# Patent

## Title
Preparation of protective antigen

## Abstract

A polynucleotide sequence is provided comprising a nucleic acid sequence encoding recombinant Protective Antigen (rPA).
Also provided are expression vectors and host cells comprising the polynucleotide sequence of the invention, and methods for producing rPA.

## Background
CROSS REFERENCE TO RELATED APPLICATION
This application is a divisional application of U.S. application Ser. No. 12/042,150, filed Mar. 4, 2008 now U.S. Pat. No. 8,101,735, which is a continuation-in-part application of U.S. application Ser. No. 11/153,865, filed Jun. 15, 2005, entitled “BACILLUS ANTHRACIS PROTECTIVE ANTIGEN”, (now U.S. Pat. No. 7,355,027), which claims the benefit of U.S. Provisional Application 60/579,687, filed Jun. 16, 2004, entitled “PREPARATION OF PROTECTIVE ANTIGEN”.


SEQUENCE LISTING INCORPORATION BY REFERENCE
A sequence listing in an ASCII text file, having the name “MSQ01-010-DIVX-US_SEQUENCE_LISTING—9-26-2011.txt”, created on 26 Sep. 2011, and having a size of 307,748 bytes, is hereby incorporated by reference in its entirety.
The present invention relates to polynucleotides and vectors encoding recombinant Bacillus anthracis protective antigen (rPA), methods of producing rPA, and uses thereof in antigenic compositions, such as vaccines.
Bacillus anthracis is a Gram positive, spore-forming bacterium and the causative agent of anthrax. Anthrax is a disease of domestic and land animals, and can affect humans through contact with infected animal products. In the lungs, anthrax can cause massive fluid build-up, tissue decay, toxic shock and death.
Anthrax vaccine has been manufactured by the present Applicant for over 40 years and, since 1979, has been the subject of a UK Product Licence (PL1511/0037) held by the Secretary of State for Health. However, within that time there has been little product development or advance in its manufacturing process.
The above vaccine preparation is now described in more detail. Cultures of the toxigenic, non-capsulating B. anthracis 34F2 “Sterne” strain [see Sterne, M. (1939). Onderstepoort J. of Veterinary Science and Animal Industry, 13, pp 307-312] are grown in multiple 500 mL volumes in a partially defined medium in Thompson bottles at 37° C. until the pH of selected culture bottles falls below pH 7.4.
At the end of the growth period (approximately 24-28 hours) the cultures are harvested by aspiration, and the pooled supernatant fluids sterilised by filtration. Potassium aluminium sulphate solution is added, and the resulting solution mixed. The pH is then adjusted to 5.8-6.2, and the resulting flocculant (‘alum-precipitation’) allowed to settle under gravity for up to one week at 5° C.
The precipitate is then concentrated 20-fold (by volume) by aspiration, and diluted 1:4 with a saline solution to provide a ‘5-fold’ concentrate of anthrax vaccine precipitate (AVP). This is the antigenic composition that is used for vaccine formulation. Although the vaccine is subjected to animal tests for potency and safety prior to human use, there is no separate routine biochemical characterisation.
One further cell-free anthrax vaccine is available for human use. This vaccine is produced in the United States of America and is broadly similar to that available under PL1511/0037, except that a different B. anthracis strain is used and grown anaerobically. The process is fermenter-based, and the culture filtrate is absorbed on to an aluminium hydroxide suspension.
Other available vaccines comprise live, attenuated spore suspensions. However, because of the inherent risks associated with attenuated pathogens, these vaccines are usually restricted to non-human use.
Anthrax toxin consists of three distinct polypeptides known as protective antigen (PA), oedema factor (EF), and lethal factor (LF). The toxin components act in specific binary combinations of PA and EF to form oedema toxin (ET), which causes tissue oedema, and of PA and LF to form lethal toxin (LT), which is lethal to laboratory animals and causes lysis of monocyte and macrophage cells. Lethal toxin is considered to be the principal cause of anthrax-associated death as a consequence of its cytotoxic effects on peripheral macrophages and other cells.
PA acts as a target cell-binding moiety and, after a site-specific N-terminal activation by a cell-associated protease (furin), oligomerises and provides a high-affinity binding component for which EF and LF compete. Following binding of EF or LF to activated PA, the resulting ET or LT complexes become internalised by an acidic endosome compartment, and the toxin factors EF and LF are thereby delivered into the cytosol of the target cell.
EF is a calcium- and calmodulin-dependent adenylyl cyclase that catalyses the conversion of intracellular ATP to cAMP. EF is active in a variety of intracellular signalling pathways, and is thereby capable of disrupting a range of cellular processes.
LF is a Zn2+-dependent metalloprotease that cleaves and inactivates the dual specificity, mitogen-activated protein kinase kinases MAPKK/1 and 2, MEK-1 and MEK-2, and probably other proteins.
A survey of in vitro or in vivo published data on anthrax vaccines for human use indicates the following:—

    1. to date, all effective anthrax vaccines contain or produce PA (i.e. either the 83 kDa pro-form, or its activated 63 kDa derivative). In fact, the current dogma is that PA is necessary and sufficient alone to produce an effective anthrax vaccine, and efforts are underway to develop such a vaccine [see, for example, Baillie, L. (2001), 91, pp 609-613];
    2. the non-capsulated, toxigenic live-spore vaccines effect a higher degree of protection against all B. anthracis strains so far tested than do the licensed cell-free vaccines [see Little, S. F. (1986) Inf. and Immunol. vol. 52, No. 2, pp 509-512];
    3. the current cell-free vaccines are generally poorly defined and may vary significantly in effectiveness on a batch-by-batch basis. Accordingly, each batch must be individually tested for efficacy in an animal model prior to human use;
    4. the current cell-free anthrax vaccine manufacturing process is evaluated only on completion of the production process and packaging of the final product. Thus, in the event that any one batch of vaccine material should not meet the validation test criteria, the contributing factors cannot be identified readily. Such factors may differ between manufactured batches and the lack of understanding exacerbates any difficulties encountered in the manufacturing process;
    5. as a result of the poorly defined nature of current cell-free vaccines, these vaccines may contain quantities of PA together with LF and/or EF which, upon in vivo (or in vitro) activation of PA to the 63 kDa form, may form LT and ET and exert adverse effects on the recipient of the vaccine. Such vaccines may, of course, also contain other B. anthracis proteins, both secreted and lysis products, peptidoglycan, nucleic acid and carbohydrate, which may compromise protective efficacy;
    6. the current cell-free vaccine compositions are highly variable in terms of LF, PA, and EF concentrations, so much so that EF may be absent from some preparations; and
    7. the current cell-free compositions are highly variable in terms of total protein content. Thus, the concentration of toxin components present in a given composition may vary significantly. This, in turn, may affect efficacy and potential toxicity in humans.


Over the last few years there has been notable academic research in the anthrax field. Sharma et al. (1996) describe the expression of native PA from E. coli. The signal sequence of the outer membrane protein A (OmpA) was added to the 5′-end of the PA gene and allowed the purification of the protein from the E. coli periplasmic space. Further research has allowed identification of the native binding sites and translocation domain of PA [see Bhatnagas, R. (2001) Critical Rev. in Microbiol., 27(3), pp 167-200; and Batra, S. (2001) Biochem. and Biophys. Res. Comm., 281, pp 186-192]. Thus, the structure and binding/translocation domains of PA have been well documented.
Recently, a second-generation “recombinant” anthrax vaccine has been proposed by The Ohio State University Research Foundation [see WO 01/45639; and Price, B. M. (2001) Inf. and Immun., vol. 69, No. 7, pp 4509-4515]. The described vaccine is based on PA and LF, wherein the LF molecule has been modified so as to be zinc metalloprotease negative. Thus, the described PA and LF components are fully capable of binding to one another to form an LT molecule, but the resulting LT molecule is not cytotoxic as there is no active zinc metalloprotease function present with the LF component.
Ahuja Nidhi et al., Biochem. and Biophys. Research Communications, Vol. 287, No. 2, 21 Sep. 2001, pp 542-549, describes PA mutants having impaired oligomerization and their potential as vaccine candidates.
Batra Smriti et al., Biochem. and Biophys. Research Communications, Vol. 281, No. 1, 16 Feb. 2001, pp 186-192 describes PA mutants having mutant residues that may have a role in membrane insertion of PA and/or translocation of LF/EF into the cytosol.
WO 02/04646 describes PA polypeptide domains capable of producing an immune response. The PA polypeptide is produced in E. coli and accumulates in the form of inclusion bodies.
DNA-based anthrax vaccine compositions are described in WO 2004/024067. The vaccine compositions contain anthrax nucleic acids that have been modified to optimise expression in a eukaryotic host—e.g. the patient to whom the vaccine composition is administered.
In view of the increasing threats of bio-terrorism and biological warfare, there is a need for alternative anthrax vaccines, and for vaccines that address one or more of the above-identified problems.
Thus, according to a first aspect of the present invention, there is provided a polynucleotide sequence comprising a nucleic acid sequence having at least 75% identity to SEQ ID NO: 1, wherein said nucleic acid sequence encodes recombinant Bacillus anthracis Protective Antigen (rPA); or a fragment of said nucleic acid sequence wherein said fragment encodes a fragment of recombinant Bacillus anthracis Protective Antigen (rPA).
In this regard, SEQ ID NO: 1 represents a modified nucleic acid that encodes rPA. The sequence of SEQ ID NO: 1 is approximately 70% identical to the wild-type Bacillus anthracis nucleic acid sequence encoding PA, provided herein as SEQ ID NO: 2.
The present inventors have found that by modifying the wild-type PA nucleic acid sequence (SEQ ID NO: 2), expression levels of rPA protein may be significantly improved. Thus, the present invention relates to non-natural nucleic acid sequences which encode for the rPA polypeptide. Particularly, the non-natural nucleic acid sequences are selected to increase expression levels of rPA expressed in heterologous systems, such as heterologous bacterial systems, e.g. E. coli. Preferably, the rPA polypeptide or fragment thereof, which is expressed from the modified, non-natural nucleic acid sequence (or fragment thereof) of the invention, is expressed at a level that is at least 110%, at least 120%, at least 150%, at least 200%, at least 250%, at least 300%, at least 400%, or at least 500% higher than that expressed from the wild-type nucleic acid sequence under equivalent conditions.
The polynucleotide of the invention comprises a nucleic acid sequence (or fragment thereof) that encodes rPA (or a fragment thereof). This rPA encoding nucleic acid sequence (or fragment thereof) is referred to herein as the rPA nucleic acid (or fragment thereof). Thus, the polynucleotide of the present invention may comprise the rPA nucleic acid, plus other coding and/or non-coding sequences. By way of example, non-coding sequences that may be comprised in the polynucleotide of the present invention include promoter sequences and transcription/translation initiation and termination sequences.
In this regard, the rPA nucleic acid sequence of the present invention may embrace a number of modifications, which result in the same translated amino acid sequence of the encoded polypeptide. Numerous factors should be taken into account when modifying a nucleic acid sequence, for example, the degree of degeneracy available, codon usage, and predicted RNA secondary structure considerations. For example, many amino acids are designated by more than one codon, due to the “degeneracy” of the genetic code. In more detail, alanine is coded for by 4 different triplets, and serine is coded for by 6 different triplets. This degeneracy allows for DNA base composition to vary over a wide range without altering the amino acid sequence of the protein encoded by the DNA.
The wild-type polypeptide sequence of Bacillus anthracis UM44 PA is provided in SEQ ID NO: 5 (see also, Vodkin, M., et al., Cell, 34:693 (1983); and Welkos, S., et al., Gene, 69(2): 287 (1988)).
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences may be then compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequent coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percentage sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
Optimal alignment of sequences for comparison may be conducted, for example, by the local homology alignment algorithm of Smith and Waterman [Adv. Appl. Math. 2: 484 (1981)], by the algorithm of Needleman & Wunsch [J. Mol. Biol. 48: 443 (1970)] by the search for similarity method of Pearson & Lipman [Proc. Nat. Acad. Sci. USA 85: 2444 (1988)], by computer implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA—Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705), or by visual inspection [see Current Protocols in Molecular Biology, F. M. Ausubel et al., eds, Current Protocols, a joint venture between Greene Publishing Associates, In. and John Wiley & Sons, Inc. (1995 Supplement) Ausubel].
Examples of algorithms suitable for determining percent sequence similarity are the BLAST and BLAST 2.0 algorithms [see Altschul (1990) J. Mol. Biol. 215: pp. 403-410; and “www.ncbi.nlm.nih.gov” of the National Center for Biotechnology Information].
In one embodiment of a polypeptide homology comparison, the identity exists over a region of the sequences that is at least 10 amino acids, preferably at least 20 amino acids, more preferably at least 35 amino acids in length. In a preferred polypeptide homology comparison, the identity exists over a region of the sequences that is at least 100 amino acids, preferably at least 200 amino acids, more preferably at least 350 amino acids in length.
The terms “peptide” or “polypeptide” throughout this specification are synonymous with the term “protein”, and do not refer to a specific length of the product. These terms may embrace post-translational modifications such as glycosylation, acetylation, and phosphorylation.
Reference throughout the present application to rPA polypeptides, polynucleotides and nucleic acids embraces fragments, variants and derivatives thereof. In particular, reference throughout the present application to rPA polypeptides embraces fragments, variants and derivatives thereof that have a common antigenic cross-reactivity with wild-type Bacillus anthracis PA (SEQ ID NO: 5). Similarly, reference throughout the present application to rPA polynucleotides and nucleic acids embraces fragments, variants and derivatives thereof that encode peptides having a common antigenic cross-reactivity with wild-type Bacillus anthracis PA (SEQ ID No. 5).
In one embodiment, the above-mentioned fragments, variants and derivatives may have a common antigenic cross-reactivity with one or more of the four domains of the mature 735 amino acid monomer (see SEQ ID NO: 5) described below:

    DOMAIN 1: amino acids 1-258. This domain binds two Ca2+ ions and is the cleavage site for proteases to activate the PA protein. The product of this cleavage is the amino terminal fragment a20 (20K fragment). A furin cleavage site is located at amino acids 164-167.
    DOMAIN 2: amino acids 259-487. This domain is involved in the formation of hexamer and has flexible loop which aids membrane insertion.
    DOMAIN 3: amino acids 488-595. This domain currently has no known function.
    DOMAIN 4: amino acids 596-735. This domain is involved in receptor binding.


In preferred embodiments, polypeptide “fragments” of the invention comprise at least one of the four domains identified above. More preferably, they comprise at least two, at least three, or all four of these domains in any combination. In a particular embodiment, they comprise at least domains 2 & 3 identified above.
Each of the four domains identified above is considered to comprise important epitope(s) of wild-type Bacillus anthracis PA. In addition, PA epitopes have been identified as shown in the two tables below (the “B Cell” table and the “T Cell” table).
In a preferred embodiment of the invention, polynucleotides are provided that encode one or more epitopes or partial epitopes of PA. By way of example, SEQ ID NOs: 36-105 encode all or part of the first, and the third to the sixth, epitopes listed in the “B Cell” table, and all three of the epitopes listed in the “T Cell” table. SEQ ID NOs: 66-105 further encode the second epitope listed in the “B-Cell” table.












B-Cell Epitopes from Human and
Epitope



Non Human Primates (NHPs)
Position











Immunized

in rPA



Species
Epitope Sequence
protein
Reference





H. sapiens
IKLNAKMNILIRDKRFHYDRN
581-601
Les Baillie et al., “Characterisation of the human immune



(SEQ ID NO: 107)

response to the UK anthrax vaccine”, FEMS Immunol. Med.





Microbiol. 2004


 


M..
PLYISNPNY 
686-694
Laffly et al., “Selection of a macaque Fab with framework


fascicularis
(SEQ ID NO: 108)

regions like those in humans, high affinity, and ability





to neutralize the protective antigen of Bacillus anthracis





by binding to the segment of PA between residues 686 and





694”, Antimicrob. Agents Chemother. 2005


 


M. mulatta
—
488-735 
E D Williamson, et al. Infect. Immun. 2005


 


M. mulatta
—
596-735
′′


 


M. mulatta
—
  1-258
′′


 


P.
—
614-735
Chen et al., Efficient neutralization of anthrax toxin by


troglodytes


chimpanzee monoclonal antibodies against protective





antigen, J. Infect. Dis. 2006





















T-Cell Epitopes from Human and 
Epitope



Non Human Primates (NHPs)
Position











Immunized

In rPA



Species
Epitope Sequence
protein
Reference





H. sapiens
PIYNVLPTTSLVLGKNQTLAT
373-393
Laughlin et al., Antigen-specific CD4+ T cells



(SEQ ID NO: 109)

recognize epitopes of protective antigen 





following vaccination, Infect. Immun. 2007


 


H. sapiens
SLVLGKNQTLAT 
381-392
Laughlin et al., Antigen-specific CD4+ T cells



(SEQ ID NO: 110)

recognize epitopes of protective antigen 





following vaccination, Infect. Immun. 2007


 


H. sapiens
RLYQIKIQYQRENPTE 
112-127
Laughlin et al., Antigen-specific CD4+ T cells



(SEQ ID NO: 111)

recognize epitopes of protective antigen 





following vaccination, Infect. Immun. 2007









The term “fragment” of a polypeptide means a peptide consisting of at least 5, preferably at least 10, more preferably at least 20, and most preferably at least 35 amino acid residues of the full-length polypeptide that is the product of the polynucleotide in question. The fragment preferably includes at least one epitope of the corresponding full-length polypeptide. The fragment may result from enzymatic break-down of the corresponding full-length polypeptide. Alternatively, a fragment of the corresponding full-length polypeptide may be produced by expressing a polynucleotide that is fragment of the corresponding full-length polynucleotide.
In preferred embodiments, the polypeptide “fragment” has an amino acid length which is at least 10%, preferably at least 20%, preferably at least 30%, preferably at least 40%, preferably at least 50%, preferably at least 70%, and more preferably at least 80%, or at least 90%, that of the length of the amino acid sequence of the corresponding full-length polypeptide. For example, the polypeptide fragment may comprise at least 100, preferably at least 150, preferably at least 200, preferably at least 300, most preferably at least 400, or at least 500, or at least 600, or at least 700, amino acid residues, of the wild-type PA polypeptide sequence (SEQ ID NO: 5).
The present invention embraces “variants”. An example of a “variant” is a peptide or peptide fragment that contains one or more analogs of an amino acid (e.g. an unnatural amino acid), or a substituted linkage. In a further embodiment, a “variant” may be a mimic of the peptide or peptide fragment, which mimic reproduces at least one epitope of the peptide or peptide fragment. The mimic may be, for example, a nucleic acid mimic, preferably a DNA mimic.
The present invention also embraces “derivatives”, meaning a protein comprising the peptide (or fragment, or variant thereof) in question. Thus, a derivative may include the peptide in question, and a further peptide sequence that may introduce one or more additional epitopes. The further sequence should preferably not interfere with the basic folding and thus conformational structure of the peptide in question.
Examples of a “derivative” are a fusion protein, a conjugate, and a graft. Thus, two or more peptides (or fragments, or variants) may be joined together to form a derivative. Alternatively, a peptide (or fragment, or variant) may be joined to an unrelated molecule (e.g. a second, unrelated peptide). Derivatives may be chemically synthesized, but will be typically prepared by recombinant nucleic acid methods. Additional components such as lipid, and/or polysaccharide, and/or polyketide components may be included in a derivative.
All of the molecules “fragment”, “variant” and “derivative” have a common antigenic cross-reactivity and/or substantially the same in vitro or in vivo biological activity as the product of the polynucleotide in question from which they are derived. By way of example, an antibody capable of binding to a fragment, variant or derivative would be also capable of binding to the product of the polynucleotide in question.
It is a preferred feature that the fragment, variant and derivative each possess the active site of the peptide in question. Alternatively, all of the above embodiments of a peptide of the present invention share a common ability to induce a “recall response” of a T-lymphocyte which has been previously exposed to an antigenic component of a Bacillus anthracis infection.
An rPA peptide fragment, variant or derivative preferably has one or more of the following properties—a) able to bind to the PA receptor on a cell membrane; b) able to bind to EF and/or LF; and c) able to be cleaved by furin protease. Thus, in one embodiment, a fragment, variant or derivative of a peptide of the present invention may be identified by carrying out simple tests for the above-mentioned properties, as described in WO 03/037370 which is incorporated by reference herein.
The terms DNA “fragment”, polynucleotide “fragment” and nucleic acid “fragment” used in this application refer to a polynucleotide that will usually comprise at least about 5 codons (15 nucleotides), more usually at least about 7 to 15 codons, and most preferably at least about 35 codons. This number of nucleotides is usually about the minimal length required for a successful probe that would hybridize specifically (e.g. under selective hybridization conditions) with such a sequence.
Preferably, the DNA “fragment” of the invention comprises nucleotides encoding at least one of the four PA protein domains identified above. More preferably, the DNA “fragment” comprises nucleotides encoding at least two, at least three, or all four of the domains identified above in any combination. The corresponding DNA base numbering for the four PA protein domains is as follows:

    DOMAIN 1: by 1-774 (774 bp)
    DOMAIN 2: by 775-1461 (687 bp)
    DOMAIN 3: by 1462-1785 (324 bp)
    DOMAIN 4: by 1786-2205 (420 bp)


In a particular embodiment, the DNA “fragment” comprises DNA encoding protein at least domains 2 & 3 as identified above. Examples of such fragments are given in SEQ ID Nos: 36-105, which relate to truncated versions of SEQ ID NO: 1. These truncated sequences encode domains 2 & 3 in their entirety and substantial portions of both domains 1 & 4.
In preferred embodiments, the DNA “fragment” has a nucleotide length which is at least 10%, preferably at least 20%, preferably at least 30%, preferably at least 40%, preferably at least 50%, preferably at least 70%, and more preferably at least 80% or at least 90% that of the coding sequence of the corresponding gene. For example, the fragment may comprise at least 200, 300, 400, 500 or 600, preferably at least 900, most preferably at least 1200, or at least 1500, or at least 1700, or at least 1900, or at least 2100 nucleotides of the full-length rPA nucleic acid sequence of the present invention. In particular embodiments, the DNA fragments have at least 1755, or at least 1806, or at least 1854, or at least 1857, or at least 1905, or at least 1953, or at least 2055 nucleotides of the full-length rPA sequence of the present invention.
The present invention embraces DNA “variants”. A DNA variant is a DNA sequence that has substantial homology or substantial similarity to a reference sequence, such as the coding sequence (or a fragment thereof) of the corresponding wild-type (natural) gene. A nucleic acid or fragment thereof is “substantially homologous” (or “substantially similar”) to another if, when optimally aligned (with appropriate nucleotide insertions or deletions) with the other nucleic acid (or its complementary strand), there is nucleotide sequence identity in at least about 60% of the nucleotide bases, usually at least about 70%, more usually at least about 80%, preferably at least about 90%, and more preferably at least about 95 to 99% of the nucleotide bases. Homology determination is performed as described supra for peptides.
Alternatively, a DNA “variant” is substantially homologous (or substantially similar) with the coding sequence (or a fragment thereof) of a wild-type (natural) gene when it is capable of hybridizing under selective hybridization conditions. Nucleic acid hybridization will be affected by such conditions as salt concentration (e.g. NaCl), temperature, or organic solvents, in addition to the base composition, length of the complementary strands, and the number of nucleotide base mismatches between the hybridizing nucleic acids, as will be readily appreciated by those skilled in the art. Stringent temperature conditions are preferably employed, and generally include temperatures in excess of 30° C., typically in excess of 37° C. and preferably in excess of 45° C. Stringent salt conditions will ordinarily be less than 1000 mM, typically less than 500 mM, and preferably less than 200 mM. The pH is typically between 7.0 and 8.3. However, the combination of parameters is much more important than the measure of any single parameter. See, for example, Wetmur and Davidson (1968) J. Mol. Biol. 31:349-370.
Selectivity of hybridization exists when hybridization occurs which is substantially more selective than total lack of specificity. Typically, selective hybridization will occur when there is at least about 65% homology over a stretch of at least about 14 nucleotides, preferably at least about 70%, more preferably at least about 75%, and most preferably at least about 90% (see, Kanehisa (1984) Nuc. Acids Res. 12: 203-213). The length of homology comparison, as described, may be over longer stretches, and in certain embodiments will often be over a stretch of at least about 17 nucleotides, usually at least about 20 nucleotides, more usually at least about 24 nucleotides, typically at least about 28 nucleotides, more typically at least about 32 nucleotides, and preferably at least about 36 or more nucleotides. In a preferred embodiment, the length of homology comparison is over a stretch of at least about 170 nucleotides, usually at least about 200 nucleotides, more usually at least about 240 nucleotides, typically at least about 280 nucleotides, more typically at least about 320 nucleotides, and preferably at least about 360 or more nucleotides.
The present invention embraces DNA “derivatives”, meaning a DNA polynucleotide which comprises a DNA sequence (or a fragment, or variant thereof) corresponding to the coding sequence of the reference gene, e.g. the wild-type Bacillus anthracis PA gene, and an additional DNA sequence which is not naturally associated with the DNA sequence corresponding to the coding sequence. The comments on peptide derivatives supra also apply to DNA “derivatives”. A “derivative” may, for example, include two or more coding sequences of an operon. Thus, depending on the presence or absence of a non-coding region between the coding sequences, the expression product(s) of such a “derivative” may be a fusion protein, or separate peptide products encoded by the individual coding regions.
The above terms DNA “fragment”, “variant”, and “derivative” have in common with each other that the resulting peptide products have cross-reactive antigenic properties, which are substantially the same as those of the corresponding wild-type peptide. Preferably all of the peptide products of the above DNA molecule embodiments of the present invention bind to an antibody which also binds to the wild-type peptide. Alternatively, all of the above peptide products are capable of inducing a “recall response” of a T lymphocyte, which has been previously exposed to an antigenic component of a Bacillus anthracis infection.
Thus, a DNA fragment, variant or derivative may be identified by way of its encoded peptide product—for example, by carrying out the simple tests mentioned above (and described in WO 03/037370).
Polynucleotides of the present invention comprise a nucleic acid having at least 75%, preferably at least 80%, more preferably at least 85%, more preferably at least 90%, even more preferably at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% and most preferably 99% or 100% identity to SEQ ID NO: 1; or a fragment of said nucleic acid.
Specific polynucleotides having between 91 and 99% identity to SEQ ID NO: 1 (minus the terminal “TAA” stop codon) are provided in SEQ ID NOs: 9 to 35 as shown in the table below.
















% Identity
No. of bases




to SEQ ID
differing from



SEQ ID NO
No. 1
SEQ ID No. 1




















SEQ ID No. 9
99.00
22



SEQ ID No. 10
99.00
22



SEQ ID No. 11
99.00
22



SEQ ID No. 12
98.00
44



SEQ ID No. 13
98.00
44



SEQ ID No. 14
98.00
44



SEQ ID No. 15
97.01
66



SEQ ID No. 16
98.00
66



SEQ ID No. 17
98.00
66



SEQ ID No. 18
96.01
88



SEQ ID No. 19
96.01
88



SEQ ID No. 20
96.01
88



SEQ ID No. 21
95.01
110



SEQ ID No. 22
95.01
110



SEQ ID No. 23
95.01
110



SEQ ID No. 24
94.01
132



SEQ ID No. 25
94.01
132



SEQ ID No. 26
94.01
132



SEQ ID No. 27
93.02
154



SEQ ID No. 28
93.02
154



SEQ ID No. 29
93.02
154



SEQ ID No. 30
92.02
176



SEQ ID No. 31
92.02
176



SEQ ID No. 32
92.02
176



SEQ ID No. 33
91.02
198



SEQ ID No. 34
91.02
198



SEQ ID No. 35
91.02
198










In one embodiment, polynucleotides of the invention comprise a nucleic acid having at least 75%, preferably at least 80%, more preferably at least 85%, more preferably at least 90%, even more preferably at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% and most preferably 99% or 100% identity to SEQ ID NO: 36. SEQ ID NO: 36 is a truncated version of SEQ ID NO: 1 and comprises base pairs 301-2055 of SEQ ID NO: 1. Specific polynucleotides having between 91 and 99% identity to SEQ ID NO: 36 are provided in SEQ ID NOs: 37 to 45 as shown in the table below.
















% Identity
No. of bases




to SEQ ID
differing from



SEQ ID NO
No. 36
SEQ ID No. 36




















SEQ ID No. 37
98.97
18



SEQ ID No. 38
98.06
34



SEQ ID No. 39
97.04
52



SEQ ID No. 40
95.90
72



SEQ ID No. 41
94.99
88



SEQ ID No. 42
93.96
106



SEQ ID No. 43
93.16
120



SEQ ID No. 44
92.02
140



SEQ ID No. 45
91.00
158










In another embodiment, polynucleotides of the invention comprise a nucleic acid having at least 75%, preferably at least 80%, more preferably at least 85%, more preferably at least 90%, even more preferably at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% and most preferably 99% or 100% identity to SEQ ID NO: 46. SEQ ID NO: 46 is a truncated version of SEQ ID NO: 1 and comprises base pairs 202-2055 of SEQ ID NO: 1. Specific polynucleotides having between 91 and 99% identity to SEQ ID NO: 46 are provided in SEQ ID NOs: 47-55 as shown in the table below.
















% Identity
No. of bases




to SEQ ID
differing from



SEQ ID NO
No. 46
SEQ ID No. 46




















SEQ ID No. 47
99.03
18



SEQ ID No. 48
97.95
38



SEQ ID No. 49
97.09
54



SEQ ID No. 50
96.12
72



SEQ ID No. 51
95.04
92



SEQ ID No. 52
93.96
112



SEQ ID No. 53
92.99
130



SEQ ID No. 54
92.13
146



SEQ ID No. 55
91.05
166










In another embodiment, polynucleotides of the invention comprise a nucleic acid having at least 75%, preferably at least 80%, more preferably at least 85%, more preferably at least 90%, even more preferably at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% and most preferably 99% or 100% identity to SEQ ID NO: 56. SEQ ID NO: 56 is a truncated version of SEQ ID NO: 1 and comprises base pairs 103-2055 of SEQ ID NO: 1. Specific polynucleotides having between 91 and 99% identity to SEQ ID NO: 56 are provided in SEQ ID NOs: 57-65 as shown in the table below.
















% Identity
No. of bases




to SEQ ID
differing from



SEQ ID NO
No. 56
SEQ ID No. 56




















SEQ ID No. 57
99.08
18



SEQ ID No. 58
97.95
40



SEQ ID No. 59
97.03
58



SEQ ID No. 60
96.01
78



SEQ ID No. 61
94.98
98



SEQ ID No. 62
94.06
116



SEQ ID No. 63
93.04
136



SEQ ID No. 64
92.01
156



SEQ ID No. 65
90.99
176










In another embodiment, polynucleotides of the invention comprise a nucleic acid having at least 75%, preferably at least 80%, more preferably at least 85%, more preferably at least 90%, even more preferably at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% and most preferably 99% or 100% identity to SEQ ID NO: 66. SEQ ID NO: 66 is a truncated version of SEQ ID NO: 1 and comprises base pairs 301-2106 of SEQ ID NO: 1. Specific polynucleotides having between 91 and 99% identity to SEQ ID NO: 66 are provided in SEQ ID NOs: 67-75 as shown in the table below.
















% Identity
No. of bases




to SEQ ID
differing from



SEQ ID NO
No. 66
SEQ ID No. 66




















SEQ ID No. 67
99.00
18



SEQ ID No. 68
97.90
38



SEQ ID No. 69
97.01
54



SEQ ID No. 70
96.12
70



SEQ ID No. 71
95.02
90



SEQ ID No. 72
94.02
108



SEQ ID No. 73
93.02
126



SEQ ID No. 74
92.03
144



SEQ ID No. 75
91.03
162










In another embodiment, polynucleotides of the invention comprise a nucleic acid having at least 75%, preferably at least 80%, more preferably at least 85%, more preferably at least 90%, even more preferably at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% and most preferably 99% or 100% identity to SEQ ID NO: 76. SEQ ID NO: 76 is a truncated version of SEQ ID NO: 1 and comprises base pairs 301-2157 of SEQ ID NO: 1. Specific polynucleotides having between 91 and 99% identity to SEQ ID NO: 76 are provided in SEQ ID NOs: 77-85 as shown in the table below.
















% Identity
No. of bases




to SEQ ID
differing from



SEQ ID NO
No. 76
SEQ ID No. 76




















SEQ ID No. 77
99.03
18



SEQ ID No. 78
98.06
36



SEQ ID No. 79
96.98
56



SEQ ID No. 80
96.02
74



SEQ ID No. 81
95.05
92



SEQ ID No. 82
93.97
112



SEQ ID No. 83
93.00
130



SEQ ID No. 84
92.03
148



SEQ ID No. 85
90.95
168










In another embodiment, polynucleotides of the invention comprise a nucleic acid having at least 75%, preferably at least 80%, more preferably at least 85%, more preferably at least 90%, even more preferably at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% and most preferably 99% or 100% identity to SEQ ID NO: 86. SEQ ID NO: 86 is a truncated version of SEQ ID NO: 1 and comprises base pairs 202-2106 of SEQ ID NO: 1. Specific polynucleotides having between 91 and 99% identity to SEQ ID NO: 86 are provided in SEQ ID NOs: 87-95 as shown in the table below.
















% Identity
No. of bases




to SEQ ID
differing from



SEQ ID NO
No. 86
SEQ ID No. 86




















SEQ ID No. 87
98.95
20



SEQ ID No. 88
98.01
38



SEQ ID No. 89
96.96
58



SEQ ID No. 90
96.01
76



SEQ ID No. 91
94.96
96



SEQ ID No. 92
94.02
114



SEQ ID No. 93
92.97
134



SEQ ID No. 94
92.02
152



SEQ ID No. 95
90.97
172










In another embodiment, polynucleotides of the invention comprise a nucleic acid having at least 75%, preferably at least 80%, more preferably at least 85%, more preferably at least 90%, even more preferably at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% and most preferably 99% or 100% identity to SEQ ID NO: 96. SEQ ID NO: 96 is a truncated version of SEQ ID NO: 1 and comprises base pairs 103-2157 of SEQ ID NO: 1. Specific polynucleotides having between 91 and 99% identity to SEQ ID NO: 96 are provided in SEQ ID NOs: 97-105 as shown in the table below.
















% Identity
No. of bases




to SEQ ID
differing from



SEQ ID NO
No. 96
SEQ ID No. 96




















SEQ ID No. 97
99.03
20



SEQ ID No. 98
97.96
42



SEQ ID No. 99
96.98
62



SEQ ID No. 100
96.01
82



SEQ ID No. 101
95.04
102



SEQ ID No. 102
93.97
124



SEQ ID No. 103
93.00
144



SEQ ID No. 104
92.02
164



SEQ ID No. 105
91.15
182










In one embodiment, polynucleotide sequences of the present invention further comprise a polynucleotide encoding a secretion sequence. The polynucleotide encoding the secretion sequence is preferably cloned upstream of the rPA nucleic acid sequence, or fragment thereof, and is most preferably operatively linked to said nucleic acid sequence, or fragment thereof.
Secretion sequences may allow the encoded protein to cross and/or lodge in cell membranes, and thus attain its functional topology or be secreted from a host cell. In this regard, the secretion sequence may be for extracellular translocation of the expressed polypeptide from a host cell (e.g. a bacterial host cell) into the extracellular environment. Alternatively, the secretion sequence may be for periplasmic translocation of the expressed polypeptide from a bacterial host cell cytoplasm into the periplasmic space.
It is particularly preferred that the secretion sequence is cleavable from the expressed polypeptide during periplasmic translocation or during extracellular translocation, in which case the periplasmic/extracellular polypeptide is free of this sequence. One example of such a ‘cleavable’ sequence is a cpg leader sequence encoded by SEQ ID NO: 3.
The cpg leader sequence illustrated in SEQ ID NO: 3 is designed such that it has a 5′-NdeI restriction site for inserting into an expression vector at a NdeI site, and a 3′-MscI site for fusion with a rPA nucleic acid sequence, or fragment thereof, where a similar MscI site has preferably been engineered. Thus, the cpg leader is cleaved from the expressed rPA protein (or protein fragment) as it passes through a host cell membrane, leaving the ‘trimmed’ mature rPA protein, or fragment thereof, in the extracellular environment or periplasmic space accordingly.
Other suitable secretion sequences for use in the present invention are described in Watson (1984) Proc. Nat. Acad. Sci. USA. vol. 12: 5145; and Makrides (1996) Microbiological Reviews 60: 512-538; and include, ompA (Denefle et al. (1989) Gene 85: 4990-510; and Ghrayeb et al. (1984) EMBO J. 3: 2437-2442.); pelB (Better et al. (1988) Science 240: 1041-1043; and Lei et al. (1987) J. Bacteriol. 169: 4379-4383); including a degenerate version thereof—see Le Calvez et al. (1996) Gene 170: 51-55; phoA (Denefle et al. (1989) Gene 85: 499-510; and Oka et al. (1985) Proc. Nat. Acad. Sci. USA. 82: 7212-7216); ompT (Johnson et al. (1996) Protein Expression Purif. 7: 104-1123); lamB (Hoffman & Wright (1985) Proc. Nat. Acad. Sci. USA. 82: 5107-5111); ompF (Hoffman & Wright (1985)); beta lactamase (Kadonaga et al. (1984) J. Biol. Chem. 259: 2149-2154; and Villa-Komaroff et al. (1977) Proc. Nat. Acad. Sci. USA. 75: 3727-3731); Staphylococcus aureus protein A (Abrahmsen (1986) Nucl. Acids Res. 14: 7487-7500; and Macyntyre & Henning (1990) Biochimmie 72: 157-167); Bacillus subtilis endoglucanase (Proudfoot et al. (1996) J. Biol. Chem. 271: 2599-2603); murine RNAse (Schein et al. (1992) Biochem. J. 283: 137-144); human growth hormone (Gray et al. (1985) Gene 39: 247-254); and enterotoxins ST-II, LT-A and LT-B (Fujimoto et al. (1988) J. Biotechnol. 8: 77-86; and Morioka-Fujimoto et al. (1991) J. Biol. Chem. 266: 1728-1732).
In one embodiment, the polynucleotide sequence of the present invention comprises a nucleic acid of the present invention, or a fragment thereof, having a 3′ and a 5′ end, and said nucleic acid or fragment thereof has a codon encoding a methionine residue cloned to the 5′ end. By way of example, the nucleic acid may be SEQ ID NO: 7 (or a fragment of SEQ ID NO: 7 that includes the 5′ terminal, met-encoding codon of SEQ ID NO: 5). This methionine-encoding codon is added in order to increase stability of the final (signal-less) protein when expressed in E. coli. Thus, rPA protein encoded by the polynucleotide of this particular embodiment of the invention is distinguished from wild-type PA protein naturally produced in Bacillus anthracis by the addition of an extra methionine residue to the N-terminus.
The present invention thus also provides a polypeptide or polypeptide fragment encoded by the polynucleotide of the present invention. Polypeptides of the present invention may therefore comprise an amino acid sequence encoding rPA, or a fragment thereof, with an extra methionine residue added at the N-terminus of the rPA amino acid sequence.
In a related aspect, the present invention also provides an isolated RNA molecule that is encoded by a DNA polynucleotide sequence of the present invention, or a fragment or variant or derivative of said DNA sequence.
Also contemplated within the invention are expression vectors comprising a polynucleotide of the present invention. Expression vectors are useful for the expression of heterologous nucleic acid sequences in a host cell. As used herein, the term “heterologous” means that the polynucleotide or polypeptide sequence concerned does not naturally exist in the cell, but has been introduced into it, for example by transformation, transfection, injection etc.
Expression vectors generally are replicable polynucleotide constructs that include coding regions for a peptide, operably linked to suitable transcriptional and translational regulatory elements. Examples of regulatory elements usually included in expression vectors are promoters, enhancers, ribosomal binding sites, and transcription and translation initiation and termination sequences. These regulatory elements are operably linked to the sequence to be translated. A nucleic acid sequence is operably linked when it is placed into a functional relationship with another nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression. Generally, “operably linked” means that the DNA sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in reading frame. The regulatory elements employed in the expression vectors containing a polynucleotide encoding a virulence factor are functional in the host cell used for expression.
It is preferred that the expression vector expresses the polynucleotide in the absence of a chemical inducer—i.e. a chemical inducer is not required for induction of expression from the expression vector. In one embodiment, the vector expresses the polynucleotide constitutively, with no induction of gene expression needed. In another embodiment, the vector expresses the polynucleotide in response to an environmental stimulus or stimuli—such as starvation, or limitation of nutrients or oxygen, such as when a component or components become exhausted in the growth medium.
The term “promoter” is well known in the art, encompasses relatively simple, minimal promoters to complex promoters having upstream elements and enhancers. Suitable promoters for expression in prokaryotic and eukaryotic host cells are well known in the art, and are described in, for example, Molecular Cloning. A laboratory Manual (Sambrook et al., Second edition, 1989) and Current Protocols in Molecular Biology (Ausubel et al., eds., 1994).
Appropriate promoter and other necessary vector sequences are selected so as to be functional in the host. By way of example, promoters such as the trp, lac and phage promoters (e.g. T7, T4, lambda, fd), tRNA promoters and glycolytic enzyme promoters may be used in prokaryotic hosts. It is preferred that the expression vector comprises a “strong” promoter,—i.e. a promoter that is selected so as to ensure that the encoded rPA polypeptide (or fragment thereof) is highly expressed. Examples of strong promoters include recA, malate dehydrogenase, T7, tac, etc. In this regard, a polypeptide is said to be “highly expressed” if it is expressed at levels above 20% of total host cell soluble protein, preferably above 30%, more preferably above 40% and most preferably above 50% total host cell soluble protein. A preferred “strong promoter” for use in accordance with the invention is the malate dehydrogenase (mdh) promoter (proprietary to CAMR; U.S. Pat. No. 5,670,333).
Expression vectors may contain a selectable marker—i.e. a gene encoding a protein necessary for the survival or growth of a host cell transformed with the vector. The presence of this gene ensures the growth on a selective medium of only those host cells that contain the desired vector and that express the selectable marker. Typical selection genes encode proteins that: (a) confer resistance to antibiotics or other toxic substances, e.g. ampicillin, tetracycline, neomycin, methotrexate, etc.; (b) complement auxotrophic deficiencies; or (c) supply critical nutrients not available from complex media. The selection of an appropriate vector and an appropriate selectable marker will depend on the host cell, and is well within the capabilities of an ordinary person of skill in the art.
Expression vectors typically contain all of the additional elements that are necessary for efficient expression of the nucleic acid in a host cell. Examples of suitable vectors for expression of heterologous proteins in bacterial include pET vectors (for example pET26b-Novagen), and pTrKHis (Invitrogen). Both these vectors achieve high-level expression of nucleic acid in E. coli. 
pMTL expression vectors are advantageous because they are capable of yielding high levels of recombinant protein, and can be very stable, even in the absence of selective pressure using antibiotics. Furthermore, those pMTL vectors based on the very strong E. coli malate dehydrogenase (mdh) promoter are particularly advantageous because induction of expression using exogenous inducer chemicals is not required (Alldread et al. (1992) Gene 14: 139-143). It is an advantage not to require an exogenous chemical inducer for regulatory reasons, since any chemical inducer may have to be rigorously and successfully removed from the final product before administration to patients.
In a particularly preferred embodiment, the expression vector is also a high copy number plasmid, such as pMTL1015 (Chambers et al. (1988) Gene 68: 139-149). pMTL1015 is a derivative of pMTL4, it replicates from a mutant of the ColE1 replicon (600 copies per cell; Minton et al. (1988) Focus 10: 56) and is encoded by SEQ ID NO: 4. Plasmid pMTL1015 is essentially identical to pMTL1003 as described by Brehm et al. (1991) Appl. Microbiol Biotechnol 36: 358-363, and has numerous advantageous features. By way of example, pMTL1015 differs from pMTL1003 in that the trp promoter has been replaced with the very powerful mdh promoter (Alldread et al. (1992) Gene 14: 139-143), and the ampicillin resistance gene has been replaced with the tetracycline resistance gene of pBR322 (Bolivar et al. (1977) Gene 2: 95). The plasmid also incorporates the pSC101 partition function (par; Miller et al. (1983) Gene 24: 309-315), the rrnB double terminator (Brosius et al. (1981) J. Mol. Biol. 148: 107-127) and the pMTL20 polylinker cloning region (Chambers et al., 1988). The par locus endows the plasmid with good segregational stability enabling antibiotic-free fermentations without plasmid loss and the tetracycline resistance marker is a biopharmaceutically acceptable drug.
An example of an expression vector suitable for use in the present invention is the vector deposited under ECACC No: 04061401.
An example of an expression vector comprising a polynucleotide according to the present invention is pMTL1015-cpg-PA-synt, deposited under ECACC No: 04052501.
The vectors containing the nucleic acids of interest can be transcribed in vitro and the resulting RNA introduced into the host cell (e.g. by injection), or the vectors can be introduced directly into host cells by methods which vary depending on the type of cellular host, including electroporation; transfection employing calcium chloride, rubidium chloride, calcium phosphate, DEAE-dextran, or other substances; microprojectile bombardment; lipofection; infection (where the vector is an infectious agent, such as a retroviral genome). The term “host cells” is meant to embrace the progeny of such cells.
The present application thus also provides a host cell comprising an expression vector as described above. It is preferred that the host cell is a bacterial cell, in particular an E. coli cell, such as E. coli strains DHS, BL21 and HMS174 (Invitrogen).
It is particularly preferred that the bacterial cell e.g. E. coli strain is a protease-deficient strain, since rPA protein is generally considered to be a protease-sensitive protein. One example of a protease-deficient strain of E. coli is E. coli RV308 (ATCC No: 31608).
Also provided by the present invention are methods for producing rPA comprising expressing the polynucleotide of the present invention.
In one embodiment, the polynucleotide is expressed—i.e. transcribed and translated, in a host cell. In another embodiment, the polynucleotide is DNA, which is transcribed into RNA in vitro, and then the RNA is then translated into protein in a host cell. The host cell may be a bacterial cell, such as an E. coli host cell. The E. coil host cell is preferably a protease-deficient strain, such as E. coli RV308 (deposited under ATCC No: 31608).
In a preferred embodiment, rPA is expressed in a host cell from the expression vector of the present invention, as described above. In this embodiment, the method may incorporate at least one, preferably two, most preferably all of the following features:—(i) the expression vector comprises the cpg leader sequence encoded by SEQ ID NO: 3; (ii) the vector is the plasmid pMTL1015, encoded by SEQ ID NO: 4; and (iii) the vector is expressed in an E. coli host cell such as E. coli RV308 (ATCC No: 31608).
In one embodiment, the method comprises the initial steps of transforming an expression vector comprising the polynucleotide of interest into a host cell, such as E. coli host cell and culturing the transformed host cell in a suitable growth medium.
Optionally, the culture is carried out under selective pressure, such as in the presence of an antibiotic, e.g. tetracycline, in which case it is an advantage for the expression vector to comprise a selectable marker that confers resistance to the antibiotic.
Culture parameters may be controlled, in order to control nutrients, pH and/or oxygen levels (dissolved oxygen tension—DOT) in the culture. For example, DOT may be controlled by agitation, back pressure, sparged airflow and/or oxygen supplementation. It is preferred that DOT is maintained at above 40%.
The temperature at which host cells are grown can have an effect on the level of protein that can be purified from the culture. For example, protein expression rate and protein degradation rate (such as due to protease activity) can both affect the amount of protein that can be extracted. Growing the cultured host cells comprising the claimed polynucleotide at a reduced temperature of less than, for example 40° C., has been found to give acceptable levels of rPA expression and stability. Thus, in one embodiment of the invention, host cells containing polynucleotides of the invention (e.g. expression vectors) are cultured at less than 40° C.; preferably at less than 37° C.; more preferably at less than 35° C.; more preferably at about 30° C., and most preferably at 25-30° C., such as 29° C., 28° C., 27° C., 26° C. and 25° C. Culturing host cells at these reduced temperatures may slow down the rate of rPA expression, but this may be useful if a high-level expression vector, such as the plasmid pMTL1015, is used for expression.
It is preferred that a growth medium is used that is free of animal products (i.e. products derived from animals), since this is advantageous for meeting the regulations for injectable products. Examples of suitable media include phytone peptone-based Terrific Broth, and soy peptone-based L-broth.
If a secretion sequence is used that enables extracellular secretion of the polypeptide into the growth medium then the growth medium may be harvested and undergo further purification steps to extract the polypeptide.
Alternatively, if the secretion sequence enables secretion of the polypeptide into the bacterial periplasm then the polypeptide product will be intracellular. In this case, the cells must be harvested from the culture medium (e.g. by centrifugation as a cell paste) and undergo further processing to extract the polypeptide from the cells. Suitable protocols for the harvesting of cell cultures, such as bacterial cultures, for the purification of polypeptides are well known in the art, and can be found in common laboratory manuals such as Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press; and Sambrook and Russell (2001) Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press.
Typically, bacterial cells can be harvested by centrifugation for extraction of either nucleic acids or polypeptides. For protein purification the conditions selected for the harvesting of cultured cells by centrifugation are generally gentler than for the extraction of nucleic acid, so as not to damage the target protein. For example, the harvesting of bacterial cells for extraction of a target polypeptide may be carried out at 4° C., by centrifugation at 4,000-5,000 g for 10-15 minutes.
It is an option for the method to further comprise testing steps, to identify the presence and/or yield of desired polypeptide, prior to further processing. In one embodiment, an ELISA-based test is carried out.
Following the fermentation (bacterial growth and harvesting) and optional testing protocols, the method may further comprise downstream processing steps in order to obtain isolated, purified, rPA protein.
The downstream processing steps employed in the present invention preferably achieve one or more of the following aims:—

    
    
        reduction in the number of chromatography steps required, compared to prior art methods;
        use of step elution rather than gradient elution for some, preferably all, chromatography steps;
        increase in the level of primary processing prior to chromatography, compared to prior art methods;
        removal of the need for the addition of conditioning agents (e.g. nucleases) where possible;
        use of techniques capable of scaling-up to at least 100 L fermentation scale; and
        use of techniques that are compatible with cGMP.
    
    


It is preferred that the purification procedure has reduced process times and volumes and/or has increased process efficiency in comparison to prior art methods. In the present invention, the number of dialysis/buffer exchange steps is preferably minimised, for example, by linking steps that generate a process stream of high conductivity with those that require a high conductivity starting material (e.g. ammonium sulphate precipitation or ion-exchange chromatography may be followed by hydrophobic interaction chromatography).
The downstream processing protocol commences with a crude mixture containing rPA polypeptide. If the rPA polypeptide is located within the host cell (e.g. within a bacterial host cell periplasm) then the cells must be treated to extract the rPA polypeptide, for example by homogenisation.
It is preferred that the method further comprises at least one separation step, carried out on the extracted rPA polypeptide. Examples of separation steps that may be included in the method are filtration steps such as diafiltration steps, and chromatography steps. In one embodiment, the method comprises at least one chromatography step and at least one filtration step.
In a particularly preferred embodiment of the present method, the extracted rPA polypeptide (together with unwanted components such as nucleic acids, other proteins, and cell debris) is subjected to diafiltration, such as tangental flow diafiltration. The purpose of this step is to alter the load of charged molecules, in preparation for subsequent separation steps, such as chromatography steps. Diafilters retain molecules of above a certain molecular weight (e.g. above 30 kDa, 40 kDa or 50 kDa) and allow dissolved substances and those below the specified molecular weight to pass through the filter. Thus, it is preferred that the method includes at least one filtration step that is a diafiltration step.
Chromatography steps may include ion-exchange chromatography (e.g. using a Q-sepharose anion exchange column) and hydrophobic charge chromatography (e.g. using a mercaptoethyl pyridine hypercel column). Other examples of suitable chromatographic techniques are known in the art and would be routinely available to a skilled person. Thus, the present method may include at least one ion-exchange chromatography step and at least one hydrophobic charge chromatography step.
In one embodiment, when the rPA polypeptide has been expressed in an E. coli host cell, there may be residual E. coli endotoxin associated with the rPA polypeptide and this can be separated from the rPA polypeptide by a (further) separation step, if necessary. In one embodiment, separation of endotoxin may be achieved by filtration, using a charged filter to which the toxin adheres.
Thus, in a specific embodiment, a method of producing rPA comprises the steps of obtaining host cells that express the polypeptide of the present invention; extracting the expressed rPA from the host cells; subjecting the extracted rPA to a diafiltration step (e.g. tangental flow diafiltration at 30 kDa); followed by at least one chromatography step selected from ion exchange chromatography and hydrophobic charge chromatography; then a further diafiltration step (which may be at a higher molecular weight cut-off e.g. 40 kDa or 50 kDa); and an optional further filtration step to remove any residual protein and/or bacterial endotoxin.
In one embodiment of the present invention, the combination of high-level gene expression (plasmid containing strong promoter), periplasmic translocation (secretion sequence), nucleic acid sequence modification (rPA nucleic acid sequence) and efficient downstream processing, results in an increase of rPA protein yields that are 10 to 20-fold above yields previously available in the prior art.
Furthermore, the downstream processing steps of the present invention allow rPA protein to be obtained that has greater than 70%, preferably greater than 80%, greater than 90%, or greater than 95%, and more preferably greater than 98% purity.
Polypeptide purity or homogeneity may be indicated by, for example, polyacrylamide gel electrophoresis of a protein sample, followed by visualizing a single polypeptide band upon staining the gel. Alternatively, higher resolution may be provided by using, for example, HPLC.
If desirable, the amino acid sequence of the polypeptides of the present invention may be determined by protein sequencing methods.
The present invention thus also provides an rPA polypeptide or fragment thereof produced by the method of the present invention. In one embodiment, the polypeptide may be identical to wild-type PA produced by Bacillus anthracis. In another embodiment, as described above, the polypeptide or fragment thereof may be distinguished from wild-type PA (or a fragment thereof) by the presence of an extra residue, such as a methionine residue, at the N-terminus of the rPA amino-acid sequence. For example, the polypeptide may be SEQ ID NO: 6, or a fragment thereof comprising the N-terminal methionine residue of SEQ ID NO: 6.
Also envisaged by the present invention is a kit, which may comprise one or more of a polynucleotide, an expression vector, a host cell, and a polypeptide of the present invention.
Also provided by the present invention are antigenic compositions, such as vaccine compositions, comprising a polypeptide according to the present invention.
The invention also provides methods of inducing an immune response against infection by Bacillus anthracis comprising administering a polypeptide of the present invention or an antigenic composition of the present invention.
Also provided by the present invention is use of a polypeptide of the present invention for manufacture of a medicament for inducing an immune response against infection by Bacillus anthracis. 
In this regard, “inducing an immune response” may embrace protecting against infection by Bacillus anthracis. The protection conferred by the method and/or use of the present invention may be 100%, or may be less than 100%. Preferably, “protecting against infection by Bacillus anthracis” provides protection against at least 50%, preferably at least 70%, more preferably at least 80%, most preferably at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% of Bacillus anthracis infections. Preferably, “protecting against infection by Bacillus anthracis” provides a level of protection that is at least 50%, preferably at least 70%, more preferably at least 80%, most preferably at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% effective against a Bacillus anthracis infection.
Furthermore, the term “protecting against infection” may embrace preventing infection and treating infection. In this regard, the term “preventing” includes reducing the severity/intensity of, or initiation of, a Bacillus anthracis infection. The term “treating” includes post-infection therapy and amelioration of a Bacillus anthracis infection.
The antigenic composition may be administered by conventional routes, e.g. intravenous, subcutaneous, intraperitoneal, and mucosal routes using methods well known in the art.
Typically, such antigenic compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared. The preparation may also be emulsified, or the peptide encapsulated in liposomes or microcapsules.
The active immunogenic ingredients are often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof. In addition, if desired, the vaccine may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and/or adjuvants which enhance the effectiveness of the vaccine. Examples of adjuvants which may be effective include but are not limited to: aluminum hydroxide, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxy phosphory loxy)-ethylamine (CGP 19835A, referred to as MTP-PE), and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trehalose dimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/Tween 80 emulsion.
The active components may be formulated into the vaccine as neutral or salt forms. Pharmaceutically acceptable salts include the acid addition salts (formed with free amino groups of the peptide) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or with organic acids such as acetic, oxalic, tartaric, maleic, and the like. Salts formed with the free carboxyl groups may also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.
The antigenic compositions are conventionally administered parenterally, by injection, for example, either subcutaneously or intramuscularly.
The antigenic compositions are for administration in a manner compatible with the dosage formulation, and in such amount as will be prophylactically and/or therapeutically effective. The quantity to be administered, which is generally in the range of 5 micrograms to 250 micrograms of antigen per dose, preferably about 50-100 μg per dose, depends on the subject to be treated, capacity of the subject's immune system to synthesize antibodies, and the degree of protection desired. Precise amounts of the active ingredient that is required to be administered may depend on the judgment of the practitioner and may be particular to each subject.
The antigenic composition may be given in a single dose schedule, or optionally in a multiple dose schedule. A multiple dose schedule is one in which a primary course of vaccination may be with 1-6 separate doses, followed by other doses given at subsequent time intervals required to maintain and or reinforce the immune response, for example, at 1-4 months for a second dose, and if needed, a subsequent dose(s) after several months. The dosage regimen will also, at least in part, be determined by the need of the individual and be dependent upon the judgment of the practitioner.
In addition, the antigenic composition containing the immunogenic antigen(s) may be administered in conjunction with other immunoregulatory agents, for example, immunoglobulins, as well as antibiotics.
Additional formulations which are suitable for other modes of administration include microcapsules, suppositories and, in some cases, oral formulations or formulations suitable for distribution as aerosols. For suppositories, traditional binders and carriers may include, for example, polyalkylene glycols or triglycerides; such suppositories may be formed from mixtures containing the active ingredient in the range of 0.5% to 10%, preferably 1%-2%.
Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders and contain 10%-95% of active ingredient, preferably 25%-70%.
In one embodiment the medicament may be administered intranasally (i.n.). An intranasal composition may be administered in droplet form having approximate diameters in the range of 100-5000 μm, which in terms of volume would have droplet sizes in the approximate range of 0.001-100 μl.
Intranasal administration may be achieved by way of applying nasal droplets or via a nasal spray. In the case of nasal droplets, the droplets may typically have a diameter of approximately 1000-3000 μm and/or a volume of 1-25 μl, whereas in the case of a nasal spray, the droplets may typically have a diameter of approximately 100-1000 μm and/or a volume of 0.001-1 μl.
It is possible that, following i.n. delivery of antibodies, their passage to the lungs may be facilitated by a reverse flow of mucosal secretions.
In a different embodiment, the medicament may be delivered in an aerosol formulation. The aerosol formulation may take the form of a powder, suspension or solution.
The size of aerosol particles is one factor relevant to the delivery capability of an aerosol. Thus, smaller particles may travel further down the respiratory airway towards the alveoli than would larger particles. In one embodiment, the aerosol particles have a diameter distribution to facilitate delivery along the entire length of the bronchi, bronchioles, and alveoli. Alternatively, the particle size distribution may be selected to target a particular section of the respiratory airway, for example the alveoli.
The aerosol particles may be delivered by way of a nebulizer or nasal spray.
In the case of aerosol delivery of the medicament, the particles may have diameters in the approximate range of 0.1-50 μm, preferably 1-5 μm.
The aerosol formulation of the medicament of the present invention may optionally contain a propellant and/or surfactant.
By controlling the size of the droplets which are to be administered to a patient to within the defined range of the present invention, it is possible to avoid/minimise inadvertent antigen delivery to the alveoli and thus avoid alveoli-associated pathological problems such as inflammation and fibrotic scarring of the lungs.
Intranasal vaccination engages both T and B cell mediated effector mechanisms in nasal and bronchus associated mucosal tissues, which differ from other mucosae-associated lymphoid tissues.
Intranasal delivery of antigens allows targeting of the antigens to submucosal B cells of the respiratory system. These B cells are the major local IgA-producing cells in mammals and intranasal delivery facilitates a rapid increase in IgA production by these cells against the anthrax antigens.
In one embodiment administration of the medicament comprising an anthrax antigen stimulates IgA antibody production, and the IgA antibody binds to the anthrax antigen. In another embodiment, a mucosal and/or Th2 immune response is stimulated.
In one embodiment, the vaccine composition comprises rPA protein adsorbed to adjuvant. In one embodiment, the vaccine is delivered by intramuscular injection.
The invention also provides a vector having the sequence SEQ ID NO:4.
The invention also provides a vector as deposited under ECACC No: 04061401.
The invention also provides a vector comprising a polynucleotide according to the present invention, as deposited under ECACC NO: 04052501.



Referring to the Figures of the present application:—
FIG. 1 depicts HPA clone pMTL1015-cpg-rPA-synt—i.e. the modified rPA nucleic acid sequence fused to the cpg2 leader in pMTL1015 (TcR). Manipulations required to generate this plasmid are as follows: (1) sub-clone synthetic ‘mature’ rPA sequence from sequence verified PCR product TOPO vector (i.e. without any leader) into HPA pET22bcpg vector; (2) sub-clone cpg-SynPA from pET22bcpgSynPA into pMTL1015.
FIG. 2 demonstrates SDS-PAGE of pMTL1015 clones expressing rPA after 16 hr Shake-flask culture in phytone peptone-based Terrific Broth. The key is as follows:—

    1. Blank.
    2. rPA Standard (DEV030IP; 100 μg/mL)
    3. pMTL1015 vector only
    4. pMTL1015-ompA-PA-wt
    5. pMTL1015-cpg-PA-wt
    6. pMTL1015-pelB-PA-wt
    7. pMTL1015-ompA-PA-synt
    8. pMTL1015-cpg-PA-synt
    9. pMTL1015-pelB-PA-synt
    10. Molecular weight markers


FIG. 3 shows a Western blot of pMTL1015 clones expressing rPA after 16 hrs Shake-flask culture in phytone peptone-based Terrific Broth. The key is as described above for FIG. 2.
FIG. 4 shows time course analysis by (A) SDS-PAGE and (B) Western Blot of samples from Shake-flask culture of E. coli (pMTL1015-cpg-PA-synt) in phytone peptone-based Terrific Broth. The negative control was E. coli RV308 (pMTL1015).
FIG. 5 shows growth curves of E. coli RV308 pMTL1015-ompA-PA-synt in phytone peptone-based Terrific Broth, Shake-flask culture, in baffled flasks (A and B) or non-baffled flasks (C).
FIG. 6 shows growth curves of E. coli RV308 pMTL1015-ompA-PA-wt (A and B) and pMTL1015-ompA-PA-synt [C and D) in Hy-soy based semi-defined medium, Shake-flask culture.
FIG. 7 shows growth curves of E. coli RV308 pMTL1015-pelB-PA-wt (A and B) and pMTL1015-pelB-PA-synt [C and D) in Hy-soy based semi-defined medium, Shake-flask culture.
FIG. 8 shows the growth curve of E. coli RV308 pMTL1015-cpg-PA-wt (A and B) and pMTL1015-cpg-PA-synt [C and D) in Hy-soy based semi-defined medium, Shake-flask culture.
FIG. 9 shows SDS-PAGE (12.5% PHAST-GEL) of pMTL1015 clones expressing rPA in Shake-flask culture using Hy-soy based semi-defined medium. The key is as follows:—

    1: Molecular Weight Markers
    2: RV308 pMTL1015 ompA-PA-synt
    3: RV308 pMTL1015 ompA-PA-wt
    4: RV308 pMTL1015 pelB-PA-synt
    5: RV308 pMTL1015 pelB-PA-wt
    6: RV308 pMTL1015 cpg-PA-synt
    7: RV308 pMTL1015 cpg-PA-wt
    8: Reference DEV0303IP (100 μg/mL)


FIG. 10 shows growth of E. coli RV308 pMTL1015-cpg-PA-synt in production medium (Phytone peptone 12 g/L, Bacto yeast extract 60 g/L, glucose 25 g/L, magnesium sulphate heptahydrate 2 g/L, K2HPO4 12.54 g/L, KH2PO4 2.31 g/L and tetracycline 1.5 mg/L, pH 7.0-7.2), with varying levels of Yeast Extract, as follows:—

    A 1× yeast extract
    B 1.5× yeast extract
    C 2× yeast extract
    D 2.5× yeast extract


FIG. 11 shows growth curves (A) and rPA production curves (B) for E. coli RV308 pMTL1015-cpg-PA-synt in production medium.
FIG. 12 is a flow chart showing the downstream processing steps for isolation of rPA.
FIG. 13 (A-D) shows the sequence alignment between SEQ ID NO: 8—“DVC.Synthetic.rP” (i.e. the wild-type PA gene sequence, SEQ ID NO: 2, plus a 5′ codon encoding a methionine residue), and SEQ ID NO: 7—“AP.PA.wt.Sequenc” (i.e. the modified rPA gene sequence of the present invention, SEQ ID NO: 1, plus a 5′ codon encoding a methionine residue). The sequence identity is 71.2%. (The consensus sequence is disclosed as SEQ ID NO: 106.)



The invention is now described by reference to the following Examples.
EXAMPLE 1
rPA Expression Systems
pMTL expression vector constructs were generated, directing expression of either the wild-type PA gene sequence or the modified rPA gene sequence, fused to either the Erwinia carotovora pelB or the pseudomonad carboxypeptidase G2 (cpg2) leader sequences. The latter sequence is described in European Patent 0 121 352, and has been shown to be efficiently processed in E. coli, directing soluble protein into the periplasmic space. These rPA expression constructs were compared with Dynport Vaccine Company (DVC)'s pET26b and Invitrogen pTrk vector-based constructs for evaluation.
Generation of novel rPA pMTL-based expression clones was as follows:

    1. PCR amplification of the two PA-encoding nucleotide sequences (wild type and modified) fused to both the pelB, ompA and cpg2 leader sequences. This generated six rPA sequence options.
    2. Primary clones were constructed in a PCR product cloning vector system (e.g. Invitrogen TA Cloning).
    3. Primary clones were authenticated by DNA sequence analysis of the composite PA/leader sequences.
    4. The six rPA sequences were sub-cloned into pMTL1015 expression vector and the recombinant plasmids were authenticated.
    5. Plasmid DNA derived from the four authenticated clones was used to transform a protease-deficient expression strain, E. coli RV308 (ATCC 31608).

Strategy for Comparison of rPA Expression Systems



The six clones based on the pMTL expression plasmid were evaluated in shake-flask culture in the current production medium. The existing DVC production organism was used as a control. Growth conditions and induction initiation/duration (where applicable) were standardised as much as possible to allow a true comparison of expression levels to be made under the given experimental conditions. For example, a standard cell density was used for inoculation. Production levels were compared by sampling cultures throughout growth and following chemical cell lysis using BugBusterTM (Novagen) of harvested cells, by densitometric analysis of SDS-PAGE. Western blotting was used to confirm the identity of the rPA protein band.
Media Selection Strategy
In addition to increasing the expression level of rPA by genetic manipulation, the final yield of product was raised by growing cultures to a higher cell density using a medium containing higher nutrient levels.
The strains showing the most promise in terms of rPA production levels in the current production medium were examined further, initially in shake-flask culture, using a range of potential production media. The analytical techniques used by DVC (SDS-PAGE, RP-HPLC) were used to estimate product levels throughout growth and at harvest.
EXAMPLE 2
Shake-Flask Comparisons of rPA Expression
EXAMPLE 2.1
Phytone Peptone-Based Terrific Broth
An experiment was performed to compare the expression of rPA by six pMTL1015 clones in phytone peptone-based Terrific Broth using shake-flask culture. Since previous work using the pMTL1015 expression system at CAMR had shown that low oxygenation rates may favour product expression, cultures were set up in both baffled flasks (high oxygenation) and non-baffled flasks (low oxygenation).
The 10 mL cultures prepared as primary seed cultures for the cell banking were used to prepare seed cultures for this study. A 50 μL aliquot of the 10 mL culture was used to inoculate 50 mL of phytone peptone-based Terrific Broth in 250 mL baffled flasks.
These seed cultures were incubated at 30° C. at 150 rpm for 17 h and then used to inoculate duplicate 200 mL cultures of the same medium in 1000 mL baffled flasks and single cultures of 250 mL in 500 mL non-baffled flasks. The inoculum for each culture was calculated to give a starting OD600 of 0.1-0.2. The cultures were incubated at 30° C. and 150 rpm for 24 h. Samples (2.5 mL) were removed at 2 hourly intervals for rPA assay when the OD600 reached 5-7. Samples were centrifuged at 4,000 rpm in a Clandon T-52 bench top centrifuge for 15 min, the supernatant decanted and the pellets stored frozen at −20° C. After 24 h growth, the duplicate baffled flask cultures were bulked and the cell mass harvested by centrifugation (Sorvall RC-3, 5000 rpm for 15 min) and the cell paste stored frozen at −20° C.
FIGS. 2 and 3 show SDS-PAGE and Western blot analysis of the 16 h samples from each of the pMTL1015 clones grown in phytone peptone-based Terrific Broth under conditions of high oxygenation (baffled flasks) following treatment with BugBusterTM. It can be seen that strong protein bands are present at the expected rPA molecular mass following SDS-PAGE for the three clones expressing the synthetic gene product, with weaker bands for those clones expressing the wild type gene (FIG. 2). The amount of rPA present was estimated by comparison with the intensity of the rPA standard and confirmed by ELISA (Table 1). The Western blot analysis demonstrated the presence of some immuno-reactive material at lower molecular weights than the rPA (FIG. 3). The amount of this material relative to intact rPA was similar for all clones. It is not known at present whether this represents proteolytic degradation products or truncated expression.







TABLE 1







Comparison of rPA expression of all 12 E. coli clones


following growth in phytone peptone-based Terrific Broth.









rPA



(μg/mL culture)















OD600
*Gel



Clone
Name
E. coli host
culture
estimate
ELISA















1
pET26b-PA
BL21 (DE3)
5.5
<100
24


2
pET26b-PA-synt
BL21 (DE3)
3.6
<100
11


3
pTrck-pelB-PA
DH5a
9.7
<100
57


4
pTrck-ompA-PA
DH5α
9.7
<100
74


5
pMTL1015-pelB-PA-wt
RV308
17.3
<100
58


6
pMTL1015-ompA-PA-wt
RV308
19.7
<100
135


7
pMTL1015-cpg-PA-wt
RV308
20.4
<100
67


8
pMTL1015-pelB-PA-synt
RV308
21.1
>>100 
394


9
pMTL1015-cpg-PA-synt
RV308
23.3
>>100 
496


10
pMTL1015-ompA-PA-synt
RV308
25.3
>>100 
476


11
pTrck-pelB-PA-synt
DH5α
8.2
>100
304


12
pTrck-ompA-PA-synt
DH5α
11
>100
252





*estimate of rPA concentration from SDS-PAGE by comparison with 100 μg/mL rPA standard.






Time course samples from the pMTL1015-cpg-PA-synt clone were analysed by SDS-PAGE (Phast-gel), Western Blot (FIG. 4) and ELISA (Table 2) to determine; (a) the point at which rPA expression was maximal, and (b) whether prolonged incubation resulted in loss of product due to proteolytic activity. It can be seen that rPA expression by ELISA was optimal after 14-16 h incubation and did not change appreciably with further incubation up to 24 h (Table 2). Western blot analysis (FIG. 4) showed that the level of lower molecular weight immuno-reactive material relative to intact rPA did not change significantly with extended incubation time.







TABLE 2







Time course analysis by ELISA of samples from shake


flask culture of E. coli (pMTL1015-cpg-PA-synt)


in phytone peptone based Terrific Broth.










Time (h)
rPA (μg/mL culture)







10
107



12
313



14
507



16
532



18
488



20
491



22
487



24
525










FIG. 5 shows the growth curves obtained for E. coli RV308 (pMTL1015-ompA-PA-synt) when grown in phytone peptone-based Terrific Broth using baffled (high oxygenation) and non-baffled (low oxygenation) flasks. It can be seen that growth was substantially better in the baffled flasks. Cultures grown in non-baffled flasks reached a much lower final cell density compared with the baffled flask cultures. rPA expression was considerably lower in the cultures grown in non-baffled flasks (data not shown).
EXAMPLE 2.2
Hy-Soy-Based Semi-Defined Medium
The experiment described above (Example 2.1) was repeated using Hy-Soy based semi-defined medium in baffled flasks only. The growth curves (FIGS. 6, 7 & 8) show that lower growth rates and final cell densities were obtained in this medium compared to Terrific Broth and a lag phase of up to 8 h was obtained for the clones expressing the synthetic gene. rPA expression levels were generally lower than observed in phytone peptone-based Terrific Broth; however, a similar pattern of superior expression levels with clones expressing the synthetic gene compared with the wild-type gene was observed by SDS-PAGE (FIG. 9) and ELISA (Table 3).







TABLE 3







Comparison of rPA expression of E. coli pMTL1015 clones


following growth in Hy-soy-based semi-defined medium.









rPA



(μg/mL culture)














E. coli
Sample
*Gel



Clone
Name
host
time (h)
estimate
ELISA















5
pMTL1015-pelB-PA-wt
RV308
16
<100
50


6
pMTL1015-ompA-PA-wt
RV308
16
<100
64


7
pMTL1015-cpg-PA-wt
RV308
16
<100
56


8
pMTL1015-pelB-PA-synt
RV308
20
>100
224


9
pMTL1015-cpg-PA-synt
RV308
20
>100
170


10
pMTL1015-ompA-PA-synt
RV308
20
>100
189





*estimate of rPA concentration from SDS-PAGE by comparison with 100 μg/mL rPA standard






EXAMPLE 3
Fermenter Level Comparisons of rPA Expression
Evaluation of the following four down-selected clones in fermenter culture was continued:

    E. coli RV308 pMTL1015-cpg-PA-synt
    E. coli RV308 pMTL1015-ompA-PA-synt
    E. coli RV308 pMTL1015-ompA-PA-wt
    E. coli DH5 pTrcK-pelB-PA-synt

Medium Selection



8 L fermentations were performed in each medium under conditions as previously described with DOT and pH control.
The growth curves obtained were similar to those seen previously with the same media (see FIG. 10), but the rPA yield from production medium (Run No: PRECRV0034: Table 4) was 2500 μg/mL by ELISA. This culture was fed with 80 mL of 50% glucose solution prior to glucose depletion in the culture. A growth curve for PRECRV0034 showing rPA production can be seen in FIG. 11, but data does not indicate whether the yield has reached a maximum when the culture was harvested.
In order to determine whether the improved rPA yields obtained for E. coli RV308 pMTL1015-cpg-PA-synt when cultured in production also occurred in the other two down-selected pMTL1015 clones, parallel fermentations were set up for all three strains under these conditions. However, the 80 mL of 50% glucose fed to the previous cultures was included from the start, raising the initial glucose concentration to 25 g/L.
E. coli RV308 pMTL1015-cpg-PA-synt again gave a yield of 2500 μg/mL and E. coli RV308 pMTL1015-ompA-PA-synt yielded 2000 μg/mL (see PRECRV0038 and 0037, Table 4).
E. coli DH5α pTrcK-pelB-PA-synt was grown in PPTBgIy at 8 L scale (see Table 4, PRECDH0013) with the exception that the OD600 at induction was raised to 15. The rPA yield was not improved significantly over previous results although more biomass was produced with a higher final OD600 of 26 at four hours post induction with IPTG.
Effect of Growth Temperature
Previous development programs incorporating the E. coli RV308 pMTL1015-cpg-host/vector system have indicated that expression of product is most efficient at temperatures between 25 and 30° C.
Assessment of the effect on yield and product stability of growth at lower temperatures of E. coli RV308 pMTL1015-cpg-PA-synt was made by culturing the strain in production medium, under conditions described above, at 30, 28 and 25° C. (see Table 4, PRECRV0039, 0040 and 0041 respectively).
The yields from production at the lower temperatures were lower than when grown at 30° C. The quality of the material produced did not improve with the reduction in temperature, with little or no reduction in minor impurity bands on SDS-PAGE/Western Blot.
Effect of Antibiotic Concentration
As a confirmation of the stability of the plasmid under reduced antibiotic selective pressure, E. coli RV308 pMTL1015-cpg-PA-synt was cultured in production medium, under conditions described above, with varying tetracycline concentration levels in the medium (see Table 4, PRECRV0042-0044). The tetracycline concentrations were 15 μg/mL (100%), 1.5 μg/mL (10%) and 0. The 2° seed cultures contained 15, 1.5 and 15 μg/mL respectively. Thus the fermenter with no added antibiotic relied on carryover from the secondary seed to supply any selective pressure, assuming no degradation of the tetracycline during the seed growth. The volume of seed transferred to the fermenter was 124 mL giving a nominal 0.23 μg/mL tetracycline in the fermentation medium at inoculation.
The yields in terms of final OD600 and biomass were within the expected range, but the yield of rPA was slightly lower than expected for the 15 μg/mL control. The levels for the reduced antibiotic cultures were slightly higher. The stability of the pMTL1015-cpg-PA-synt plasmid was confirmed by tooth-picking final fermentation sample colony isolates onto selective (L-agar with 15 μg/mL tetracycline) and non-selective media. The results of 100, 98 and 96% growth on selective medium for 15, 1.5 and 0 μg/mL tetracycline fermentations respectively, indicate good stability under the conditions used. The viable count results for PPTBgIuc2.5xYE fermentations are in the 2×1010-5×1010 cfu/mL range.







TABLE 4







Summary Table of fermentations.


















SDS-






Seed
Fermenter
PAGE
ELISA


Run no.
Clone
Medium (No.)
OD600
OD600
(mg/L)
(mg/L)
















PRECRV
pMTL1015-
PPTBgluc
12.6
34.8
100+ 
 320


0031
cpg-PA-synt


PRECRV
pMTL1015-
PPTBgluc
13.0
44.2*
100* 
  84*


0032
cpg-PA-synt
YEx1.5


PRECRV
pMTL1015-
PPTBgluc
14.7
59.8
500++
1630


0033
cpg-PA-synt
YEx2


PRECRV
pMTL1015-
PPTBgluc
14.2
71.6
500++
2500


0034
cpg-PA-synt
YEx2.5


PRECDH
pTrcK-pelB-
PPTBgly
2.67
26.2
100++
360-465


0013
PA-synt


PRECRV
pMTL1015-
PPTBgluc
14.8
43.9*
<100* 
  90*


0036
ompA-PA-wt
YEx2.5


PRECRV
pMTL1015-
PPTBgluc
8.7
56.6
500++
2000


0037
ompA-PA-
YEx2.5



synt


PRECRV
pMTL1015-
PPTBgluc
14.7
62.6
500++
2500


0038
cpg-PA-synt
YEx2.5


PRECRV
pMTL1015-
PPTBgluc
15.6
62.4
500++
2300


0039
cpg-PA-synt
YEx2.5


PRECRV
pMTL1015-
PPTBgluc
15.6
62.2
500++
1600


0040
cpg-PA-synt
YEx2.5


PRECRV
pMTL1015-
PPTBgluc
15.6
63.6
500++
1500


0041
cpg-PA-synt
YEx2.5


PRECRV
pMTL1015-
PPTBgluc
12.9
62.4
500++
1720


0042
cpg-PA-synt
YEx2.5


PRECRV
pMTL1015-
PPTBgluc
13.2
66.4
500++
1800


0043
cpg-PA-synt
YEx2.5


PRECRV
pMTL1015-
PPTBgluc
12.9
63.8
500++
2120


0044
cpg-PA-synt
YEx2.5





PPTB—Phytone Peptone-based Terrific Broth;


gluc—glucose;


YE—Yeast Extract






Selection of Production Strain

The results obtained to date for the clones investigated after the initial down-selection have shown that of the four, E. coli RV308 pMTL1015-cpg-PA-synt has, in most cases, shown the highest yield when compared with the other pMTL1015 clones under equivalent conditions.
The largest proportion of information generated has been from the E. coli RV308 pMTL1015-cpg-PA-synt clone, for both fermentation and DSP development and with yields in the 1.5-2.5 mg/mL range when production medium has been used. This has allowed the present applicant to select this clone as their preferred production organism for all future work.
Table 5 shows a summary of all cultures grown to date in production medium. The figures indicate that although 2500 μg/mL is achievable, a more realistic value for the yield is 2000 μg/mL.







TABLE 5







Comparison of rPA levels relative to cell wet weight and


optical density at harvest for cultures of E. coli RV308


pMTL1015-cpg-PA-synt containing 2.5x yeast extract.














Cell
rPA

mg rPA/g



Culture
Weight
Yield
mg rPA/
wet


Run No.
OD600
(g/L)
(mg/L)
OD unit
weight















PRECRV0030
69.8
85.8
1900
27.2
22.1


PRECRV0034
71.6
102
2500
34.9
24.5


PRECRV0038
62.6
86.5
2500
39.9
28.9


PRECRV0039
62.4
77.5
2300
36.9
29.7


PRECRV0040
62.2
80.4
1600
25.7
19.9


PRECRV0041
63.6
98.5
1500
23.5
15.2


PRECRV0042
62.4
89.1
1720
27.6
19.3


PRECRV0043
66.4
88.8
1800
27.1
20.3


PRECRV0044
63.8
83.9
2120
33.2
25.3


MEAN
65.0
88.1
1993
30.7
22.8









EXAMPLE 4
Upstream Process for rPA Production
Seed Banks for Clone of Interest—Clone pMTL1015-cpg-PA-synt Transformed into E. coli RV308 (ATCC 31608).
After sequence confirmation, a research seed bank was prepared by growth under selective pressure of tetracycline (15 mg/L) in soy peptone based L-broth (Phytone peptone 15 g/L, Bacto yeast extract 5 g/L, NaCl 5 g/L, pH 6.8-7.0). A single colony from a nutrient agar plate with tetracycline was inoculated into 100 mL medium in 500 mL baffled shake flasks and incubated at 30° C. and 150 rpm in a shaking incubator until OD600 reached 1.5. The culture was then mixed with sterile 50% glycerol in growth medium (see above) to give a final glycerol concentration of 10%, and stored frozen at −80° C. as 1 mL aliquots in 1.8 mL cryovials.
A working research cell bank (WRCB) of 250 vials was prepared from above seed bank using the same conditions and medium for growth, however 250 μL of thawed vial contents were inoculated into 200 mL medium in 1000 mL baffled shake flasks.
Primary Seed Culture.
1 vial of WRCB was thawed and 100 μL inoculated into 10 mL soy peptone based L-Broth (see above) containing tetracycline at 15 mg/L in a 25 mL universal bottle, incubated at 30° C. with shaking at 150 rpm for 7-9 hours. This was a recovery step to ensure that the organism is viable and to give a more consistent seed production process. The final OD600 of this step was 0.7-1.0.
Secondary Seed Culture.
This step produces the inoculum for the fermentation, and with a reasonably sized shaking incubator is capable of producing inocula sufficient for 5-250 L cultures in shake flasks. At 50 L scale, 200 μL of primary seed was inoculated into 200 mL of production medium in each of 5×1000 mL baffled shake flasks. The cultures were incubated with shaking at 150 rpm and 30° C. for 11-12 hours giving a final OD600 of 13-16.
To prevent precipitation and caramelisation of some components during sterilisation by autoclaving, production medium is prepared by sterilising the complex component as a bulk and then adding the glucose, phosphate, magnesium and tetracycline aseptically as sterile solutions when the temperature of the components has fallen to lower than 25° C.
Production Fermentation
The seed cultures were then bulked and a volume sufficient to give a starting OD600 of 0.2 in the fermenter was inoculated into 50 L production medium (see above) in a 72 L Applikon stirred tank fermenter. The complex medium components were sterilised, as a 40 L bulk, in situ at 121-123° C. for 30 minutes, cooled to below 25° C. and then supplemented with the remaining components to bring the total volume to 50 L.
The culture was then grown as a batch at a temperature of 30(±0.5)° C., pH 7.0 controlled by addition of sodium hydroxide and phosphoric acid. Dissolved oxygen tension was maintained at >40% by cascade step control of the following parameters: agitation (200-800 rpm), backpressure (3-7 psi), sparged airflow (25-50 Lpm) and oxygen supplementation (0-20 Lpm), in the order described.
When growth had ceased (12-14 hours), as measured by OD (OD600 60-65), the culture was chilled to below 15° C. and harvested by batch centrifugation (Sorvall RC-3B, H6000A rotor, 5000 rpm for 15 minutes). The harvested cell paste was stored at −20° C. until required for downstream processing. Product expression was assessed by ELISA assay from samples removed hourly from the culture.
EXAMPLE 5
Downstream Processing Steps
Cell Breakage
Approximately 4.5 kg of frozen cell paste harvest were suspended into a smooth paste with, initially, a minimum volume of 20 mM tris/1 mM EDTA pH 8.5. Further buffer was added to give an overall suspended volume of 16 L.
The suspended cells were broken by passing twice through an ‘APV Gaulin’ high-pressure homogeniser at a pressure of 7000 psi. The homogenate was then centrifuged for 1 hour at 5000 rpm in a ‘Sorval’ RC3 centrifuge. The pellet was discarded, and the supernatant (16 L approx) was retained.
Diafiltration
The centrifuged homogenate was diafiltered with 3 times its volume of purified water using a ‘Millipore Pellicon’ concentrator fitted with two ‘Pall’ OS030F07 0.5 m2 ‘Centrasette 2 Omega’ suspended screen channel 30 kDa membranes. The concentrator was operated at a flow-rate of 17 L/min with a trans-membrane pressure of 1.6 Bar. The pH was adjusted to 8.0 and the conductivity to 2 mS/cm.
Anion Exchange and Chromatography
A 25 cm diameter chromatography column was packed with 5 L of ‘Amersham’ ‘Q-Sepharose Fast Flow’ anion exchanger to give a bed height of 10 cm. An industrial UV monitor was then connected to the effluent line. The column was operated at a flow-rate of 330 mL/min throughout. The packed column was washed with 10 L of water, then 5 L of 0.5 M sodium hydroxide, followed by purified water. 10 L of 0.5 M tris, pH 8.0, was pumped, and the column was then equilibrated with start buffer (20 mM tris, pH 8.0).
The diafiltrate was loaded, and then the loaded column was washed to baseline resolution with start buffer. The bound rPA was eluted with increasing salt steps of 10, 20, and 65 mM sodium chloride in start buffer, and the eluted peaks were collected in separate appropriately sized vessels. The eluates were assayed by SDS-PAGE and SEC-HPLC, and the fractions containing rPA at a purity of >40% were retained.
The column was regenerated by passing sequentially 10 L of 2 M sodium chloride, followed by 10 L of 1 M sodium acetate, 10 L of 0.5 M sodium hydroxide, then 10 L of 50 mM sodium hydroxide for storage.
Hydrophobic Charge Induction Chromatography
A 30 cm diameter column connected to UV monitor was packed with 20 L of ‘Ciphergen’ ‘MEP HyperCel’ at a flow rate of 7 L /min. Once packed, all further steps were performed at 800 mL/min. The column was washed with 5 L of 1 M sodium hydroxide with a contact time of no more than 40 min. The column was then washed with water, and then equilibrated with 20 L loading buffer (50 mM tris, pH 8.0). The Q pool (i.e. the pool from the previous Q chromatography step) was loaded, the column was washed with loading buffer to baseline, then the bound rPA was eluted with purified water. The collected product was assayed by SDS-PAGE and SEC-HPLC. The MEP pool (i.e. the pool from the MEP Hypercel column) was filtered through a 0.22 μm, 2000 cm2 Pall ‘Posidyne’ filter. The column was regenerated with 10 L of 1 M sodium hydroxide, washed with purified water, and then stored in 0.2 μm filtered 50 mM sodium hydroxide.
Diafiltration and Formulation
The purified rPA was diafiltered using a ‘Pall Centramate’ medium screen ‘Omega’ 50 kDa cartridge (part No. OS0350C12, 0.093 m2). A flow-rate of 800 mL/min, and a trans-membrane pressure of 1.6 Bar were used. The diafiltration was performed versus 5 L of formulation buffer; 25 mM sodium phosphate, 150 mM sodium chloride, pH 8.0. A further filtration was performed using a 0.22 μm Pall ‘Posidyne’ filter of 5000 cm2 area, and then the final product was dispensed into appropriate vials.
EXAMPLE 6
Construction of Variant Synthetic rPA Gene Constructs
The variant sequences set out in SEQ ID NOS: 9-105 are synthesized using solid phase chemical synthesis using nucleoside phosphoramidites. This is a well-established method in the field (see Brown T, Brown D J S. 1991. in Oligonucleotides and Analogues. A Practical Approach, ed. F Eckstein, pp. 1-24. Oxford: IRL). Typically, the synthetic gene sequences are constructed from a number of oligonucletide sequences (40-80 bp in length) that have been generated using this chemical synthesis methodology. These oligonucleotide sequences represent both strands of the gene sequence and have their termini designed such that, post hybridization of complementary oligonucleotide pairs, the double stranded elements are bound by unique complementary overhanging sequences that enable their correct ordered assembly to generate the rPA gene “sub-fragment” sequences, typically  ̃500 base pairs in length. This is performed by mixing the hybridized oligonucleotide pairs with an appropriately cleaved plasmid vector (for example, a PUC or Invitrogen TOPO vector) with the addition of bacteriophage T4 ligase; both plasmid and rPA sub-fragments having compatible restriction site termini. These ligation products are used to transform competent E.coli host cells, generating E.coli clones for screening. Screening of clones is carried out using restriction enzyme analysis of isolated plasmid DNA, and selected clones authenticated by DNA sequence analysis of the cloned insert of the plasmid.
The final rPA-encoding gene product is then assembled via the isolation of the plasmid-borne “sub-fragment” DNA segments as specifically bound restriction fragments, which are then ligated together with an appropriately cleaved plasmid vector (for example, a PUC or Invitrogen TOPO vector) and the ligation mixture used to transform competent E.coli cells. The E.coli clones generated are then screened by restriction analysis and the entire cloned rPA-encoding gene sequence verified by DNA sequence analysis.
The synthetic rPA-encoding gene sequence may be generated with or without a 5′-leader sequence DNA moiety. If generated without a leader sequence, a unique MscI restriction site is engineered at the 5′-end of the coding sequence as this will enable “in-frame” cloning to some leader sequences (e.g., ompA, pelB) which already reside in some commercially available E.coli expression plasmids. More typically, the choice of a larger range of leader sequences (e.gs, cpg2, ompA, pelB, phoA, ompT, lamb, omp F, beta lactamase, Staphylococcus aureus Protein A, Bacillus subtilus endoglucanase, murine RNAase, human growth hormone, enterotoxins ST-II, LT-A and LT-B) is incorporated in the original design and DNA synthesis strategy. This way, the leader sequence-rPA “cassette” is generated as a single genetic element that can then be sub-cloned into a variety of E.coli expression vectors for production of the rPA polypeptide product. By virtue of engineering a unique MscI restriction site at the leader sequence-rPA-encoding gene sequence, different leader sequences may be substituted via simple sub-cloning procedures (Sambrook, J., Fritsch, E. F., Maniatis, T. Molecular Cloning: a Laboratory Manual, 2nd Ed. 1989. Cold Spring Harbour Laboratory Press).
EXAMPLE 7
Expression of Variant Synthetic rPA Gene Constructs
The rPA gene encoding sequences depicted in SEQ ID NOs: 9 to 105 are cloned as leader sequence-rPA sequence “cassettes” into E.coli expression plasmids.
Cloning of these leader sequence-rPA sequence “cassettes” is facilitated by virtue of unique restriction sites engineered at the 5′- and 3′-ends for compatibility with the E.coli expression vector of choice. Typically, this would be either a NdeI or NcoI restriction site at the 5-end as this facilitates optimal positioning of the ATG initiation (metheionine) codon to the vector borne ribosome binding site (RBS) to enable efficient translation initiation of the RNA message originating from the expression vector moiety of the constructs. Restriction enzyme sites at the 3′-ends of the leader sequence-rPA sequence “cassettes” are variable and engineered to be compatible with choice of E.coli expression vector. The choice of available E.coli expression vectors is varied and examples include: pMTL series of vectors (proprietary to HPA), pET series (Novagen), pRSET, pET and pBAD series (Invitrogen), pQE series (Qiagen), pMaI series (New England Biolabs), pPROTet series (Clontech), pGEX series (GE Healthcare), pEK/LIC series (EMD Biosciences), pIVEX series for cell-free expression (Roche) and bacteriophage Lambda gt11 and Lambda ZAP expression vectors (Stratagene).
Expression of the rPA polypeptides elaborated from rPA-coding sequences SEQ ID Nos 9 to 105 is conducted in shake flasks or in fermenter bioreactors as described in Examples 2 and 3. The latter of these (i.e. the fermenter) attains levels of periplasmically located rPA polypeptide product at levels typically exceeding 2 grams per liter. Particularly good levels of rPA polypeptide (in the range 2.1-2.4 grams per liter) are achieved using SEQ ID NOs: 36, 46, 56, 66, 76, 86 and 96. SEQ ID NO: 36, for example, achieves a typical yield of at least 2.2 grams per liter.
Purification of the rPA polypeptide is achieved using the methods described in Example 5.
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## Claims

1. A method for producing rPA comprising expressing a polynucleotide having at least 90% sequence identity to SEQ ID NO: 36,
wherein the polynucleotide is an rPA polynucleotide,
with the proviso that the polynucleotide does not comprise the nucleic acid sequence of SEQ ID NO: 1.

2. A method according to claim 1, wherein said polynucleotide is expressed in a host cell.

3. A method according to claim 1, wherein said polynucleotide is DNA, and is optionally first transcribed into RNA in vitro and the RNA is then translated in a host cell.

4. A method according to claim 2, wherein the host cell is an E. coli host cell.

5. A method according to claim 4, wherein the E. coli host cell is E. coli RV308.

6. A method according to claim 1, comprising expressing rPA from an expression vector comprising the polynucleotide.

7. A method according to claim 6, wherein the expression vector comprises the cpg leader sequence encoded by SEQ ID NO: 3.

8. A method according to claim 6, wherein the vector is plasmid pMTL1015, encoded by SEQ ID NO: 4.

9. A method according to claim 6, wherein the vector is expressed in E. coli RV308.

10. A method according to claim 6, further comprising initial steps of transforming the expression vector into a host cell, and culturing the transformed host cell in a growth medium.

11. A method according to claim 10, wherein said growth medium is free of animal products.

12. A method according to claim 10, comprising culturing the transformed host cells at a temperature of less than 40° C.

13. A method according to claim 10, further comprising harvesting the host cell.

14. A method according to claim 13, further comprising extracting rPA from the host cell.

15. A method according to claim 14, further comprising a separation step.

16. A method according to claim 15, wherein the separation step is selected from one or more chromatography steps, and one or more filtration steps.

17. A method according to claim 16, wherein at least one of said filtration step(s) is a diafiltration step.

18. A method according to claim 16, wherein at least one of said chromatography step(s) is selected from an ion-exchange chromatography step and a hydrophobic charge chromatography step.

19. A method according to claim 2, comprising:
(a) obtaining host cells that express the polynucleotide or an expression vector comprising the polynucleotide;
(b) extracting the expressed rPA from the host cells;
(c) subjecting the extracted rPA to a diafiltration step;
(d) subjecting the diafiltered rPA to at least one chromatography step selected from anion exchange and hydrophobic charge chromatography; and
(e) carrying out a further diafiltration step.