Patent Application
20150273042
The invention provides methods of forming pili in vitro and mutant sortase enzymes and proteins suitable for use in these methods. The invention also provides pili produced by these methods and compositions comprising these pili for the treatment and prevention of bacterial disease, in particular of conditions caused by Streptococcus. The invention also provides general methods of ligating proteins and sortase enzymes for use in same.
Most bacterial pathogens comprise pili (also known as fimbrae), long filamentous structures extending from their surface, that are often responsible for initial adhesion of bacteria to tissues during host colonization. Gram-negative bacteria have been known for many years to have pili, typically formed by non-covalent interactions between pilin subunits. More recently, Gram-positive bacteria, including Streptococcus bacteria, have also been shown to have pili typically formed through covalent association of subunits by sortases that are encoded by pilus-specific pathogenicity islands.
The Gram-positive bacterium Streptococcus agalactiae (or “group B streptococcus”, abbreviated to “GBS”), for example, has three pilus variants, each encoded by a distinct pathogenicity island, PI-1, PI-2a or PI-2b [1, 2]. Each pathogenicity island consists of: i) genes encoding the three structural components of the pilus (the pilus backbone protein (BP) and 2 ancillary proteins (AP1 and AP2)); and ii) genes encoding 2 sortase proteins (SrtC1 and SrtC2) that are involved in the assembly of the pilus. All GBS strains carry at least one of these 3 pathogenicity islands.
Similar pathogenicity islands are present in other Gram-positive bacteria including Streptococcus pyogenes or “group A streptococcus”, abbreviated to “GAS”), and Streptococcus pneumoniae (also known as pneumococcus). The pathogenicity island in pneumococcus encodes the 3 structural components of the pilus (RrgA, RrgB and RrgC) and three sortases (SrtC1, SrtC2 and SrtC3) which catalyse pilus formation. In GAS, the FCT regions encode the backbone and accessory proteins and polymerisation of these proteins is also mediated by a sortase (SACT).
Pilus structures in these Gram-positive bacteria are considered to be interesting vaccine candidates and work has been done on assessing the immunogenicity of purified recombinant proteins from pilus structures. It is also desirable to study these proteins in their native form within assembled pili but currently, the only way to do this is by the laborious process of purifying wild-type pili from the bacteria. One object of the invention is therefore to provide a process for producing recombinant pili in vitro without the need to purify wild-type pili.
The streptococcal bacteria discussed above are associated with serious disease. GBS causes bacteremia and meningitis in immunocompromised individuals and in neonates. GAS is a frequent human pathogen, estimated to be present in between 5-15% of normal individuals without signs of disease. When host defences are compromised or when GAS is introduced to vulnerable tissues or hosts, however, an acute infection occurs. Diseases caused by GAS include puerperal fever, scarlet fever, erysipelas, pharyngitis, impetigo, necrotising fasciitis, myositis and streptococcal toxic shock syndrome. Pneumococcus is the most common cause of acute bacterial meningitis in adults and in children over 5 years of age
Investigations have been conducted into the development of protein-based vaccines against these Streptococcal bacteria but currently, no protein-based vaccines are commercially available. There therefore remains a need for effective vaccines against Streptococcal infection. It is a further object of the invention to provide immunogenic compositions which can be used in the development of vaccines against streptococcal infection.
In a first aspect the invention provides a method of ligating at least two moieties comprising contacting the at least two moieties with a pilus-related sortase C enzyme in vitro under conditions suitable for a sortase mediated transpeptidation reaction to occur, wherein the pilus-related sortase C enzyme comprises an exposed active site.
Particularly the pilus-related sortase C enzyme is from Streptococcus, more particularly from Streptococcus agalactiae (GBS), Streptococcus pneumonia (pneumococcus) and Streptococcus pyogenes (GAS). Yet more particularly the pilus-related sortase C enzyme is a sortase C1 enzyme (srtC1), sortase C2 enzyme (SrtC2) or a sortase C3 enzyme (SrtC3).
In certain embodiments the pilus-related sortase C enzyme mutation comprises a deletion of part or all of the lid. Particularly the mutation comprises a deletion of the amino acids at positions 84, 85 and/or 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3), or the deletion of amino acids at corresponding positions in the amino acid sequence of another pilus-related sortase C enzyme.
In other embodiments the mutation comprises substitution of the amino acids at positions 84, 85 and/or 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3), or the substitution of amino acids at corresponding positions in the amino acid sequence of another sortase C enzyme.
Particularly the pilus-related sortase C enzyme comprises or consists of an amino acid sequence selected from the group consisting of SEQ ID NO: 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70 and 71.
In one embodiment of the invention, the method is a method of forming a recombinant or artificial pilus in vitro. This, the at least two moieties comprise an LPxTG motif and a pilin motif. For example, the pilin motif may comprise the amino acids YPAN. ‘X’ in any sortase recognition motif disclosed herein may be any standard or non-standard amino acid and every variation is disclosed. In some embodiments, X is selected from the 20 standard amino acids found most commonly in proteins found in living organisms. Where the recognition motif is LPXTG or LPXT, X may be D, E, A, N, Q, K, or R. In particular, X is selected from K, S, E, L, A, N in an LPXTG or LPXT motif.
Particularly the at least two moieties are from Gram-positive bacteria. The at least two moieties may be from the same strain or type of Gram-positive bacteria or from different strains or types of Gram positive bacteria. Yet more particularly, the at least two moieties are Streptococcal polypeptides. Still yet more particularly, the at least two moieties are Streptococcal backbone proteins and/or ancillary proteins.
For example, the at least two moieties comprise or consist of an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to a polypeptide having the amino acid sequence of any one of SEQ ID NOs: 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, or 97; or (b) that is a fragment of at least ‘n’ consecutive amino acids of one of these sequences wherein ‘n’ is 20 or more (e.g. 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150 or more; e.g. 20 or more; or e.g. 50 or more; or e.g. 80 or more).
In other aspects of the invention, there is provided an artificial or recombinant pilus obtained or obtainable from the aforementioned method. In one embodiment there is provided an artificial or recombinant pilus which comprises at least two variants of backbone protein GBS59. Particularly the at least two variants are selected from Group B Streptococcus strains 2603, H36B, 515, CJB111, CJB110 and DK21. Yet more particularly, the artificial or recombinant pilus is a chimeric pilus comprising at least one variant of GBS backbone protein GBS59 selected from Streptococcus strains 2603, H36B, 515, CJB111, CJB110 and DK21 and at least one backbone protein from Streptococcus pneumonia selected from the group consisting of RrgA, RrgB and RrgC. In other embodiments artificial or recombinant pili further comprise GBS80 and/or GBS1523.
In particular aspects of the invention, the artificial or recombinant pilus is for use in medicine, yet more particularly for use in preventing or treating Streptococcal infection. Thus, in another embodiment there is provided a method of treating or preventing Streptococcal infection in a patient in need thereof comprising administering an effective amount of an artificial or recombinant pilus formed by the methods of the invention to a patient.
In a second aspect of the invention, there is provided a method wherein the at least two moieties comprise a first moiety comprising the amino acid motif LPXTG, wherein X is any amino acid, and a second moiety comprising at least one amino acid.
Particularly the first moiety is a first polypeptide and the second moiety is a second polypeptide. In certain embodiments, the first polypeptide and the second polypeptide are from Gram-positive bacteria. For example, the first polypeptide and the second polypeptide may be from the same type or strain of Gram-positive bacteria or from different types or strains of Gram positive bacteria. In some embodiments, the first polypeptide and the second polypeptide are Streptococcal polypeptides. For example, the first polypeptide and the second polypeptide may be Streptococcal backbone proteins and/or ancillary proteins.
In some embodiments of the invention, either the first moiety or the second moiety comprises a detectable label. By way of non-limiting example, the detectable label may be a fluorescent label, a radiolabel, a chemiluminescent label, a phosphorescent label, a biotin label, or a streptavidin label. In some embodiments, the first moiety or the second moiety may be a polypeptide and the other moiety may be a protein or glycoprotein on the surface of a cell. In yet further embodiments, either the first moiety or the second moiety is a polypeptide and the other moiety comprises amino acids conjugated to a solid support. In still yet further embodiments, either the first moiety or the second moiety is a polypeptide and the other moiety comprises at least one amino acid conjugated to a polynucleotide.
The method of the invention may be used to ligate the N-terminus of a first moiety to the N-terminus of a second moiety. The method of the invention may be used to ligate the C-terminus of a first moiety to the C-terminus of a second moiety. Alternatively, the first moiety and the second moiety are the N-terminus and C-terminus of a moiety such as a polypeptide chain, and ligation results in the formation of a circular polypeptide. Thus, there is provided conjugate obtained or obtainable from the method described herein.
In other aspects of the invention, there is provided a kit comprising a sortase C1 or a sortase C2 enzyme from Streptococcus agalactiae and a moiety comprising the amino acid motif LPXTG, wherein X is any amino acid.
In another aspect of the invention, there is provided a sortase C enzyme from Streptococcus comprising a mutation in its lid region, particularly a sortase C enzyme from Streptococcus which is from Streptococcus agalactiae (GBS), Streptococcus pneumonia (pneumococcus) or Streptococcus pyogenes (GAS). Yet more particularly a sortase C enzyme from Streptococcus wherein the sortase C enzyme from Streptococcus is a sortase C1 enzyme, sortase C2 enzyme or a sortase C3 enzyme. In certain embodiments, there is provided a sortase C enzyme from Streptococcus wherein the mutation comprises deletion of part or all of the lid region of the sortase C enzyme. Particularly the mutation comprises deletion of the amino acids at positions 84, 85 and/or 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3), or the deletion of amino acids at corresponding positions in the amino acid sequence of another sortase C enzyme. In other embodiments there is provided a sortase C enzyme from Streptococcus wherein the mutation comprises substitution of the amino acids at positions 84, 85 and/or 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3), or the substitution of amino acids at corresponding positions in the amino acid sequence of another sortase C enzyme
Particularly there is provided a sortase C enzyme from Streptococcus which comprises a mutation in its lid region and wherein the sortase C enzyme comprises or consists of an amino acid sequence selected from SEQ ID NO: 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70 or 71.
Structural studies of pilus-related C-sortases in gram positive bacteria have demonstrated that the active site of many of these enzymes contains a catalytic triad of amino acids that are covered by a mobile “lid” region in the absence of substrate. Thus, a feature of pilus-related sortases is the presence of a lid that not only blocks active site access, i.e. it encapsulates the active site, but also carries two key residues, generally an Asp and a hydrophobic amino acid, that interact within the catalytic cleft itself, serving as ‘anchors’. Generally sequences corresponding to lid regions can be identified in all pilus-related sortases characterized to date. In particular, this lid structure has been demonstrated to be present in the sortase C1 enzymes from GBS PI-1, PI-2a and PI-2b [3], in the sortase C1, sortase C2 and sortase C3 enzymes from Streptococcus pneumoniae [4, 5], and in the sortase C1 enzyme from GAS. Mutation of the lid region in the sortase C1 enzyme from GBS PI-2a has been shown not to have an adverse impact on pilus production in complementation studies [3] but until now, no studies have been conducted into the ability of mutant sortases to polymerise proteins in vitro.
The inventors have now found that sortase C enzymes are capable of polymerising proteins in vitro more effectively than wild-type sortase C enzyme, for example, resulting in the production of recombinant pili. Wild type sortase C enzyme comprise a “mobile lid” region encapsulating the active site in a closed conformation in the absence of substrate. For example, the lid of SrtC1 harbors 3 residues, Asp84, Pro85, and Tyr86 which make interactions with residues of the active site and surroundings. Thus, sortase C enzymes are inactive in vitro and unable to ligate or polymerise moieties such as pilin backbone and ancillary proteins. The inventors have now discovered that by mutating the lid region, the catalytic site can be exposed rendering these mutated enzymes active in vitro. As discussed below, and surprisingly, these mutated enzymes are more active than their wild-type counterparts and yet more surprisingly are capable of recognising a broader range of amino acids. Particularly, mutated enzymes of the invention possess or comprise an exposed catalytic site which is not encapsulated by a “lid” and is available to catalyze a transpeptidation reaction to form an acyl enzyme intermediate in vitro.
The methods of the invention can thus be used to produce artificial or recombinant pili without the need for the labourious purification procedures currently used. Surprisingly, these mutant sortase C enzymes can also be used to polymerise proteins from a variety of sources such as gram positive bacteria, not just proteins derived from the same bacteria as the mutant sortase C enzyme itself. Furthermore, the pili resulting from these methods are immunogenic and may be used in the development of vaccines to treat or prevent diseases caused by the gram positive bacteria from which the component proteins of the pili are derived.
Some pilin subunits within the pilus contain intra-protein isopeptide bonds that form spontaneously, presumably stabilizing the structure of the pilus. Thus, in the context of vaccines, immunisation of a subject with proteins in the form of an artificial or recombinant pilus structure mimicking those encountered by the immune system during invasion/infection may also have advantages in terms of the presence of additional epitopes, such as structural or conformational epitopes based on three-dimensional structure. Such structural or conformational epitopes may be absent from subunit vaccines when the pilus proteins are provided in compositions comprising the isolated, purified forms or as conjugates, such as glycoconjugates. Thus, the polymerised pili proteins may comprise three-dimensional epitopes not predictable from the structure of the proteins alone.
Mutant Sortase C Enzymes
The mutant sortase C enzyme used in the methods of the invention is derived from a wild-type sortase C enzyme from Streptococcus. The mutant sortase C enzyme may, for example, be derived from a wild-type sortase C enzyme from Streptococcus agalactiae (GBS), Streptococcus pneumonia (pneumococcus) or Streptococcus pyogenes (GAS). The mutant sortase C enzyme may be derived from a sortase C1 enzyme, a sortase C2 enzyme or a sortase C3 enzyme. The mutant sortase C enzyme is derived from a wild-type streptococcal sortase C enzyme that comprises a lid region. The lid region is the structural loop of about 15-18 amino acids that covers the catalytic triad of amino acids found in the active site of a sortase C enzyme in the absence of a substrate. The lid region is located within the soluble core domain of the sortase C enzyme, between the signal peptide and transmembrane (TM) region located at the N-terminal of the enzyme and the positively charged domain located at the C-terminal of the enzyme. The location of the lid region in a variety of wild-type Streptococcal sortase C enzymes is summarised in the table below. These sequences are all wild-type sequences which include the N-terminal signal peptide.
Pneumococcus sortase C1
Pneumococcus sortase C2
Pneumococcus sortase C3
The location of the lid region in other Streptococcal sortase C enzymes can readily be determined by the skilled person by structural analysis or more simply, by alignment of the sequences of these enzyme with the sequences of the Streptococcal proteins having lid regions at known locations shown in Table 1.
The sortase C enzyme from Streptococcus used in the methods of the invention comprises a mutation in its lid region. The mutation may be a substitution, deletion or insertion in the amino acid sequence of the lid region of the mutant sortase C-enzyme relative to the amino acid sequence of the wild-type sortase C enzyme.
Deletion Mutants
Where the mutation is a deletion, the mutation may comprise deletion of part or all of the lid region of the wild-type sortase C enzyme. The lid region is typically around 15-18 amino acids long and the mutation may comprise deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 or more amino acids from the lid region, or deletion of all of the amino acids in the lid region.
The mutation may comprise deletion of amino acids at positions predicted to interact with the catalytic triad in the active site of the sortase C enzyme. For example, the mutation may comprise the deletion of amino acids at positions 84, 85 and/or 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3), or the deletion of amino acids at corresponding positions in the amino acid sequence of other sortase C enzymes. The mutation may thus comprise the deletion of: i) an amino acid at position 84; ii) an amino acid at position 85; iii) an amino acid at position 86; iv) two amino acids at positions 84 and 85; v) two amino acids at positions 84 and 86; vi) two amino acids at positions 85 and 86; or vii) three amino acids at positions 84, 85 and 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3), or the deletion of amino acids at corresponding positions in the amino acid sequence of another sortase C enzyme. Amino acids at positions corresponding to positions 84, 85 and 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3) can readily be determined by alignment.
Amino acids at positions corresponding to positions 84, 85 and 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3) are found at:
Alternatively, the mutation may comprise the deletion of all of amino acids in the lid region. The deletion may comprise further changes at positions within the remaining sortase sequence. For example, the sortase may comprise substitutions, deletions or insertions at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more additional amino acid positions. By way of further example, the sortase may comprise substitutions, deletions or insertions at fewer than, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 additional amino acid positions or any range therebetween.
In particular, the mutation may additionally comprise deletion of part or all of the signal peptide and/or transmembrane domain of the wild-type sortase C enzyme which is N-terminal of the lid region in the wild-type enzyme. The transmembrane domain comprises two alpha-helices. The mutation may comprise deletion of one or both of these two alpha-helices and, optionally, may also comprise deletion of the signal peptide N-terminal of the transmembrane domain. For example, the mutation may comprise deletion of part or all of the lid region and the deletion of 10, 20, 30, 40, 50, 60, 70, 80, 90 or more amino acids N-terminal of the lid region. By way of further example, the mutation may comprise deletion of part or all of the lid region and the deletion of less than 10, 20, 30, 40, 50, 60, 70, 80, 90 amino acids N-terminal of the lid region or any range therebetween. In some embodiments, the mutation comprises the deletion of all of amino acids in the lid region and all of amino acids N-terminal of the lid region. The sortase C enzyme in this embodiment of the invention thus consists of the C-terminal/positively charged domain of the wild-type sortase C enzyme.
The mutation may consist of the deletions described above in the absence of any further mutations. For example, the mutation may consist of deletion of part or all of the lid region, deletion of part or all of the lid region and the signal peptide and/or transmembrane domain, or deletion of part or all of the lid region and the entre N-terminal region in the absence of any further mutations. Examples of sequences of sortase C enzymes where the mutation consists of a) deletion of all of the lid region and the signal peptide/transmembrane domain, b) deletion of all of the lid region and the entire N-terminal regions, and c) deletion of the signal peptide/transmembrane domain and amino acids in the catalytic triad which are suitable for use in the methods of the invention are provided in Table 2 below.
Pneumococcus sortase C1
Pneumococcus sortase C2
Pneumococcus sortase C3
Mutant sortase enzymes used in the methods of the invention may thus comprise or consist of an amino acid sequence selected from SEQ ID NO: 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36. Mutant sortase enzymes used in the methods of the invention may also comprise or consist of an amino acid sequence selected from SEQ ID NO: 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36 except for the substitution, deletion or insertion of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids.
Substitution Mutants
The mutation may comprise one or more amino acid substitutions in the lid region compared to the wild-type sortase C enzyme sequence. The substitution(s) may be at positions in the lid region predicted to interact with amino acids in the catalytic site such that the substitutions abolish normal lid function. The mutation may comprise the substitution of amino acids at positions 84, 85 and/or 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3), or the substitution deletion of amino acids at corresponding positions in the amino acid sequence of other sortase C enzymes. The mutation may thus comprise the substitution of: i) an amino acid at position 84; ii) an amino acid at position 85; iii) an amino acid at position 86; iv) two amino acids at positions 84 and 85; v) two amino acids at positions 84 and 86; vi) two amino acids at positions 85 and 86; or vii) three amino acids at positions 84, 85 and 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3), or the substitution of amino acids at corresponding positions in the amino acid sequence of another sortase C enzyme. Amino acids at positions corresponding to positions 84, 85 and 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3) can readily be determined by alignment.
Amino acids at positions corresponding to positions 84, 85 and 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3) are found at:
The substitutions at positions corresponding to position 84 and/or position 85 and/or position 86 may comprise replacement of the wild-type residue at these positions with an alanine residue.
Where the sortase is GBS sortase C1 of PI-1 (SEQ ID NO:1), the mutation may comprise replacement of the aspartate residue at position 90 with an alanine residue (D90A) and/or replacement of the proline residue at position 91 with an alanine residue (P91A), and/or replacement of the tyrosine residue at position 92 with an alanine residue (Y92A).
Where the sortase is GBS sortase C2 of PI-1 (SEQ ID NO:2), the mutation may comprise replacement of the aspartate residue at position 84 with an alanine residue (D84A) and/or replacement of the proline residue at position 85 with an alanine residue (P85A), and/or replacement of the phenylalanine residue at position 86 with an alanine residue (F86A).
Where the sortase is GBS sortase C1 of PI-2a (SEQ ID NO:3), the mutation may comprise replacement of the aspartate residue at position 84 with an alanine residue (D84A) and/or replacement of the proline residue at position 85 with an alanine residue (P85A), and/or replacement of the tyrosine residue at position 86 with an alanine residue (Y86A).
Where the sortase is GBS sortase C2 of PI-2a (SEQ ID NO:4), the mutation may comprise replacement of the aspartate residue at position 88 with an alanine residue (D88A) and/or replacement of the proline residue at position 89 with an alanine residue (P89A), and/or replacement of the tyrosine residue at position 90 with an alanine residue (Y90A).
Where the sortase is GBS sortase C1 of PI-2b (SEQ ID NO:5), the mutation may comprise replacement of the methionine residue at position 53 with an alanine residue (M53A) and/or replacement of the lysine residue at position 54 with an alanine residue (K54A), and/or replacement of the tryptophan residue at position 55 with an alanine residue (W55A).
Where the sortase is pneumococcal sortase C1 (SEQ ID NO:6), the mutation may comprise replacement of the aspartate residue at position 58 with an alanine residue (D58A) and/or replacement of the proline residue at position 59 with an alanine residue (P59A), and/or replacement of the tryptophan residue at position 60 with an alanine residue (W55A).
Where the sortase is pneumococcal sortase C2 (SEQ ID NO:7), the mutation may comprise replacement of the aspartate residue at position 50 with an alanine residue (D50A) and/or replacement of the proline residue at position 51 with an alanine residue (P51A), and/or replacement of the phenylalanine residue at position 52 with an alanine residue (F52A).
Where the sortase is pneumococcal sortase C2 (SEQ ID NO:8), the mutation may comprise replacement of the aspartate residue at position 74 with an alanine residue (D74A) and/or replacement of the proline residue at position 75 with an alanine residue (P75A), and/or replacement of the phenylalanine residue at position 76 with an alanine residue (F76A).
Where the sortase is GAS sortase C1 (SEQ ID NO:9), the mutation may comprise replacement of the aspartate residue at position 46 with an alanine residue (D46A) and/or and/or replacement of the phenylalanine residue at position 48 with an alanine residue (F48A). The GAS sortase C1 enzyme already comprises an alanine residue at position 47.
The mutation may comprise further amino acid changes at positions other than at positions corresponding to positions 84 and/or 85 and/or 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3). For example, the mutation may comprise substitutions at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more additional amino acid positions. Alternatively or in addition to these further substitutions, the mutation may comprise deletions and/or insertions. In particular, the mutation may comprise substitutions at positions corresponding to positions 84 and/or 85 and/or 86 of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3) and deletion of a) the signal peptide and/or transmembrane domain, or b) deletion of the entire N-terminal region of the wild-type sortase enzyme.
The sortase may consist of substitutions at positions 84 and/or 85 and/or 86 in the absence of any further mutations. Examples of sequences of sortase C enzymes consisting of substitutions at positions that are equivalent to positions 84 and/or 86 of the lid region of the amino acid sequence of the GBS sortase C1 enzyme of PI-2a (SEQ ID NO:3) and also consisting of deletion of the signal peptide/transmembrane region which are suitable for use in the methods of the invention are provided in Table 3 below.
Pneumococcus
Pneumococcus
Pneumococcus
Mutant sortase enzymes used in the methods of the invention may thus comprise or consist of an amino acid sequence selected from SEQ ID NO: 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70 or 71. Mutant sortase enzymes used in the methods of the invention may also comprise or consist of an amino acid sequence selected from SEQ ID NO:37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70 or 71 except for the substitution, deletion or insertion of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids.
The mutant sortase C enzymes suitable for use in the methods of the invention described above are also embodiments of the invention in their own right. Particularly sortase mutants are the SrtC1Y92A and SrtC2F86A because the stability of these enzymes is higher, they are better expressed and more soluble in comparison with, for example SrtC1-ΔNT and SrtC2-ΔNT deletion mutants. This is surprising since the Vmax of the cleavage reaction for the Y92A and F86A mutants was lower than that of the SrtC1-ΔNT and SrtC2-ΔNT mutants which are also more difficult to purify.
Sortase Action
Sortases cleave the LPXTG motif of, for example, pilin proteins and covalently join the C terminus of one moiety, such as a pilin subunit, to a Lys side-chain NH2 group on the next moiety or subunit. Two recognition events are involved in this sortase action. Firstly, the sortase recognition motif (LPXTG or a variant) of the substrate protein must be recognised and bound. Secondly, the acceptor substrate, to which the substrate protein will be transferred, must be recognised and bound, and a specific amino group brought into position to attack the thioacyl intermediate.
Bacterial Polypeptides Polymerised by the Mutant Sortase C Enzymes
The mutant sortase C enzymes described above may be used to polymerise one or more polypeptides. The mutant sortase C enzymes are brought into contact with the one or more polypeptides in vitro and following a period of incubation, polymerised polypeptides are detected, for example by identifying a pattern of high molecular weight bands on SDS gels. Incubation may be carried out at 37° C. Incubation may be carried out for 1, 2, 3, 4, 5, 6, 7 days or more. The polypeptides and the mutant sortase C enzymes may be incubated in the presence of a reducing agent, for example DTT 1 mM, to keep the catalytic cysteine of the mutant sortase C enzyme active. Incubation may be carried out at around pH 7-8.
In contrast to the mutant sortase C enzymes of the invention, the wild-type sortase C enzymes fail to polymerise polypeptides in vitro. For the avoidance of doubt, use of the term “in vitro” refers to the use of isolated and/or purified components of a cell, such as an enzyme, to effect pilus polymerisation without requiring the presence of the cell itself.
The polypeptides polymerised by the mutant sortase C enzymes of the invention typically comprise the LPxTG motif. They may further comprise a pilin motif (consensus WxxxVxVyPK) and/or an E-Box motif (consensus YxLxETxAPxGY) shown to be important for pilus assembly [6]. In particular, the polypeptides may comprise a conserved lysine (K) residues, for example, found in the pilin motif. In other embodiments the polypeptides do not comprise a conserved lysine (K) residue in the pilin motif, i.e. wherein the presence of the conserved lysine residue is excluded. In some embodiments, the polypeptides polymerised by the mutant sortase C enzymes of the invention may comprise an N-terminal glycine residue. Other sequence motifs will be apparent to one skilled in the art and may include, by way of non-limiting example: LPETGG, LPXT, LPXTG, LPKTG, LPATG, LPNTG, IPQTG, IQTGGIGT.
Examples of polypeptides that may be polymerised by the mutant sortase C enzymes of the invention include polypeptides from Gram-positive bacteria, such as the backbone proteins and ancillary proteins that are found in the pili of Gram-positive bacteria. In particular, the mutant sortase C enzyme may be brought into contact with a backbone protein found in a pilus from GBS, GAS or Streptococcus pneumoniae. For example, the mutant sortase C enzyme may be brought into contact with the backbone protein from GBS PI-1 (GBS80/SAG0645), the backbone protein from GBS PI-2a (GBS59/SAG1407), the backbone protein from GBS PI-2b (Spb1/SAN1518), the backbone protein from Streptococcus pneumoniae (RrgB), or the backbone protein from GAS (fee6, spy128, orf80, eftLSLA).
Alternatively or in addition, the mutant sortase C enzyme may be brought into contact with an ancillary protein found in a pilus from GBS, GAS or Streptococcus pneumoniae. For example, the mutant sortase C enzyme may be brought into contact with the ancillary protein 1 (AP-1) from GBS PI-1 (GBS104), the AP-1 from GBS PI-2a (GBS67/SAG1408), the AP-1 from GBS PI-2b (SAN1519), the AP-1 from Streptococcus pneumoniae (RrgA) or the AP-1 from GAS (cpa), the ancillary protein 2 (AP-2) from GBS PI-1 (GBS52), the AP-2 from GBS PI-2a (GBS150/SAG1404), the AP-2 from GBS PI-2b (SAN1516), the AP-2 from Streptococcus pneumoniae (RrgC) or the AP-2 from GAS spy130, orf82, orf2).
The mutant sortase C enzymes of the invention may be used to polymerise homologues, fragments or variants of the wild-type backbone protein and ancillary protein sequences, provided that these homologues, fragments and variants retain the sequences described above necessary for polymerisation by mutant sortase C enzymes. For example, variants of these polypeptides that may be used in the methods of the invention include backbone proteins and/or ancillary protein sequences from which the transmembrane domain has been deleted compared to the wild-type sequence. In addition or instead of the deletion of the transmembrane domain, variants may comprise the additional of a glycine residue at the N-terminal to promote polymerisation.
By way of non-limiting example, the sequences some of these polypeptides which may be polymerised by the mutant sortase enzymes of the invention are provided below for reference. The sequences of additional polypeptides which may be polymerised by the mutant sortases of the invention can be readily determined by the skilled person. Further details of these polypeptides are provided in reference [7].
BP from PI-1 (GBS80)
The amino acid sequence of full length GBS80 as found in the 2603 strain is given as SEQ ID NO: 72 herein. Wild-type GBS80 contains a N-terminal leader or signal sequence region at amino acids 1-37 of SEQ ID NO:72. One or more amino acids from the leader or signal sequence region of GBS80 can be removed, e.g. SEQ ID NO:73.
BP from PI-2b (GBS1523/SAN1518)
The original ‘GBS1523’ (SAN1518; Spb1) sequence was annotated as a cell wall surface anchor family protein (see GI: 77408651). For reference purposes, the amino acid sequence of full length GBS 1523 as found in the COH1 strain is given as SEQ ID NO: 110 herein. Preferred GBS1523 polypeptides for use with the invention comprise an amino acid sequence: (a) having 60% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:110; and/or (b) comprising a fragment of at least ‘n’ consecutive amino acids of SEQ ID NO: 110, wherein ‘n’ is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more).
The wild-type sequence contains an amino acid motif indicative of a cell wall anchor (LPSTG) at amino acids 468-472 of SEQ ID NO:110. An E box containing a conserved glutamic residue has also been identified at amino acids 419-429 of SEQ ID NO:110, with a conserved glutamic acid at residue 423. The E box motif may be important for the formation of oligomeric pilus-like structures, and so useful fragments of GBS1523 may include the conserved glutamic acid residue. A mutant of GBS1523 has been identified in which the glutamine (Q) at position 41 of SEQ ID NO:110 is substituted for a lysine (K), as a result of a mutation of a codon in the encoding nucleotide sequence from CAA to AAA. This substitution may be present in the GBS1523 sequences and GBS1523 fragments (e.g. SEQ ID NO:112). A further variant of GBS1523 COH1 without signal sequence region is provided as SEQ ID NO:111.
BP from GBS PI-2a (GBS59)
The amino acid sequence of full length GBS59 as found in the 2603 strain is given as SEQ ID NO: 74 herein. Variants of GBS59 exist in strains H36B, 515, CJB111, DK21 and CJB110. The amino acid sequence of full length GBS59 as found in the H36B, 515, CJB111, CJB110 and DK21 strains are given as SEQ ID NOs: 75, 76, 77, 78, and 79.
BP from GBS PI-2b (Spb1)
The amino acid sequence of full length Sbp1 as found in the COH1 strain is given as SEQ ID NO:80 herein. Wild-type Spb1 contains a N-terminal leader or signal sequence region. One or more amino acids from the leader or signal sequence region of Spb1 can be removed, e.g. SEQ ID NO:81.
BP from Streptococcus pneumoniae (RrgB)
The RrgB pilus subunit has at least three clades. Reference amino acid sequences for the three clades are SEQ ID NOs: 82, 83 and 84 herein.
AP-1 from GBS PI-1 (GBS104/SAG0649)
The amino acid sequence of full length GBS104 as found in the 2603 strain is given as SEQ ID NO:85 herein.
AP-1 from GBS PI-2a (GBS67)
The amino acid sequence of full length GBS67 as found in the 2603 strain is given as SEQ ID NO: 86 herein. A variant of GBS67 (SAI1512) exists in strain H36B. The amino acid sequence of full length GBS67 as found in the H36B strain is given as SEQ ID NO: 87. Variants of GBS67 also exists in strains CJB111, 515, NEM316, DK21 and CJB110. The amino acid sequences of full length GBS67 as found in the CJB111, 515, NEM316, DK21 and CJB110 strains are given as SEQ ID NOS: 88, 89, 90, 91, and 92 herein.
AP-1 from GBS PI-2b (GBS1524/SAN1519)
The amino acid sequence of full length GBS1524 (SAN1519) as found in the COH1 strain is given as SEQ ID NO:93 herein.
AP-1 from Streptococcus pneumoniae (RrgA)
The amino acid sequence of full length RrgA is given as SEQ ID NO:94 herein.
AP-2 from GBS PI-1 (GBS052/SAG0646)
The amino acid sequence of full length GBS052/SAG0646 as found in the 2603 strain is given as SEQ ID NO:95 herein.
AP-2 from GBS PI-2a (GBS150/SAG1404)
The amino acid sequence of full length GBS150/SAG1404 as found in the 2603 strain is given as SEQ ID NO:96 herein.
AP-2 from Streptococcus pneumonia (RrgC)
The amino acid sequence of full length RrgC is given as SEQ ID NO:97 herein.
Polypeptides for use with the invention may thus comprise or consist of an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to a polypeptide having the amino acid sequence of any one of SEQ ID NOs: 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, or 97 or to any other backbone or ancillary protein sequences described above; or (b) that is a fragment of at least ‘n’ consecutive amino acids of one of these sequences wherein ‘n’ is 20 or more (e.g. 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150 or more; e.g. 20 or more; or e.g. 50 or more; or e.g. 80 or more). Alternatively, ‘n’ is less than 20 or less than 25, 30, 35, 40, 50, 60, 70, 80, 90, 100 or less than 150.
The methods of the invention may involve polymerisation of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 polypeptides having 50% identity to a polypeptide having the amino acid sequence of any one of SEQ ID NOs: 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, or 97, or of or of fragments of at least ‘n’ consecutive amino acids of one of these sequences wherein ‘n’ is 20 or more (e.g. 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150 or more; e.g. 20 or more; or e.g. 50 or more; or e.g. 80 or more).
The methods of the invention may involve polymerisation of 1, 2, 3, 4, 5 or 6 polypeptides having 50% identity e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to a polypeptide having the amino acid sequence of any one of SEQ ID NOs: 74, 75, 76, 77, 78 and 79, or of fragments of at least ‘n’ consecutive amino acids of one of these sequences wherein ‘n’ is 20 or more (e.g. 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150 or more; e.g. 20 or more; or e.g. 50 or more; or e.g. 80 or more).
The methods of the invention may involve polymerisation of 1, 2, or 3 polypeptides having 50% identity e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to a polypeptide having the amino acid sequence of any one of SEQ ID NOs: 82, 83 and 84, or of fragments of at least ‘n’ consecutive amino acids of one of these sequences wherein ‘n’ is 20 or more (e.g. 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150 or more; e.g. 20 or more; or e.g. 50 or more; or e.g. 80 or more).
Amino acid fragments of these backbone and ancillary proteins may comprise an amino acid sequence of e.g up to 30, up to 40, up to 50, up to 60, up to 70, up to 80, up to 90, up to 100, up to 125, up to 150, up to 175, up to 200, up to 250, up to 300, up to 350, up to 400, up to 450, up to 500, up to 550, up to 600, up to 650, up to 700, up to 750, up to 800, up to 850, up to 900, up to 950, up to 1000, up to 1100, up to 1200, up to 1300, up to 1400, up to 1500, consecutive amino acid residues of the sequences provided above. Other fragments omit one or more polypeptide domains, for example the transmembrane domain.
The mutant sortase C enzymes of the invention polymerise these polypeptides in a manner that is analogous to the polymerisation of backbone proteins and accessory proteins by wild-type Streptococcal sortase C enzymes in vivo to form a pilus. The polymerised polypeptides produced according to these methods are thus structurally similar to a pilus produced by a Streptococcal bacterium in vivo.
Pili in Gram-positive bacteria are constructed from either two or three types of pilin subunits. In two-component pili the shaft of the pilus is formed by multiple copies of a major pilin subunit, while the tip of the pilus contains a single copy of a minor ‘tip’ pilin subunit that typically functions as an adhesin. Three-component pili are similar, but they also contain a minor ‘basal’ pilin subunit that is covalently attached to the cell wall. Several transmission electron microscopy (EM) and immuno-gold labelling studies have led to the conclusion that the minor ‘basal’ pilin subunits are also interspersed throughout the shaft of the pilus, presumably because the sortase enzymes are promiscuous in the substrates they recognize.
The mutant sortase C enzymes may be brought into contact with 1 polypeptide, leading to the formation of a monomeric pilus. For example, the mutant sortase enzyme may be brought into contact with GBS80, GBS59 or RrgB, leading to the formation of a monomeric pilus comprising subunits of GBS80, GBS59 or RrgB respectively. Where the polypeptide is from a Gram positive bacterium, the mutant sortase enzyme that is used to polymerise that polypeptide need not be from the same Gram positive bacterium. Thus, a mutant sortase C enzyme derived from GBS can be used to polymerise proteins not just from GBS but also from Streptococcus pneumoniae and/or GAS. Variants of some pilus proteins, such as GBS59 are not generally cross-protective. Therefore, the ability to polymerise combinations of at least 2, 3, 4, 5, 6 or more of these variants within an individual pilus is advantageous, for example avoiding the need for more complex compositions or use of protein fusions to achieve cross-protection. Particularly, pili polymerised in vitro may include a combination of GBS59 variants from GBS strains 515, CJB111, H36B, 2603, DK21 and 090, more particularly a combination of GBS59 variants from GBS strains 515, CJB111, H36B and 2603. Such pili comprising two or more variants of GBS59 are not found in nature because strains of wild type bacteria express only one variant of back-bone protein (BP-2a/GBS59).
Alternatively, the mutant sortase C enzymes may be brought into contact with 2, 3, 4, 5 or more different polypeptides which may be from 1, 2, 3, 4, 5 or more Gram positive bacteria, leading to the formation of a chimeric pilus. The mutant sortase C enzymes may be brought into contact with the backbone and accessory proteins from a single Gram positive bacterium which are found in combination in a natural Streptococcal pilus from that bacterium, resulting in a chimeric pilus that is equivalent in structure to a naturally-occurring pilus. Such chimeric pili are a useful tool to enable the study of pilus properties without the laborious purification process currently used to isolate pili from Gram positive bacteria.
In addition, as discussed above, the three-dimensional structures of the monomeric and chimeric pili produced by the methods of the invention make them particularly convenient and effective for immunisation purposes compared to the administration of individual recombinant proteins. Indeed, protection assays have shown that these pili are more effective at inducing protection against the Streptococcus bacteria from which they are derived than monomeric recombinant proteins. It is postulated that this may be because the pili contain epitopes present in pili in vivo that are not replicated in monomeric recombinant proteins, particularly such epitopes are structural epitopes.
The invention includes pili obtained or obtainable using the methods of the invention. In some aspects, the combinations of polypeptides found in these pili differ from the combination of polypeptides found in naturally-occurring pili in Streptococcal bacteria. Examples of pili that may be produced according to the methods of the invention include pili comprising or consisting of the backbone proteins and/or the ancillary proteins from Streptococcus described above. In some embodiments, these pili do not contain the combinations of polypeptides found in naturally-occurring pili found in GBS, GAS or Streptococcal pneumoniae. Particularly, pili polymerised in vitro differ from naturally-occurring pili in terms of their composition, for example, because the acyl enzyme intermediate is not attached to a wild type sortase but is attached to a mutant sortase of the invention. In other cases, pili polymerised in vitro do not comprise cell wall/membrane components such as lipid II or precursors of peptidoglycan such as MurNAc—N-acetyl-muramic acid. In yet other cases, pili polymerised in vitro comprise combinations of pilus proteins not found in nature. Thus, pili polymerised in vitro can be differentiated from those occurring naturally. Thus, the term “artificial” refers to a synthetic, or non-cell derived composition, particularly a structure which is synthesized in vitro and which is not identical to structures found in native bacteria such as Streptococcus.
Immunogenic Compositions Comprising Pili
The invention provides immunogenic compositions comprising the pili described above, which may be obtained or obtainable by the methods of the invention. The term “immunogenic” is used to mean that the pilus is capable of eliciting an immune response, such as a cell-mediated and/or an antibody response, against the polypeptide or polypeptides making up the pilus when used to immunise a subject (preferably a mammal, more preferably a human or a mouse). Particularly, the immune response is a protective immune response which provides protective immunity.
Immunogenic compositions of the invention may be useful as vaccines. Vaccines according to the invention may either be prophylactic (i.e. to prevent infection) or therapeutic (i.e. to treat infection), but will typically be prophylactic. Prophylactic vaccines do not guarantee complete protection from disease because even if the patient develops antibodies, there may be a lag or delay before the immune system is able to fight off the infection. Therefore, and for the avoidance of doubt, the term prophylactic vaccine may also refer to vaccines that ameliorate the effects of a future infection, for example by reducing the severity or duration of such an infection.
The terms “protection against infection” and/or “provide protective immunity” means that the immune system of a subject has been primed (e.g by vaccination) to trigger an immune response and repel infection. Particularly, the immune response triggered is capable of repelling infection against a number of different strains of bacteria. A vaccinated subject may thus get infected, but is better able to repel the infection than a control subject.
Compositions may thus be pharmaceutically acceptable. They will usually include components in addition to the antigens e.g. they typically include one or more pharmaceutical carrier(s) and/or excipient(s). A thorough discussion of such components is available in reference [8].
Compositions will generally be administered to a mammal in aqueous form. Prior to administration, however, the composition may have been in a non-aqueous form. For instance, although some vaccines are manufactured in aqueous form, then filled and distributed and administered also in aqueous form, other vaccines are lyophilised during manufacture and are reconstituted into an aqueous form at the time of use. Thus a composition of the invention may be dried, such as a lyophilised formulation.
The composition may include preservatives such as thiomersal or 2-phenoxyethanol. It is preferred, however, that the vaccine should be substantially free from (i.e. less than 5 μg/ml) mercurial material e.g. thiomersal-free. Vaccines containing no mercury are more preferred. Preservative-free vaccines are particularly preferred.
To improve thermal stability, a composition may include a temperature protective agent. Further details of such agents are provided below.
To control tonicity, it is preferred to include a physiological salt, such as a sodium salt. Sodium chloride (NaCl) is preferred, which may be present at between 1 and 20 mg/ml e.g. about 10±2 mg/ml NaCl. Other salts that may be present include potassium chloride, potassium dihydrogen phosphate, disodium phosphate dehydrate, magnesium chloride, calcium chloride, etc.
Compositions will generally have an osmolality of between 200 mOsm/kg and 400 mOsm/kg, preferably between 240-360 mOsm/kg, and will more preferably fall within the range of 290-310 mOsm/kg.
Compositions may include one or more buffers. Typical buffers include: a phosphate buffer; a Tris buffer; a borate buffer; a succinate buffer; a histidine buffer (particularly with an aluminum hydroxide adjuvant); or a citrate buffer. Buffers will typically be included in the 5-20 mM range.
The pH of a composition will generally be between 5.0 and 8.1, and more typically between 6.0 and 8.0 e.g. 6.5 and 7.5, or between 7.0 and 7.8.
The composition is preferably sterile. The composition is preferably non-pyrogenic e.g. containing <1 EU (endotoxin unit, a standard measure) per dose, and preferably <0.1 EU per dose. The composition is preferably gluten free.
The composition may include material for a single immunisation, or may include material for multiple immunisations (i.e. a ‘multidose’ kit). The inclusion of a preservative is preferred in multidose arrangements. As an alternative (or in addition) to including a preservative in multidose compositions, the compositions may be contained in a container having an aseptic adaptor for removal of material.
Human vaccines are typically administered in a dosage volume of about 0.5 ml, although a half dose (i.e. about 0.25 ml) may be administered to children.
Immunogenic compositions of the invention may also comprise one or more immunoregulatory agents. Preferably, one or more of the immunoregulatory agents include one or more adjuvants. The adjuvants may include a TH1 adjuvant and/or a TH2 adjuvant, further discussed below.
Adjuvants which may be used in compositions of the invention include, but are not limited to:
Immunogenic compositions and vaccines of the invention may also comprise combinations of aspects of one or more of the adjuvants identified above. For example, the following adjuvant compositions may be used in the invention: (1) a saponin and an oil-in-water emulsion [55]; (2) a saponin (e.g. QS21)+a non-toxic LPS derivative (e.g. 3dMPL) [56]; (3) a saponin (e.g. QS21)+a non-toxic LPS derivative (e.g. 3dMPL)+a cholesterol; (4) a saponin (e.g. QS21)+3dMPL+IL-12 (optionally+a sterol) [57]; (5) combinations of 3dMPL with, for example, QS21 and/or oil-in-water emulsions [58]; (6) SAF, containing 10% squalane, 0.4% Tween 80™, 5% pluronic-block polymer L121, and thr-MDP, either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion. (7) Ribi™ adjuvant system (RAS), (Ribi Immunochem) containing 2% squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL+CWS (Detox™); and (8) one or more mineral salts (such as an aluminum salt)+a non-toxic derivative of LPS (such as 3dMPL). Other substances that act as immunostimulating agents are disclosed in chapter 7 of ref 9.
The use of an aluminium hydroxide and/or aluminium phosphate adjuvant is particularly preferred, and antigens are generally adsorbed to these salts. Calcium phosphate is another preferred adjuvant. Other preferred adjuvant combinations include combinations of Th1 and Th2 adjuvants such as CpG & alum or resiquimod & alum. A combination of aluminium phosphate and 3dMPL may be used (this has been reported as effective in pneumococcal immunisation [59]).
The compositions of the invention may elicit both a cell mediated immune response as well as a humoral immune response. This immune response will preferably induce long lasting (e.g. neutralising) antibodies and a cell mediated immunity that can quickly respond upon exposure to infection.
Two types of T cells, CD4 and CD8 cells, are generally thought necessary to initiate and/or enhance cell mediated immunity and humoral immunity. CD8 T cells can express a CD8 co-receptor and are commonly referred to as Cytotoxic T lymphocytes (CTLs). CD8 T cells are able to recognized or interact with antigens displayed on MHC Class I molecules.
CD4 T cells can express a CD4 co-receptor and are commonly referred to as T helper cells. CD4 T cells are able to recognize antigenic peptides bound to MHC class II molecules. Upon interaction with a MHC class II molecule, the CD4 cells can secrete factors such as cytokines. These secreted cytokines can activate B cells, cytotoxic T cells, macrophages, and other cells that participate in an immune response. Helper T cells or CD4+ cells can be further divided into two functionally distinct subsets: TH1 phenotype and TH2 phenotypes which differ in their cytokine and effector function.
Activated TH1 cells enhance cellular immunity (including an increase in antigen-specific CTL production) and are therefore of particular value in responding to intracellular infections. Activated TH1 cells may secrete one or more of IL-2, IFN-γ, and TNF-β. A TH1 immune response may result in local inflammatory reactions by activating macrophages, NK (natural killer) cells, and CD8 cytotoxic T cells (CTLs). A TH1 immune response may also act to expand the immune response by stimulating growth of B and T cells with IL-12. TH1 stimulated B cells may secrete IgG2a.
Activated TH2 cells enhance antibody production and are therefore of value in responding to extracellular infections. Activated TH2 cells may secrete one or more of IL-4, IL-5, IL-6, and IL-10. A TH2 immune response may result in the production of IgG1, IgE, IgA and memory B cells for future protection.
An enhanced immune response may include one or more of an enhanced TH1 immune response and a TH2 immune response.
A TH1 immune response may include one or more of an increase in CTLs, an increase in one or more of the cytokines associated with a TH1 immune response (such as IL-2, IFN-γ, and TNF-β), an increase in activated macrophages, an increase in NK activity, or an increase in the production of IgG2a. Preferably, the enhanced TH1 immune response will include an increase in IgG2a production.
A TH1 immune response may be elicited using a TH1 adjuvant. A TH1 adjuvant will generally elicit increased levels of IgG2a production relative to immunization of the antigen without adjuvant. TH1 adjuvants suitable for use in the invention may include for example saponin formulations, virosomes and virus like particles, non-toxic derivatives of enterobacterial lipopolysaccharide (LPS), immunostimulatory oligonucleotides. Immunostimulatory oligonucleotides, such as oligonucleotides containing a CpG motif, are preferred TH1 adjuvants for use in the invention.
A TH2 immune response may include one or more of an increase in one or more of the cytokines associated with a TH2 immune response (such as IL-4, IL-5, IL-6 and IL-10), or an increase in the production of IgG1, IgE, IgA and memory B cells. Preferably, the enhanced TH2 immune resonse will include an increase in IgG1 production.
A TH2 immune response may be elicited using a TH2 adjuvant. A TH2 adjuvant will generally elicit increased levels of IgG1 production relative to immunization of the antigen without adjuvant. TH2 adjuvants suitable for use in the invention include, for example, mineral containing compositions, oil-emulsions, and ADP-ribosylating toxins and detoxified derivatives thereof. Mineral containing compositions, such as aluminium salts are preferred TH2 adjuvants for use in the invention.
Preferably, the invention includes a composition comprising a combination of a TH1 adjuvant and a TH2 adjuvant. Preferably, such a composition elicits an enhanced TH1 and an enhanced TH2 response, i.e., an increase in the production of both IgG1 and IgG2a production relative to immunization without an adjuvant. Still more preferably, the composition comprising a combination of a TH1 and a TH2 adjuvant elicits an increased TH1 and/or an increased TH2 immune response relative to immunization with a single adjuvant (i.e., relative to immunization with a TH1 adjuvant alone or immunization with a TH2 adjuvant alone).
The immune response may be one or both of a TH1 immune response and a TH2 response. Preferably, immune response provides for one or both of an enhanced TH1 response and an enhanced TH2 response.
The enhanced immune response may be one or both of a systemic and a mucosal immune response. Preferably, the immune response provides for one or both of an enhanced systemic and an enhanced mucosal immune response. Preferably the mucosal immune response is a TH2 immune response. Preferably, the mucosal immune response includes an increase in the production of IgA.
The compositions of the invention may be prepared in various forms. For example, the compositions may be prepared as injectables, either as liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection can also be prepared (e.g. a lyophilised composition or a spray-freeze dried composition). The composition may be prepared for topical administration e.g. as an ointment, cream or powder. The composition may be prepared for oral administration e.g. as a tablet or capsule, as a spray, or as a syrup (optionally flavoured). The composition may be prepared for pulmonary administration e.g. as an inhaler, using a fine powder or a spray. The composition may be prepared as a suppository or pessary. The composition may be prepared as a solid dosage form for parenteral or needleless administration, for example intra-dermal administration. The composition may be prepared for nasal, aural or ocular administration e.g. as drops. The composition may be in kit form, designed such that a combined composition is reconstituted just prior to administration to a patient. Such kits may comprise one or more antigens in liquid form and one or more lyophilised antigens.
Where a composition is to be prepared extemporaneously prior to use (e.g. where a component is presented in lyophilised form) and is presented as a kit, the kit may comprise two vials, or it may comprise one ready-filled syringe and one vial, with the contents of the syringe being used to reactivate the contents of the vial prior to injection.
Immunogenic compositions used as vaccines comprise an immunologically effective amount of the pilus, as well as any other components, as needed. By ‘immunologically effective amount’, it is meant that the administration of that amount to an individual, either in a single dose or as part of a series, is effective for treatment or prevention. This amount varies depending upon the health and physical condition of the individual to be treated, age, the taxonomic group of individual to be treated (e.g. non-human primate, primate, etc.), the capacity of the individual's immune system to synthesise antibodies, the degree of protection desired, the formulation of the vaccine, the treating doctor's assessment of the medical situation, and other relevant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials. Examples of an immunologically effective amount are around 0.1 μg-10 μg pilus, for example 0.5 μg-10 μg pilus.
As mentioned above, a composition may include a temperature protective agent, and this component may be particularly useful in adjuvanted compositions (particularly those containing a mineral adjuvant, such as an aluminium salt). As described in reference 60, a liquid temperature protective agent may be added to an aqueous vaccine composition to lower its freezing point e.g. to reduce the freezing point to below 0° C. Thus the composition can be stored below 0° C., but above its freezing point, to inhibit thermal breakdown. The temperature protective agent also permits freezing of the composition while protecting mineral salt adjuvants against agglomeration or sedimentation after freezing and thawing, and may also protect the composition at elevated temperatures e.g. above 40° C. A starting aqueous vaccine and the liquid temperature protective agent may be mixed such that the liquid temperature protective agent forms from 1-80% by volume of the final mixture. Suitable temperature protective agents should be safe for human administration, readily miscible/soluble in water, and should not damage other components (e.g. antigen and adjuvant) in the composition. Examples include glycerin, propylene glycol, and/or polyethylene glycol (PEG). Suitable PEGs may have an average molecular weight ranging from 200-20,000 Da. In a preferred embodiment, the polyethylene glycol can have an average molecular weight of about 300 Da (PEG-300′).
Methods of Treatment, and Administration of the Vaccine
The invention also provides a method for raising an immune response in a mammal comprising the step of administering an effective amount of a composition of the invention, or a pilus of the invention. The immune response is preferably protective and preferably involves antibodies and/or cell-mediated immunity. The method may raise a booster response.
The invention also provides immunogenic combinations or compositions for use as a medicament e.g. for use in raising an immune response in a subject, such as a mammal.
The invention also provides the use of the pilus of the invention in the manufacture of a medicament for raising an immune response in a mammal.
By raising an immune response in the mammal by these uses and methods, the mammal can be protected against diseases caused by the bacteria from which the polypeptides in the pilus are derived. In particular, the mammal can be protected against disease caused by Streptococcal bacteria, including GAS, GBS and Streptococcus pneumoniae. The invention also provides a delivery device pre-filled with an immunogenic composition of the invention.
The mammal is preferably a human, a large veterinary mammal (e.g. horses, cattle, deer, goats, pigs) and/or a domestic pet (e.g. dogs, cats, gerbils, hamsters, guinea pigs, chinchillas). Most preferably, the mammal is a human, e.g. human patient. Where the vaccine is for prophylactic use, the human may be a child (e.g. a toddler or infant) or a teenager; where the vaccine is for therapeutic use, the human may be a teenager or an adult. A vaccine intended for children may also be administered to adults e.g. to assess safety, dosage, immunogenicity, etc. A mammal (e.g. human, e.g. a patient) may either be at risk from the disease themselves or may be a pregnant female, e.g. woman (‘maternal immunisation’). Vaccination of pregnant females may be advantageous as a means of providing antibody mediated passive protection to new born mammals. Maternal passive immunity is a type of naturally acquired passive immunity, and refers to antibody-mediated immunity conveyed to a fetus by its mother during pregnancy. Maternal antibodies (MatAb) are passed through the placenta to the fetus by an FcRn receptor on placental cells. This occurs around the third month of gestation. Particularly the antibodies are Immunoglobulin G (IgG) or Immunoglobulin A (IgA). IgGy antibody isotypes can pass through the placenta during pregancy. Passive immunity may also provided through the transfer of IgA antibodies found in breast milk that are transferred to the gut of the infant, protecting against bacterial infections, until the newborn can synthesize its own antibodies.
One way of checking efficacy of therapeutic treatment involves monitoring infection after administration of the compositions of the invention. One way of checking efficacy of prophylactic treatment involves monitoring immune responses, systemically (such as monitoring the level of IgG1 and IgG2a production) and/or mucosally (such as monitoring the level of IgA production), against the antigen(s) in the pilus of the invention after administration of the composition. Typically, antigen-specific serum antibody responses are determined post-immunisation but pre-challenge whereas antigen-specific mucosal antibody responses are determined post-immunisation and post-challenge.
Another way of assessing the immunogenicity of the compositions of the present invention is to express the proteins recombinantly for screening patient sera or mucosal secretions by immunoblot and/or microarrays. A positive reaction between the protein and the patient sample indicates that the patient has mounted an immune response to the protein in question. This method may also be used to identify immunodominant antigens and/or epitopes within antigens.
The efficacy of compositions of the invention can also be determined in vivo by challenging animal models of infection, e.g., guinea pigs or mice, with the vaccine compositions.
Compositions of the invention will generally be administered directly to a patient. Direct delivery may be accomplished by parenteral injection (e.g. subcutaneously, intraperitoneally, intravenously, intramuscularly, or to the interstitial space of a tissue), or mucosally, such as by rectal, oral (e.g. tablet, spray), vaginal, topical, transdermal or transcutaneous, intranasal, ocular, aural, pulmonary or other mucosal administration.
The invention may be used to elicit systemic and/or mucosal immunity, preferably to elicit an enhanced systemic and/or mucosal immunity.
Preferably the enhanced systemic and/or mucosal immunity is reflected in an enhanced TH1 and/or TH2 immune response. Preferably, the enhanced immune response includes an increase in the production of IgG1 and/or IgG2a and/or IgA.
Dosage can be by a single dose schedule or a multiple dose schedule. Multiple doses may be used in a primary immunisation schedule and/or in a booster immunisation schedule. In a multiple dose schedule the various doses may be given by the same or different routes e.g. a parenteral prime and mucosal boost, a mucosal prime and parenteral boost, etc. Multiple doses will typically be administered at least 1 week apart (e.g. about 2 weeks, about 3 weeks, about 4 weeks, about 6 weeks, about 8 weeks, about 10 weeks, about 12 weeks, about 16 weeks, etc.).
Vaccines prepared according to the invention may be used to treat both children and adults. Thus a human patient may be less than 1 year old, 1-5 years old, 5-15 years old, 15-55 years old, or at least 55 years old. Preferred patients for receiving the vaccines are the elderly (e.g. ≧50 years old, ≧60 years old, and preferably ≧65 years), the young (e.g. ≦5 years old), hospitalised patients, healthcare workers, armed service and military personnel, pregnant women, the chronically ill, or immunodeficient patients. The vaccines are not suitable solely for these groups, however, and may be used more generally in a population.
Vaccines produced by the invention may be administered to patients at substantially the same time as (e.g. during the same medical consultation or visit to a healthcare professional or vaccination centre) other vaccines e.g. at substantially the same time as a measles vaccine, a mumps vaccine, a rubella vaccine, a MMR vaccine, a varicella vaccine, a MMRV vaccine, a diphtheria vaccine, a tetanus vaccine, a pertussis vaccine, a DTP vaccine, a conjugated H. influenzae type b vaccine, an inactivated poliovirus vaccine, a hepatitis B virus vaccine, a meningococcal conjugate vaccine (such as a tetravalent A-C-W135-Y vaccine), a respiratory syncytial virus vaccine, etc.
Further Antigenic Components of Compositions of the Invention
The invention also provides compositions further comprising at least one further antigen.
In particular, the invention also provides a composition comprising a polypeptide of the invention and one or more of the following further antigens:
The composition may comprise one or more of these further antigens.
Toxic protein antigens may be detoxified where necessary (e.g. detoxification of pertussis toxin by chemical and/or genetic means [70]).
Where a diphtheria antigen is included in the composition it is preferred also to include tetanus antigen and pertussis antigens. Similarly, where a tetanus antigen is included it is preferred also to include diphtheria and pertussis antigens. Similarly, where a pertussis antigen is included it is preferred also to include diphtheria and tetanus antigens. DTP combinations are thus preferred.
Saccharide antigens are preferably in the form of conjugates. Carrier proteins for the conjugates include diphtheria toxin, tetanus toxin, the N. meningitidis outer membrane protein [80], synthetic peptides [81,82], heat shock proteins [83,84], pertussis proteins [85,86], protein D from H. influenzae [87], cytokines [88], lymphokines [88], streptococcal proteins, hormones [88], growth factors [88], toxin A or B from C. difficile [89], iron-uptake proteins [90], etc. A preferred carrier protein is the CRM197 mutant of diphtheria toxin [91].
Antigens in the composition will typically be present at a concentration of at least 1 μg/ml each. In general, the concentration of any given antigen will be sufficient to elicit an immune response against that antigen.
As an alternative to using proteins antigens in the immunogenic compositions of the invention, nucleic acid (preferably DNA e.g. in the form of a plasmid) encoding the antigen may be used.
Antigens are preferably adsorbed to an aluminium salt.
Surprisingly, the Inventors have discovered that the pilin motif is not required for polymerisation by mutant sortases of the invention in contrast to the wild type sortases (from which the mutants are derived) wherein the presence of this motif is essential. In addition, mutant sortases of the invention can use different nucleophile/s to resolve the acyl-intermediate between the enzyme and the LPXTG-like sorting signal. In contrast, wild type sortases from which the mutant sortases are derived require the presence of a lysine residue. Mutant sortases of the invention are effective in vitro at catalysing transpeptidation reactions and forming polymers of GBS pilus proteins. Mutant sortases of the invention are further useful in a variety of protein engineering applications. The structural differences between the sortases of the present invention and other pilus-related sortases in gram positive bacteria may provide new functionality and enable new in vitro methods to be performed, or may allow polymerisation and ligation reactions to be performed more efficiently.
The mutant sortase enzymes of the invention are useful for performing ligation reactions between any moiety that comprises the LPXTG recognition motif (or those listed above) and any moiety that comprises an amino acid residue that can provide the nucleophile to complete the transpeptidation reaction. As shown in the Examples, mutant sortases of the invention are able to cleave and polymerise backbone proteins and ancillary proteins comprising the LPXTG motif. Previous work has demonstrated that bacterial sortases require only a single amino acid to provide the nucleophile to complete the transpeptidation reaction (Proft., Biotechnology Letters, 2010, 32:1-10; Popp et al., Current Protocols in Protein Science, 2009, 15, WO2010/087994).
In certain embodiments of the methods of the invention, either the first moiety or the second moiety in the ligation is a polypeptide and the other moiety is a protein or glycoprotein on the surface of a cell. The sortases of the invention can be used to attach polypeptides to proteins on the cell surface. This can be particularly useful for, for example, labelling specific proteins on the cell surface. In certain embodiments, the cell has been transfected to express the surface protein of interest with a LPXTG motif. This motif can then be targeted for ligation using a sortase of the invention. Alternatively, the protein label may comprise the motif.
Use of Sortases for Ligation of Substrates Other than Pilus Proteins
In other embodiments of the invention, mutant sortases of the invention are used to ligate proteins to a solid support and either the first moiety or the second moiety is a polypeptide and the other moiety comprises amino acids conjugated to a solid support. Such covalent attachment allows extensive washing to be carried out. In certain such embodiments, the protein comprises the LPXTG motif and the solid support has amino acids, such as lysine, conjugated to it. In certain embodiments the solid support is a bead, such as a polystyrene bead or gold bead or particle such as a nanoparticle.
Similarly, the methods of the invention allow circularisation of polypeptide chains. In such embodiments the first moiety and the second moiety are the N-terminus and C-terminus of a polypeptide chain, and ligation results in the formation of a circular polypeptide.
Bacterial sortases are also of significant interest for protein modification and engineering applications. Sortases promote pilin formation in vivo by catalysing a transpepditation reaction between backbone and ancillary proteins. Sortases recognise and cleave a recognition motif (for example, LPXTG) and form an amide linkage with a target protein. By utilising the recognition motif, a variety of protein engineering functions can be performed. Ligation reactions performed using sortases are flexible, efficient and require fewer steps than comparable chemical ligation techniques. Therefore, another object of the invention is to provide improved sortases for protein engineering applications. The techniques of Sortagging are known in the art.
In addition to the sortase mutants described above, other sortase enzymes may be used for ligation. For example, the sortases SrtC1 and SrtC2 from GBS pathogenicity island PI-2b.
The amino acid sequence of wild type SrtC1 from PI-2b is presented in SEQ ID NO:5. Particularly, SrtC1 as used in the methods of the invention does not comprise a signal peptide or N-terminal transmembrane domain (as in SEQ ID NO:98, SEQ ID NO:99 or SEQ ID NO:100). In certain preferred embodiments, SrtC1 as used in the methods of the invention comprises SEQ ID NO:101, which corresponds to the cloned soluble domain. SrtC1 comprising SEQ ID NO:101, which corresponds to the cloned soluble domain. In certain embodiments, SrtC1 may have a W55F mutation (as in SEQ ID NO:102). W55 may be important in regulating the activity of SrtC1, because it is located in the region that the canonical sortases lid motif is normally found in Streptococcal sortases. W55 may mimic the function of the lid found in other sortases. In certain embodiments, the SrtC1 as used in the methods of the invention may have a C188A mutation (as in SEQ ID NO:103). C188 may be a catalytic cysteine.
The amino acid sequence of wild type SrtC2 from PI-2b is presented in SEQ ID NO:105. In certain embodiments, the SrtC2 as used in the methods of the invention may have its cysteines substituted with alanines (as in SEQ ID NO:106). In certain embodiments of the invention, SrtC2 as used in the methods of the invention does not comprise a signal peptide or N-terminal transmembrane domain (as in SEQ ID NO:108 or SEQ ID NO:109). The skilled person is capable of identifying any signal peptide or N-terminal transmembrane domain.
PI-2b sortase C1 and sortase C2 enzymes for use with the invention may thus comprise or consist of an amino acid sequence: (a) having 70% or more identity (e.g. 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to a polypeptide having the amino acid sequence of any one of SEQ ID NOs:5, 98, 100, 101, 102, 103, 105, 106, 108 and 109; or (b) that is a fragment of at least ‘n’ consecutive amino acids of one of these sequences wherein ‘n’ is 100 or more (e.g. 120, 150, 170 or 190 or more). PI-2b sortase C1 and sortase C2 enzymes for use with the invention retain the ability to perform ligation and polymerisation reactions. The nucleotide sequences encoding SrtC1 and SrtC2 are provided in SEQ ID NO:104 and SEQ ID NO:107. Particular recognition motifs may include LPETGG, LPXTG, LPXT, LPKTG, LPATG, LPNTG, LPET, VPDT, IPQT, YPRR, LPMT, LAFT, LPQT, NSKT, NPQT, NAKT, NPQS, LPKT, LPIT, LPDT, SPKT, LAET, LAAT, LAET, LAST, LPLT, LSRT.
General
The practice of the present invention will employ, unless otherwise indicated, conventional methods of chemistry, biochemistry, molecular biology, immunology and pharmacology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., references 92-99, etc. The term “comprising” encompasses “including” as well as “consisting” e.g. a composition “comprising” X may consist exclusively of X or may include something additional e.g. X+Y.
The term “consisting essentially of” means that the composition, method or structure may include additional ingredients, steps and/or parts, but only if the additional ingredients, steps and/or parts do no materially alter the basic and novel characteristics of the claimed composition, method or structure. The term “consisting of” is generally taken to mean that the invention as claimed is limited to those elements specifically recited in the claim (and may include their equivalents, insofar as the doctrine of equivalents is applicable).
The term “about” in relation to a numerical value x means, for example, x+10%.
References to a percentage sequence identity between two amino acid sequences means that, when aligned, that percentage of amino acids are the same in comparing the two sequences. This alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in section 7.7.18 of ref. 100. A preferred alignment is determined by the Smith-Waterman homology search algorithm using an affine gap search with a gap open penalty of 12 and a gap extension penalty of 2, BLOSUM matrix of 62. The Smith-Waterman homology search algorithm is disclosed in ref. 101. The percent identity of a first polypeptide and a second polypeptide is generally determined by counting the number of matched positions between the first and second polypeptides and dividing that number by the total length of the shortest polypeptide followed by multiplying the resulting value by 100. For fragments of polypeptides this value is usually around 100% and therefore has little meaning. Therefore, in the context of fragments of the present invention, the term “proportion of reference polypeptide” (expressed as a percentage) is used. Proportion of reference polypeptide is calculated by counting the number of matched positions between the fragment and reference polypeptides and dividing that number by the total length of the reference polypeptide followed by multiplying the resulting value by 100. Particularly, fragments will comprise less than 90, 80, 70, 65, 60, 55, 50, 45, 40, 35, 30, 25 or less than 20% of the sequence of the reference polypeptide.
Cell-surface pili are important virulence factors and promising vaccine candidates. Gram-positive bacteria elaborate pili via a sortase C-catalyzed transpeptidation mechanism from backbone and ancillary pilin substrates. For the covalent crosslinking of individual subunits, specific residues and/or motifs, such as the pilin motif and the conserved LPxTG sorting signal are absolutely necessary. Site-directed mutagenesis of GBS sortase C1 of Pi-2a (SrtC1) reveals the specific involvement of Tyr86 in the lid-regulatory site in the activation of recombinant SrtC1. This example shows that recombinant BP high molecular weight pili structures can be obtained in vitro using catalytic enzyme concentrations. This provides direct evidence of self-inhibition of sortase C enzymes by the presence of the lid and opens a field for studying pili assembly by using recombinant pili polymerized by a sortase-active mutant, reducing the necessity to purify high amount of wild type pili from pathogenic bacteria.
Group B Streptococcus (GBS), or Streptococcus agalactiae, is the leading cause of life-threatening diseases in newborn and is also becoming a common cause of invasive disease in nonpregnant, elderly or immune-compromised adults [102]. Pili, long filamentous fibers protruding from bacterial surface, have been discovered in Gram-Positive pathogens as important virulence factors and potential vaccine candidates. From the analysis of the eight sequenced genomes of GBS, two genomic islands, each coding for three different pili, have been identified [103; 1]. Moreover, the srtA locus that encodes the ‘housekeeping’ sortase A (SrtA) is present in a different genome region in all analyzed GBS strains [103]. Each pilus genomic island codes for three LPXTG proteins: the backbone protein (BP) representing the main pilus subunit, and two ancillary proteins (AP1 and AP2). Moreover, each island encodes at least two class C sortases, each having specificity for one of the ancillary proteins [1; 104]. The crystal structures of several pilin related sortases, SrtC1-3 from S. pneumoniae [4], AcSrtC-1 from Actinomyces oris [105] and SrtC1 from S. suis (106) have been recently solved, with only the S. suis SrtC1 in an open active-site conformation Moreover, the crystal structure of S. pyogenes Spy 0129 has been solved, showing that it belongs to the class B sortase family, different to the other characterized pilin-specific sortases, which belong to class C. We have previously reported a structural and functional characterization of GBS SrtC1-2a. The crystal structure of the soluble core of GBS SrtC1-2a, containing its catalytic domain indicates that SrtC1 employs a catalytic triad composed of His157-Cys219-Arg228, essential for pilus fiber formation and covered by a loop, known as “lid”, which is dispensable for sortase activity in vivo [3]. Moreover, the crystal structure suggests that SrtC1 is folded as an auto-inactivated enzyme, by the presence of the lid that sterically blocks the active site. The function of the lid region in enzyme regulation and activity is still unclear, but is supposed to have a role in selecting the proper pilus proteins for polymerization. In this work we show, for the first time, efficient recombinant BP high molecular weight structures by using catalytic enzyme concentrations.
GBS 515 strain and mutants were grown in Todd Hewitt Broth (THB) or in Trypticase soy agar (TSA) supplemented with 5% sheep blood at 37° C.
The proteins SrtC143-292, (SEQ ID NO:3 without signal and transmembrane domains), SrtC1Y86A (SEQ ID NO:48) and SrtC1ΔLID (SEQ ID NO:12) were expressed as His-MBP, TEV cleavable, fusion proteins and purified as previously described [3]. Recombinant BP30-649, containing both the pilin motif and the sorting signal, was cloned in speedET vector and expressed as previously described [107], and BPK189A was generated by PIPE site-directed mutagenesis using wild type BP30-649. Recombinant BP30-640, lacking the C-terminal LPxTG motif was cloned in speedET vector and expressed and purified as N terminal His-tag, TEV cleavable, fusion protein using the same protocol used for wild type BP.
Antisera
Antisera specific for the BP-2a and AP1-2a proteins were produced by immunizing CD1 mice with the purified recombinant proteins [107, 108].
Construction of Complementation Vectors and Site-Specific Mutagenesis
GBS knock-out (KO) mutant strain for BP was generated as previously reported [1]. For the generation of complementation vectors DNA fragments corresponding to wild type BP (SAL—1486), gene was PCR amplified from GBS 515 genome and the product was cloned into the E. coli-streptococcal shuttle vector pAM401/gbs80P+T, previously described [11, 27] and containing the promoter and terminator regions of the gbs80 gene (TIGR annotation SAG—0645). Site-directed mutagenesis of pAM_BP was performed using the PIPE (Polymerase Incomplete Primer Extension) method [19]. The complementation vectors pAM_BPΔLPXTG and pAM_BPK189A were electroporated into the KO strain ΔBP. Complementation was confirmed by checking BP expression by Western Blotting.
Western Blotting Analysis
Mid-exponential phase bacterial cells were resuspended in 50 mM Tris-HCl containing 400 U of mutanolysin (Sigma-Aldrich) and COMPLETE protease inhibitors (Roche). The mixtures were then incubated at 37° C. for 1 h and cells lysed by three cycles of freeze-thawing. Cellular debris were removed by centrifugation and protein concentration was determined using BCA protein assay (Pierce, Rockford, Ill.). Total protein extracts (20 μg) or recombinant pili were resolved on 3-8% or 4-12% NuPAGE precast gels (Invitrogen) by SDS-PAGE and transferred to nitrocellulose. Membranes were probed with mouse antiserum directed against BP and AP1 proteins (1:1,000 dilution) followed by a rabbit anti-mouse horseradish peroxidase-conjugated secondary antibody (Dako, Glostrup, Denmark). Bands were then visualized using an Opti-4CN substrate kit (Bio-Rad).
Results
Lysine 189 in the Putative Pilin Motif and IPQTG Sorting Signal of BP-2a are Essential for Pilus Formation by Wild-Type Sortase C.
In the backbone protein of GBS pilus 2a, BP-2a (strain 515, TIGR annotation SAL—1486) we identified a putative pilin motif containing a highly conserved lysine residue (Lys189) and the IPQTGG motif at residue 641-646 as the C terminus sorting motif (
To evaluate the role of the Lys189 in the pilin motif and the IPQTGG motif in the cell wall sorting signal (CWSS) of BP-2a we generated a plasmid (pAM_BPK189A) expressing a mutated backbone protein carrying a substitution of the pilin motif lysine residue with an alanine and a second plasmid (pAM_BPΔIPQTG) carrying the entire deletion of the IPQTG sorting signal. Both the K189 and the C terminus sorting signal of BP-2a were absolutely required for pilus polymerization and ancillary proteins incorporation into the high molecular weight structures (
The LPXTG-Like Sorting Signal is Essential for the Transpeptidation Reaction Mediated In Vitro by the SrtC1Y86A Mutant but the Pilin Motif is NOT.
To investigate the specific contribution of the Lys189 in the pilin motif and the IPQTG sorting signal in the in vitro polymerization reaction, we expressed in E. coli and purified mutated forms of the BP-2a protein, BPΔIPQTG and BPK189A, carrying the deletion of the IPQTG region and the substitution of the Lys189 with an alanine, respectively. After mixing the active SrtC1Y86A with the recombinant BPΔIPQTG mutant, HMW polymers could not be detected, confirming that the polymerization reaction occurs through the cleavage of the sorting signal and the formation of the acyl-intermediate between SrtC1Y86A and the IPQTG motif (
Wild-Type SrtC1-2a is not Able to Induce Recombinant BP Polymerization In Vitro.
The presence of pili on GBS surface is characterized by a ladder of high-molecular-weight bands on SDS-PAGE by immunoblotting analysis of cell-wall preparations, in which GBS BP monomers are covalently linked forming the pilus backbone [1]. To test the hypothesis that it is the interaction with the backbone-protein substrate that induce the lid-open-active conformation of SrtC1, we tested the functional activity in vitro of recombinant SrtC1 (r-SrtC1) and recombinant backbone protein (r-BP) (107), by searching for a pattern of high-molecular-weight bands on gradient SDS gels. Recombinant GBS major pilin subunit BP carrying the pilin motif K189 and the C-terminal LPxTG recognition site, was mixed with WT SrtC1, at various ratios and incubated at 37° C. for different times reaching also the high enzyme amounts used for S. pneumoniae SrtC1 [4]. SDS-page analysis of these samples, however, showed no formation of high molecular weight bands that could represent pilus polymers (
BP High Molecular Weight Structures can be Assembled In Vitro by Recombinant SrtC1 Lid Mutant.
To confirm our hypothesis that the catalytic cysteine is locked by the aromatic ring of Tyr86, we performed the same experiment by mixing recombinant SrtC-1Y86A [3], with recombinant purified BP and we tested the ability of this sortase mutant to polymerize GBS BP monomers. The typical pili pattern of bands with molecular weights above 260 kDa, visible by SDS-page, could be generated when monomeric r-BP was incubated with rSrtC1Y86A (
As part of the BP monomer still remains unprocessed after 10 days of reaction, we tested if higher enzyme amounts could achieve a complete conversion of monomeric BP in polymeric structures.
We found that enzyme concentrations from 10 to 100 μM mixed with a fixed BP concentration did not change the rate of recombinant BP polymers formation (
Using a fixed enzyme concentration of 2504 for the polymerization reaction, varying concentration of monomeric BP were also tested (
BP High Molecular Weight Structures Formation In Vitro by Recombinant SrtC1y86A Mutant is Mediated by LPXTG and Pilin Motives.
To confirm that the polymerization of the BP occurs through the correct motives, the polymerization in vitro was tested by incubating r-BPΔLPXTG and r-BPK189A with SrtC1Y86A confirming that the polymerization occurs through the cleavage of the LPXTG sorting signal and the subsequent linking to the pilin motif of the next subunit.
Large-Scale Recombinant BP HMW Structures Production and Purification.
Pili purification from gram positive pathogens is very challenging and time consuming and allows the purification of low amounts of material only. As we could achieve BP polymerization in a 50 μl reaction volume, we tried to scale-up the production of recombinant pili production. We found that the best reaction conditions were achieved by using the enzyme at 25 μM and the BP at 100 μM. The reaction volume is also important, as using up to 100 μl of the reaction decreases the efficiency of BP polymerization. We performed 10 reactions using these concentrations of substrate and enzyme in 100 μl each, for a total amount of 6.5 mg of pure BP, and we incubated the reaction for 7 days in presence of reducing agent. After this time, the pool of the reactions (1 ml total) was separated by gel filtration. Two fractions, containing mostly high molecular weight pili, were isolated from the monomeric BP and SrtC1, and were quantified to contain 0.5 mg of pili (
In Gram-positive bacteria the covalent association of pili requires the action of specific sortases. The pilus 2a biosynthesis in GBS is promoted by two sortase enzymes (SrtC-1 and SrtC-2) that polymerize the BP and display ancillary-proteins substrate specificity. Previously, we have shown that a triad composed of His, Cys and Arg residues is essential for SrtC-1 activity. Moreover, the crystal structure clearly indicates that GBS SrtC1 is auto-inhibited by the presence of the lid in the catalytic pocket. Recently, our group measured the catalytic activity for GBS SrtC1 by using a self-quenched fluorescent peptide mixed with recombinant GBS SrtC1 WT and lid mutants to monitor substrate cleavage, and we found that the lid-mutants are even more active than the WT. These data, in accordance with in vivo experiments with lid mutants, suggested that the activation of sortases C might occur by a conformational change that results in the movement of the lid away from the catalytic site that could be induced by the protein substrates.
Starting from these observations, we performed in vitro experiments using recombinant GBS SrtC1 WT and lid mutants mixed with recombinant backbone pilus protein and we observed that WT SrtC1 enzyme was not able to induce recombinant BP protein polymerization. Enzyme activation was achieved, in vitro, through a single mutation in the lid region of recombinant SrtC1-2a that enhances BP polymerization in vitro and recombinant pili formation. These experiments suggest that for SrtC, the mechanism behind recognition and polymerization of pilus subunits could not depend only on the interaction between the fimbrial shaft protein and the sortase, as the enzyme activation could not be achieved in vitro simply by mixing SrtC1WT with the BP. The experiments with the lid mutants indicate that the presence of the lid, and in particular of the Tyr86 in this loop, prevent BP polymerization. Our work provides the first direct evidence of self-inhibition of sortase C enzymes by the presence of the lid and opens a field for studying pili assembly by using recombinant pili polymerized by a sortase-active mutant, reducing the necessity to purify high amount of wild type pili from pathogenic bacteria. Moreover, the anchoring of many surface virulence factors on Gram-positive bacteria is mediated by sortase-activity and, therefore, these enzymes are attractive targets for the design of novel anti-infective therapeutics.
The in vitro polymerized pili structures may be used in immunisation studies in mice. For example, 10 μg of purified recombinant pili may be mixed with an adjuvant (e.g. alum) and injected into mice in a final volume of 200 μl. This may be followed by one or more booster immunisations. The mice may then be analysed for an immune response to the pili structures. This immune response may be protective against the bacteria from which the monomeric pilus proteins were originally derived.
An immunisation study has been conducted in which mice were immunised with monomeric pili comprising GBS59 generated according to the methods of the invention in combination with alum, and the protective immune response was assessed following subsequent challenge with GBS. The results were compared to immunisation using a similar protocol with recombinant GBS59 not in pilus form and alum, the SrtCM1 (Y86A) mutant and alum, Crmla and alum. The results of the immunisation experiment are provided in Table 4 below.
These results show that the GBS59 pili generated using the mutant sortase C enzymes according to the methods of the invention are significantly more effective at generating a protective immune response to GBS than the recombinant monomeric protein and are equivalent to the use of CRM Ia.
We tested the ability of the sortase mutant to polymerize variants of GBS BP monomers of GBS59 corresponding to SEQ IDs: 74, 75, 76, 77, 78 and 79.
Bacterial Strains and Growth Conditions
The GBS strains used in this work were 2603 V/R (serotype V), 515 (Ia), CJB111 (V), H36B (serotype Ib), 5401 (II) and 3050 (II). Bacteria were grown at 37° C. in Todd Hewitt Broth (THB; Difco Laboratories) or in trypticase soy agar supplemented with 5% sheep blood.
Cloning, Expression, Purification of Recombinant Proteins and Antisera.
Genomic DNA was isolated by a standard protocol for gram-positive bacteria using a Nucleo Spin Tissue kit (Macherey-Nagel) according to the manufacturer's instructions. The full length recombinant BP-2a proteins, corresponding to 515, CJB111 and 2603 allelic variants (TIGR annotation SAL1486, SAM1372 and SAG1407, respectively), were produced as reported in Margarit et al, Journal of Infectious Diseases, 2009, 199: 108-115, whilst the full length H36B variant (TIGR annotation SAI—1511) was cloned in pET24b+(Novagen) using strain H36B as source of DNA. Primers were designed to amplify the coding regions without the signal peptide and the 3′ terminal sequence starting from the LPXTG motif.
For recombinant protein expression, the cultures were maintained at 25° C. for 5h after induction with 1 mM IPTG for the pET clones or with 0.2% arabinose for the SpeedET clones. All recombinant proteins were purified by affinity chromatography and gel filtration. Briefly, cells were harvested by centrifugation and lysed in “lysis buffer”, containing 10 mM imidazole, 1 mg\ml lysozyme, 0.5 mg\ml DNAse and COMPLETE inhibitors cocktail (Roche) in PBS. The lysate was clarified by centrifugation and applied onto His-Trap HP column (Armesham Biosciences) pre-equilibrated in PBS containing 10 mM imidazole. Protein elution was performed using the same buffer containing 250 mM imidazole, after two wash steps using 20 mM and 50 mM imidazole buffers. The eluted proteins were then concentrated and loaded onto HiLoad 16/60 Superdex 75 (Amersham Biosciences) pre-equilibrated in PBS.
Antisera specific for each protein were produced by immunizing CD1 mice with the purified recombinant proteins as previously described (WO90/07936). Protein-specific immune responses (total Ig) in pooled sera were monitored by ELISA.
As before, we found that enzyme concentrations from 10 to 100 μM mixed with a fixed BP concentration did not change the rate of recombinant GBS59 polymer formation. GBS59 variant monomers were mixed at a 1:1:1:1:1:1 ratio. Using a fixed enzyme concentration of 25 μM for the polymerization reaction, varying concentrations of the mixture of variants of monomeric BP GBS59 were also tested.
In Vitro Polymerization with Three Variants of BP-2a (H36B, 515, CJB111):
BP-2a (variants H36B, 515, CJB111) concentrations: 35 μM each—105 μM tot.
SrtC1Y86A concentration: 25 μM
Buffer: 25 mM Tris-HCl pH 7.5-100 mM NaCl-1 mM DTT
Total volume of reaction 100 μl
Incubation at 37° C. for 48 h
The typical pili pattern of bands with molecular weights above 260 kDa, visible by SDS-page, could be generated when the mixture of variants of monomeric r-BPs was incubated with rSrtC1Y86A (
Following the procedures outlined above, chimeric pili comprising backbone proteins from both Streptococcus agalactiae and Pneumococcus were prepared:
BP concentrations: 50 μM each—100 μM tot.
SrtC1Y86A concentration: 25 μM
Buffer: 25 mM Tris-HCl pH 7.5-100 mM NaCl-1 mM DTT
Total volume of reaction 100 μl
Incubation at 37° C. for 48 h
As shown in
The “IQTGGIGT” sequence was added at the C-terminus of the GFP protein DNA sequence using mutagenesis:
Primers Used:
Mutagenesis DNA template: SpeedET vector+GFP
EGFP DNA sequence below (from pSpeedET):
EGFP amino acid sequence below (from pSpeedET):
Nucleic acid sequence after mutagenesis:
Amino acid sequence after mutagenesis:
Production of Recombinant “GFP-IQTGGIGT”: Expression and Purification
GFP-IPQTGGIGT Expression in HK100 in LB+kanamicine 30 ug\ml using biosilta media at 30° C., induction with arabinose 0.15% final. Purification: standard IMAC
GFP-IQTGGIGT and SrtC1Y86A Polymerization Reaction:
mix 25 uM SrtC1Y86A with 25-50 or 100 uM GFP-IPQTGGIGT in buffer 25 mM Tris pH7.5, 150 mM NaCl, DTT1 mM for 72h at 37° C. in termomixer. Reaction volume 50 ul.
As shown in
Full-length SrtC1 and C2 were cloned (using strain COH1 as template) in fusion with a His-MBP-tag. Recombinant enzymes were then expressed in E. coli and purified with IMAC or IMAC and MBP-trap column. FRET assays with purified sortases were carried out using synthetic fluorescent peptides carrying the LPXTG sorting motif of PI-1 backbone protein and of PI-1 minor ancillary protein in order to assess the catalytic activity. The PI-2b SrtC1 and SrtC2 enzymes are able to cleave the fluorescent peptides. These data demonstrate that the PI-2b SrtC1 and SrtC2 enzymes are active in vitro and are suitable for use in ligating and polymerising proteins.
The following protocols and conditions were used:
Purification of SrtC1 Enzyme—IMAC
Purification of SrtC2 Enzyme—IMAC
Purification of SrtC2 Enzyme—MBP-Trap
FRET Analysis
Closed plate with termofluor plastic.
1) 50 μl buffer (300 mM NaCl+50 mM Tris pH8)+50 μl 11515+1 μl BP peptide
2) 50 μl buffer (300 mM NaCl+50 mM Tris pH8)+50 μl 11515+1 μl AP2 peptide
3) 100 μl 11515+1 μl BP peptide
4) 100 μl 11515+1 μl AP2 peptide
5) 100 μl 1 elution buffer (300 mM Imidazole)+1 μl BP peptide
6) 100 μl 1 elution buffer (300 mM Imidazole)+1 μl AP2 peptide
We used 200 μl [1.78 mg/ml] of concentrated protein+2 μl LPXTG peptide of BP and AP2, and as control used the elution buffer 300 mM Imidazole instead of protein.
Tecan plate reader—300 cycles with a measurement every 10 minutes, temperature [34-37.5° C.°] with 37° C. for optimum and wavelength [400 nm-600 nm] have been obtained with maximum absorption provided to 500 nm.
The activity of SrtC1 was further assayed by using a mutant GBS strain that does not express any pili (515Δ2a). This strain was transformed with complementation vectors PAMp80/t80 carrying genes coding for BP alone or BP with PI-2b SrtC1. The ability of the complementation vectors to restore pili polymerisation was analysed by western blot. As shown in
These data demonstrate that PI-2b SrtC1 is effective at polymerising pili.
The following protocols and conditions were used:
Electroporation
100 μl of the A909 and 515Δ2a strains were transformed with 3/7 μl of Spb1 (BP-PI-2b) or Spb1+SrtC1 (PI-2b).
Inoculation
In 10 ml THB+clm glycerol.
Cells were pelleted and washed with 25 ml PBS
Gel and Western Blot GBS Extracts
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2013/053644 | 2/23/2013 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 61602827 | Feb 2012 | US | |
| 61704866 | Sep 2012 | US |
