protein A
• SpsA Streptococcus pneumoniae secretory IgA binding protein
• GST glutathione S-transferase
• PCR polymerase chain reaction
• SDS-PAGE sodium dodecyl sulphate polyacrylamide gel electrophoresis.
• the present application relates to proteins and peptides binding fH.
• proteins and peptides are all comprise a derivative of the subsequence from thr38 to lysl49 of amino-terminal of the Hie protein, whose amino acid sequence is enclosed herein as SEQ ID NO: 1.
• Peptides and proteins according to this first aspect show a homology of at least 50 %, preferably at least 60
• polypeptides according to the first aspect of the invention have one or more of the following properties. Firstly, they may have the ability to bind to fH. As will be shown below, this feature makes them interesting as vaccine candidates against pneumococci. Secondly, peptides according to the invention may have the ability to stimulate a T-cell response. Thirdly, the peptides of the invention may stimulate a B-cell response.
• the present invention relates to peptides and proteins comprising at least 15 amino acids and which peptides and proteins show a homology of at least 85 %, preferably at least 95 %, and most preferably at least 99 % with the amino acid sequence of the Hie protein disclosed as SEQ ID NO: 1.
• polypeptides according to the second aspect of the invention show a high homology to the Hie protein, which makes them interesting as vaccine candidates against pneumococci.
• peptides according to this aspect of the invention may have the ability to stimulate a T-cell response.
• the peptides of this aspect of the invention may stimulate a B-cell response.
• the invention provides a polypeptide which comprises: (a) the amino acid sequence of Thr38 to Lys 149 of SEQ ID NO : 1 ,
• the invention relates to a vaccine composition
• the ability to bind factor H can be monitored by any suitable method.
• assays can be carried out using labelled factor H, for example, labelled with a radio label and monitoring binding to a peptide under investigation.
• the ability of the peptides to bind anti-Hic antibodies can be monitored using any suitable assay, and in particular using antibodies which have been generated against full length protein Hie as shown in SEQ ID NO: 1 or a fragment thereof comprising the sequence of Thr38 to Lysl49 of SEQ ID NO: 1.
• the capability of the peptide to generate an immune response can be tested using a suitable animal model such as a murine model comprising administering the peptide under investigation to the animal, monitoring the generation of an immune response, either through the production of antibodies or through the production of T-cell responses such as cytotoxic T-cell responses.
• Preferred peptides which are able to generate a protective immune response can be identified by subjecting an animal so vaccinated with a lethal challenge of pneumococci.
• the ability of the peptide to bind to anti- protein Hie antibodies can be assayed in vitro.
• An anti-protein Hie antibody can be generated by standard techniques using a protein of SEQ ID NO: 1 to generate a suitable antibody.
• the invention relates to a novel polynucleotide having a sequence which is: (i) the nucleotide coding sequence of SEQ ID NO: 4 or a sequence complementary thereto,
• Polypeptides are provided which are encoded by a polynucleotide of the invention.
• the invention also relates to polynucleotides which encode a polypeptide of the invention.
• the invention also provides: a recombinant vector comprising a polynucleotide of the invention, such as an expression vector in which the polynucleotide is operably linked to a regulatory sequence; a host cell which is transformed for the polynucleotide of the invention; a process of producing a polypeptide of the invention comprising maintaining a host cell transformed with a polynucleotide of the invention under conditions to provide expression of the polypeptide; an antibody, monoclonal or polyclonal, specific for a polypeptide in accordance with the invention; a method of vaccinating a patient against pneumococcal infection which method comprises administering to the patient an effective amount of a polypeptide or polynucleotide according to the invention.
• the invention in another aspect, relates to an assay to identify an agent which inhibits the binding of factor H to protein Hie.
• the assay may comprise incubating a polypeptide of the invention having the ability to bind factor H with factor H in the presence of the substance under test and monitoring for binding of the polypeptide of the invention to factor H. Methods for monitoring protein interactions are well known in the art.
• the polypeptide of the invention may be provided in isolated form.
• a bacterium expressing a polypeptide of the invention may be provided and incubated with factor H.
• Substances which are identified which inhibit the binding of factor H to a polypeptide of the invention may be used as an antibiotic or in the treatment of an individual suffering from pneumococcal infection.
• the invention also provides formulating an agent identified as an inhibitor of the binding of factor H to a polypeptide of the invention with a pharmaceutically acceptable carrier.
• the present invention provides a method for the treatment of a Streptococcus pneumoniae infection, which method comprises identifying a substance which inhibits binding of factor H to a polypeptide of the invention and administering a therapeutically effective amount of the substance to a patient in need thereof.
• a therapeutically effective amount of the substance is an amount which alleviates the symptoms of the Streptococcus pneumoniae infection or otherwise improves the condition of the patient suffering from a Streptococcus pneumoniae infection.
• the substance administered to a patient is formulated with a pharmaceutically acceptable carrier.
• a DNA sequence encoding the Hie protein is disclosed as SEQ ID NO: 4.
• the nucleic acid sequences of the present invention are preferably DNA, though they may be RNA.
• Nucleic acid sequences of the invention will typically be in isolated or substantially isolated form. For example up to 80, up to 90, up to 95 or up to 100% of the nucleic acid material in a preparation of a nucleic acid of the invention will typically be nucleic acid according to the invention. Alterations, isolations or syntheses of nucleic acid sequences according to the invention may be performed by any conventional method, for example by the methods of Sambrook et al (Molecular Cloning: A Laboratory Manual; 1989).
• sequences of the invention include sequences that are capable of selective hybridisation to those encoding the proteins or peptides of the invention or the complementary strands thereof and that encode a polypeptide having one or more of the properties defined above.
• Such hybridisation may be carried out under any suitable conditions known in the art (see Sambrook et al (1989): Molecular Cloning: A Laboratory Manual). For example, if high stringency is required, suitable conditions include 0.2 X SSC at 60 °C. If lower stringency is required, suitable conditions include 2X SSC at 60 °C.
• a polynucleotide of the invention can hybridize to SEQ ID NO: 4, or its complement at a level significantly above background. Background hybridization may occur, for example, because of other cDNAs present in a cDNA library.
• the signal level generated by the interaction between a polynucleotide of the invention and the sequence of SEQ ID NO: 4 is typically at least 10 fold, preferably at least 100 fold, as intense as interactions between other polynucleotides and the sequence of SEQ ID NO: 4.
• the intensity of interaction may be measured, for example, by radiolabelling the probe, e.g. with 32 P.
• Selective hybridization is typically achieved using conditions of medium to high stringency (for example 0.1 to 0.2 x SSC at from about 50°C to about 60°C).
• a nucleotide sequence capable of selectively hybridizing to the DNA sequence of SEQ ID NO: 4 or to the sequence complementary to that coding sequence will be generally at least 80%), preferably at least 90%> and more preferably at least 95%), homologous to the sequence of SEQ ID NO: 4 or its complement over a region of at least 20, preferably at least 30, for instance at least 40, 60 or 100 or more contiguous nucleotides or, indeed, over the full length of the coding sequence. Thus there may be at least 85%, at least 90%) or at least 95% nucleotide identity over such regions.
• polynucleotides of the invention Any combination of the above mentioned degrees of homology and minimum size may be used to define polynucleotides of the invention, with the more stringent combinations (i.e. higher homology over longer lengths) being preferred.
• a polynucleotide which is at least 85% homologous over 25, preferably over 30, nucleotides forms one aspect of the invention, as does a polynucleotide which is at least 90%> homologous over 40 nucleotides.
• the UWGCG Package provides the BESTFIT program which can be used to calculate homology (for example used on its default settings) (Devereux et al (1984) Nucleic Acids Research 12, p387-395).
• the PILEUP and BLAST algorithms can be used to calculate homology or line up sequences (such as identifying equivalent or corresponding sequences (typically on their default settings), for example as described in Altschul S. F. (1993) J Mol Evol 36:290-300; Altschul, S, F et al (1990) J Mol Biol 215:403-10.
• HSPs high scoring sequence pair
• T some positive-valued threshold score
• Altschul et al, supra these initial neighbourhood word hits act as seeds for initiating searches to find HSP's containing them.
• the word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased.
• Extensions for the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
• the BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
• the BLAST algorithm performs a statistical analysis of the similarity between two sequences; see e.g., Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-5787.
• One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance.
• P(N) the smallest sum probability
• a sequence is considered similar to another sequence if the smallest sum probability in comparison of the first sequence to the second sequence is less than about 1, preferably less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
• sequences that differ from those defined above because of the degeneracy of the genetic code and encode the same polypeptide having one or more of the properties defined above.
• Nucleic acid sequences of the invention will preferably be at least 30 bases in length, for example up to 50, up to 100, up to 200, up to 300, up to 400, up to 500, up to 600, up to 800, up to 1000 bases, up to 2000 bases or up to 3000 bases.
• Nucleic acid sequences of the invention may be extended at either or both of the 5' and 3' ends. Such extensions may be of any length.
• an extension may comprise up to 10, up to 20, up to 50, up to 100, up to 200 or up to 500 or more nucleic acids.
• the nucleic acid sequences of the invention may be extended at either or both of the 5' and 3' ends by any non- wild-type sequence.
• polypeptides of the invention are derived from the amino acid sequence shown as SEQ ID NO: 1.
• the polypeptides of the invention are not limited to the polypeptide of SEQ ID NO: 1.
• the polypeptides of the invention also include polypeptides with sequences closely related to that of SEQ ID NO: 1 that are able to bind fH.
• the polypeptides of the invention comprises very similar or identical antigenic determinants compared to the Hie protein despite the fact that they do not bind to fH. All these sequences may be prepared by altering that of SEQ ID NO: 1 by any conventional method, or isolated from any organism or made synthetically.
• polypeptides related to that of SEQ ID NO: 1 may be prepared by modifying a DNA sequence encoding the Hie protein expressing them recombinantly.
• polypeptides of the invention may accordingly have less than 100%> sequence identity with that of SEQ ID NO: 1.
• polypeptides of the invention may include substitutions, deletions, or insertions that distinguish them from SEQ ID NO: 1 as long as these do not destroy the ability to bind fH, or as long as they show similar antigenic properties as the Hie protein.
• a substitution, deletion or insertion may suitably involve one or more amino acids, typically from one to five, one to ten or one to twenty amino acids, for example, a substitution, deletion or insertion of one, two, three, four, five, eight, ten, fifteen, or twenty amino acids.
• a fH-binding polypeptide of the first aspect of the invention has at least 50%>, at least 60%o, or at least 70% sequence identity to the subsequence from thr38 to lys 149 of SEQ ID NO: 1.
• the polypeptide has at least 80%, 90%, 95%, 97% or 99% identity with SEQ ID NO: 1.
• a polypeptide of the second aspect of the invention has at least 85 %, at least 95, or at least 99 %> sequence identity to a subsequence that can be derived from all parts of the sequence of SEQ ID NO: 1 , and preferably to a sequence of 15 to 600 contiguous amino acids of SEQ ID NO: 1.
• sequences of SEQ ID NO: 1 should be preserved in a polypeptide of the invention. Such sequences will generally be similar in charge, hydrophobicity and size to that of SEQ ID NO: 1. Examples of substitutions that do not greatly affect the physicochemical nature of amino acid sequences are those in which an amino acid from one of the following groups is substituted by a different amino acid from the same group:
• D-amino acids may be incorporated into the amino acid sequence at sites where they do not affect the polypeptides biological properties. This reduces the polypeptides' susceptibility to proteolysis by the recipient's proteases.
• nucleic acid sequences encoding the polypeptides of the invention may be extended at one or both ends by any non-wild-type sequence.
• polypeptides of the invention may be extended at the C-terminal by an amino acid sequence of any length.
• an extension may comprise up to 5, up to 10, up to 20, up to 50, or up to 100 or 200 or more amino acids.
• a C- terminal extension may have any sequence apart from that which is C-terminal to the sequence of the invention (or the native sequence from which it is derived) in native Hie protein.
• the polypeptides of the invention may be extended at the C- terminal by any non- wild-type sequence.
• polypeptides of the invention may be attached to other polypeptides, proteins or carbohydrates that enhance their antigenic properties.
• polypeptides of the invention may be attached to one or more other antigenic polypeptides.
• additional antigenic polypeptides may be derived from S. pneumoniae or from another organism.
• Possible additional antigenic polypeptides include heterologous T- cell epitopes derived from other S. pneumoniae proteins or from species other than S. pneumoniae. Heterologous B-cell epitopes may also be used. Such heterologous T- cell and or B-cell epitopes may be of any length and epitopes of up to 5, up to 10 or up to 20 amino acids in length are particularly preferred.
• Possible carbohydrates that can be added are capsular antigens.
• These additional antigenic polypeptides may be attached to the polypeptides of the invention chemically.
• one or more additional antigenic sequences or carbohydrate groups may comprise an extension to a polypeptide of the invention.
• a polypeptide of the invention may be subjected to one or more chemical modifications, such as glycosylation, sulphation, COOH-amidation or acylation.
• polypeptides that are acetylated at the N-terminus are preferred, as are polypeptides having C-terminal amide groups.
• Preferred polypeptides may have one or more of these modifications.
• particularly preferred peptides may have a C-terminal amide group and N-terminal acetylation.
• a polypeptide of the invention may form part of a larger polypeptide comprising multiple copies of the sequence of one or more of SEQ ID NO: 1 or a sequences related to them in any of the ways defined herein.
• Polypeptides of the invention typically comprise at least 15 amino acids, for example 15 to 20, 20 to 50, 50 to 100 or 100 to 200 or 200 to 300 or 300 to 400 or 400 to 500 or 500 to 600 or 600 to 700 or 700 to 800 amino acids.
• Polypeptides according to the invention may be purified or substantially purified. Such a polypeptide in substantially purified form will generally form part of a preparation in which more than 90%), for example up to 95%, up to 98% or up to 99%o of the peptide material in the preparation is that of a polypeptide or polypeptides according to the invention.
• nucleic acid sequences and polypeptides of the invention were originally derived from S. pneumoniae. However, nucleic acid sequences and/or polypeptides of the invention may also be obtained from other organisms, typically bacteria, especially other streptococci. They may be obtained either by conventional cloning techniques or by probing genomic or cDNA libraries with nucleic acid sequences according to the invention. This can be done by any conventional method, such as the methods of Sambrook et al (Molecular Cloning: A Laboratory Manual; 1989).
• a nucleic acid sequence according to the invention may be included within a vector, suitably a replicable vector, for instance a replicable expression vector.
• a replicable expression vector comprises an origin of replication so that the vector can be replicated in a host cell such as a bacterial host cell.
• a suitable vector will also typically comprise the following elements, usually in a 5' to 3' arrangement: a promoter for directing expression of the nucleic acid sequence and optionally a regulator of the promoter, a translational start codon and a nucleic acid sequence according to the invention encoding a polypeptide having one or more of the biological properties of Hie protein.
• a non-replicable vector lacks a suitable origin of replication whilst a non-expression vector lacks an effective promoter.
• the vector may also contain one or more selectable marker genes, for example an ampicillin resistance gene for the identification of bacterial transformants. Another possible marker gene is the kanamycin resistance gene.
• the vector may also comprise an enhancer for the promoter. If it is desired to express the nucleic acid sequence of the invention in a eucaryotic cell, the vector may also comprise a polyadenylation signal operably linked 3' to the nucleic acid encoding the functional protein. The vector may also comprise a transcriptionai terminator 3' to the sequence encoding the polypeptide of the invention.
• the vector may also comprise one or more non-coding sequences 3' to the sequence encoding the polypeptide of the invention. These may be from S. pneumoniae (the organism from which the sequences of the invention are derived) or the host organism, which is to be transformed with the vector or from another organism.
• the nucleic acid sequence of the invention is operably linked to a promoter capable of expressing the sequence.
• "Operably linked” refers to a juxtaposition wherein the promoter and the nucleic acid sequence encoding the polypeptide of the invention are in a relationship permitting the coding sequence to be expressed under the control of the promoter.
• there may be elements such as 5' non-coding sequence between the promoter and coding sequence. These elements may be native either to S. pneumoniae or to the organism from which the promoter sequence is derived or to neither organism. Such sequences can be included in the vector if they enhance or do not impair the correct control of the coding sequence by the promoter.
• the vector may be of any type.
• the vector may be in linear or circular form.
• the vector may be a plasmid vector.
• plasmid vector Those of skill in the art will be able to prepare suitable vectors comprising nucleic acid sequences encoding polypeptides of the invention starting with widely available vectors which will be modified by genetic engineering techniques such as those described by Sambrook et al (Molecular Cloning: A Laboratory Manual; 1989).
• Preferred starting vectors include plasmids that confer kanamycin resistance and direct expression of the polypeptide of the invention via a tac promoter.
• any promoter capable of directing expression of a sequence of the invention in a host cell may be operably linked to the nucleic acid sequence of the invention. Suitable promoters include the tac promoter.
• Such vectors may be used to transfect or transform a host cell. Depending on the type of vector, they may be used as cloning vectors to amplify DNA sequences according to the invention or to express this DNA in
• a further embodiment of the invention provides host cells harbouring vectors of the invention, i.e. cells transformed or transfected with vectors for the replication and/or expression of nucleic acid sequences according to the invention.
• the cells will be chosen to be compatible with the vector and may for example be bacterial cells.
• Transformed or transfected bacterial cells for example E. coli cells, will be particularly useful for amplifying nucleic acid sequences of the invention as well as for expressing them as polypeptides.
• the cells may be transformed or transfected by any suitable method, such as the methods described by Sambrook et al (Molecular cloning: A Laboratory Manual; 1989).
• vectors comprising nucleic acid sequences according to the invention may be packaged into infectious viral particles, such as retroviral particles.
• the constructs may also be introduced, for example, by electroporation, calcium phosphate precipitation, and biolistic methods or by contacting naked nucleic acid vectors with the cells in solution.
• the nucleic may be DNA or RNA, preferably DNA.
• the vectors with which the host cells are transformed or transfected may be of any suitable type.
• the vectors may be able to effect integration of nucleic acid sequences of the invention into the host cell genome or they may remain free in the cytoplasm.
• the vector used for transformation may be an expression vector as defined herein.
• the present invention also provides a process of producing polypeptides according to the invention. Such a process will typically comprise transforming or transfecting host cells with vectors comprising nucleic acid sequences according to the invention and expressing the nucleic acid sequence in these cells.
• the nucleic acid sequence will be operably linked to a promoter capable of directing its expression in the host cell.
• a promoter will be a "strong" promoter capable of achieving high levels of expression in the host cell. It may be desirable to overexpress the polypeptide according to the invention in the host cell.
• Suitable host cells for this purpose include yeast cells and bacterial cells, for example E. coli cells, a particularly preferred E. coli strain being E. coli K12 strain BL 21.
• expression systems can also be used, for example baculovirus systems in which the vector is a baculovirus having in its genome nucleic acid encoding a polypeptide of the invention and expression occurs when the baculovirus is allowed to infect insect cells.
• the thus produced polypeptide of the invention may he recovered by any suitable method known in the art.
• the thus recovered polypeptide may be purified by any suitable method, for example a method according to Sambrook et al (Molecular Cloning: A Laboratory Manual).
• polypeptides of the invention may also be synthesised chemically using standard techniques of peptide synthesis. For shorter polypeptides, chemical ' synthesis may be preferable to recombinant expression. In particular, peptides of up to 20 or up to 40 amino acid residues in length may desirably be synthesised chemically.
• the nucleic acid sequences of the invention may be used to prepare probes and primers. These will be useful, for example, in the isolation of genes having sequences similar to that of SEQ ID NO: 4.
• Such probes and primers may be of any suitable length, desirably from 10 to 100, for example from 10 to 20, 20 to 50 or 50 to 100 bases in length. Examples of such probes are disclosed herein as SEQ ID NO: 2 and SEQ ID NO: 3.
• Polynucleotides or primers of the invention may carry a revealing label.
• Suitable labels include radioisotopes such as 32 P or 35 S, enzyme labels or other protein labels such as biotin. Such labels may be added to polynucleotides or primers of the invention and may be detected using techniques known per se.
• Polynucleotides or primers of the invention or fragments thereof, labelled or unlabelled, may be used by a person skilled in the art in nucleic acid-based tests for detecting or sequencing protein Hie in a sample.
• Such tests for detecting generally comprise bringing a sample containing DNA or RNA into contact with a probe comprising a polynucleotide or primer of the invention under hybridizing conditions and detecting any duplex formed between the probe and nucleic acid in the sample.
• detection may be achieved using techniques such as PCR or by immobilizing the probe on a solid support, removing nucleic acid in the sample which is not hybridized to the probe, and then detecting nucleic acid which has hybridized to the probe.
• the sample nucleic acid may be immobilized on a solid support, and the amount of probe bound to such a support can be detected.
• the probes of the invention may conveniently be packaged in the form of a test kit in a suitable container.
• the probe may be bound to a solid support where the assay formats for which the kit is designed requires such binding.
• the kit may also contain suitable reagents for treating the sample to be probed, hybridizing s the probe to nucleic acid in the sample, control reagents, instructions, and the like.
• Polynucleotides of the invention can be incorporated into a recombinant replicable vector. The vector may be used to replicate the nucleic acid in a compatible host cell.
• the invention provides a method of making polynucleotides of the invention by introducing a polynucleotide of the invention into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which bring about replication of the vector.
• the vector may be recovered from the host cell. Suitable host cells are described in connection with expression vectors.
• the present invention also provides antibodies to the polypeptides of the invention. These antibodies may be monoclonal or polyclonal.
• antibody includes fragments of whole antibodies which retain their binding activity for a target antigen. Such fragments include Fv, F(ab') and F(ab') 2 fragments, as well as single chain antibodies.
• the antibodies may be produced by any method known in the art, such as the methods of Sambrook et al (Molecular Cloning: A Laboratory Manual; 1989). For example, they may be prepared by conventional hybridoma techniques or, in the case of modified antibodies or fragments, by recombinant DNA technology, for example by the expression in a suitable host vector of a DNA construct encoding the modified antibody or fragment operably linked to a promoter. Suitable host cells include bacterial (for example E. coli), yeast, insect and mammalian cells. Polyclonal antibodies may also be prepared by conventional means which comprise inoculating a host animal, for example a rat or a rabbit, with a peptide of the invention and recovering immune serum.
• compositions comprising polypeptides of the invention.
• Compositions comprising polypeptides of the invention that include T-cell and/or B-cell epitopes may be used as vaccines against infections caused by pneumococci.
• compositions of the invention may be administered to mammals including humans by any route appropriate. Suitable routes include topical application in the mouth, oral delivery by means of tablets or capsule and parenteral delivery, including subcutaneous, intramuscular, intravenous and intradermal delivery. Preferred routes of administration are injection, typically subcutaneous or intramuscular injection, with a view to effecting systemic immunisation.
• polypeptides according to the invention may also be mixed with other antigens of different immunogenicity.
• compositions of the invention may be administered to the subject alone or in a liposome or associated with other delivery molecules.
• the effective dosage depends on many factors, such as whether a delivery molecule is used, the route of delivery and the size of the mammal being vaccinated. Typical doses are from 0.1 to 100 mg of the polypeptide of the invention per dose, for example 0.1 to 1 mg, and 1 to 5 mg, 5 to 10 mg and 10 to 100 mg per dose. Doses of from 1 to 5 mg are preferred. Dosage schedules will vary according to, for example, the route of administration, the species of the recipient and the condition of the recipient. However, single doses and multiple doses spread over periods of days, weeks or months are envisaged.
• a regime for administering a vaccine composition of the invention to young human patients will conveniently be :6 months, 2 years, 5 years and 10 years, with the initial dose being accompanied by adjuvant and the subsequent doses being about 1/2 to 1/4 the level of polypeptide in the initial dose.
• the frequency of administration can, however, be determined by monitoring the antibody levels in the patient.
• polypeptides of the invention While it is possible for polypeptides of the invention to be administered alone it is preferable to present them as pharmaceutical formulations.
• the formulations of the present invention comprise at least one active ingredient, a polypeptide of the invention, together with one or more acceptable carriers thereof and optionally other therapeutic ingredients.
• the carrier or carriers must be "acceptable” in the sense of being compatible with the other ingredients of the formulation and not deleterious to the recipients thereof, for example, liposomes.
• the preparation of vaccines which contain an immunogenic polypeptide(s) as active ingredient(s), is known to one skilled in the art. Typically, such vaccines are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared.
• the preparation may also be emulsified, or the protein encapsulated in liposomes.
• the active immunogenic ingredients are often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof.
• the vaccine may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and/or adjuvants which enhance the effectiveness of the vaccine.
• adjuvants which may be effective include but are not limited to: aluminium hydroxide, N-acetyl-muramyl-L-threonyl-D-isoglutamin (thr-MDP), N- acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutamnyl-L-alanine-2-(r-2'-dipalmitoyl-sn- glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP 19835A, referred to as MTP- PE), and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trehalose dimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/Tween 80 emulsion.
• an adjuvant may be determined by measuring the amount of antibodies directed against an immunogenic polypeptide containing Hie antigenic sequence resulting from administration of this polypeptide in vaccines which are also comprised of the various adjuvants.
• the vaccines are conventionally administered parentally, by injection, for example, either subcutaneously or intramuscularly. Additional formulations which are suitable for other modes of administration include suppositories and, in some cases, oral formulations.
• suppositories traditional binders and carriers may include, for example, polyalkylene glycols or triglycerides; such suppositories may be formed from mixtures containing the active ingredient in the range of 0.5%> to 10%, preferably 1% to 2%>.
• Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccarine, cellulose, magnesium carbonate, and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders and contain 10%> to 95% of active ingredient, preferably 25%> to 70%.
• the vaccine composition is lyophilised, the lyophilised material may be reconstituted prior to administration, e.g. as a suspension. Reconstitution is preferably effected in buffer.
• Capsules, tablets and pills for oral administration to a patient may be provided with an enteric coating comprising, for example, Eudragit "S”, Eudragit "L”, cellulose acetate, cellulose acetate phthalate or hydroxypropylmethyl cellulose.
• the polypeptides of the invention may be formulated into the vaccine as neutral or salt forms.
• Pharmaceutically acceptable salts include the acid addition salts (formed with free amino groups of the peptide) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids such as acetic, oxalic, tartaric and maleic. Salts formed with the free carboxyl groups may also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine and procaine.
• Formulations suitable for parenteral administration include aqueous and non- aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostatis, bactericidal antibiotics and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents, and liposomes or other microparticulate systems which are designed to target the compound to blood components or one or more organs.
• sterile pyrogen-free aqueous and non-aqueous solutions are preferred.
• formulations in which the polypeptides of 5 the invention are contained in liposomes.
• Injection solutions and suspensions may be prepared extemporaneously from sterile powders, granules and tablets of the kind previously described.
• Oral methods of administration may produce a systemic effect.
• Orally active preparations can be formulated in any suitable carrier, such as a gel, toothpaste, 10 mouthwash or chewing gum. .
• formulations of this invention may include other agents conventional in the art having regard to the type of formulation in question.
• the present invention provides a method of vaccinating a 15 . mammalian host against infections caused by pneumococci or treating such infections, which method comprises administering to the host an effective amount of a pharmaceutical composition as described above, for example a vaccine composition.
• Antibodies including monoclonal antibodies, and fragments thereof such as 0 Fab fragments can be formulated for passive immunisation as indicated above for the formulation of including polypeptides of the invention.
• Preferred formulations for passive immunisation include solid or liquid formulations such as gels, toothpastes, mouth-washes or chewing gum.
• a further aspect of the present invention is a naked nucleic acid vaccine.
• the vaccine composition comprises a nucleic acid, typically an isolated nucleic acid, preferably DNA, rather than a polypeptide.
• the nucleic acid is injected in to a mammalian host and expressed in vivo, generating a polypeptide of the invention. This stimulates a T-cell response, which leads to protective immunity against Streptococcus pneumoniae, for example against dental caries, in the same 0 way as direct vaccination with a polypeptide of the invention.
• Nucleic acid vaccination can be carried out with any nucleic acid according to the invention as long as it encodes a polypeptide that stimulates a T-cell and or B- cell response.
• These nucleic acids will typically be included within an expression vectors as defined above.
• the nucleic acid according to the invention will typically be operably linked to a promoter capable of directing its expression in a mammalian host cell.
• a promoter capable of directing its expression in a mammalian host cell.
• promoters from viral genes that are expressed in the mammalian cells such as the cytomegalovirus (CMV) immediate early gene promoter are suitable.
• CMV cytomegalovirus
• promoters from mammalian genes that are expressed in many or all mammalian cell types such as the promoters of "housekeeping" genes.
• nucleic acid sequence according to the invention is incorporated into a plasmid vector, since it has been found that covalent closed circle (CCC) plasmid DNA can be taken up directly by muscle cells and expressed without being integrated into the cells' genomic DNA (Ascadi et al (1991): The New Biologist; 3, 71-81).
• Naked nucleic acid vaccine may be prepared as any of the types of formulation mentioned above in respect of conventional polypeptide-based vaccines.
• nucleic acid vaccines may be delivered in any of the ways mentioned above in respect of conventional polypeptide-based vaccines but intramuscular injection is preferred.
• nucleic acid vaccines may be provided suitable for administration by particle bombardment, or in formulations comprising liposomes or cationic lipid formulation such as lipofectin or other suitable carriers.
• the present invention provides a vaccine composition comprising a nucleic acid sequence or vector as described above and an acceptable carrier.
• Complement-dependent opsonophagocytosis is a crucial defense against infection with Streptococcus pneumoniae (33).
• Two recent studies discuss how type 3 pneumococci may subvert the normal function of the complement system.
• One study (14) showed that the alternative pathway of complement is essential for efficient clearance of bacteria, and that pneumococcal interference with complement activation is a virulence determinant. Based on comparisons of PspA-negative mutants with wild type bacteria the researchers claim that PspA blocks recruitment of the alternative pathway, by an unknown mechanism.
• Another study (15) describes the binding of complement factor H to trypsin-sensitive structures at the surface of pneumococci, independent of previous activation of complement. Notably, the study rules out any major contribution of PspA with respect to binding of fH.
• the findings indicate that factor H binding proteins might constitute an independent virulence factor.
• the present investigation describes a novel pneumococcal surface protein, responsible for the binding of fH in type 3 pneumococci.
• the gene encoding the protein (Hie) is found in the locus of pspC, a possible virulence determinant and protective antigen, but shows highly atypical characteristics compared to previously described pspC alleles.
• the type 3 strain was considered pspC-negative, since there was no protein reacting with PspC-antibodies and PCR experiments failed to amplify thspspC gene.
• Hie is similar to the M protein in S. pyogenes, also known to bind fH (11).
• a Hic-deficient mutant failed to absorb fH from human plasma, in contrast to the wild type strain. This mutant did not bind radiolabelled fH, indicating that most or all of the fH binding to PR218 bacteria is due to the presence of Hie at the pneumococcal surface.
• Hie By accumulating an active complement inhibitor at the pneumococcal surface, Hie may act alone or in concert with PspA to block deposition of C3b and concomitant opsonophagocytosis. As previously described, a putative C3 proteinase in types 3, 4 and 14 pneumococci (35) should have similar effects. The present observation that a region of Hie shows an intrinsic capacity to inhibit the alternative pathway further underlines the significance of this virulence mechanism. In conclusion, pneumococci appear highly prone to interfere with the complement system. Binding of fH, by different mechanisms, has also been described for group A streptococci (11), Y. enterocolitica (13), and N. gonorrhoeae (36,37) and may represent a widespread theme in bacterial adaptation to the human host.
• Bacteria used for binding assays were grown in Todd-Hewitt broth (Difco), supplemented with 0.2%> Yeast extract (Difco).
• Escherichia coli strain DH5 ⁇ was grown in Luria-Broth (Difco) or on LB -agar, supplemented with ampicillin (50 ⁇ g/ml) when containing pGEX.
• OHgonucleotides HICfl (5'-TGGGATCCCAGAGAAGGAGGTAAC TAC- 3', SEQ ID NO: 2) and HICrl (5'-GGAGCCTGAATTCGACGAAG-3 ⁇ SEQ ID NO: 3), containing Bam ⁇ l and EcoRI restriction sites respectively, were used in a polymerase chain reaction (PCR) to amplify DNA corresponding to amino acids 39 to 261 in Hie.
• the PCR was performed with Taq polymerase (Gibco BRL), and consisted of 30 cycles at 94°C for 1 min., 50°C for 1 min., and 72°C for 1 min., followed by a final extension at 72°C for 7 min.
• Template was prepared by resuspending bacterial colonies in water, boiling for 5 min., and removal of bacterial debris by centrifuging at 13000 x g.
• the PCR-amplified fragment was gel-purified with Sephaglas Bandprep (Pharmacia Biotech), digested with BamHI and Eco ⁇ I (Pharmacia Biotech) and ligated with likewise digested vector pGEX-5X-3 (Pharmacia Biotech) using T4 DNA ligase (Pharmacia Biotech). Plasmid pGEX-5X- 3:hic(39-261) was then electroporated into DH5 ⁇ E. coli according to the GST gene fusion system protocol (Pharmacia Biotech).
• Transformants were screened for presence of insert by plasmid mini-preps and restriction. enzyme digestion.
• the clone used for overexpression of the fusion protein GST:Hic 39"261 was verified by purifying the plasmid and sequencing the complete insert. Fusion protein was affinity purified according to the instructions in the GST gene fusion system manual (Pharmacia Biotech).
• Plasma absorption experiments were performed with log-phase pneumococci (OD 60 o appr. 0.4). Bacteria were washed twice in PBS, pH 7.4, containing 0.05 % Tween 20 (PBST), and the bacterial concentration was adjusted to 2 x 10 10 cells/ml. 100 ⁇ l of bacteria were incubated for 1 h with 100 ⁇ l of human plasma. Bacteria were washed five times with PBST, and bound proteins were eluted from the cells with 100 ⁇ l 0.1 M glycine/HCl, pH 2.0. The pH of the eluted material was adjusted to appr. 7 with 1 M Tris. C3 -deficient serum was obtained from a patient with selective complete C3 deficiency (C3 ⁇ 1 mg/liter), kindly provided by Dr. G. Eggertsen, Huddinge Hospital, Sweden.
• C3 -deficient serum was obtained from a patient with selective complete C3 deficiency (C3 ⁇ 1 mg/liter), kindly provided by Dr
• Protein samples were separated by SDS-PAGE (20) containing 8-12%) acrylamide. Proteins were blotted onto an Immobilon-PTM PVDF-membrane (Millipore) as described (21). Rabbit polyclonal antiserum against fH diluted 1 :1000 was the source of primary antibodies. Horseradish peroxidase-conjugated anti-rabbit goat antibodies (Bio-Rad, Bio-Rad Laboratories, CA) were used as secondary antibodies, and detection of immuno-reactive bands was performed by c emiluminescence as described (22).
• the membrane was washed for 4 x 20 min. in PBST, 0.5 M NaCl, and membrane-associated radioactivity was visualized by exposure onto a phosphoimaging plate (Fuji Photo Film). Western blot membranes were treated in the same way. Binding assays with pneumococci were performed as described (23), using log-phase bacteria (OD 60 o appr. 0.4).
• Final incubation mixtures contained C2-deficient serum diluted 1/12 (200 ⁇ l) with or without additional proteins (fH, GST, or GST:Hic 39"261 , at 30, 90 or 60 ⁇ M, respectively) and 2.5 x 10 7 rabbit erythrocytes (50 ⁇ l). The erythrocytes were added 5 min after the other reagents. After 5-40 min reactions were stopped by the addition of 750 ⁇ l cold VBS, 10 mM EDTA. Samples were centrifuged at 3000 rpm for 5 min., and the supernatants were removed for measurement of light absorbance at 412 nm.
• Encapsulated strains generally bound somewhat less than the corresponding unencapsulated strains.
• binding of fH to strain PR218 was examined following treatment of bacteria with different proteases (data not shown). Binding was almost completely abolished by pretreatment with papain. Trypsin also caused a major decrease, whereas pepsin had a moderate effect ( ⁇ 50%> decrease).
• Previously described bacterial surface proteins known to interact with fH include streptococcal M proteins (11) and YadA (13) from Y. enterocolitica. Nucleotide and amino acid sequences of YadA, Ml, M 1.1 (26), M6 (27), and the M- like protein H (28), were used to search a pneumococcal (type 4 strain JNR. 7/87) genome database obtained from The Institute for Genomic Research (http://www.tigr.org).
• the highest scoring homology for all the probes was found in a 2106 bp open reading frame (ORF), encoding a putative protein of 702 amino acids (aa).
• ORF open reading frame
• the degree of homology between the pneumococcal protein and the. fH-binding proteins used for searching was low, but significant, when comparing the full sequences. However, there were several limited regions of markedly higher homology.
• a GENB ANK search with this putative protein identified it as an allele of PspC, also denoted SpsA, CbpA,- or PbcA (16). PspC was then conversely used to search the Streptococcus pyogenes genome sequencing project, and the highest scoring match was found to encode the Ml protein.
• the locus contained a 1836 bp ORF, encoding a putative protein of 612 aa.
• the gene was tentatively named hie, for factor H binding inhibitor of complement (GenBank accession number AF252857).
• the Hie protein (schematically depicted in fig. 1, top) contains a proline-rich region consisting of 22 repeats of 11 amino acids.
• SpsA2, CbpA, and PbcA together form the D39-lineage of PspC alleles (16).
• Hie Fig. 1, bottom
• the PspC proteins contain a series of repeats with choline- binding motifs, a different mechanism for surface attachment.
• Computer predictions (31,32) of the secondary structure resulted in strong predictions of ⁇ -helical structure in the NH 2 -terminal region of both Hie (aa 40 - 270) and PspC (aa 50 - 250).
• the unencapsulated strain PR218 (serotype 3), showing the most pronounced absorption of fH from human plasma, was chosen for further studies.
• Splicing by overlap extension (gene SOEing) (19) was used to flank an antibioticum resistance cassette with sequences found up- and downstream of the hie gene.
• PR218 was transformed with this construct and the hie gene was deleted by double cross-over mutagenesis.
• the resulting strain, FP13 grew as well as the parent strain in ordinary growth media. The deletion of hie was confirmed by PCR experiments.
• the mutant strain was subjected to plasma absorption experiments identical to those described above.
• the hie region encoding the NH 2 -terminal part of Hie (aa 39 - 261) was cloned into the vector pGEX, resulting in a fusion with the gene encoding GST.
• Control sequencing of the insert verified the presence of the partial hie gene, showing 100 % identity with the DNA sequence from strain A66.
• GST:Hic 39"251 and GST were overexpressed, affinity purified, and analysed by SDS-PAGE. Although partly degraded, the main protein band had the expected mass (54 kDa).

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