Link:  Pharm/Biotech Resources

Title:  Virulence genes, proteins, and their use

United States Patent:  6,951,732

Issued:  October 4, 2005

Inventors:  Clarke; Enda Elizabeth (Berkshire, GB); Zhou; Liqing (Berkshire, GB); Shea; Jacqueline Elizabeth (Berkshire, GB); Feldman; Robert Graham (Berkshire, GB); Holden; David William (Berkshire, GB)

Assignee:  VMAX Ltd. (GB)

Appl. No.:  169048

Filed:  December 22, 2000

PCT Filed:  December 22, 2000

PCT NO:  PCT/GB00/04997

371 Date:  September 23, 2002

102(e) Date:  September 23, 2002

PCT PUB.NO.:  WO01/48208

PCT PUB. Date:  July 5, 2001

A series of genes from Streptococcus pyogenes are shown to encode products which are implicated in virulence. The identification of these genes therefore allows attenuated microorganisms to be produced. Furthermore, the genes or their encoded products can be used in the manufacture of vaccines for therapeutic application.

FIELD OF THE INVENTION

This invention relates to virulence genes and proteins, and their use. More particularly, it relates to genes and proteins/peptides obtained from Streptococcus pyogenes, and their use in therapy and in screening for drugs.

BACKGROUND OF THE INVENTION

Group A Streptococcus (GAS) is responsible for the majority of Streptococcal illnesses. An organism of particular interest is S. pyogenes, which is implicated in a wide range of non-invasive and invasive infections, such as impetigo, pharyngitis, necrotizing fasciitis, bacteraemia, streptococcal toxic shock syndrome (STSS), pneumonia and rheumatic fever.

Some GAS infections can be treated with antibiotics, including penicillin and erythromycin. However, due to the problems associated with resistance to antibiotics, and antibiotic-allergic patients, there is a need for further therapeutics which may be useful in treating of preventing GAS infection.

SUMMARY OF THE INVENTION

The present invention is based on the discovery of virulence genes in S. pyogenes.

According to a first aspect of the invention, a peptide of the invention is encoded by an operon including any of the nucleotide sequences identified herein as SEQ ID NOS. 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59 and 61 of S. pyogenes or a homologue thereof in a Gram-positive bacterium, or a functional fragment thereof, for therapeutic or diagnostic use.

The peptides may have many therapeutic uses for treating Group A Streptococcal infections, including use in vaccines for prophylactic application.

According to a second aspect, a polynucleotide encoding a peptide defined above, may also be useful for therapy or diagnosis.

According to a third aspect, the genes that encode the peptides may be utilised to prepare attenuated microorganisms. The attenuated microorganisms will usually have a mutation that disrupts the expression of one or more of the genes identified herein, to provide a strain that lacks virulence. These microorganisms will also have use in therapy and diagnosis.

According to a fourth aspect, the peptides, genes and attenuated microorganisms according to the invention may be used in the treatment or prevention of a condition associated with infection by Streptococcal or Gram-positive bacteria.

DESCRIPTION OF THE INVENTION

The present invention is based on the discovery of genes encoding peptides which are implicated in virulence. The peptides and genes of the invention are therefore useful for the preparation of therapeutic agents to treat infection. It should be understood that references to therapy also include preventative treatments, e.g. vaccination. Furthermore, while the products of the invention are intended primarily for treatment of infections in human patients, veterinary applications are also considered to be within the scope of the invention.

The present invention is described with reference to Streptococcus pyogenes. However, all the Group A streptococcal strains, and many other Gram-positive bacterial strains are likely to include related peptides or proteins having amino acid sequence identity or similarity to those identified herein. Organisms likely to contain the peptides include, but are not limited to the genera Lactococcus, Enterococcus, Streptococcus and Staphylococcus.

Preferably, the peptides that may be useful in the various aspects of the invention have greater than a 40% similarity with the peptides identified herein. More preferably, the peptides have greater than 60% sequence similarity. Most preferably, the peptides have greater than 80% sequence similarity, e.g. 95% similarity. With regard to the polynucleotide sequences identified herein, related polynucleotides that may be useful in the various aspects of the invention may have greater than 40% identity with the sequences identified herein. More preferably, the polynucleotide sequences have greater than 60% sequence identity. Most preferably, the polynucleotide sequences have greater than 80% sequence identity, e.g. 95% identity.

The terms "similarity" and "identity" are known in the art. The use of the term "identity" refers to a sequence comparison based on identical matches between correspondingly identical positions in the sequences being compared. The term "similarity" refers to a comparison between amino acid sequences, and takes into account not only identical amino acids in corresponding positions, but also functionally similar amino acids in corresponding positions. Thus similarity between polypeptide sequences indicates functional similarity, in addition to sequence similarity.

Levels of identity between gene sequences and levels of identity or similarity between amino acid sequences can be calculated using known methods. In relation to the present invention, publicly available computer based methods for determining identity and similarity include the BLASTP, BLASTN and FASTA (Atschul et al., J. Molec. Biol., 1990; 215:403-410), the BLASTX program available from NCBI, and the Gap program from Genetics Computer Group, Madison Wis. The levels of similarity and identity provided herein, were obtained using the Gap program, with a Gap penalty of 12 and a Gap length penalty of 4 for determining the amino acid sequence comparisons, and a Gap penalty of 50 and a Gap length penalty of 3 for the polynucleotide sequence comparisons.

Having characterised a gene according to the invention, it is possible to use the gene sequence to search for related genes or peptides in other microorganisms. This may be carried out by searching in existing databases, e.g. EMBL or GenBank.

Peptides or proteins according to the invention may be purified and isolated by methods known in the art. In particular, having identified the gene sequence, it will be possible to use recombinant techniques to express the genes in a suitable host. Active fragments and related molecules can be identified and may be useful in therapy. For example, the peptides or their active fragments may be used as antigenic determinants in a vaccine, to elicit an immune response. They may also be used in the preparation of antibodies, for passive immunisation, or diagnostic applications. Suitable antibodies include monoclonal antibodies, or fragments thereof, including single chain Fv fragments. Methods for the preparation of antibodies will be apparent to those skilled in the art.

Active fragments of the peptides are those that retain the biological function of the peptide. For example, when used to elicit an immune response, the fragment will be of sufficient size, such that antibodies generated from the fragment will discriminate between that peptide and other peptides on the bacterial microorganism. Typically, the fragment will be at least 30 nucleotides (10 amino acids) in size, preferably 60 nucleotides (20 amino acids) and most preferably greater than 90 nucleotides (30 amino acids) in size.

It should also be understood, that in addition to related molecules from other microorganisms, the invention encompasses modifications made to the peptides and polynucleotides identified herein which do not significantly alter the biological function. It will be apparent to the skilled person that the degeneracy of the genetic code can result in polynucleotides with minor base changes from those specified herein, but which nevertheless encode the same peptides. Complementary polynucleotides are also within the invention. Conservative replacements at the amino acid level are also envisaged, i.e. different acidic or basic amino acids may be substituted without substantial loss of function.

The preparation of vaccines based on attenuated microorganisms is known to those skilled in the art. Vaccine compositions can be formulated with suitable carriers or adjuvants, e.g. alum, as necessary or desired, to provide effective immunisation against infection. The preparation of vaccine formulations will be apparent to the skilled person. The attenuated microorganisms may be prepared with a mutation that disrupts the expression of any of the genes identified herein. The skilled person will be aware of methods for disrupting expression of particular genes. Techniques that may be used include insertional inactivation or gene deletion techniques. Attenuated microorganisms according to the invention may also comprise additional mutations in other genes, for example in a second gene identified herein or in a separate gene required for growth of the microorganism, e.g. an aro mutation. Attenuated microorganisms may also be used as carrier systems for the delivery of heterologous antigens, therapeutic proteins or nucleic acids (DNA or RNA). In this embodiment, the attenuated microorganisms are used to deliver a heterologous antigen, protein or nucleic acid to a particular site in vivo. Introduction of a heterologous antigen, peptide or nucleic acid into an attenuated microorganism can be carried out by conventional techniques, including the use of recombinant constructs, e.g. vectors, which comprise polynucleotides that express the heterologous antigen or therapeutic protein, and also include suitable promoter sequences. Alternatively, the gene that encodes the heterologous antigen or protein may be incorporated into the genome of the organism and the endogenous promoters used to control expression.

More generally, and as is well known to those skilled in the art, a suitable amount of an active component of the invention can be selected, for therapeutic use, as can suitable carriers or excipients, and routes of administration. These factors would be chosen or determined according to known criteria such as the nature/severity of the condition to be treated, the type and/or health of the subject etc.

In a separate embodiment, the products of the invention may be used in screening assays for the identification of potential antimicrobial drugs or for the detection for virulence. Routine screening assays are known to those skilled in the art, and can be adapted using the products of the invention in the appropriate way. For example, the products of the invention may be used as the target for a potential drug, with the ability of the drug to inactivate or bind to the target indicating its potential antimicrobial activity.

The various products of the invention may also be used in veterinary applications.

The following is a brief overview of the experimental procedure used to identify the virulence genes. The virulence genes in S. pyogenes were identified by using signature-tagged mutagenesis (STM) to screen an S. pyogenes mutant bank for attenuated mutants (Hensel et al., 1995. Science 269(5222):400-3).

Mutants were generated via Tn917 transposon insertion, using a plasmid vector. In addition to a fragment of Tn917, the vector comprised a spectromycin-resistance gene, a chloramphenicol-resistance gene (CAT gene) with a synthetic promoter, a Gram-negative origin of replication (rop.ori) and a cloning site for the STM tags. After ligating the tags into the vector, E. coli transformation was carried out, and 96 plasmids that hybridised with the original tags were selected.

The S. pyogenes strain B514-SM (type M50) was transformed with each of the 96 tagged plasmids, and transformants were selected by resistance to spectinomycin and chloramphenicol. For each of the transformed S. pyogenes strains, 20 mutants were generated via Tn917 transposon insertion to create a mutant bank.

The mutant bank was screened in either a skin invasive lesion model of mouse infection (Schrager et al., J. Clinical Investigation 1996; 98:1954-1958) or from a throat colonisation model of mouse infection (Husmann et al., Infection and Immunity, 1997; 65 (4):935-944).

In the skin model, five CD1 mice were each inoculated intradermally with 1×10⁸ cells in a volume of 50 μl representing the collection of 96 distinct and readily distinguishable mutants. 48 hours after inoculation, samples were taken and bacteria recovered. The skin lesions were macerated in 2×BHI medium and bacteria liberated from the lesion by treatment in a stomacher for 10 minutes. The released bacteria were plated out and a minimum of 10,000 colonies recovered from a minimum of 3 mice. DNA was isolated from these samples and used to amplify the tagged DNA present in the recovered bacteria. The DNA isolated from each recovered pool was used as a hybridisation probe to reveal those mutants in each pool that failed to be recovered from the animals and which were therefore attenuated in this animal model of infection.

In the throat colonisation model, 2×10⁸ cells were inoculated intranasally into six C57BL/6 mice and samples taken after 48 hours. As with the skin model, bacteria containing a transposon Tn917 insertion within a virulence gene failed to be recovered from mice inoculated with a mixed population of mutants, and were therefore likely to be attenuated.

Additional experiments were carried out on mutants identified through the STM screen to determine the competitive index (CI). Individual mutants were tested in mixed infections with the wild-type strain in the skin lesion model of infection (Chiang, S. L. and Mekalanos, J. J. Molecular Microbiology 1998; 27(4):797-805). As for the initial screen, groups of four CD1 mice were inoculated with equal numbers of both wild-type and mutant cells, to a total number of 1×10⁸ cells. Bacteria recovered after 48 hours were plated out onto selective media that allows the wild-type and mutant colonies to be distinguished. The ratio of mutant bacteria to wild-type bacteria seen in the inoculum compared with the ratio in recovered bacteria is the competitive index (ratio of mutants versus wild-type in the inoculum divided by the ratio of mutants versus wild-type bacteria recovered from the animal model).

The following Examples illustrate the invention.

EXAMPLE 1

A first mutant was identified and the nucleotide sequence immediately following the transposon insertion was cloned.

The nucleotide sequence shows 100% identity at the nucleotide level to a coding sequence within the S. pyogenes genome, shown as SEQ ID NO. 1, with the putative protein sequence shown as SEQ ID NO. 2.

The amino acid sequence of the predicted protein product shows 43% identity to the putative NAD(P)H nitroreductase of H. influenzae (accession number: SW: Q57431).

Given the similarity of the putative NAD(P)H nitroreductase gene in S. pyogenes to the gene in H. influenzae, the skilled person will appreciate that similar sequences in other Streptococci and Gram-positive bacteria may also be implicated in virulence.

In the test for attenuation of virulence, the mutated microorganism was shown to be attenuated with a competitive index (CI) of 0.644.

EXAMPLE 2

A further mutant was identified and the nucleotide sequence immediately following the transposon insertion was cloned.

The nucleotide sequence has 98% identity at the nucleotide level to a sequence within the S. pyogenes genome, shown as SEQ ID NO. 3. The putative amino acid sequence is shown as SEQ ID NO. 4.

The amino acid sequence shows 81% identity to a probable integrase enzyme of S. mutans (accession number: TREMBL: 069155).

This demonstrates that the disrupted gene is at least partially identical to a probable integrase gene of S. mutans. However, this gene was previously unknown in S. pyogenes, and has not been assigned a role in virulence.

Given the similarity of the S. pyogenes gene to the probable integrase gene of S. mutans, the skilled person will appreciate that similar sequences in other Steptococci and Gram-positive bacteria may also be virulence determinants.

In the test for attenuation of virulence, the mutated microorganism was shown to be attenuated with a competitive index (CI) of 0.229.

EXAMPLE 3

A further mutant was identified and the nucleotide sequence immediately following the transposon insertion was cloned.

The nucleotide sequence has 97% identity at the nucleotide level to a sequence within the S. pyogenes genome, shown as SEQ ID NO. 5. The predicted amino acid sequence is shown as SEQ ID NO. 6.

The amino acid sequence shows 37% identity at the amino acid level to the GlgP protein of the unicellular cyanobacterium Synechocystis spp. (accession number: TREMBL: P73511).

This demonstrates that the disrupted gene is at least partially identical to the glgP gene of Synechocystis spp.

Given the similarity of the gene of S. pyogenes to the glgP gene of Synechocystis spp., the skilled person will appreciate that similar sequences in other Streptococci and Gram-positive bacteria may also be virulence determinants.

In the test for attenuation of virulence, the mutated microorganism was shown to be attenuated with a competitive index (CI) of 0.011.

EXAMPLE 4

A further mutant was identified and the nucleotide sequence immediately following the transposon insertion was cloned.

The nucleotide sequence has 97% identity at the nucleotide level to a sequence within the S. pyogenes genome, shown as SEQ ID NO. 7. The predicted amino acid sequence is shown as SEQ ID NO. 8.

The amino acid sequence shows 35% identity at the amino acid level to the BraB protein of B. subtilis (accession number: TREMBL: 034545).

This demonstrates that the disrupted gene is at least partially identical to the braB gene of B. subtilis.

Given the similarity of the braB gene of S. pyogenes to the braB gene in B. subtilis, the skilled person will appreciate that similar sequences in other Streptococci and Gram-positive bacteria may also be implicated in virulence.

In the test for attenuation of virulence, the mutated microorganism was shown to be attenuated with a competitive index (CI) of 0.88.

EXAMPLE 5

A further mutant was identified and the nucleotide sequence immediately following the transposon insertion was cloned.

The nucleotide sequence shows 99% identity at the nucleotide level to a sequence within the S. pyogenes genome, shown as SEQ ID NO. 9. The predicted amino acid sequence is shown as SEQ ID NO. 10.

A still further attenuated mutant was also identified with a nucleotide sequence having 98% identity at the nucleotide level to a sequence within the S. pyogenes genome, shown as SEQ ID NO. 11. The predicted amino acid sequence is shown as SEQ ID NO. 12.

The predicted protein of the first mutant shows 53% identity at the amino acid level to the AdcR protein of S. pneumoniae (accession number: TREMBL:033703). That of the second mutant shows 79% identity at the amino acid level to the AdcC protein of S. pneumoniae (accession number: TREMBL: 087862).

This demonstrates that the disrupted genes are at least partially identical to the adcR and adcC genes of S. pneumoniae. The adcR and adcC genes are part of the adc operon (including adcR, adcC, adcB, and adcA) in S. pneumoniae. Therefore the attenuation of S. pyogenes adcR and adcC mutants could result from a failure to express the adcR and adcC genes, or the predicted downstream genes (adcB and abcA homologues). These genes have not previously been assigned a role in-virulence in S. pyogenes.

Given the similarity of the S. pyogenes genes to the adcR and adcC genes in S. pneumoniae, the skilled person will appreciate that similar sequences in other Steptococci and Gram-positive bacteria may be implicated in virulence.

In the test for attenuation of virulence, the mutated microorganisms were shown to be attenuated with a competitive index (CI) of 0.548 (adcR) and 0.028 (adcC).
 

Claim 1 of 1 Claim

1. A screening assay for the identification of an antimicrobial drug, comprising:

(i) contacting a citrate lyase acyl carrier protein (citD) with a potential drug, wherein the citD protein comprises the amino acid sequence of SEQ ID NO:22; and

(ii) determining whether the potential drug inhibits citD protein activity, wherein inhibition of citD protein activity is indicative of an antimicrobial drug.

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