Patent Application
20230322870
The present invention relates to microorganisms comprising each of an ApxIA, ApxIIA and ApxIIIA toxin, related vaccines and methods of production thereof, as well as uses thereof for the immunisation and protection of mammals.
Actinobacillus pleuropneumoniae (APP) is a Gram-negative bacterium and a member of the family Pasteurellaceae. APP is the etiological agent of porcine pleuropneumonia, a severe pulmonary disease of pigs that causes high economic losses in pig production worldwide. The disease is often characterised by haemorrhagic, fibrinous and necrotic lung lesions. Pigs surviving the disease often become asymptomatic carriers of APP and are the main cause of bacterial dissemination.
To date, 19 serotypes of APP have been identified on the basis of the antigenic properties of capsular polysaccharides (CPS) and as a result of genetic analysis. Main virulence factors of APP are exotoxins, CPS, lipopolysaccharide (LPS) and membrane proteins. The most important virulence factors are Apx-exotoxins, which belong to the pore-forming repeats in toxin (RTX) family. The toxins are known to be highly immunogenic and are very important to obtain a protective immunity against APP-related pleuropneumonia. At least four different Apx toxins are produced by APP, designated ApxI, ApxII, ApxIII and ApxIV. ApxI shows strong haemolytic activity, whereas ApxII shows low haemolytic activity. Both are cytotoxic and active against a broad range of cells of different host species. ApxIII is non-haemolytic but strongly cytotoxic, with porcine alveolar macrophages and neutrophils as major targets. ApxIV shows no cytotoxic activity and only weak haemolytic activity. No serotypes of APP produce all four Apx toxins, or even all three of ApxI, ApxII and ApxIII. All serotypes produce ApxIV and one or two of ApxI-III. The pattern of Apx toxin production is associated with virulence, with serotypes 1, 5, 9 and 11 producing ApxI and ApxII being the most virulent.
At least four genes are responsible for production and secretion of active Apx toxins. Gene A encodes the structural toxin. Gene C encodes an acyltransferase which is required for post-translational activation of the toxin. Genes B and D encode two membrane proteins that are required for secretion of the mature protein. The Apx genes are organised as operons. Operons of ApxI and ApxIII consist of genes CABD, whilst the ApxII operon contains only the genes CA (
Presently, pleuropneumonia resulting from APP infection of pigs is usually treated with antibiotics. However, it has been found that APP often exhibits antibiotic resistance against at least one of the antibiotics commonly used to treat APP infection.
Vaccination against APP is a promising prophylactic strategy to prevent pleuropneumonia. Several vaccines have been commercialised. Commercially available vaccines are either chemically inactivated whole cell vaccines or subunit vaccines or a combination of both. The immunological reactions of animals vaccinated with whole cell vaccines is directed mainly against surface structures such as CPS and LPS. The absence of secreted proteins such as Apx toxins which are known to be highly immunogenic and essential for protection explains the limited protection observed with APP whole cell vaccines. Furthermore, APP whole cell vaccines confer only homologous protection against the serotype used to prepare the vaccine.
The commercially available subunit vaccine (described in EP 0453024 B1) contains chemically inactivated ApxA toxins as well as an outer membrane protein. The inactivation of ApxA toxins with denaturising substances such as formaldehyde potentially leads to a decreased immunogenicity of the toxoids. The disadvantages of such a vaccine are insufficient protection due to denaturising the toxins, as well as concomitant serious side reactions, probably due to residual toxicity from incomplete inactivation of ApxA toxins. Subsequently, due to decreased immunogenicity after inactivation, higher amounts of toxins need to be used. This can result in increased amounts of contaminating LPS in the vaccines. High LPS content can also cause side effects, as seen with the commercial APP subunit vaccines.
Thus, the current commercially available APP vaccines do not possess satisfactory safety and or efficacy profiles against APP infection.
Other experimental approaches for APP vaccines are also under development.
WO 2004/045639 discloses a live attenuated vaccine against porcine pleuropneumonia containing an APP strain which is modified in transmembrane domains of genes encoding the toxins ApxIA and ApxIIA. To test the degree of attenuation, three-month old pigs were inoculated with modified live APP strains. Seven days after the inoculation the animals were sacrificed, and macroscopic lesions were recorded in the respiratory organs. All animals showed a modification of their behaviour and lung lesions at necropsy. The efficacy of this live vaccine was not examined.
EP 0810283(A2) and EP0861319(B1) describe live attenuated APP strains having deletions in ApxA activator (apxC) genes. The modified APP strain does not produce the ApxC activator proteins in a functional form and therefore the toxins ApxIA and ApxIIA were not activated by acylation. Mice were vaccinated with a ΔapxC strain and challenged with virulent APP field strains. Vaccinated mice were protected against homologous challenge and partially protected against heterologous challenge. One study in pigs was performed. One out of six vaccinated pigs had lung lesions after heterologous challenge and necropsy. These attenuated live vaccines seem to be efficacious, but bear a significant safety risk. The vaccine strains produce Apx toxins which are not activated by acylation due to lacking apxC. However, these toxins have the original amino acid sequence of toxic ApxA. Very likely heterologous acyltransferases can acylate the ApxA converting it into its active, toxic form. In most pig farms worldwide, there are asymptomatic carriers of virulent APP strains as well as pigs infected with low virulent APP strains. If such pigs were vaccinated with a ΔapxC vaccine strain, the non-activated ApxA toxins of the vaccine strain could be activated by functional ApxC proteins of field strains. Furthermore, there is the possibility of complementation of the apxC deletion by uptake of functional apxC genes. Therefore, there is the possibility that the attenuated strains could revert to virulence, causing disease in the vaccinated animals.
The present inventors have previously developed recombinant ApxIA, ApxIIA and ApxIIIA toxins expressed in Escherichia coli, which are modified at their acylation sites to create inactive but fully immunogenic toxoid forms of these proteins.
To-date, the issue of providing protection against heterologous serotypes, particularly for live attenuated and inactivated whole cell vaccines, remains. Further, even with subunit vaccines this remains problematic from a commercial perspective, as it is costly to grow sufficient volumes of multiple different serotypes and then purify their respective ApxA proteins to produce subunit vaccines that provide protection against all known APP serotypes.
Accordingly, there is a need for improved vaccines against APP which are safe, can be produced at scale by an economically viable process, and which are safe and able to induce cross-protection against all relevant APP serotypes in pigs and/or young piglets.
It is therefore an object of the invention to provide microorganisms comprising each of each of an ApxIA, ApxIIA and ApxIII toxin, related vaccines and methods of production, as well as uses thereof for the immunisation and protection of mammals.
The present inventors are the first to produce APP bacteria expressing all three of ApxIA, ApxIIA and ApxIIIA in a single strain. In particular, the inventors have constructed APP strains that produce non-functional forms of each of ApxIA, ApxIIA and ApxIIIA, with the genes encoding each modified toxin integrated into the APP chromosome. These APP strains have been generated by the introduction of unmarked mutations using two-step natural transformation. The advantage of the inventors' modified APP strains is that these triple mutants can be used as a single live attenuated vaccine strain, that will induce antibodies against all three of ApxIA, ApxIIA and ApxIIIA, and hence that will give protection against all known serovars of APP. In addition, these strains can be used to streamline the production of Apx toxoid vaccines, enabling a single APP strain to be used to produce all three of ApxIA, ApxIIA and ApxIIIA. Using the inventors' methodology it would be equally possible to produce APP strains producing all three of ApxIA, ApxIIA and ApxIIIA, either in wild-type or modified forms for the production of inactivated whole cell or subunit vaccines, wherein either the bacteria or the individual ApxIA, ApxIIA and ApxIIIA can be inactivated using suitable inactivants for use as vaccines.
Accordingly, the present invention provides a microorganism comprising: (a) a nucleic acid sequence encoding ApxIA of Actinobacillus pleuropneumoniae; (b) a nucleic acid sequence encoding ApxIIA of A. pleuropneumoniae; and (c) a nucleic acid sequence encoding ApxIIIA of A. pleuropneumoniae.
The nucleic acid sequences of (a), (b) and/or (c) may be: (i) comprised within the genome of the microorganism; or (ii) comprised extra-chromosomally.
The ApxIA, ApxIIA and ApxIIIA may be: (a) inactive ApxIA, ApxIIA and ApxIIIA which have common antigenic cross-reactivity with wild-type ApxIA, ApxIIA and ApxIIIA; or (b) wild-type ApxIA, ApxIIA and ApxIIIA. In particular, the microorganism may comprise: (a) (i) the inactive ApxIA has an amino acid sequence corresponding to the wild-type ApxIA amino acid sequence of SEQ ID NO: 1, modified in at least one amino acid selected from the group consisting of K560 and K686, or a variant or fragment thereof which is at least 90% homologous to said inactive ApxIA amino acid sequence, said fragment comprising at least 30% of the consecutive amino acids of said inactive ApxIA amino acid sequence, wherein said variant or fragment comprises the at least one modified amino acid; (ii) the inactive ApxIIA has an amino acid sequence corresponding to the wild-type ApxIIA amino acid sequence of SEQ ID NO: 2, modified in at least one amino acid selected from the group consisting of K557 and N687, or a variant or fragment thereof which is at least 90% homologous to said inactive ApxIIA amino acid sequence, said fragment comprising at least 30% of the consecutive amino acids of said inactive ApxIIA amino acid sequence, wherein said variant or fragment comprises the at least one modified amino acid; and (iii) the inactive ApxIIIA has an amino acid sequence corresponding to the wild-type ApxIIIA amino acid sequence of SEQ ID NO: 3, modified in at least one amino acid selected from the group consisting of K571 and K702, or a variant or fragment thereof which is at least 90% homologous to said inactive ApxIIIA amino acid sequence, said fragment comprising at least 30% of the consecutive amino acids of said inactive ApxIIIA amino acid sequence, wherein said variant or fragment comprises the at least one modified amino acid; and the at least one modified amino acid is substituted by an amino acid not susceptible to acylation; or (b) (i) the inactive ApxIA has an amino acid sequence corresponding to the wild-type ApxIA amino acid sequence of SEQ ID NO: 1, containing deletions comprising at least one amino acid selected from the group consisting of K560 and K686, or a variant or fragment thereof which is at least 90% homologous to said inactive ApxIA amino acid sequence, said fragment comprising at least 30% of the consecutive amino acids of said inactive ApxIA amino acid sequence, wherein said variant or fragment comprises the deletion; (ii) the inactive ApxIIA has an amino acid sequence corresponding to the wild-type ApxIIA amino acid sequence of SEQ ID NO: 2, containing deletions comprising at least one amino acid selected from the group consisting of K557 and N687, or a variant or fragment thereof which is at least 90% homologous to said inactive ApxIIA amino acid sequence, said fragment comprising at least 30% of the consecutive amino acids of said inactive ApxIIA amino acid sequence, wherein said variant or fragment comprises the deletion; and (iii) the inactive ApxIIIA has an amino acid sequence corresponding to the wild-type ApxIIIA amino acid sequence of SEQ ID NO: 3, containing deletions comprising at least one amino acid selected from the group consisting of K571 and K702, or a variant or fragment thereof which is at least 90% homologous to said inactive ApxIIIA amino acid sequence, said fragment comprising at least 30% of the consecutive amino acids of said inactive ApxIIIA amino acid sequence, wherein said variant or fragment comprises the deletion. Wherein either or both of the acylation sites are substituted by amino acids not susceptible to acylation, each amino acid not susceptible to acylation may be independently selected from the group consisting of alanine, glycine, isoleucine, leucine, methionine, valine, serine, threonine, asparagine, glutamine, aspartic acid, histidine, aspartic acid, cysteine, proline, phenylalanine, tyrosine, tryptophan and glutamic acid; preferably selected from the group consisting of alanine, glycine, serine, isoleucine and leucine, valine and threonine; most preferably selected from the group consisting of alanine, glycine and serine. The inactive ApxIA may have substitutions at both K560 and K686. The inactive ApxIIA may have substitutions at both K557 and N687. The inactive ApxIIIA may have substitutions at both K571 and K702. The inactive ApxIA may comprise the amino acid sequence of SEQ ID NO: 4. The inactive ApxIIA may comprise the amino acid sequence of SEQ ID NO: 5. The inactive ApxIIIA may comprise the amino acid sequence of SEQ ID NO: 6. Wherein the acylation sites are deleted: (i) the inactive ApxIA has deletions at both K560 and K686; (ii) the inactive ApxIIA has deletions at both K557 and N687; and (iii) the inactive ApxIIIA has deletions at both K571 and K702.
Wherein the microorganism comprises wild-type ApxA polypeptides: (a) the wild-type ApxIA has an amino acid sequence corresponding to SEQ ID NO: 1, or a variant or fragment thereof which is at least 90% homologous to said wild-type ApxIA amino acid sequence, said fragment comprising at least 30% of the consecutive amino acids of said wild-type ApxIA amino acid sequence; (b) the wild-type ApxIIA has an amino acid sequence corresponding to SEQ ID NO: 2, or a variant or fragment thereof which is at least 90% homologous to said wild-type ApxIIA amino acid sequence, said fragment comprising at least 30% of the consecutive amino acids of said wild-type ApxIIA amino acid sequence; and (c) the wild-type ApxIIIA has an amino acid sequence corresponding to SEQ ID NO: 3, or a variant or fragment thereof which is at least 90% homologous to said wild-type ApxIIIA amino acid sequence, said fragment comprising at least 30% of the consecutive amino acids of said wild-type ApxIIIA amino acid sequence.
The microorganism of the invention may be an Escherichia coli strain or an Actinobacillus strain, preferably an Actinobacillus pleuropneumoniae strain. The A. pleuropneumoniae strain may be produced from: (a) an A. pleuropneumoniae strain which expresses an endogenous ApxIIA and ApxIIIA, preferably a serotype 2, 8, or 15 strain; or (b) an A. pleuropneumoniae strain which expresses an endogenous ApxIA and ApxIIA, preferably a serotype 1, 5 or 9 strain.
The microorganism may be an A. pleuropneumoniae strain in which at least one additional gene is modified, wherein preferably: (a) said one or more additional gene is selected from the group consisting of apxIVA, sxy, nlpD and/or ssrA; and/or (b) said modification results in the inactivation of said one or more additional gene. The at least one additional gene which is modified maybe (i) apxIVA; (ii) sxy; or (iii) apxIVA and sxy, wherein preferably: (a) the apxIVA gene is modified by an unmarked in-frame deletion of an N-terminal immunogenic domain sequence; and/or (b) the sxy gene is deleted.
The invention also provides a vaccine composition comprising a microorganism of the invention and at least a pharmaceutical carrier, a diluent and/or an adjuvant. Said vaccine may be a live vaccine, wherein preferably: (a) the microorganism is an Actinobacillus pleuropneumoniae strain; and/or (b) the ApxIA, ApxIIA and ApxIIIA are inactive ApxIA, ApxIIA and ApxIIIA which have common antigenic cross-reactivity with wild-type ApxIA, ApxIIA and ApxIIIA. Said vaccine may be an inactivated vaccine, wherein preferably: (a) the microorganism is an Actinobacillus pleuropneumoniae strain; and/or (b) the ApxIA, ApxIIA and ApxIIIA are wild-type ApxIA, ApxIIA and ApxIIIA which have been subsequently inactivated, preferably by chemical and/or heat treatment.
The invention also provides a method of producing a live vaccine composition of the invention, comprising: (a) culturing a microorganism of the invention, wherein the ApxIA, ApxIIA and ApxIIIA are inactive ApxIA, ApxIIA and ApxIIIA which have common antigenic cross-reactivity with wild-type ApxIA, ApxIIA and ApxIIIA; (b) isolating the microorganism; and (c) formulating the microorganism with a pharmaceutical carrier, a diluent and/or an adjuvant.
The invention further provides a method of producing an inactivated vaccine composition of the invention, comprising: (a) culturing a microorganism of the invention, wherein the ApxIA, ApxIIA and ApxIIIA are wild-type ApxIA, ApxIIA and ApxIIIA; (b) isolating the microorganism; (c) inactivating the microorganism, preferably by chemical and/or heat treatment; and (d) formulating the inactivated microorganism with a pharmaceutical carrier, a diluent and/or an adjuvant.
The invention also provides a method of producing a subunit vaccine composition, comprising: (a) (i) culturing a microorganism of the invention, wherein the ApxIA, ApxIIA and ApxIIIA are inactive ApxIA, ApxIIA and ApxIIIA which have common antigenic cross-reactivity with wild-type ApxIA, ApxIIA and ApxIIIA; (ii) isolating the inactive ApxIA, ApxIIA and ApxIIIA from the cultured microorganism; and (iii) formulating the inactive ApxIA, ApxIIA and ApxIIIA with a pharmaceutical carrier, a diluent and/or an adjuvant; or (b) (i) culturing a microorganism of the invention, wherein the ApxIA, ApxIIA and ApxIIIA are wild-type ApxIA, ApxIIA and ApxIIIA; (ii) isolating the wild-type ApxIA, ApxIIA and ApxIIIA from the cultured microorganism; (iii) inactivating the wild-type ApxIA, ApxIIA and ApxIIIA, preferably by chemical and/or heat treatment; and (iv) formulating the inactivated wild-type ApxIA, ApxIIA and ApxIIIA with a pharmaceutical carrier, a diluent and/or an adjuvant.
The invention also provides a vaccine composition of the invention for use in a method of prophylactic, metaphylactic or therapeutic treatment of a pneumonia, a pleurisy or a pleuropneumonia, in particular, of a pneumonia, a pleurisy or a pleuropneumonia caused by Actinobacillus pleuropneumoniae, wherein optionally the vaccine composition is to be administered intramuscularly, intradermally, intravenously, subcutaneously, or by mucosal administration.
The invention further provides an expression system comprising a microorganism of the invention, further comprising at least one additional nucleic acid which encodes one or more additional swine pathogen antigen, wherein preferably the at least one additional nucleic acid is comprised within the genome of the microorganism.
The invention further provides a vector or set of vectors comprising nucleic acids encoding for: (a) wild-type ApxIA, ApxIIA and ApxIIIA as defined herein; or (b) inactive ApxIA, ApxIIA and ApxIIIA which have common antigenic cross-reactivity with wild-type ApxIA, ApxIIA and ApxIIIA as defined herein.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Singleton, et al., DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY, 20 ED., John Wiley and Sons, New York (1994), and Hale & Marham, THE HARPER COLLINS DICTIONARY OF BIOLOGY, Harper Perennial, NY (1991) provide the skilled person with a general dictionary of many of the terms used in this disclosure. The meaning and scope of the terms should be clear; however, in the event of any latent ambiguity, definitions provided herein take precedent over any dictionary or extrinsic definition. It should be understood that this invention is not limited to the particular methodology, protocols, and reagents, etc., described herein and as such can vary.
This disclosure is not limited by the exemplary methods and materials disclosed herein, and any methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of this disclosure. The terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention, which is defined solely by the claims.
The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize. For example, while method steps or functions are presented in a given order, alternative embodiments may perform functions in a different order, or functions may be performed substantially concurrently. The teachings of the disclosure provided herein can be applied to other procedures or methods as appropriate. The various embodiments described herein can be combined to provide further embodiments. Aspects of the disclosure can be modified, if necessary, to employ the compositions, functions and concepts of the above references and application to provide yet further embodiments of the disclosure. Moreover, due to biological functional equivalency considerations, some changes can be made in protein structure without affecting the biological or chemical action in kind or amount. These and other changes can be made to the disclosure in light of the detailed description. All such modifications are intended to be included within the scope of the appended claims.
Numeric ranges are inclusive of the numbers defining the range. Unless otherwise indicated, any nucleic acid sequences are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.
The headings provided herein are not limitations of the various aspects or embodiments of this disclosure.
As used herein, the term “capable of” when used with a verb, encompasses or means the action of the corresponding verb. For example, “capable of interacting” also means interacting, “capable of cleaving” also means cleaves, “capable of binding” also means binds and “capable of specifically targeting . . . ” also means specifically targets.
Other definitions of terms may appear throughout the specification. Before the exemplary embodiments are described in more detail, it is to be understood that this disclosure is not limited to particular embodiments described, and as such may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present disclosure will be defined only by the appended claims.
Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limits of that range is also specifically disclosed. Each smaller range between any stated value or intervening value in a stated range and any other stated or intervening value in that stated range is encompassed within this disclosure. The upper and lower limits of these smaller ranges may independently be included or excluded in the range, and each range where either, neither or both limits are included in the smaller ranges is also encompassed within this disclosure, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in this disclosure.
As used herein, the articles “a” and “an” may refer to one or to more than one (e.g. to at least one) of the grammatical object of the article. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. In this application, the use of “or” means “and/or” unless stated otherwise. Furthermore, the use of the term “including”, as well as other forms, such as “includes” and “included”, is not limiting.
“About” may generally mean an acceptable degree of error for the quantity measured given the nature or precision of the measurements. Exemplary degrees of error are within 20 percent (%), typically, within 10%, and more typically, within 5% of a given value or range of values. Preferably, the term “about” shall be understood herein as plus or minus (±) 5%, preferably ±4%, ±3%, ±2%, ±1%, ±0.5%, ±0.1%, of the numerical value of the number with which it is being used.
The term “consisting of” refers to compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the invention.
As used herein the term “consisting essentially of” refers to those elements required for a given invention. The term permits the presence of elements that do not materially affect the basic and novel or functional characteristic(s) of that invention (i.e. inactive or non-immunogenic ingredients).
Embodiments described herein as “comprising” one or more features may also be considered as disclosure of the corresponding embodiments “consisting of” and/or “consisting essentially of” such features.
The term “pharmaceutically acceptable” as used herein means approved by a regulatory agency of the Federal or a state government, or listed in the U.S. Pharmacopeia, European Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in pigs.
Concentrations, amounts, volumes, percentages and other numerical values may be presented herein in a range format. It is also to be understood that such range format is used merely for convenience and brevity and should be interpreted flexibly to include not only the numerical values explicitly recited as the limits of the range but also to include all the individual numerical values or sub-ranges encompassed within that range as if each numerical value and sub-range is explicitly recited.
Amino acids are referred to herein using the name of the amino acid, the three-letter abbreviation or the single letter abbreviation.
As used herein, the terms “protein” and “polypeptide” are used interchangeably herein to designate a series of amino acid residues, connected to each other by peptide bonds between the alpha-amino and carboxyl groups of adjacent residues. The terms “protein”, and “polypeptide” refer to a polymer of amino acids, including modified amino acids (e.g., phosphorylated, glycated, glycosylated, etc.) and amino acid analogues, regardless of its size or function. “Protein” and “polypeptide” are often used in reference to relatively large polypeptides, whereas the term “peptide” is often used in reference to small polypeptides, but usage of these terms in the art overlaps. The terms “protein” and “polypeptide” are used interchangeably herein when referring to a gene product and fragments thereof. Thus, exemplary polypeptides or proteins include gene products, naturally occurring proteins, homologs, orthologs, paralogs, fragments and other equivalents, variants, fragments, and analogues of the foregoing.
Minor variations in the amino acid sequences of proteins of the invention are contemplated as being encompassed by the present invention, providing that the variations in the amino acid sequence(s) maintain at least 60%, at least 70%, more preferably at least 80%, at least 85%, at least 90%, at least 95%, and most preferably at least 97% or at least 99% sequence identity to the proteins of the invention or an immunogenic fragment thereof as defined anywhere herein. The term homology is used herein to mean identity. As such, the sequence of a variant or analogue sequence of a protein of the invention may differ on the basis of substitution (typically conservative substitution) deletion or insertion.
Proteins of the invention may include variants in which amino acid residues from one species are substituted for the corresponding residue in another species, either at the conserved or non-conserved positions. Variants of protein molecules disclosed herein may be produced and used in the present invention. Following the lead of computational chemistry in applying multivariate data analysis techniques to the structure/property-activity relationships [see for example, Wold, et al. Multivariate data analysis in chemistry. Chemometrics-Mathematics and Statistics in Chemistry (Ed.: B. Kowalski); D. Reidel Publishing Company, Dordrecht, Holland, 1984 (ISBN 90-277-1846-6] quantitative activity-property relationships of proteins can be derived using well-known mathematical techniques, such as statistical regression, pattern recognition and classification [see for example Norman et al. Applied Regression Analysis. Wiley-Interscience; 3rd edition (April 1998) ISBN: 0471170828; Kandel, Abraham et al. Computer-Assisted Reasoning in Cluster Analysis. Prentice Hall PTR, (May 11, 1995), ISBN: 0133418847; Krzanowski, Wojtek. Principles of Multivariate Analysis: A User's Perspective (Oxford Statistical Science Series, No 22 (Paper)). Oxford University Press; (December 2000), ISBN: 0198507089; Witten, Ian H. et al Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations. Morgan Kaufmann; (Oct. 11, 1999), ISBN:1558605525; Denison David G. T. (Editor) et al Bayesian Methods for Nonlinear Classification and Regression (Wiley Series in Probability and Statistics). John Wiley & Sons; (July 2002), ISBN: 0471490369; Ghose, Arup K. et al. Combinatorial Library Design and Evaluation Principles, Software, Tools, and Applications in Drug Discovery. ISBN: 0-8247-0487-8]. The properties of proteins can be derived from empirical and theoretical models (for example, analysis of likely contact residues or calculated physicochemical property) of proteins sequence, functional and three-dimensional structures and these properties can be considered individually and in combination.
Amino acids are referred to herein using the name of the amino acid, the three-letter abbreviation or the single letter abbreviation. The term “protein”, as used herein, includes proteins, polypeptides, and peptides. As used herein, the term “amino acid sequence” is synonymous with the term “polypeptide” and/or the term “protein”. In some instances, the term “amino acid sequence” is synonymous with the term “peptide”. The terms “protein” and “polypeptide” are used interchangeably herein. In the present disclosure and claims, the conventional one-letter and three-letter codes for amino acid residues may be used. The 3-letter code for amino acids as defined in conformity with the IUPACIUB Joint Commission on Biochemical Nomenclature (JCBN). It is also understood that a polypeptide may be coded for by more than one nucleotide sequence due to the degeneracy of the genetic code.
Amino acid residues at non-conserved positions may be substituted with conservative or non-conservative residues. In particular, conservative amino acid replacements are contemplated.
A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art, including basic side chains (e.g., lysine, arginine, or histidine), acidic side chains (e.g., aspartic acid or glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, or cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, or tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, or histidine). Thus, if an amino acid in a polypeptide is replaced with another amino acid from the same side chain family, the amino acid substitution is considered to be conservative. The inclusion of conservatively modified variants in a protein of the invention does not exclude other forms of variant, for example polymorphic variants, interspecies homologs, and alleles.
“Non-conservative amino acid substitutions” include those in which (i) a residue having an electropositive side chain (e.g., Arg, His or Lys) is substituted for, or by, an electronegative residue (e.g., Glu or Asp), (ii) a hydrophilic residue (e.g., Ser or Thr) is substituted for, or by, a hydrophobic residue (e.g., Ala, Leu, Ile, Phe or Val), (iii) a cysteine or proline is substituted for, or by, any other residue, or (iv) a residue having a bulky hydrophobic or aromatic side chain (e.g., Val, His, Ile or Trp) is substituted for, or by, one having a smaller side chain (e.g., Ala or Ser) or no side chain (e.g., Gly).
“Insertions” or “deletions” are typically in the range of about 1, 2, or 3 amino acids. The variation allowed may be experimentally determined by systematically introducing insertions or deletions of amino acids in a protein using recombinant DNA techniques and assaying the resulting recombinant variants for activity. This does not require more than routine experiments for a skilled person.
A “fragment” of a polypeptide comprises at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or more of the original polypeptide. These fragments may be used as active ingredients in APP vaccines as described herein.
The proteins of the invention, or immunogenic fragments thereof, include both intact and modified forms of the proteins disclosed herein. For example, a protein of the invention or immunogenic fragment thereof can be functionally linked (e.g. by chemical coupling, genetic fusion, noncovalent association, or otherwise) to one or more other molecular entities, such as a pharmaceutical agent, a detection agent, and/or a protein or peptide that can mediate association of a binding molecule disclosed herein with another molecule (e.g. a streptavidin core region or a polyhistidine tag) Non-limiting examples of detection agents include: enzymes, such as alkaline phosphatase, glucose-6-phosphate dehydrogenase (“G6PDH”), alpha-D-galactosidase, glucose oxydase, glucose amylase, carbonic anhydrase, acetylcholinesterase, lysozyme, malate dehydrogenase and peroxidase, e.g., horseradish peroxidase; dyes; fluorescent labels or fluorescers, such as fluorescein and its derivatives, fluorochrome, rhodamine compounds and derivatives, GFP (GFP for “Green Fluorescent Protein”), dansyl, umbelliferone, phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde, and fluorescamine; fluorophores such as lanthanide cryptates and chelates, e.g., Europium etc., (Perkin Elmer and Cis Biointernational); chemoluminescent labels or chemiluminescers, such as isoluminol, luminol and the dioxetanes; bio-luminescent labels, such as luciferase and luciferin; sensitizers; coenzymes; enzyme substrates; radiolabels, including but not limited to, bromine77, carbon14, cobalt57, fluorine8, gallium67, gallium68, hydrogen3 (tritium), indium111, indium113m, iodine123m, iodine125, iodine126, iodine131, iodine133, mercury107, mercury203, phosphorous32, rhenium99m, rhenium101, rhenium105, ruthenium95, ruthenium97, ruthenium103, ruthenium105, scandium47, selenium75, sulphur35, technetium99, technetium99m, tellurium121m, tellurium122m, tellurium126m, thulium165, thulium167, thulium168 and yttrium199; particles, such as latex or carbon particles, metal sol, crystallite, liposomes, cells, etc., which may be further labelled with a dye, catalyst or other detectable group; molecules such as biotin, digoxygenin or 5-bromodeoxyuridine; toxin moieties, such as for example a toxin moiety selected from a group of Pseudomonas exotoxin (PE or a cytotoxic fragment or mutant thereof), Diptheria toxin or a cytotoxic fragment or mutant thereof, a Botulinum toxin A, B, C, D, E or F, ricin or a cytotoxic fragment thereof e.g. ricin A, abrin or a cytotoxic fragment thereof, saporin or a cytotoxic fragment thereof, pokeweed antiviral toxin or a cytotoxic fragment thereof and bryodin 1 or a cytotoxic fragment thereof.
The proteins of the invention or immunogenic fragments thereof also include derivatives that are modified (e.g., by the covalent attachment of any type of molecule to the protein) such that covalent attachment does not prevent the protein from binding to antibodies specific for said protein, or otherwise impair the biological activity of the protein. Examples of suitable derivatives include, but are not limited to fucosylated proteins, glycosylated proteins, acetylated proteins, PEGylated proteins, phosphorylated proteins, and amidated proteins.
As used herein, the terms “polynucleotides”, “nucleic acid” and “nucleic acid sequence” refers to any molecule, preferably a polymeric molecule, incorporating units of ribonucleic acid, deoxyribonucleic acid or an analogue thereof. The nucleic acid can be either single-stranded or double-stranded. A single-stranded nucleic acid can be one nucleic acid strand of a denatured double-stranded DNA Alternatively, it can be a single-stranded nucleic acid not derived from any double-stranded DNA. In one aspect, the nucleic acid can be DNA. In another aspect, the nucleic acid can be RNA Suitable nucleic acid molecules are DNA, including genomic DNA or cDNA. Other suitable nucleic acid molecules are RNA, including mRNA.
The terms “decrease”, “reduced”, “reduction”, or “inhibit” are all used herein to mean a decrease by a statistically significant amount. The terms “reduce,” “reduction” or “decrease” or “inhibit” typically means a decrease by at least 10% as compared to a reference level (e.g. the absence of a given treatment) and can include, for example, a decrease by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, at least about 99%, or more. As used herein, “reduction” or “inhibition” does not encompass a complete inhibition or reduction as compared to a reference level. “Complete inhibition” is a 100% inhibition as compared to a reference level. A decrease can be preferably down to a level accepted as within the range of normal for an individual without a given disorder.
The terms “increased”, “increase”, “enhance”, or “activate” are all used herein to mean an increase by a statically significant amount. The terms “increased”, “increase”, “enhance”, or “activate” can mean an increase of at least 10% as compared to a reference level, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% increase or any increase between 10-100% as compared to a reference level, or at least about a 2-fold, or at least about a 3-fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10-fold increase, or any increase between 2-fold and 10-fold or greater as compared to a reference level. In the context of a marker or symptom, an “increase” is a statistically significant increase in such level.
References herein to the level of a particular molecule (specifically any of the Apx proteins described herein) encompass the actual amount of the molecule, such as the mass, molar amount, concentration or molarity of the molecule. Preferably in the context of the invention, references to the level of a particular molecule refer to the concentration of the molecule.
The level of a molecule may be determined in any appropriate physiological compartment. Preferred physiological compartments include plasma, blood and/or bronchoalveolar lavage (BAL). The level of a molecule may be determined from any appropriate sample from a patient, e.g. a plasma sample, a blood sample, a serum sample and/or a BAL sample. Other non-limiting examples of samples which may be tested are tissue or fluid samples urine and biopsy samples. Thus, by way of non-limiting example, the invention may reference the level (e.g. concentration) of a molecule (e.g. an antibody to ApxIA, ApxIIA or ApxIIIA) in the plasma and/or BAL of a subject. The level of a molecule pre-treatment with a vaccine of the invention may be interchangeably referred to as the “baseline”.
The level of a molecule may be measured directly or indirectly, and may be determined using any appropriate technique. Suitable standard techniques are known in the art, for example Western blotting and enzyme-linked immunosorbent assays (ELISAs).
A subject can be one who has been previously diagnosed with or identified as suffering from or having a condition in need of treatment or one or more complications related to such a condition, and optionally, have already undergone treatment for a condition as defined herein or the one or more complications related to said condition. Alternatively, a subject can also be one who has not been previously diagnosed as having a condition as defined herein or one or more complications related to said condition. For example, a subject can be one who exhibits one or more risk factors for a condition, or one or more complications related to said condition or a subject who does not exhibit risk factors.
A “subject in need” of treatment for a particular condition can be a subject having that condition, diagnosed as having that condition, or at risk of developing that condition.
A “subject” may be any mammal, particularly a pig. A “subject” may be an adult, juvenile or infant, such as a pig or piglet. A “subject” may be male or female.
As used herein, the term “vaccine” is used to refer to a composition which induces an immune response. For example, the composition may induce an immune response in a subject to which it is administered. Unless explicitly stated, the term “vaccine” includes live vaccines (attenuated and vectored), inactivated vaccines (including whole cell inactivated vaccines and inactivated subunit vaccines) and subunit vaccines.
A live attenuated vaccine comprises whole bacteria which are capable of infecting and replicating in host cells, but have been modified in some way so that they do not cause disease.
A live vectored vaccine comprises a live vector, which is typically non-pathogenic, that has been modified to express one or more antigen from the bacteria against which an immune response is to be raised. Typically, the one or more antigen is a key antigen against which an immune response would be generated if a subject were exposed to the wild-type bacterium (i.e. is infected with the disease) or vaccinated with a live attenuated or inactivated vaccine. The antigen may be a protein antigen, or fragment thereof, or a polysaccharide antigen, or fragment thereof. The antigen may be expressed recombinantly or as a conjugate or fusion protein.
An inactivated whole cell vaccine comprises whole bacteria which have been killed or inactivated (e.g. by heat or chemical treatment). Inactivated bacteria are not capable of infecting or replicating in host cells and do not cause disease.
A subunit vaccine comprises one or more component of the bacterium against which an immune response is to be raised. Typically, the one or more component is a key antigen against which an immune response would be generated if a patient were exposed to the wild-type bacteria (i.e. is infected with the disease) or vaccinated with a live attenuated or inactivated vaccine. The component may be a protein antigen, or fragment thereof, or a polysaccharide antigen, or fragment thereof. The component may be expressed recombinantly or as a conjugate or fusion protein. In the case of subunit vaccines comprising toxin components, these may either be (i) modified such that the toxin no longer has toxic (e.g. cytotoxic or haemolytic activity), or (ii) wild-type toxins which have been inactivated (e.g. by heat or chemical treatment).
As used herein, the terms Apx polypeptides or Apx toxins are used interchangeably and encompass any one, two, or three of ApxIA, ApxIIA and ApxIIIA (e.g. ApxIA; ApxIIA; ApxIIIA; ApxIA and ApxIIA; ApxIA and ApxIIA; ApxIIA and ApxIIIA; and/or ApxIA, ApxIIA and ApxIIIA), unless expressly stated to the contrary. Typically, reference herein to Apx polypeptides or Apx toxins encompasses all of ApxIA, ApxIIA and ApxIIIA unless expressly stated otherwise.
A wild-type APP “toxin” is a polypeptide that consists of the amino acid sequence of ApxI, ApxIIA or ApxIIIA (e.g. as set forth in SEQ ID Nos: 1 to 3 respectively) and exhibits cytolytic and/or haemolytic activity. A “toxoid” in this disclosure is a polypeptide that is a modified form of the “toxin” wherein the modification is achieved by the replacement or deletion of one or more amino acid that is susceptible to acylation in vivo in APP, said toxoid does not exhibit any cytotoxic or haemolytic activity.
The genus Actinobacillus comprises Gram-negative, non-spore forming and predominantly encapsulated bacterial species that colonise mucosal surfaces of the respiratory and urogenital tracts. Relevant veterinary species are for example APP, Actinobacillus suis, Actinobacillus equuli and Actinobacillus lignieresii which are the preferred Actinobacillus spp. of the disclosure. Actinobacillus spp. normally show strong host species specificity. Preferred APP serotypes are serotypes 1, 5, 7, 8, 9 and 11.
The terms “strain”, “serovar” and “serotype” are used interchangeably herein to describe a distinct group or classification of APP.
The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that such publications constitute prior art to the claims appended hereto.
The present invention relates to microorganisms which express one of each of ApxIA, ApxIIA and ApxIIIA polypeptides (hereafter collectively and exchangeably designated ApxA toxins or polypeptides for brevity). Whilst conventional approaches have been able to produce a series of contructs each expressing individual ApxA toxins (for example Hur et al. J. Vet. Med. Sci. 77(12):1693-1696, 2015; and Hur and Lee Vet. Res. Commun. 38:87-91, 2014; which are herein incorporated by reference in its entirely), this is very different to providing a single microorganism expressing one each of ApxIA, ApxIIA and ApxIIIA polypeptides. The former is technically straightforward, whereas the present inventors have pioneered the natural transformation methodology and so are the first to provide a technique by which microorganisms expressing one of each of ApxIA, ApxIIA and ApxIIIA polypeptides can be produced. Linear template DNA is used in natural transformation, ensuring that allele exchange occurs via a double-cross over event, resulting in correct directional insertion of the gene replacement without incorporation of any extra (e.g. plasmid backbone) DNA. Other approaches described in the art are also unsuitable for the production of microorganisms according to the invention, and are typically associated with one or more disadvantages. For example, some prior art techniques are dependent on the particular APP strain, or rely on serial single cross-over events which do not reliably result in the production of the desired gene in a predictable manner (e.g., Oswald et al. FEMS Microbiol. Lett. 179:153-160, 1999, which is herein incorporated by reference in its entirety).
The ApxIA, ApxIIA and ApxIIIA polypeptides expressed by microorganisms of the invention may be wild-type ApxA polypeptides as described herein. The ApxIA, ApxIIA and ApxIIIA polypeptides may be variants of wild-type ApxA polypeptides as described herein which retain the cytotoxic and/or haemolytic activity of the wild-type ApxA polypeptide from which they are derived. The ApxIA, ApxIIA and ApxIIIA polypeptides may be modified ApxA polypeptides which have reduced cytotoxic and/or haemolytic activity compared with the wild-type ApxA polypeptide from which they are derived. In particular, the ApxIA, ApxIIA and ApxIIIA polypeptides may be modified ApxA polypeptides as described herein. Typically, all three of ApxIA, ApxIIA and ApxIIIA polypeptides are either wild-type ApxA polypeptides or modified ApxA polypeptides.
One or more of the ApxA polypeptides expressed by a microorganism of the invention are typically in their native conformation, preferably all of the ApxA polypeptides expressed by a microorganism of the invention are in their native conformation.
The ApxA polypeptides of the invention can induce a humoral and/or cellular immunological response against one or more serotypes of AAP in a mammal, in particular a pig, when administered to said mammal. The ApxA polypeptides can induce a humoral and/or cellular immunological response against at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least 12, at least 15 or more, up to all known serotypes (currently 19) of APP in a mammal, in particular a pig, when administered to said mammal. Preferably the ApxA polypeptides of the invention induce a sterile immunity (i.e. provide complete protection) against APP, APP strains, APP serotypes or APP serovars.
The microorganisms, vectors and vaccines of the invention may comprise wild-type ApxIA, ApxIIA and ApxIIIA polypeptides, or a fragment or variant thereof, provided that said variants do not encompass modifications at either acylation site as described herein in the context of modified ApxIA, ApxIIA and ApxIIIA polypeptides of the invention (i.e. amino acids corresponding to K560 and/or K686 in ApxIA; K557 and/or N687 in ApxIIA; and K571 and/or K702 in ApxIIIA).
A wild-type ApxIA polypeptide typically has an amino acid sequence corresponding to SEQ ID NO: 1. A variant of this wild-type ApxIA polypeptide may have at least 60%, at least 70%, more preferably at least 80%, at least 85%, at least 90%, at least 95%, and most preferably at least 97% or at least 99% sequence identity with the wild-type ApxIA sequence (e.g. SEQ ID NO: 1). By way of non-limiting example, a variant of an ApxIA wild-type polypeptide is at least 90% homologous to the wild-type ApxIA amino acid sequence. A fragment of the wild-type ApxIA comprises at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or more of the wild-type ApxIA polypeptide from which it is derived (e.g. SEQ ID NO: 1).
A wild-type ApxIIA polypeptide typically has an amino acid sequence corresponding to SEQ ID NO: 2. A variant of this wild-type ApxIIA polypeptide may have at least 60%, at least 70%, more preferably at least 80%, at least 85%, at least 90%, at least 95%, and most preferably at least 97% or at least 99% sequence identity with the wild-type ApxIIA sequence (e.g. SEQ ID NO: 2). By way of non-limiting example, a variant of an ApxIIA wild-type polypeptide is at least 90% homologous to the wild-type ApxIIA amino acid sequence. A fragment of the wild-type ApxIIA comprises at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or more of the wild-type ApxIIA polypeptide from which it is derived (e.g. SEQ ID NO: 2). A particular example of a fragment of a wild-type ApxIIA polypeptide is set out in SEQ ID NO: 7. Approximately 62% of the full-length wild-type ApxIIA sequence has been deleted to produce this wild-type ApxIIA fragment.
A wild-type ApxIIIA polypeptide typically has an amino acid sequence corresponding to SEQ ID NO: 3. A variant of this wild-type ApxIIIA polypeptide may have at least 60%, at least 70%, more preferably at least 80%, at least 85%, at least 90%, at least 95%, and most preferably at least 97% or at least 99% sequence identity with the wild-type ApxIIIA sequence (e.g. SEQ ID NO: 3). By way of non-limiting example, a variant of an ApxIIIA wild-type polypeptide is at least 90% homologous to the wild-type ApxIIIA amino acid sequence. A fragment of the wild-type ApxIIIA comprises at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or more of the wild-type ApxIIIA polypeptide from which it is derived (e.g. SEQ ID NO: 3).
Variants of the wild-type ApxA polypeptides typically comprise conservative substitutions or deletions as defined in the general definitions section above. These variants do not comprise substitutions or deletions which reduce or abrogate the cytotoxicity and/or haemolytic activity of the wild-type ApxA polypeptides (instead, ApxA polypeptides with reduced or abrogated cytotoxicity and/or haemolytic activity are encompassed by the modified ApxA polypeptides of the invention, described herein).
In particular, variants of the wild-type ApxA polypeptides do not comprise conservative substitutions or deletions of either amino acid susceptible to acylation (i.e. amino acids corresponding to K560 and/or K686 in ApxIA; K557 and/or N687 in ApxIIA; and K571 and/or K702 in ApxIIIA). In other words, variants of the wild-type ApxA polypeptides comprise both amino acids susceptible to acylation. Thus, variants of the wild-type ApxA polypeptides may comprise substitutions and/or deletions provided the one or two amino acids susceptible to acylation (or any other amino acids required for cytotoxic and haemolytic activity) are not substituted and/or deleted.
The wild-type ApxA polypeptide variants may comprise any number of substitutions or deletions, provided the cytotoxic and/or haemolytic activity of the wild-type ApxA polypeptides is retained. Typically, the wild-type ApxA polypeptide variants will comprise less than ten amino acid deletions, nine amino acid deletions, eight amino acid deletions, seven amino acid deletions, six amino acid deletions, five amino acid deletions, four amino acid deletions, three amino acid deletions, two amino acid deletions or one amino acid deletion. Preferably, the wild-type ApxA polypeptide variants will comprise only one, two or three amino acid deletions. Typically the wild-type ApxA polypeptide variants will comprise less than ten conservative amino acid substitutions, nine conservative amino acid substitutions, eight conservative amino acid substitutions, seven conservative amino acid substitutions, six conservative amino acid substitutions, five conservative amino acid substitutions, four conservative amino acid substitutions, three conservative amino acid substitutions, two conservative amino acid substitutions or one conservative amino acid substitution. Preferably, the wild-type ApxA polypeptide variants will comprise only one, two or three conservative amino acid substitutions. The wild-type ApxA polypeptide variants may comprise less than ten conservative amino acid substitutions and deletions in total, nine conservative amino acid substitutions and deletions in total, eight conservative amino acid substitutions and deletions in total, seven conservative amino acid substitutions and deletions in total, six conservative amino acid substitutions and deletions in total, five conservative amino acid substitutions and deletions in total, four conservative amino acid substitutions and deletions in total, three conservative amino acid substitutions and deletions in total, two conservative amino acid substitutions and deletions in total or one conservative amino acid substitution or deletion.
Fragments of the wild-type ApxA polypeptides also comprise both amino acids susceptible to acylation.
Any combination of these wild-type ApxA polypeptides may be used together, provided that each of an ApxIA, ApxIIA and ApxIIIA polypeptide is used.
The present inventors have previously developed modified forms of ApxIA, ApxIIA and ApxIIIA which may be used in the present invention.
These modified ApxA toxins have been modified at at least one of the two acylation sites of ApxIA, ApxIIA and ApxIIIA (typically amino acids corresponding to K560 and/or K686 in ApxIA; K557 and/or N687 in ApxIIA; and K571 and/or K702 in ApxIIIA), creating inactive but fully immunogenic toxoid forms of these proteins. The modification at either or both acylation sites may be by amino acid substitution or deletion at the position of the amino acid susceptible to acylation in the wild-type polypeptide. The substitution or deletion of the amino acids at either or both of the two acylation sites prevents them from being acylated by any endogenous or exogeneous acyltransferase (e.g. an ApxC of APP). Preferably, both of the acylation sites of ApxIA, ApxIIA and/or ApxIIIA are substituted or deleted.
As a result of this inability to be acylated (whether by substitution or deletion of either or both of the amino acids at the acylation positions within ApxA polypeptides), these modified Apx toxins cannot initiate binding to the target cell membrane and consequently have substantial pathological effect, particularly no cytotoxic or haemolytic activity. These inactive ApxA polypeptides are safer to use in vaccine compositions than vaccines in which the acyltransferase ApxC is deleted because in the acyltransferase deletion vaccines the Apx polypeptides remain pathological if an acyltransferase is provided exogenously, either by a naturally occurring strain of APP or any other source of acyltransferase in vivo. The modified ApxA proteins of the invention typically elicit fewer side effects (e.g. fever, vomiting, apathy) when used to vaccinate a mammal whilst conferring immunological protection against APP. These modified ApxA may therefore be considered as inactivated toxins (also referred to as toxoids). A further benefit is that these modified Apx toxins, whether in subunit or whole cell vaccine form do not need to be chemically inactivated, resulting in highly immunogenic vaccines, such that lower doses may be used.
Accordingly, the microorganisms, vectors and vaccines of the invention may comprise modified ApxIA, ApxIIA and ApxIIIA polypeptides, or a fragment or variant thereof, provided that said modified ApxA polypeptides comprise a modification at either or both acylation site as described. These modified ApxA polypeptides are also referred interchangeably herein as inactive ApxA polypeptides. These modified ApxA polypeptides typically retain common antigenic cross-reactivity with the corresponding wild-type ApxA polypeptide from which they are derived.
An inactive ApxIA typically has an amino acid sequence corresponding to the wild-type ApxIA amino acid sequence of SEQ ID NO: 1, modified by an amino acid substitution at at least one amino acid selected from the group consisting of K560 and K686. Preferably the inactive ApxIA comprises substitutions at both K560 and K686. Variants of this inactive ApxIA are also encompassed. A variant of this inactive ApxIA polypeptide may have at least 60%, at least 70%, more preferably at least 80%, at least 85%, at least 90%, at least 95%, and most preferably at least 97% or at least 99% sequence identity with the inactive ApxIA sequence, provided that said variant comprises the at least one modified (substituted) amino acid. By way of non-limiting example, a variant of an inactive ApxIA polypeptide is at least 90% homologous to the inactive ApxIA amino acid sequence, wherein said variant comprises an amino acid substitution at position K560 and/or K686. A fragment of the inactive ApxIA comprises at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or more of the inactive ApxIA polypeptide from which it is derived, provided that said variant comprises the at least one modified (substituted) amino acid. Preferably variants and/or fragments of the inactive ApxIA comprise substitutions at both K560 and K686.
An inactive ApxIIA typically has an amino acid sequence corresponding to the wild-type ApxIIA amino acid sequence of SEQ ID NO: 2, modified by an amino acid substitution at least one amino acid selected from the group consisting of K557 and N687. Preferably the inactive ApxIIA comprises substitutions at both K557 and N687. Variants of this inactive ApxIIA are also encompassed. A variant of this inactive ApxIIA polypeptide may have at least 60%, at least 70%, more preferably at least 80%, at least 85%, at least 90%, at least 95%, and most preferably at least 97% or at least 99% sequence identity with the inactive ApxIIA sequence, provided that said variant comprises the at least one modified (substituted) amino acid. By way of non-limiting example, a variant of an inactive ApxIIA polypeptide is at least 90% homologous to the inactive ApxIIA amino acid sequence, wherein said variant comprises an amino acid substitution at position K557 and/or N687. A fragment of the inactive ApxIIA comprises at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or more of the inactive ApxIIA polypeptide from which it is derived, provided that said variant comprises the at least one modified (substituted) amino acid. Preferably variants and/or fragments of the inactive ApxIIA comprise substitutions at both K557 and N687. A particular example of a fragment of an inactive ApxIIA polypeptide is set out in SEQ ID NO: 8. Approximately 62% of the full-length inactive ApxIIA sequence has been deleted to produce this inactive ApxIIA fragment.
An inactive ApxIIIA typically has an amino acid sequence corresponding to the wild-type ApxIIA amino acid sequence of SEQ ID NO: 3, modified by an amino acid substitution at least one amino acid selected from the group consisting of K571 and K702. Preferably the inactive ApxIIIA comprises substitutions at both K571 and K702. Variants of this inactive ApxIIIA are also encompassed. A variant of this inactive ApxIIIA polypeptide may have at least 60%, at least 70%, more preferably at least 80%, at least 85%, at least 90%, at least 95%, and most preferably at least 97% or at least 99% sequence identity with the inactive ApxIIIA sequence, provided that said variant comprises the at least one modified (substituted) amino acid. By way of non-limiting example, a variant of an inactive ApxIIIA polypeptide is at least 90% homologous to the inactive ApxIIIA amino acid sequence, wherein said variant comprises an amino acid substitution at position K571 and/or K702. A fragment of the inactive ApxIIIA comprises at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or more of the inactive ApxIIIA polypeptide from which it is derived, provided that said variant comprises the at least one modified (substituted) amino acid. Preferably variants and/or fragments of the inactive ApxIIIA comprise substitutions at both K571 and K702.
An exemplary inactive ApxIA polypeptide of the invention comprises the amino acid sequence of SEQ ID NO: 4.
An exemplary inactive ApxIIA polypeptide of the invention comprises the amino acid sequence of SEQ ID NO: 5.
An exemplary inactive ApxIIIA polypeptide of the invention comprises the amino acid sequence of SEQ ID NO: 6.
An inactive ApxIA may have an amino acid sequence corresponding to the wild-type ApxIA amino acid sequence of SEQ ID NO: 1, modified by a deletion at at least one amino acid selected from the group consisting of K560 and K686. Preferably the inactive ApxIA comprises deletions at both K560 and K686. Variants of this inactive ApxIA are also encompassed. A variant of this inactive ApxIA polypeptide may have at least 60%, at least 70%, more preferably at least 80%, at least 85%, at least 90%, at least 95%, and most preferably at least 97% or at least 99% sequence identity with the inactive ApxIA sequence, provided that said variant comprises the at least one deletion. By way of non-limiting example, a variant of an inactive ApxIA polypeptide is at least 90% homologous to the inactive ApxIA amino acid sequence, wherein said variant comprises a deletion at position K560 and/or K686. A fragment of the inactive ApxIA comprises at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or more of the inactive ApxIA polypeptide from which it is derived, provided that said variant comprises the at least one deletion. Preferably variants and/or fragments of the inactive ApxIA comprise deletions at both K560 and K686.
An inactive ApxIIA typically has an amino acid sequence corresponding to the wild-type ApxIIA amino acid sequence of SEQ ID NO: 2, modified by a deletion at at least one amino acid selected from the group consisting of K557 and N687. Preferably the inactive ApxIIA comprises deletions at both K557 and N687. Variants of this inactive ApxIIA are also encompassed. A variant of this inactive ApxIIA polypeptide may have at least 60%, at least 70%, more preferably at least 80%, at least 85%, at least 90%, at least 95%, and most preferably at least 97% or at least 99% sequence identity with the inactive ApxIIA sequence, provided that said variant comprises the at least one deletion. By way of non-limiting example, a variant of an inactive ApxIIA polypeptide is at least 90% homologous to the inactive ApxIIA amino acid sequence, wherein said variant comprises a deletion at position K557 and/or N687. A fragment of the inactive ApxIIA comprises at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or more of the inactive ApxIIA polypeptide from which it is derived, provided that said variant comprises the at least one deletion. Preferably variants and/or fragments of the inactive ApxIIA comprise deletions at both K557 and N687.
An inactive ApxIIIA typically has an amino acid sequence corresponding to the wild-type ApxIIA amino acid sequence of SEQ ID NO: 3, modified by a deletion at at least one amino acid selected from the group consisting of K571 and K702. Preferably the inactive ApxIIIA comprises deletions at both K571 and K702. Variants of this inactive ApxIIIA are also encompassed. A variant of this inactive ApxIIIA polypeptide may have at least 60%, at least 70%, more preferably at least 80%, at least 85%, at least 90%, at least 95%, and most preferably at least 97% or at least 99% sequence identity with the inactive ApxIIIA sequence, provided that said variant comprises the at least one deletion. By way of non-limiting example, a variant of an inactive ApxIIIA polypeptide is at least 90% homologous to the inactive ApxIIIA amino acid sequence, wherein said variant comprises a deletion at position K571 and/or K702. A fragment of the inactive ApxIIIA comprises at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or more of the inactive ApxIIIA polypeptide from which it is derived, provided that said variant comprises the at least one deletion. Preferably variants and/or fragments of the inactive ApxIIIA comprise deletions at both K571 and K702.
In inactive ApxA polypeptides, where one or both of the amino acids which are susceptible to acylation (i.e. the acylation sites) are deleted, the deletion may comprise point deletions where only either the one or the two amino acids susceptible to acylation in each wild-type ApxA sequence are deleted. Alternatively, the deletions may also delete amino acids in an area adjacent to the one or two amino acids susceptible to acylation. Thus, the respective deletions may comprise a deletion of two, three, four, five, six, seven, eight, nine, ten, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 200, 300, 350 or 400 amino acids, provided that the deletion comprises one of the two amino acids susceptible to acylation. When both of the amino acids which are susceptible to acylation are deleted, the size of the deletion for each amino acid susceptible to acylation may be independent from each other, or the two deletions may be the same size. Deletions which cover a consecutive stretch of amino acids between the two amino acids susceptible to acylation are also disclosed.
Whether either or both of the amino acids which are susceptible to acylation are deleted, the deletion(s) do not delete more than 70% of the corresponding wild-type amino acid sequence.
Other modified ApxA polypeptides may be used in the present invention. The methods of the present invention may be used to produce a microorganism which expresses inactive forms of each of ApxIA, ApxIIA and ApxIIIA. By way of non-limiting example, WO 2013/068629 (herein incorporated by reference in its entirety) describes modified apxIIA and ApxIIIA genes which are mutated in their transmembrane domains and the encoded modified ApxIIA and ApxIIIA retain their immunogenicity whilst being haemolytically and cytotoxically inactive. These modified apxIIA and ApxIIIA genes may be used in the present invention as alternatives to or in combination with the modified ApxA polypeptides with one or more deleted/substituted acylation site.
Variants of the inactive ApxA polypeptides typically comprise conservative substitutions or deletions as defined in the general definitions section above. Thus, variants of the inactive ApxA polypeptides may comprise further deletions outside the deletion region comprising the one or two amino acids susceptible to acylation.
The inactive ApxA polypeptide variants may comprise any number of substitutions or deletions, provided the cytotoxic and/or haemolytic activity of the wild-type ApxA polypeptides is still abrogated or reduced. Typically, the inactive ApxA polypeptide variants will comprise less than ten amino acid deletions, nine amino acid deletions, eight amino acid deletions, seven amino acid deletions, six amino acid deletions, five amino acid deletions, four amino acid deletions, three amino acid deletions, two amino acid deletions or one amino acid deletion. Preferably, the inactive ApxA polypeptide variants will comprise only one, two or three amino acid deletions. Typically the inactive ApxA polypeptide variants will comprise less than ten conservative amino acid substitutions, nine conservative amino acid substitutions, eight conservative amino acid substitutions, seven conservative amino acid substitutions, six conservative amino acid substitutions, five conservative amino acid substitutions, four conservative amino acid substitutions, three conservative amino acid substitutions, two conservative amino acid substitutions or one conservative amino acid substitution. Preferably, the inactive ApxA polypeptide variants will comprise only one, two or three conservative amino acid substitutions. The inactive ApxA polypeptide variants may comprise less than ten conservative amino acid substitutions and deletions in total, nine conservative amino acid substitutions and deletions in total, eight conservative amino acid substitutions and deletions in total, seven conservative amino acid substitutions and deletions in total, six conservative amino acid substitutions and deletions in total, five conservative amino acid substitutions and deletions in total, four conservative amino acid substitutions and deletions in total, three conservative amino acid substitutions and deletions in total, two conservative amino acid substitutions and deletions in total or one conservative amino acid substitution or deletion.
Any combination of these inactive ApxA polypeptides may be used together, provided that each of an ApxIA, ApxIIA and ApxIIIA polypeptide is used.
In an inactive ApxIA, ApxIIA or ApxIIIA polypeptide of the invention, the one or two amino acids susceptible to acylation may be each be independently substituted with any amino acid that is not susceptible to acylation.
Amino acids susceptible to acylation are naturally occurring amino acids such as lysine and/or asparagine. Amino acids not susceptible to acylation are known to the skilled person and can be used to substitute one or both of the amino acids susceptible to acylation. The amino acid to be substituted at each amino acid susceptible to acylation in the wild-type ApxA polypeptides, i.e. amino acids corresponding to K560 and/or K686 in ApxIA; K557 and/or N687 in ApxIIA; and K571 and/or K702 in ApxIIIA, may be independently selected from the group consisting of alanine, glycine, isoleucine, leucine, methionine, valine, serine, threonine, asparagine, glutamine, aspartic acid, histidine, cysteine, proline, phenylalanine, tyrosine, tryptophan and glutamic acid. More preferably, each amino acid to be substituted at each amino acid susceptible to acylation in the wild-type ApxA polypeptides, i.e. K560 and/or K686 in ApxIA; K557 and/or N687 in ApxIIA; and K571 and/or K702 in ApxIIIA, may be independently selected from the group consisting of alanine, glycine, serine, isoleucine and leucine, valine and threonine. Even more preferably, each amino acid to be substituted at each amino acid susceptible to acylation in the wild-type ApxA polypeptides, i.e. K560 and/or K686 in ApxIA; K557 and/or N687 in ApxIIA; and K571 and/or K702 in ApxIIIA, may be independently selected from the group consisting of alanine, glycine and serine. The most preferred amino acid not susceptible to acylation (for each of ApxIA, ApxIIA and ApxIIIA) is alanine.
Preferably, for each inactive ApxA polypeptide, i.e. each of ApxIA, ApxIIA and ApxIIIA, both of the two amino acids susceptible to acylation are modified. Accordingly, the wild-type sequence of ApxIA (exemplified by SEQ ID NO: 1) is modified at amino acids corresponding to K560 and K686. The wild-type sequence of ApxIIA (exemplified by SEQ ID NO: 2) is modified at amino acids corresponding to K557 and N687. The wild-type sequence of ApxIIIA (exemplified by SEQ ID NO: 3) is modified at amino acids corresponding to K571 and K702. Preferably, both of the two amino acids susceptible to acylation in each of ApxIA, ApxIIA and ApxIIIA are substituted with alanine. Thus, preferred inactive ApxA polypeptides have the amino acid sequence set forth in SEQ ID: 4 (inactive ApxIA); SEQ ID NO: 5 (inactive ApxIIA) and SEQ ID NO: 6 (inactive ApxIIIA). Variants and fragments of these sequences are also encompassed as described above.
Nucleic acids comprising a nucleic acid sequence capable of coding for the above described wild-type and inactive ApxA polypeptides are also disclosed. The disclosed nucleic acid can be cDNA, DNA, RNA, cRNA or PNA (peptide nucleic acid). The term “nucleic acid sequence” refers to a heteropolymer of nucleotides or the sequence of these nucleotides. The nucleic acid can comprise a nucleic acid as set forth in SEQ ID NO: 9, 10, or 11 (for wild-type apxIA, apxIIA and apxIIIA respectively) or 12, 13 or 14 (for inactive apxIA, apxIIA and apxIIIA respectively). Variants and fragments of said nucleic acids which encode variants and fragments of wild-type and inactive ApxA polypeptides as disclosed herein are also encompassed.
Said nucleic acids may be comprised in a microorganism of the invention, as described herein.
The nucleic acid may be comprised in a vector suitable for cloning or expressing the nucleic acids of the disclosure. Exemplary vectors are pEX-A258 (SEQ ID NO: 15), pQE-80L (SEQ ID NO: 16) and/or pQE-60 (SEQ ID NO: 17). The nucleic acids or vectors may comprise additional regulatory non-coding elements like inducible or non-inducible promoters, operators (e.g. lac-operator) or nucleic acids coding for other APP proteins.
One or more nucleic acids of the invention may encode for each of an ApxIA, an ApxIIA and an ApxIIIA polypeptide (wild-type or inactive) as disclosed herein. All three ApxA polypeptides may be encoded by a single nucleic acid. Alternatively, each ApxA polypeptide may be encoded by a separate nucleic acid. Alternatively, any two of the ApxA polypeptides may be encoded by a first nucleic acid, with the remaining ApxA polypeptide being encoded by a second nucleic acid. By way of non-limiting example, ApxIA and ApxIIA polypeptides of the invention may be encoded by a first nucleic acid, with ApxIIIA encoded by a second nucleic acid. By way of a further non-limiting example, ApxIA and ApxIIIA polypeptides of the invention may be encoded by a first nucleic acid, with ApxIIA encoded by a second nucleic acid. By way of a further non-limiting example, ApxIIA and ApxIIIA polypeptides of the invention may be encoded by a first nucleic acid, with ApxIA encoded by a second nucleic acid. Thus, the present invention provides a nucleic acid or set of nucleic acids (i.e. one or more nucleic acid) encoding for an ApxIA, an ApxIIA and an ApxIIIA polypeptide (wild-type or inactive) of the invention.
The one or more nucleic acid may be integrated into one or more vector, wherein the one or more nucleic acid is operably linked to an expression control region of the vector(s). Each nucleic acid may be operably linked to a separate expression control region, or the nucleic acids may be operably linked to the same expression control region, forming a polycistronic cassette. Thus, expression vectors are also disclosed, wherein the expression vector preferably comprises one or more regulatory sequences in addition to the nucleic acid(s) encoding for the ApxIA, ApxIIA and ApxIIIA polypeptides. The present invention therefore provides a vector or set of vectors (i.e. one or more vector) encoding for an ApxIA, an ApxIIA and an ApxIIIA polypeptide (wild-type or inactive) of the invention.
One or more vector of the invention may encode for each of an ApxIA, an ApxIIA and an ApxIIIA polypeptide (wild-type or inactive) as disclosed herein. All three ApxA polypeptides may be encoded by a vector. Alternatively, each ApxA polypeptide may be encoded by a separate vector. Alternatively, any two of the ApxA polypeptides may be encoded by a first vector, with the remaining ApxA polypeptide being encoded by a second vector. By way of non-limiting example, ApxIA and ApxIIA polypeptides of the invention may be encoded by a first vector, with ApxIIIA encoded by a second vector. By way of a further non-limiting example, ApxIA and ApxIIIA polypeptides of the invention may be encoded by a first vector, with ApxIIA encoded by a second vector. By way of a further non-limiting example, ApxIIA and ApxIIIA polypeptides of the invention may be encoded by a first vector, with ApxIA encoded by a second vector. The nucleic acid encoding each ApxA polypeptide in said one or more vector may be operably linked to the same expression control region as described herein, or maybe operably linked to separate expression control regions.
The term “expression vector” generally refers to a plasmid, phage, virus or vector for expressing a polypeptide from a DNA (RNA) sequence. An expression vector may comprise a transcriptional unit comprising an assembly of (1) a genetic element or elements having a regulatory role in gene expression, for example promoters or enhancers; (2) a structural or coding sequence which is transcribed into mRNA and translated into protein; and (3) appropriate transcription initiation and termination sequences. Structural units intended for use in yeast or eukaryotic expression systems preferably include a leader sequence enabling extracellular secretion of translated protein by a host cell. Alternatively, where recombinant protein is expressed without a leader or transport sequence, it may include an N-terminal methionine residue. This residue may or may not be subsequently cleaved from the expressed recombinant protein to provide a final product.
Any of these one or more nucleic acid combinations or one or more vector combinations may be comprised in a vaccine composition of the invention. Preferably for such vaccine combinations the one or more nucleic acid is integrated into one or more vector as disclosed herein.
The present invention particularly relates to microorganisms which comprise each of an ApxIA, an ApxIIA and an ApxIIIA polypeptide. These ApxA polypeptides may be wild-type or inactive ApxA polypeptides as described herein. Preferably, the microorganism comprises either all wild-type ApxA polypeptides or all inactive ApxA polypeptides as disclosed herein. As used herein, references to a microorganism “comprising” (wild-type or inactive) ApxA encompass microorganisms producing, encoding or expressing said ApxA.
The APP ApxA polypeptides may be provided via nucleic acids or vectors of the invention. Accordingly, the invention provides a microorganism comprising: (a) a nucleic acid sequence encoding ApxIA; (b) a nucleic acid sequence encoding ApxIIA; and (c) a nucleic acid sequence encoding ApxIIIA. Said nucleic acids may be comprised within one or more vector as described herein.
The nucleic acid encoding each of the ApxIA, ApxIIA and ApxIIIA polypeptides may be comprised within the genome of the microorganism. This may involve integration of the nucleic acid within the genome of the microorganism, such as by using molecular biological techniques. The nucleic acid encoding each of the ApxIA, ApxIIA and ApxIIIA polypeptides may be comprised separately (e.g. extra-chromosomally) from the genome of the microorganism. In such instances, expression of the ApxIA, ApxIIA and/or ApxIIIA polypeptides expressed by an extra-chromosomal nucleic acid may be transient. By way of non-limiting example, extra-chromosomal expression of one or more of the ApxIA, ApxIIA and ApxIIIA polypeptides may be achieved when the nucleic acid encoding one or more of the ApxIA, ApxIIA and ApxIIIA polypeptides is part of a (non-integrating) plasmid. One benefit of integrating the ApxA polypeptides (wild-type or inactive) into the genome of the microorganism is that expression of the ApxA polypeptides is stable and does not require antibiotic selection for maintenance. Introduction of ApxA polypeptides according to the invention, particularly when the apxA genes are stably integrated into the genome of the microorganism, such as when introduced via natural transformation, is typically not associated with a selection marker (e.g. antimicrobial or antibiotic-resistance marker). Instead, in such embodiments, the apxA genes are typically unmarked within the chromosome of the microorganism.
Any combination of ApxA polypeptides encoding nucleic acids comprised with the genome of a microorganism or comprised separately from the genome is encompassed herein. By way of non-limiting example, a microorganism may comprise one or more nucleic acid encoding for ApxIA and ApxIIA within its genome, with a nucleic acid encoding for ApxIIIA comprised separately from its genome (e.g. in a separate plasmid). By way of a further non-limiting example, a microorganism may comprise one or more nucleic acid encoding for ApxIIA and ApxIIIA within its genome, with a nucleic acid encoding for ApxIA comprised separately from its genome (e.g. in a separate plasmid). By way of a further non-limiting example, a microorganism may comprise one or more nucleic acid encoding for ApxIA and ApxIIIA within its genome, with a nucleic acid encoding for ApxIIA comprised separately from its genome (e.g. in a separate plasmid).
The microorganism may be any appropriate bacterial species. Non-limiting examples include Actinobacillus species, for example APP, Actinobacillus suis, an Actinobacillus species strain, for example a strain of APP or a strain A. suis, or a particular serotype (ST) of an Actinobacillus species, such a strain of a serotype of APP or a strain of a serotype of A. suis. Other examples of appropriate bacteria include E. coli, for example an E. coli strain, particularly E. coli Top10F′ strain. Preferably the microorganism is an APP or an APP strain, e.g. serotype 2 (ST2 e.g. APP23 or 07/07), serotype 5 (ST5, e.g. DZY47), serotype 7 (ST7, e.g. DZY33) or serotype 8 (ST8, e.g. DZY49). References herein to an Actinobacillus species encompass references to strains and serotypes (also called serovars) of said Actinobacillus species. For example, references herein to APP also encompass references to strains, serotypes/serovars of APP.
The microorganism may be an APP strain which is produced by modification of an existing APP strain, such as naturally occurring APP strains. The resulting microorganism may comprise (express/produce) wild-type or inactive ApxA polypeptides as described herein.
A microorganism of the invention may be produced from an APP strain which expresses only one of ApxIA, ApxIIA and ApxIIIA endogenously. In such instances, the additional two ApxA polypeptides may be introduced to the microorganism, either in wild-type form if the endogenous ApxA is retained in wild-type form, or in inactive form if the endogenous ApxA is replaced or modified to produce an inactive form.
A microorganism of the invention may be produced from an APP strain which expresses only two of ApxIA, ApxIIA and ApxIIIA endogenously. In such instances, the additional ApxA polypeptide may be introduced to the microorganism, either in wild-type form if the endogenous ApxA are retained in wild-type form, or in inactive form if the endogenous ApxA are replaced or modified to produce the inactive forms.
A microorganism of the invention may be produced from an APP strain which expresses endogenous ApxIIA and ApxIIIA polypeptides, such as a serotype 2, 8 or 15 strain. By way of non-limiting example, a nucleic acid encoding a wild-type ApxIA polypeptide as disclosed herein may be introduced to said APP strain to produce a microorganism according to the invention (the nucleic acid encoding the wild-type ApxIA polypeptide may be integrated into the genome of the APP strain, or may be present extra-chromosomally within the microorganism).
A microorganism of the invention may be produced from an APP strain which expresses endogenous ApxIA and ApxIIA polypeptides, such as a serotype 1, 5 or 9 strain. By way of non-limiting example, a nucleic acid encoding a wild-type ApxIIIA polypeptide as disclosed herein may be introduced to said APP strain to produce a microorganism according to the invention (the nucleic acid encoding the wild-type ApxIIIA polypeptide may be integrated into the genome of the APP strain, or may be present extra-chromosomally within the microorganism).
A microorganism of the invention may be produced from an APP strain which expresses endogenous ApxIIA and ApxIIIA polypeptides, such as a serotype 2, 8 or 15 strain, and the endogenous ApxIIA and ApxIIIA polypeptides may be replaced by or modified to form inactive ApxIIA and ApxIIIA polypeptides. A nucleic acid encoding an inactive ApxIA polypeptide may be introduced to produce the microorganism of the invention. By way of non-limiting example, a nucleic acid encoding an inactive ApxIA polypeptide as disclosed herein may be introduced to said APP strain to produce a microorganism according to the invention (the nucleic acid encoding the inactive ApxIA, ApxIIA and/or ApxIIIA polypeptides may be integrated into the genome of the APP strain, or may be present extra-chromosomally within the microorganism).
A microorganism of the invention may be produced from an APP strain which expresses ApxIA and ApxIIA polypeptides, such as a serotype 1, 5 or 9 strain, and the endogenous ApxIA and ApxIIA polypeptides may be replaced by or modified to form inactive ApxIA and ApxIIA polypeptides. A nucleic acid encoding an inactive ApxIIIA polypeptide may be introduced to produce the microorganism of the invention. By way of non-limiting example, a nucleic acid encoding an inactive ApxIIIA polypeptide as disclosed herein may be introduced to said APP strain to produce a microorganism according to the invention (the nucleic acid encoding the inactive ApxIA, ApxIIA and/or ApxIIIA polypeptides may be integrated into the genome of the APP strain, or may be present extra-chromosomally within the microorganism).
The introduction, replacement or modification of a nucleic acid encoding an ApxIA, ApxIIA and/or ApxIIIA polypeptide may be carried out by any appropriate technique. Non-limiting examples of suitable techniques include those described in Baltes et al. (FEMS Microbiol. Lets. (2003b) 220(1):41-48), the single-step transconjugation system described in Oswald et al. (FEMS Microbiol. Lets. (1999) 179(1):153-160) and the allele exchange methodology used in Sheehan et al. (Infect Immun (2000) 68(8):4778-478), each of which is herein incorporated by reference in its entirety. Preferably, the introduction, replacement or modification of a nucleic acid encoding an ApxIA, ApxIIA and/or ApxIIIA polypeptide is carried out using natural transformation. This technique is preferred as it allows for the production of precise APP mutant strains. Exemplary natural transformation methodology is described in Bosse et al. FEMS Microbiol Lett. 2004 Apr. 15; 233(2):277-81 and Bosse et al. 2014 PLoS ONE 9(11): e111252, which are herein incorporated by reference in its entirety. Typically, a two-step natural transformation protocol is used, such as that exemplified herein. One example of a cassette that may be used in the first step of such a two-step natural transformation protocol is the dfrA14sacB cassette (SEQ ID NO: 18), as exemplified herein. This preferred dfrA14sacB cassette consists of the trimethoprim resistance allele dfrA14 (identified in endogenous APP plasmids), preceded by the promoter for the sodC gene of APP, followed by a 9-bp sequence required for uptake of DNA during natural transformation by APP, and the sucrose sensitivity gene, sacB. Gene replacement and mutation/deletion constructs (along with all of the primer sequences used in generation of these constructs) for the preferred natural transformation method are given in SEQ ID Nos: 19 to 46 in the sequence information section below.
The invention therefore provides a method for the production of an APP strain producing all three ApxA toxins (ApxI, ApxII, ApxIII) as described herein. Said method typically involves the introduction of one or more apxA gene into a microorganism by natural transformation, typically by two-step natural transformation. The dfrA14sacB cassette described herein is an exemplary, non-limiting cassette that may be used in such methods. Non-limiting examples of production methods are described in more detail below. The Examples herein provide non-limiting descriptions of methods according to the invention.
The methods of the invention can be used to generate APP strains producing all three ApxA toxins (ApxI, ApxII and ApxIII), in either wild-type or inactive form, regardless of the original apx gene profile of the APP strain. By way of non-limiting example, for a transformable APP isolate producing ApxII and ApxIII, to produce a strain comprising inactive forms of all three of ApxI, ApxII and ApxIII according to the invention, the appropriate mutations/deletions to remove or inactivate the one or both acylation sites in the respective toxin apxIIA and apxIIIA genes (as described herein) will be introduced, together with a mutated apxI operon (comprising a deletion/modification of one or both acylation sites as described herein) using natural transformation, such as the two-step transformation process described in the Examples. This can be done by amplifying the entire mutated apxI operon and 500 bp of flanking sequence and transforming this sequence into the strain in which the apxIIA and apxIIIA genes have already been mutated. The 500 bp flanking sequence to either side of the operon may be modified as appropriate to target a desired insertion site. As another non-limiting example, for a transformable APP isolate producing ApxI and ApxII, to produce a strain comprising inactive forms of all three of ApxI, ApxII and ApxIII according to the invention, the appropriate mutations/deletions to remove the one or both acylation sites in the respective toxin apxIA and apxIIA genes (as described herein) will be introduced, together with a mutated apxIII operon (comprising a deletion/modification of one or both acylation sites as described herein) using natural transformation, such as the two-step transformation process described in the Examples. This may easily be done by amplifying the entire mutated apxIII operon and 500 bp of flanking sequence (e.g. from one of the serotype 8 or 15 mutants) and transforming this sequence into the strain in which the apxIA and apxIIA genes have already been mutated. By way of further non-limiting example, if using a strain that normally only possesses genes for one of the ApxA toxins, the other two operons (with one or both acylation sites mutated or deleted in the respective toxin genes) could be introduced using this same method.
Similarly, this two-step method may be used to generate a microorganism in which all three ApxIA, ApxIIA and ApxIIIA are present in wild-type form. By way of non-limiting example, whether starting from an APP strain which endogenously expresses wild-type ApxIIA and ApxIIIA, two step-transformation may be carried out by amplifying the entire wild-type apxI operon and 500 bp of flanking sequence and transforming this sequence into the strain already comprising wild-type apxIIA and apxIIIA genes. As a further non-limiting example, if the starting strain endogenously expresses ApxIA and ApxIIA, the two-step natural transformation process involves the amplification of the entire wild-type apxIII operon and 500 bp of flanking sequence and transforming this sequence into the strain already comprising wild-type apxIA and apxIIA genes. The 500 bp flanking sequence to either side of the operon may be modified as appropriate to target a desired insertion site.
Microorganisms of the present invention may also comprise nucleic acids and/or vectors encoding one or more additional genes.
The one or more additional antigen may be from APP or may be from one or more other swine pathogens. Non-limiting examples of other swine pathogens and antigens therefrom that may be expressed using microorganisms, nucleic acids and/or vectors of the invention include bacterial antigens from: Bordetella bronchiseptica, Brachyspira hyodysenteriae, Brachyspira pilosicoli, Brucella suis, Clostridium difficile, Clostridium perfringens, Escherichia coli [e.g Heat labile (LT)-toxin, heat-stable (ST)-toxins], Lawsonia intracellularis Shigella-like toxin type II variant (SLT-Ile), verotoxin, cell wall (O antigens) and fimbriae (F antigens), Erysipelothrix rhusiopathiae, Haemophilus parasuis, Leptospira spp., Mycoplasma hyopneumoniae, Mycoplasma hyosynoviae, Mycoplasma hyorhinis, Pasteurella multocida, Salmonella spp, Staphylococcus hyicus, Streptococcus suis (e.g. IdeS).
Non-limiting examples of other swine pathogens and antigens therefrom that may be expressed using microorganisms, nucleic acids and/or vectors of the invention include viral antigens from: African Swine Fever Virus (ASFV), Atypical Porcine Pestivirus (APPV, e.g. E1 and or E2), Classical Swine Fever Virus (CSFV, e.g. E1 and or E2), Foot and Mouth Disease Virus (FMDV, e.g. VP1, VP2, VP3, VP4, P2A and/or 3C), Porcine Epidemic Diarrhea Virus (PEDV, e.g. spike protein), Encephalomyocarditis virus, Parvovirus (e.g. VP2), Porcine Circovirus (PCV1, PCV2 or PCV2, e.g. ORF2 or cap protein respectively), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), Suid Herpes Virus, Rotavirus Type A and C (RVA, RVC, e.g. VP4 and or Vp7), Swine Herpes Virus, Swine Influenza Virus (SIV, e.g. Haemmagglutinin (HA) and or Neuraminidase NA), Swine Pox Virus, Swine Vesicular Disease Virus, Transmissible Gastroenteritis Virus (TGEV).
Microorganisms of the present invention may also comprise one or more additional modification or deletion to inactivate/knock out at least one additional polypeptide within the microorganism. Such additional modifications are typically comprised in microorganisms comprising inactive ApxA polypeptides as disclosed herein, particularly wherein said additional modifications provide a further means to attenuate the microorganism. Inactivation/deletion of at least one additional polypeptide is therefore preferable in the context of attenuated vaccines as described herein. Without being bound by theory, it is believed that combining additional modifications with the microorganisms of the invention, particularly those with inactive ApxIA, ApxIIA and ApxIIIA, as described herein will result in a synergistic attenuation of APP. Modification or deletion of ApxIVA as described herein may be used for either live (attenuated) microorganisms comprising inactive ApxA polypeptides or microorganisms comprising wild-type ApxA polypeptides, as in either the deleted/modified ApxIVA polypeptide may be used as a marker for a DIVA vaccine as described herein.
Non-limiting examples of other genes which may be modified according to the invention include apxIVA, sxy (e.g. as encoded by DRF63_RS09615, version as of 30 Jul. 2020), ssrA (e.g. as encoded by DRF63_RS10030, version as of 16 Jul. 2020) and nlpD (also known as DRF63_RS10540, version as of 16 Jul. 2020), which is the gene encoding a LysM peptidoglycan-binding domain containing protein. Any combination of these genes may be modified. For example, apxIVA and sxy may be modified, apxIVA, sxy and ssrA may be modified, apxIVA, sxy and nlpD may be modified, apxIVA, sxy, ssrA and nlpD may be modified or nlpD and ssrA may be modified.
Typically, where the sxy gene is modified according to the invention, the sxy gene product is inactivated or deleted, preferably deleted. Inactivation or deletion of sxy prevents natural transformation. Thus, when producing microorganisms of the invention, inactivation or deletion of sxy is typically the last modification made to the microorganism, as further modification via natural transformation will not be possible once sxy is inactivated or deleted. Inactivation or deletion of sxy is particularly preferred when a microorganism of the invention comprises inactive ApxA (ApxIA, ApxIIA and ApxIIIA) polypeptides, as deletion of sxy prevents the microorganism reacquiring a wild-type ApxA polypeptide by natural transformation and so regaining virulence. Particularly preferred are microorganisms in which (i) both amino acids that are susceptible to acylation in each ApxA (ApxIA, ApxIIA and ApxIIIA) polypeptide have been substituted for amino acids that are not susceptible to acylation or deleted; and (ii) sxy has been inactivated or deleted, preferably deleted. This combination effectively precludes the possibility of the microorganism reverting to wild-type and hence virulence.
Microorganisms of the invention where the apxIVA gene is modified according to the invention allow for the differentiation of infected from vaccinated animals. Vaccines comprising appropriately modified apxIVA may therefore be described as DIVA vaccines.
ApxIV polypeptide is a weakly-haemolytic toxin that is unique to APP. In vivo it is expressed by all serotypes and can therefore be used to assign species and as an antigen for serological surveillance. Use of a modified ApxIV polypeptide (or nucleic acid encoding therefor) has the potential to act as a marker for live attenuated vaccine strains (or for subunit vaccines which comprise an ApxIV component), via a DIVA strategy. DIVA vaccines have at least one less antigenic protein than the corresponding wild-type microorganism. The ability to differentiate between subjects which have been immunised with the vaccine and subjects which have been exposed to the pathogenic form of the microorganism are based on detecting the serological response either toward a protein (or epitope) whose gene (or part thereof) has been deleted in the vaccine strain. Thus, subjects which have bene exposed to the pathogenic form of the microorganism exhibit a positive serological response to the antigen or epitope, whereas subjects which have been immunised with the vaccine do not. ApxIVA can therefore be used as a marker for a DIVA vaccine according to the invention.
Typically, when the apxIVA gene is modified according to the invention, the apxIVA gene is deleted or modified by an unmarked in-frame deletion of a sequence encoding an N-terminal immunogenic domain in the ApxIVA protein. One non-limiting example of such a deletion is the 2586 base pair (bp) deletion described in the Examples herein. An exemplary wild-type ApxIVA polypeptide (serotype 8) is given in SEQ ID NO: 47. The exemplified N-terminal in-frame deletion is given in SEQ ID NO: 48. Vaccinated subjects will not exhibit a serological response to the N-terminal immunogenic domain of ApxIVA.
A microorganism of the invention (comprising either wild-type or inactive ApxA polypeptides as described herein) may preferably comprise a deletion of the sxy gene and/or a modification of the apxIVA gene, such as an unmarked in-frame deletion of an N-terminal immunogenic domain sequence in the apxIVA as exemplified herein (or a deletion of the apxIVA gene). Most preferably the microorganism may comprise both a deletion of the sxy gene and a modification of the apxIVA gene, such as an unmarked in-frame deletion of an N-terminal immunogenic domain sequence in the apxIVA as exemplified herein (or a deletion of the apxIVA gene).
A microorganism of the invention, particularly an APP may comprises one or at least two of the following additional modifications (e.g. single or multiple deletions): ΔtpbA, ΔtonB2, ΔsodC, ΔdsbA, Δfur, ΔmlcA, ΔmglA, ΔexbB, ΔureC, double mutant ΔexbBΔureC, double mutant ΔfhuAΔhlyX, double mutant ΔapxICΔapxIIC, triple mutant ΔapxICΔapxIICΔorf1, hexamutant ΔapxIIAΔureCΔdmsAΔhybBΔaspAΔfur, double mutant ΔapxIIIBΔapxIIID, double mutant ΔclpPΔapxIIC, ΔznuA, ΔapfA, double mutant ΔapxIIAΔureC, pentamutant ΔapxICΔapxIICΔorf1ΔcpxARΔarcA, double mutant ΔapxICΔompP2, double mutant ΔapxIICΔapxIVA, inactivated apxIIC, inactivated apxIC, Δlip40, ΔcpxA/cpxR, ΔpotD2, ΔtolC2, ΔsapA and/or ΔpdxS/pdxT. These modifications are described in Baltes et al. FEMS Microbiol Let (2002) 209(2):283-287; Sheehan et al. Infect Immun (2003) 71(7):3960-3970; Baltes et al Infect. Immun (2001) 69(1):472-478; Jaques Can J Vet Res (2004) 68(2):81-85; Baltes et al. Infect Immun (2005) 73(8):4614-4619; Lin et al. FEMS Microbiol Let (2007) 274(1):55-62; Yuan et al. Current Microbiol (2011) 63(6):574-580; Maas et al. Infect Immun (2006) 74(7):4124-4132; Park et al. J Vet Med Sci (2009) 71(10:1317-1323; Xie et al. BMC Vet Res (2017) 13(1)p14; Yuan et al. Vet Microbiol (2014) 174(3-4):531-539; Zhou et al. Clin Vaccine Immunol (2013) 20(2):287-294; Tonpitak et al. Infect Immun (2002) 70(12):7120-7125; Yuan et al. Vaccine (2018) 36(14):1830-1836; Liu et al. Onderstepoort J of Vet Res (2013) 80(1):519; Liu et al. Vaccine (2007) 25(44):7696-7705; Bei et al. FEMS Microbiol Let (2005) 243(1):21-37; Xu et al. Acta Microbiologica Sinca (2007) 47(5):923-927; Prideaux et al. Infect Immun (1999) 67(4):1962-1966; Liu Front Microbiol 2018 Jul. 3:9:1472; Li et al. Front Cell Infect Microbiol 2018 Mar. 20:8:72; Zhu Antonie Van Leeuwenhoek (2017) 110(12):1647-1657; Li J Med Microbiol (2017) DOI: 10/1099/imm.0.000544; and Xie Front Microbiol 2017 May 10:8:911; Xie PLoS One (2017) 12(4):e0176374; each of which is herein incorporated by reference in its entirety.
It is expected that the combination of the microorganisms, particularly those with inactive ApxIA, ApxIIA and ApxIIIA, as described herein will result in a synergistic attenuation of APP.
Also disclosed herein is a vaccine composition comprising one or more microorganism of the invention, one or more nucleic acid of the invention or one or more vector of the invention. In particular, the present invention provides live (attenuated) vaccines and whole cell inactivated vaccines comprising microorganisms of the invention.
Live (attenuated) vaccines typically comprise microorganisms comprising inactive ApxA polypeptides of the invention as described herein. Thus, whilst the microorganisms of live (attenuated) vaccines are able to infect and replicate in host cells, they have substantially no haemolytic and/or cytotoxic activity. In live (attenuated) vaccines of the invention preferably (a) the microorganism is an APP strain; and/or (b) the ApxIA, ApxIIA and ApxIIIA are inactive ApxIA, ApxIIA and ApxIIIA which have common antigenic cross-reactivity with wild-type ApxIA, ApxIIA and ApxIIIA as described herein.
Whole cell inactivated vaccines typically comprise microorganisms comprising wild-type ApxA polypeptides as described herein, wherein the microorganisms are subsequently inactivated by a suitable means (such as chemical or thermal inactivation). Thus, the microorganisms in whole cell inactivated vaccines are immunogenic, are unable to infect or replicate in host cells. In whole cell inactivated vaccines of the invention preferably (a) the microorganism is an APP strain; and/or (b) the ApxIA, ApxIIA and ApxIIIA are wild-type ApxIA, ApxIIA and ApxIIIA which have been subsequently inactivated, preferably by chemical and/or heat treatment.
One advantage of the vaccine compositions of the invention is that a single microorganism, particularly a single strain of a microorganism may be used to provide all three of ApxIA, ApxIIA and ApxIIA, and hence to provide protection against all APP serovars. This is the case for both live (attenuated) vaccines and whole cell inactivated vaccines. The invention also allows for the production of subunit vaccines against APP using a single microorganism, or single microorganism strain as described herein.
The microorganism comprised in a vaccine of the invention may be of any bacterial species as described herein. Actinobacillus species (e.g. APP and A. suis), including strains, serotypes/serovars thereof are preferred. APP and strains, serotypes/serovars thereof are particularly preferred. Typically, a vaccine of the invention comprises a single microorganism, or strain, species or serotype/serovar thereof. As a non-limiting example, a vaccine may comprise a single APP strain, serotype/serovar thereof. This is because the microorganism comprises each of ApxIA, ApxIIA and ApxIIIA, providing protection against all APP strains, serotypes/serovars, and avoiding the need for multiple APP strains, serotypes/serovars to be included in the vaccine.
The microorganism (comprising either wild-type or inactive ApxA polypeptides as described herein) comprised in a vaccine of the invention may comprise one or more additional modification as described herein. The microorganism (comprising either wild-type or inactive ApxA polypeptides as described herein) comprised in a vaccine of the invention preferably comprise a deletion of the sxy gene and/or a modification or deletion of the apxIVA gene as described herein. Most preferably the microorganism may comprise both a deletion of the sxy gene and a modification of the apxIVA gene, such as an unmarked in-frame deletion of an N-terminal immunogenic domain sequence in the apxIVA as exemplified herein (or a deletion of the apxIVA gene).
A vaccine composition of the invention may comprise at least a pharmaceutical carrier, a diluent and/or an adjuvant.
Non-limiting examples of pharmaceutically acceptable carriers, diluents or adjuvants which may be used in accordance with the invention include: mineral salt adjuvants (e.g. alum-, calcium-, iron- and zirconium-based adjuvants), tensoactive adjuvants (e.g. Quil A, QS-21 and other saponins), bacterial-derived adjuvants (e.g. N-acetyl muramyl-L-alanyl-D-isoglutamine (MDP), lipopolysaccharide (LPS), monophosphoryl lipid A, trehalose dimycolate (TDM), DNA, CpGs and bacterial toxins), adjuvant emulsions (e.g. FIA, Montande, Adjuvant 65, Lipovant), liposome adjuvants, polymeric adjuvants and carriers, cytokines (e.g. Granulocyte-macrophage colony stimulating factor (GM-CSF)), carbohydrate adjuvants, living antigen delivery systems (e.g. bacteria, especially modified APP). Furthermore, carriers can also comprise dry formulations such as coated patches made from titan or polymer. Techniques for formulation and administration of the vaccines of the present application may also be found in “Remington, The Science and Practice of Pharmacy”, 22nd edition.
The vaccine compositions as a unit composition may comprise 0.001-2.0 mg of protein, 0.001-2.0 mg of nucleic acid, or 0.5-200 mg (or 1×104-1×109 colony forming units (CFU)) of microorganism. The required active amount of the protein, nucleic acid or microorganism may be determined by routine testing methods by the skilled person, e.g. in pigs or piglets.
A vaccine composition of the invention may substantially only contain one or more nucleic acid or one or more vector of the invention. By way of non-limiting example, the vaccine may be a DNA vaccine. DNA vaccines are third generation vaccines. Nucleic acid or DNA APP vaccines contain DNA/nucleic acid that encodes specific proteins from APP, particularly ApxA polypeptides. DNA/nucleic acid vectors of the invention typically contain one or more nucleic acid of the invention or one or more vector of the invention which encode for all three of ApxIA, ApxIIA and ApxIIIA, preferably in inactive form as described herein. DNA/nucleic acid vaccines are administered to a mammalian subject (typically by injection) and the DNA/nucleic acid is taken up by subject's cells, whose normal metabolic processes synthesise proteins based on the genetic code in the DNA/nucleic acid of the vaccine which they have taken up. Because these proteins contain regions of amino acid sequences that are characteristic of APP, they are recognised as foreign when they are processed by the host cells and displayed on their surface, altering the subject's immune system and triggering an immune response. When the APP proteins encoded by a DNA/nucleic acid vaccine are inactive ApxA polypeptides, an immune response is triggered, but the ApxA polypeptides do not have any haemolytic or cytotoxic activity, and so are themselves non-pathogenic.
DNA/nucleic acid vaccines may be encapsulated in protein to facilitate entry to the mammalian subject's cells. If this capsid protein is comprised within the DNA/nucleic acid of the DNA/nucleic acid vaccine, the resulting vaccine can combine the potency of a live vaccine without reversion risks.
Standard methods and techniques for the production of vaccines are known in the art and are described in handbooks known to the person of skill in the art. One advantage provided by vaccines of the present invention is the simplification of the production protocol, with the consequent reduction in cost. This simplification and cost saving typically results from the fact that a single microorganism can be used to produce all three of ApxIA, ApxIIA and ApxIIIA, and thus provide protection against all known serovars of APP. Conventional production protocols require at least two APP strains, which requires multiple production steps (such as the culturing and purification of the at least two APP strains, or the ApxA polypeptides therefrom), and hence increased production costs.
Accordingly, the invention provides a method of producing a live (attenuated) vaccine composition of the invention, comprising: (a) culturing a microorganism of the invention, wherein the ApxIA, ApxIIA and ApxIIIA are inactive ApxIA, ApxIIA and ApxIIIA which have common antigenic cross-reactivity with wild-type ApxIA, ApxIIA and ApxIIIA; (b) isolating the microorganism; and (c) formulating the microorganism with a pharmaceutical carrier, a diluent and/or an adjuvant.
The invention also provides a method of producing an inactivated vaccine composition of the invention, said method comprising: (a) culturing a microorganism as defined herein, wherein the ApxIA, ApxIIA and ApxIIIA are wild-type ApxIA, ApxIIA and ApxIIIA; (b) isolating the microorganism; (c) inactivating the microorganism, preferably by chemical and/or heat treatment; and (d) formulating the inactivated microorganism with a pharmaceutical carrier, a diluent and/or an adjuvant. Standard means and protocols for inactivating microorganisms, such as by heat (thermal inactivation) and/or chemical inactivation are known in the art and would be routine to one of skill in the art.
The invention also provides a method of producing subunit vaccine comprising each of ApxIA, ApxIIA and ApxIIIA using a single microorganism or strain thereof. The ApxIA, ApxIIA and ApxIIIA may be produced as wild-type polypeptides (as described herein) and subsequently inactivated. Alternatively, the ApxIA, ApxIIA and ApxIIIA may be produced in an inactive form (as described herein), such that they do not require further inactivation (e.g. chemical or thermal) prior to use.
Accordingly, the invention provides a method of producing a subunit vaccine composition, comprising: (a) culturing a microorganism of the invention which comprises inactive ApxIA, ApxIIA and ApxIIIA which have common antigenic cross-reactivity with wild-type ApxIA, ApxIIA and ApxIIIA; (b) isolating the inactive ApxIA, ApxIIA and ApxIIIA from the cultured microorganism; and (c) formulating the inactive ApxIA, ApxIIA and ApxIIIA with a pharmaceutical carrier, a diluent and/or an adjuvant.
Alternatively, the invention provides a method of producing a subunit vaccine composition, comprising: (a) culturing a microorganism of the invention which comprises wild-type ApxIA, ApxIIA and ApxIIIA; (b) isolating the wild-type ApxIA, ApxIIA and ApxIIIA from the cultured microorganism; (c) inactivating the wild-type ApxIA, ApxIIA and ApxIIIA; and (d) formulating the inactivated wild-type ApxIA, ApxIIA and ApxIIIA with a pharmaceutical carrier, a diluent and/or an adjuvant. Standard means and protocols for inactivating microorganisms, such as by heat (thermal inactivation) and/or chemical inactivation are known in the art and would be routine to one of skill in the art.
Any appropriate culture conditions, media and/or protocols may be used in the production methods of the invention. Standard culture conditions, media and protocols are known in the art. Any appropriate means may be used to isolate the microorganism. Again, routine isolation means and protocols are also known in the art and would be routine to one of skill in the art.
The production methods of the invention preferably relate to the production of a microorganism that is an Actinobacillus species (e.g. APP and A. suis), including strains, serotypes and serovars thereof are particularly preferred. In addition, microorganisms comprising one or more additional modifications are preferred, particularly microorganisms (even more particularly an Actinobacillus species (e.g. APP)) comprising the modifications/deletions sxy and/or apxIVA as described herein.
The invention also encompasses vaccines (particularly live attenuated vaccines) which comprise multiple different microorganisms, each of which provides one or more inactive ApxA poplypeptide of the invention. Each microorganism typically does not express any wild-type ApxA polypeptides. Further, where multiple different microorganisms are used, each microorganism will also comprise modification of sxy and ApxIVA as described herein. Accordingly, the invention provides a vaccine comprising three different microorganisms, each which expresses an inactive form of one of ApxIA, ApxIIA and ApxIIIA, wherein each microorganism also encompasses the the modifications/deletions sxy and/or apxIVA as described herein.
The invention also provides a vaccine comprising two different microorganisms; a first microorganism which expresses inactive forms of any two of ApxIA, ApxIIA and ApxIIIA polypeptides, and a second microorganism which expresses at least an inactive form of the ApxA polypeptide not expressed by the first microorganism (and may also express inactive forms of other ApxA polypeptides), wherein both the first and second microorganism also encompass the modifications/deletions of sxy and apxIVA as described herein. By way of non-limiting example, a vaccine may comprise: (i) a first microorganism (e.g. a serotype 2 APP strain) expressing inactive forms of ApxIIA and ApxIIIA, a modified apxIVA and a deleted sxy; and (ii) a second microorganism (e.g. a serotype 9 APP strain) expressing inactive forms of ApxIA and ApxIIA, a modified apxIVA and a deleted sxy. By way of further non-limiting example, a vaccine may comprise: (i) a first microorganism (e.g. a serotype 2 APP strain) expressing inactive forms of ApxIIA and ApxIIIA, a modified apxIVA and a deleted sxy; and (ii) a second microorganism (e.g. a serotype 14 APP strain) expressing an inactive form of ApxIA, a modified apxIVA and a deleted sxy.
Any and all disclosure herein in relation to microorganisms in the context of a single strain provide all three of ApxIA, ApxIIA and ApxIIA applies equally and without restriction to vaccines comprising multiple different microorganisms. For example, the microorganisms may each be independently any bacterial species as described herein, preferably each independently selected from an Actinobacillus species, more preferably each independently selected from APP strains.
The disclosed vaccine compositions may be used in the prophylactic, metaphylactic and/or therapeutic treatment of a pneumonia, a pleurisy or a pleuropneumonia, in particular a pneumonia, a pleurisy or a pleuropneumonia caused by APP in a subject. The subject to be treated is typically a mammal, particularly a pig.
The vaccine composition may be administered by any appropriate means. Non-limiting examples of suitable means of administration include intramuscular, intradermal, intravenous, subcutaneous and/or mucosal (e.g. intranasal) administration.
The vaccine composition may be administered via at least one, for example one or two administrations using a unit composition as described above. In particular, the composition may be administered for the first time on the day of birth of the subject, within three days, one week, two weeks, four weeks, six weeks, eight weeks, ten weeks or 12 weeks of the birth of the subject. Accordingly, the vaccine, or the first administration thereof, may be advantageously administered at an early point in time of the life of the subject. Alternatively, the vaccine may be administered (including second or subsequent administrations) at any time point in the life of the subject.
The vaccine composition may be administered for a second time or subsequent time, wherein the time period between the two administrations (e.g. the first and second administrations) may be between one and four weeks, between one and three weeks, or between one and two weeks. Preferably, a vaccine composition comprising a microorganism of the invention is to be administered once only. The invention encompasses the passive immunisation of piglets through the colostrum of sows who have been vaccinated according to the present invention. The invention also encompasses the vaccination of piglets by maternally-derived antibodies from sows who have been vaccinated according to the present invention. The invention further encompasses vaccination of piglets having maternally-derived antibodies at the time of vaccination.
The microorganisms, nucleic acids and/or vectors of the invention may be used as a means to express one or more additional antigen from a swine pathogen. Thus, the invention provides an expression system for antigens from other swine pathogens. This expression system may be used to produce the swine pathogen antigen in vitro for subsequent clinical application (e.g. to produce an (additional) component for a subunit vaccine) or research use. Alternatively, this expression system may be used in vivo as a vaccine against said one or more additional swine pathogen. In this way, subjects could be immunised against multiple swine pathogens using a single vaccine comprising a single microorganism or strain thereof.
Accordingly, the invention provides an expression system comprising a microorganism of the invention which comprises each of ApxIA, ApxIIA and ApxIIIA (either in wild-type or inactive form), further comprising at least one additional nucleic acid which encodes one or more additional swine pathogen antigen. The at least one additional nucleic acid may be comprised within the genome of the microorganism or be present extra-chromosomally, as described herein in the context of nucleic acids encoding for the (wild-type or inactive) ApxIA, ApxIIA and ApxIIIA polypeptides. That disclosure applies equally and without restriction to the at least one additional nucleic acid encoding one or more additional swine pathogen antigen. Preferably the at least one additional nucleic acid is comprised within the genome of the microorganism
The one or more additional antigen may be from APP or may be from one or more other swine pathogens. Non-limiting examples of other swine pathogens and antigens therefrom that may be expressed using microorganisms, nucleic acids and/or vectors of the invention include bacterial antigens from: Bordetella bronchiseptica, Brachyspira hyodysenteriae, Brachyspira pilosicoli, Brucella suis, Clostridium difficile, Clostridium perfringens, Escherichia coli [e.g Heat labile (LT)-toxin, heat-stable (ST)-toxins], Lawsonia intracellularis Shigella-like toxin type II variant (SLT-Ile), verotoxin, cell wall (O antigens) and fimbriae (F antigens), Erysipelothrix rhusiopathiae, Haemophilus parasuis, Leptospira spp., Mycoplasma hyopneumoniae, Mycoplasma hyosynoviae, Mycoplasma hyorhinis, Pasteurella multocida, Salmonella spp, Staphylococcus hyicus, Streptococcus suis (e.g. IdeS).
Non-limiting examples of other swine pathogens and antigens therefrom that may be expressed using microorganisms, nucleic acids and/or vectors of the invention include viral antigens from: African Swine Fever Virus (ASFV), Atypical Porcine Pestivirus (APPV, e.g. E1 and or E2), Classical Swine Fever Virus (CSFV, e.g. E1 and or E2), Foot and Mouth Disease Virus (FMDV, e.g. VP1, VP2, VP3, VP4, P2A and/or 3C), Porcine Epidemic Diarrhea Virus (PEDV, e.g. spike protein), Encephalomyocarditis virus, Parvovirus (e.g. VP2), Porcine Circovirus (PCV1, PCV2 or PCV2, e.g. ORF2 or cap protein respectively), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), Suid Herpes Virus, Rotavirus Type A and C (RVA, RVC, e.g. VP4 and or Vp7), Swine Herpes Virus, Swine Influenza Virus (SIV, e.g. Haemmagglutinin (HA) and or Neuraminidase NA), Swine Pox Virus, Swine Vesicular Disease Virus, Transmissible Gastroenteritis Virus (TGEV).
Sequence Homology
Any of a variety of sequence alignment methods can be used to determine percent identity, including, without limitation, global methods, local methods and hybrid methods, such as, e.g., segment approach methods. Protocols to determine percent identity are routine procedures within the scope of one skilled in the art. Global methods align sequences from the beginning to the end of the molecule and determine the best alignment by adding up scores of individual residue pairs and by imposing gap penalties. Non-limiting methods include, e.g., CLUSTAL W, see, e.g., Julie D. Thompson et al., CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment Through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice, 22(22) Nucleic Acids Research 4673-4680 (1994); and iterative refinement, see, e.g., Osamu Gotoh, Significant Improvement in Accuracy of Multiple Protein. Sequence Alignments by Iterative Refinement as Assessed by Reference to Structural Alignments, 264(4) J. Mol. Biol. 823-838 (1996). Local methods align sequences by identifying one or more conserved motifs shared by all of the input sequences. Non-limiting methods include, e.g., Match-box, see, e.g., Eric Depiereux and Ernest Feytmans, Match-Box: A Fundamentally New Algorithm for the Simultaneous Alignment of Several Protein Sequences, 8(5) CABIOS 501-509 (1992); Gibbs sampling, see, e.g., C. E. Lawrence et al., Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment, 262(5131) Science 208-214 (1993); Align-M, see, e.g., Ivo Van Walle et al., Align-M—A New Algorithm for Multiple Alignment of Highly Divergent Sequences, 20(9) Bioinformatics:1428-1435 (2004).
Thus, percent sequence identity is determined by conventional methods. See, for example, Altschul et al., Bull. Math. Bio. 48: 603-16, 1986 and Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:10915-19, 1992. Briefly, two amino acid sequences are aligned to optimize the alignment scores using a gap opening penalty of 10, a gap extension penalty of 1, and the “blosum 62” scoring matrix of Henikoff and Henikoff (ibid.) as shown below (amino acids are indicated by the standard one-letter codes).
The “percent sequence identity” between two or more nucleic acid or amino acid sequences is a function of the number of identical positions shared by the sequences. Thus, 15% identity may be calculated as the number of identical nucleotides/amino acids divided by the total number of nucleotides/amino acids, multiplied by 100. Calculations of % sequence identity may also take into account the number of gaps, and the length of each gap that needs to be introduced to optimize alignment of two or more sequences. Sequence comparisons and the determination of percent identity between two or more sequences can be carried out using specific mathematical algorithms, such as BLAST, which will be familiar to a skilled person.
The percent identity is then calculated as:
Substantially homologous polypeptides are characterized as having one or more amino acid substitutions, deletions or additions. These changes are preferably of a minor nature, that is conservative amino acid substitutions (as described herein) and other substitutions that do not significantly affect the folding or activity of the polypeptide; small deletions, typically of one to about 30 amino acids; and small amino- or carboxyl-terminal extensions, such as an amino-terminal methionine residue, a small linker peptide of up to about 20-25 residues, or an affinity tag.
In addition to the 20 standard amino acids, non-standard amino acids (such as 4-hydroxyproline, 6-N-methyl lysine, 2-aminoisobutyric acid, isovaline and α-methyl serine) may be substituted for amino acid residues of the polypeptides of the present invention. A limited number of non-conservative amino acids, amino acids that are not encoded by the genetic code, and unnatural amino acids may be substituted for polypeptide amino acid residues. The polypeptides of the present invention can also comprise non-naturally occurring amino acid residues.
Non-naturally occurring amino acids include, without limitation, trans-3-methylproline, 2,4-methano-proline, cis-4-hydroxyproline, trans-4-hydroxy-proline, N-methylglycine, allo-threonine, methyl-threonine, hydroxy-ethylcysteine, hydroxyethylhomo-cysteine, nitro-glutamine, homoglutamine, pipecolic acid, tert-leucine, norvaline, 2-azaphenylalanine, 3-azaphenyl-alanine, 4-azaphenyl-alanine, and 4-fluorophenylalanine. Several methods are known in the art for incorporating non-naturally occurring amino acid residues into proteins. For example, an in vitro system can be employed wherein nonsense mutations are suppressed using chemically aminoacylated suppressor tRNAs. Methods for synthesizing amino acids and aminoacylating tRNA are known in the art. Transcription and translation of plasmids containing nonsense mutations is carried out in a cell free system comprising an E. coli S30 extract and commercially available enzymes and other reagents. Proteins are purified by chromatography. See, for example, Robertson et al., J. Am. Chem. Soc. 113:2722, 1991; Ellman et al., Methods Enzymol. 202:301, 1991; Chung et al., Science 259:806-9, 1993; and Chung et al., Proc. Natl. Acad. Sci. USA 90:10145-9, 1993). In a second method, translation is carried out in Xenopus oocytes by microinjection of mutated mRNA and chemically aminoacylated suppressor tRNAs (Turcatti et al., J. Biol. Chem. 271:19991-8, 1996). Within a third method, E. coli cells are cultured in the absence of a natural amino acid that is to be replaced (e.g., phenylalanine) and in the presence of the desired non-naturally occurring amino acid(s) (e.g., 2-azaphenylalanine, 3-azaphenylalanine, 4-azaphenylalanine, or 4-fluorophenylalanine). The non-naturally occurring amino acid is incorporated into the polypeptide in place of its natural counterpart. See, Koide et al., Biochem. 33:7470-6, 1994. Naturally occurring amino acid residues can be converted to non-naturally occurring species by in vitro chemical modification. Chemical modification can be combined with site-directed mutagenesis to further expand the range of substitutions (Wynn and Richards, Protein Sci. 2:395-403, 1993).
A limited number of non-conservative amino acids, amino acids that are not encoded by the genetic code, non-naturally occurring amino acids, and unnatural amino acids may be substituted for amino acid residues of polypeptides of the present invention.
Essential amino acids in the polypeptides of the present invention can be identified according to procedures known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham and Wells, Science 244: 1081-5, 1989). Sites of biological interaction can also be determined by physical analysis of structure, as determined by such techniques as nuclear magnetic resonance, crystallography, electron diffraction or photoaffinity labeling, in conjunction with mutation of putative contact site amino acids. See, for example, de Vos et al., Science 255:306-12, 1992; Smith et al., J. Mol. Biol. 224:899-904, 1992; Wlodaver et al., FEBS Lett. 309:59-64, 1992. The identities of essential amino acids can also be inferred from analysis of homologies with related components (e.g. the translocation or protease components) of the polypeptides of the present invention.
Multiple amino acid substitutions can be made and tested using known methods of mutagenesis and screening, such as those disclosed by Reidhaar-Olson and Sauer (Science 241:53-7, 1988) or Bowie and Sauer (Proc. Natl. Acad. Sci. USA 86:2152-6, 1989). Briefly, these authors disclose methods for simultaneously randomizing two or more positions in a polypeptide, selecting for functional polypeptide, and then sequencing the mutagenized polypeptides to determine the spectrum of allowable substitutions at each position. Other methods that can be used include phage display (e.g., Lowman et al., Biochem. 30:10832-7, 1991; Ladner et al., U.S. Pat. No. 5,223,409; Huse, WIPO Publication WO 92/06204) and region-directed mutagenesis (Derbyshire et al., Gene 46:145, 1986; Ner et al., DNA 7:127, 1988).
Multiple amino acid substitutions can be made and tested using known methods of mutagenesis and screening, such as those disclosed by Reidhaar-Olson and Sauer (Science 241:53-7, 1988) or Bowie and Sauer (Proc. Natl. Acad. Sci. USA 86:2152-6, 1989). Briefly, these authors disclose methods for simultaneously randomizing two or more positions in a polypeptide, selecting for functional polypeptide, and then sequencing the mutagenized polypeptides to determine the spectrum of allowable substitutions at each position. Other methods that can be used include phage display (e.g., Lowman et al., Biochem. 30:10832-7, 1991; Ladner et al., U.S. Pat. No. 5,223,409; Huse, WIPO Publication WO 92/06204) and region-directed mutagenesis (Derbyshire et al., Gene 46:145, 1986; Ner et al., DNA 7:127, 1988).
The invention will now be illustrated by the following non-limiting examples. The Examples that follow are illustrative of specific embodiments of the disclosure, and various uses thereof. They are set forth for explanatory purposes only and should not be construed as limiting the scope of the disclosure in any way.
Unmarked mutations have been introduced to an APP strain via use of two-step natural transformation method, resulting in the systematic alteration of the codons for both acylation sites in each of the endogenous apxIIA and apxIIIA genes present in said strain. Subsequently, generation of an unmarked in-frame deletion of an N-terminal immunogenic domain sequence in the apxIVA gene was used to generate DIVA vaccine candidates. Finally, an unmarked deletion of the competence regulatory gene, sxy, may be generated to render the strains unable to undergo further natural transformation, and so eliminate the most likely source of reversion to wild-type for any of the introduced mutations.
The inventors have previously described the use of a catsacB cassette (encoding a promoterless chloramphenicol resistance gene and sucrose sensitivity gene transcribed from the promoter of the omlA gene of APP) for generation of successive unmarked mutations in APP (Bossé et al. 2014 PLoS ONE 9(11): e111252). In the present example, a more refined dfrA14sacB cassette, encoding the trimethoprim resistance allele dfrA14, identified in endogenous APP plasmids (Bosse et al. (2015) J Antimicrob Chemother 70(8):2217-2222), and the sucrose sensitivity gene, sacB. The dfrA14sacB cassette was generated by overlap extension-PCR (OE-PCR) to combine a synthetic trimethoprim selection cassette (generated by Eurofins Genomics and consisting of the dfrA14 gene, preceded by the promoter for the sodC gene of APP, known to be active under all tested conditions, and followed by the 9-bp sequence required for uptake of DNA during natural transformation by APP) to the sacB gene PCR amplified from the previous catsacB cassette. Linker sequences, tri_OE_for (GTTAATGCCGTCTGAAGTGCGAAG, SEQ ID NO: 19) and sac_OE_rev (GAAGCAGTTGCACGTTCATGTCTC, SEQ ID NO: 20) were added on either end of the dfrA14sacB cassette to facilitate addition of all synthetically generated gene-specific left and right flanking sequences (comprising approx. 500 bases to either side of the region to be mutated) to which the complementary linker sequences (tri_OE_rev or sac_OE_for, as appropriate, described below) are added—see
For generation of unmarked acylation site mutations, gene replacement constructs (to be used in the second round of natural transformation to remove the dfrA14sacB cassette added in the first round natural transformation—see below) were synthesised by Eurofins Genomics consisting of approx. 1500 bases of sequence comprising the full left and right flanking regions (see below) as well as the central acylation-site containing region in which the acylation site codons were altered (K to A and N to A for the respective acylation sites in ApxIIA; K to A for both acylation sites in each of ApxIA and ApxIIIA). These mutation constructs were synthesised with the 9 bp uptake signal sequence (USS) required for efficient natural transformation into APP (Redfield et al., 2006. BMC Evolutionary Biology 2006, 6:82) at the 3′, and were supplied already cloned into a pEX4K vector (with the resulting plasmids designated pExapxIAmut, pExapxIIAmut, and pExapxIIIAmut), each of which was linearised with XhoI prior to use in natural transformation for removal of the dfrA14sacB in the respective toxin gene mutants described below.
For sequential mutation of the acylation sites in the endogenous apxIIA and apxIIIA genes in the naturally transformable strains of serotype 8 and serotype 15, synthetic left and right flanking sequences (approximately 500 bases to the left and right of a central region of approximately 465 bp containing both acylation sites) were synthesised for both apxIIA and apxIIIA by Eurofins Genomics such that both left flank sequences were flanked on the 5′ end with a 24 bp left_flank_for priming site (ATTGGGTACCGAGCTCGC, SEQ ID NO: 21), and on the 3′ end with a 24 bp tri_OE_rev priming site (CTTCGCACTTCAGACGGCATTAAC, SEQ ID NO: 22) complementary to the linker sequence present at the 5′ end of the dfrA14sacB cassette. Similarly, both apxIIA and apxIIIA right flank sequences were synthesised by Eurofins Genomics such that the 5′ ends contained a 24 bp sac_OE_for primer sequence (GAGACATGAACGTGCAACTGCTTC, SEQ ID NO: 23) complementary to the 24 bp linker present at the 3′ end of the dfrA14sacB cassette, and the 3′ ends contained a 24 bp right_flank_rev primer site (CCATTTCACACAGGAATTCGGATC, SEQ ID NO: 24). In this way, the same primer pairs, i.e. left_flank_forward/tri_OE_rev were used to reamplify all synthetic left flank sequences, and sac_OE_for/right_flank_rev were used to reamplify all synthetic right flank sequences, prior to OE-PCR fusion of the flanks to the central dfrA14sacB cassette which had been amplified using tri_OE_for/sac_OE_rev primers. All PCR amplifications were performed using the CloneAmp proof-reading polymerase and, where necessary, template DNA was subsequently removed by treatment with DpnI.
Overlap extension PCRs were performed by combining roughly equimolar concentrations of the left and right flanking sequences (used as primers) and the dfrA14sacB in a total volume of 15 μl of 1× CloneAmp PCR mix. Following an initial amplification of 12 cycles of 98° C./10 sec, 60° C./10 sec, 72° C./3 min, a 1 μl aliquot of the fused overlap product was then used as template for a subsequent 15 cycle PCR amplification (using the same cycling conditions) with the terminal left_flank_forward/right_flank_rev primers (at a final concentration of 1 μM each) in a total volume of 30 μl 1× CloneAmp mix. The resulting fused gene replacement constructs were cleaned using the Qiamp PCR cleanup kit and used directly as template DNA for natural transformation (or, alternatively, were A-tailed and cloned into pGEMT, with the resulting verified clones linearised by digestion with SpeI prior to use in natural transformation) for replacement of the central approx. 465 bp sequences of the respective toxin genes (containing the acylation sites) with the dfrA14sacB cassette. Transformants were selected on Columbia agar plates containing 0.01% nicotinamide adenine dinucleotide and 10 μg/ml trimethoprim (Col-NAD-Tri10) and subsequently screened for sensitivity to sucrose on salt-free LB agar supplemented with 10% sucrose, 5% horse serum and 0.01% NAD (LB-SSN). Sequencing was used to confirm correct insertion of the dfrA14sacB cassette replacing the respective toxin gene regions. Gene replacement constructs delta_apxIIA_dfrA14sacB and delta_apxIIIA_dfrA14sacB are shown in SEQ ID Nos: 37 and 39 respectively.
The dfrA14sacB cassette was subsequently removed in a second round of natural transformation using the appropriate mutation constructs (i.e. apxIIA_mut or apxIIIA_mut, as required; see SEQ ID NOs: 38 and 40, respectively) to leave unmarked mutants, selected for sucrose resistance by plating on LB-SSN plates. Sensitivity to trimethoprim following loss of the dfrA14sacB cassette was confirmed by plating onto Col-NAD-Tri10 plates and selected clones were sequenced across the modified region of the respective toxin sequence to confirm the presence of both modified acylation sites and no other mutation. See
Unmarked apxIIA mutants were generated first, followed by mutation of apxIIIA, to generate double toxin mutants (apxIIA_mut/apxIIIA_mut) in which both acylation sites were altered in each of the ApxII and ApxIII proteins. Secretion of immunogenic non-toxic ApxIIA and ApxIIIA proteins was confirmed by SDS-PAGE analysis of cell free culture supernatants and cytotoxicity assays using cultured BL3 cells, with wild-type active ApxII and ApxIII toxins used as positive controls. As shown in
An alternative to having two different strains to produce the full complement of detoxified Apx proteins is to generate a single strain secreting all three proteins. To do this, a mutated apxIA gene (along with the apxIC gene) was introduced to replace the truncated apxIA sequence present in isolates in which the endogenous apxIIA and apxIIIA genes were already mutated to remove acylation sites, as described in Example 1 above. The resulting mutants therefore expressed all three ApxI-ApxIII proteins, each of which is an inactive toxin.
Briefly, a dfrA14sacB-containing construct (i.e. delta_apxIA_trunc_dfrA14sacB; SEQ ID NO: 41) was generated to replace the existing truncated apxIA sequence (see
The correct gene replacement/insertion of the dfrA14sacB cassette (replacing the truncated apxIA) was confirmed by sequencing. To remove the dfrA14sacB cassette in the mutant, an extended 4.7 kb unmarked mutation (apxIAmut_long; SEQ ID NO: 42), capable of reconstituting an intact apxI operon (in which both acylation sites of the apxIA gene are mutated) was then generated as follows. Extended left (2773 bp) and right (1481 bp) flanking sequences were PCR amplified from genomic DNA extracted from Shope 4074 (serotype 1 strain with complete apxI operon) using primers aaacaagcggtCCGGATCTTGGAATTTCGGC (SEQ ID NO: 25)/TGCCTTCAAGCGGATCAAACAC (SEQ ID NO: 26) for the left flank, and TCGAACTTGGGAACGGTATCAG (SEQ ID NO: 27)/ttacaagcggtACTTTGCCAGCTTACCTACGATG (SEQ ID NO: 28) for the right flank. Copies of the 9 bp USS was appended to the 5′ ends of both the left flank forward and right flank reverse primers (shown underlined in both sequences); the left flank reverse and right flank forward primers were complementary to those used to amplify 566 bp of the apxIA sequence (containing both mutated acylation sites) from the synthetic construct in the plasmid pExapxIAmut, i.e. primers apxIA_mut_for_OE (GTGTTTGATCCGCTTGAAGGCA, SEQ ID NO: 29) and apxIA_mut_rev_OE (CTGATACCGTTCCCAAGTTCGA, SEQ ID NO: 30). The left and right flanks were combined in equimolar ratios with the central 566 bp amplicon and fused by OE-PCR as described in Example 1. The resulting fusion product was cleaned, A-tailed and cloned into pGEMT. Sequencing was used to confirm the correct gene replacement construct in the resulting plasmid pTapxIAmut_long, which was linearised with SpeI prior to use in the second round of natural transformation to remove the dfrA14sacB cassette and leave a reconstituted, but mutated, apxI operon in the chromosome, with selection of transformants on LB-SSN plates. Confirmation of trimethoprim sensitivity due to loss of the dfrA14sacB cassette was assessed by sub-culturing onto Col-NAD-Tri10 plates. Sequencing across the insertion site confirmed reconstitution of the mutated apxI operon (i.e., insertion of the apxICA genes, with the apxIA gene having both acylation sites mutated).
Secretion of all three immunogenic non-toxic proteins in the resulting triple toxin mutants was confirmed by Western blot (
Following confirmation of creation of triple toxin mutants in Example 2, a 2586 bp in-frame N-terminal deletion in the apxIVA gene was generated. Similar to creation of the acylation site mutations described in Examples 1 and 2 above, synthetic left and right flanking sequences of approx. 500 bp (to either side of the 2586 bp region to be deleted) were generated by Eurofins Genomics. In this instance, the left_flank_for_USS primer sequence (ATCC√{square root over (ACAAGCGGT)}CATCTGGC, SEQ ID NO: 31) added to the 5′ end of the apxIV left flank construct was modified to incorporate the 9 bp USS (underlined) required for natural transformation; all other linker priming sites for the left and right flank sequences were as used in Examples 1 and 2. The gene replacement construct delta_apxIVA_dfrA14sacB is shown in SEQ ID NO: 43. A 1043 bp deletion construct (apxIV_int_del, SEQ ID NO: 44), consisting of the left and right flanking regions fused together at the site of the 2586 bp in-frame deletion was generated by Eurofins Genomics, with the same terminal left_flank_for USS and right_flank_rev priming sites to allow re-amplification of the synthetic strand.
Following amplification of the synthetic left and right flank constructs using left_flank_for_USS/tri_OE_rev and sac_OE_for/right_flank_rev, and the dfrA14sacB cassette using tri_OE_for/sac_OE_rev, the three cleaned sequences were fused by OE-PCR, as above. This construct was introduced into the triple toxin mutants by natural transformation with selection on Col-NAD-Tri10 plates. Following confirmation of the correct insertion site, the dfrA14sacB cassette was removed using the amplified apxIV_int_del sequence in a second round of natural transformation, with selection of transformants on LB-SSN plates. Loss of the dfrA14sacB cassette was confirmed by plating on Col-NAD-Tri10 plates to show trimethoprim sensitivity, and by PCR to show the 2586 bp in-frame N-terminal deletion.
Following confirmation of creation of the DIVA (internal ApxIV deletion) triple toxin mutants in Example 3, the sxy gene is deleted using a modified version of the method for generating the in-frame apxIV deletion. As the Sxy protein is required for the second round of natural transformation, the construct for the first round of natural transformation to introduce the dfra14sacB cassette is not designed using flanking regions that would replace the sxy gene with the cassette, but rather to introduce the cassette immediately downstream of the sxy gene. The construct to remove the dfra14sacB cassette in the second round of transformation is designed to also remove the entire sxy gene, leaving an unmarked deletion (
Due to complex secondary structure of the sequence upstream of the sxy gene, generation of a synthetic left flank was not possible. In order to PCR amplify an appropriate left flank sequence that would be amenable for use in natural transformation, the sequence upstream of sxy was analysed for the presence of a natural USS (
A right flank sequence, comprising approximately 500 bp of sequence downstream of the sxy gene was synthesised by Eurofins, with the appropriate sac_OE_for and right_flank_rev priming sites at the 5′ and 3′ ends, respectively, as described in Example 1. Following amplification of both the left and right flanking sequences, as well as the dfra14sacB cassette, the three fragments were fused by OE-PCR, as described in Example 1. The product of this OE-PCR is used in the first round of natural transformation, to introduce the dfra14sacB cassette downstream of the sxy gene, with selection on Col-NAD-Tri10 plates.
A sxy deletion construct was synthesised by Eurofins, comprising the same 500 bp downstream of sxy used in generating the right flank sequence fused on the 5′ end to approximately 500 bp sequence upstream of sxy, bounded by the left_flank_for_USS and right_flank_rev priming sites, as described in Examples 3 and 1, respectively, to allow re-amplification of the synthetic construct. Following confirmation of the correct insertion site in the mutants generated by the first round of natural transformation, the dfrA14sacB cassette is removed along with the entire sxy gene, by transformation with the amplified sxy deletion construct. Transformants are selected on LB-SSN plates. Loss of the dfrA14sacB cassette is confirmed by plating on Col-NAD-Tri10 plates to show trimethoprim sensitivity, and by PCR and sequencing to confirm the clean deletion of the sxy gene.
In the event of identification of a naturally transformable isolate encoding ApxI and ApxII, the structural genes for these two toxins is similarly be inactivated using the same protocol as described in Example 1. Following mutation of the apxIIA gene, as described in Example 1, the apxIA gene is similarly mutated using the gene replacement and mutation constructs delta_apxIA_dfrA14sacB and the apxIA_mut, respectively, shown in SEQ ID Nos: 35 and 36. This is followed by the introduction of genes encoding for inactive ApxIIIA, amplified from a suitable apxIIIA mutant as generated in Example 1. Lastly, this is followed by introduction of the apxIVA and sxy mutations (as per Examples 2 and 4).
| Number | Date | Country | Kind |
|---|---|---|---|
| 2011902.0 | Jul 2020 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/IB2021/000549 | 7/30/2021 | WO |
