# Patent

## Title
Antibiotic resistance free vaccines and methods for constructing and using same

## Abstract

The present invention provides Listeria strains that express a heterologous antigen and a metabolic enzyme, and methods of generating same.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a Continuation-in-Part of U.S. application Ser. No. 11/203,415, filed Aug. 15, 2005, which claims priority of U.S. Provisional Application Ser. No. 60/601,492, filed Aug. 13, 2004. This application is hereby incorporated in its entirety by reference herein.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This research was supported in whole or in part by U.S. Government funds (RAID NSC 715814 and CA69632). The U.S. Government has certain rights in the invention.


FIELD OF INVENTION
The present invention provides Listeria strains that express a heterologous antigen and a metabolic enzyme, and methods of generating same.
BACKGROUND OF THE INVENTION
Vaccines represent the most beneficial and cost effective public health measure currently known. However, as the understanding of neoplasias and infectious diseases grows, it has become apparent that traditional vaccine strategies may not be completely effective. Traditional vaccines have employed killed or attenuated organisms or antigen subunits in order to elicit immunity in an animal. A limit with these approaches, especially with killed or subunit vaccines, is that the immune response is primarily humoral in nature, and therefore not effective in combating intracellular organism or tumors that require cell mediated immunity for their destruction. Similarly, attenuated or inactivated bacteria often only induce immunization for a short period of time and immunity is limited to a humoral response. Further, traditional attenuated or inactivated bacterial vaccines do not elicit the cytotoxic T-lymphocyte (CTL) immune response necessary for the lysis of tumor cells and cells infected with intracellular pathogens.
Viral vaccines are often used to induce a CTL response in a vaccine. Viral vaccines are usually pathogenic viruses attenuated by serial passage in cell culture or viruses killed through heat or chemical inactivation. Killed viruses are incapable of infecting cells, and thus, like subunit vaccines, primarily elicit a humoral immune response. Attenuated viruses are capable of infecting cells, and can induce a CTL response in an individual. However, attenuated virus vaccines are not without drawbacks. First, attenuating a virus is often a process of trial and error. Second, there is a serious safety issue in using attenuated viruses, especially in children, the elderly, and the immuno-compromised. A solution to the problems of traditional bacterial and viral vaccines exists with bacterial vaccine vectors such as Listeria monocytogenes (LM). LM is a beta hemolytic gram positive facultative intracellular microbe.
Three methods are currently used to express a heterologous antigen in Listeria monocytogenes, and include plasmid-based expression systems and chromosome expression systems. One chromosomal based method is described in Frankel et al. (1995, J. Immunol. 155:4775-4782) and Mata et al. (2001, Vaccine 19:1435-1445). Briefly, a gene encoding the antigen of interest is placed, along with a suitable promoter and signal sequence, between two regions of DNA homologous to a region of the Listeria chromosome. This homologous recombination allows specific integration of the antigen in the Listeria chromosome. The cassette comprising the antigen and the homologous DNA is ligated into a temperature sensitive plasmid incapable of replication at temperatures above 40° C. The plasmid further comprises drug resistance markers for selection and plasmid maintenance purposes. The manipulation and replication of this plasmid usually takes place in E. coli, because of its rapid replication and ease of transformation compared to Listeria. Because Listeria is a gram positive organism and E. coli is a gram negative organism, the drug resistance genes can be specific to each category of organism, or there may be two copies of the same drug resistance gene effective in both types of organism, but under the control of separate gram positive and gram negative promoters. After assembly, the plasmid is transformed into LM by direct conjugation with the E. coli comprising the plasmid, or by lysis and isolation of the plasmid from the E. coli, followed by electroporation of competent LM.
In order to integrate the plasmid into the desired region of the Listeria chromosome, the two-step allelic exchange method of Camilli et al. (1992, Mol. Microbiol. 8:143-157) is followed. Briefly, the Listeria is passaged at greater than 40° C. to prevent plasmid replication. Integration of the plasmid into the Listeria chromosome is selected by growth at 40° C. in the presence of a selecting drug, e.g. chloramphenicol. After selection of transformants, bacteria are passaged at 30° C. and selected for drug sensitivity to screen for Listeria in which excision of extraneous vector sequences has occurred. The disadvantage of this method is that the double allelic exchange method is time consuming and requires the selection of many clones in order to arrive at a suitable vaccine strain. A second chromosomal method of producing Listeria strains comprising a heterologous antigen is described by Lauer et al. (2002, J. Bacteriol. 184:4177-4186). This method does not require allelic exchange, but instead requires two phage-based integration vectors. This method utilizes one or two drug resistance genes, resulting in a Listeria organism comprising resistance to one or more drugs. The disadvantage of the methods of Lauer et al is the presence of drug resistance genes, which are not considered safe because of concern over the spread of antibiotic resistance to microorganisms previously susceptible to antibiotic therapy. Therefore, the presence of antibiotic resistance genes in a vaccine vector is considered a liability from a safety perspective.
A third method of expressing foreign antigen in Listeria is to express the antigen episomally from a plasmid. This method is described in Ikonomidis et al. (1994 J. Exp. Med. 180: 2209-2218) and Gunn et al. (2001, J Immunol 167: 6471-6479). This method has the advantage that the gene does not have to be integrated into the chromosome and can be expressed in multiple copies, which may enhance immunogenicity. However, in order to select for plasmid transformants and ensure the retention of the plasmid during propagation in vitro it is necessary to include two drug resistance genes on the plasmid, one for the construction of the plasmid in E. coli and one for the propagation of the transformed Listeria monocytogenes. 
Thus, given the demonstrated uses of Listeria as a vaccine vector, methods for constructing Listeria vaccine vectors without antibiotic resistance, yet capable of eliciting a strong immune response, are needed in the field.
BRIEF SUMMARY OF THE INVENTION
The present invention provides Listeria strains that express a heterologous antigen and a metabolic enzyme, and methods of generating same.
In one embodiment, the present invention provides a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises a protein antigen, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant Listeria strain. In another embodiment, the strain is a Listeria vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of inducing an immune response against a protein antigen of interest in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby inducing an immune response against a protein antigen of interest in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of inducing an immune response against a tumor of interest in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, whereby said tumor expresses said antigen, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby inducing an immune response against a protein antigen of interest in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of treating a cancer in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, the cancer expresses the protein antigen of interest, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby treating a cancer in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of reducing an incidence of a cancer in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, the cancer expresses the protein antigen of interest, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby reducing an incidence of a cancer in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of treating an infectious disease in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, the infectious disease organism expresses the protein antigen of interest, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby treating an infectious disease in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of reducing an incidence of an infectious disease in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, the infectious disease organism expresses the protein antigen of interest, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby reducing an incidence of an infectious disease in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a schematic map of E. coli-Listeria shuttle plasmids pGG55 (above) and pTV3 (below). CAT(−): E. coli chloramphenicol transferase; CAT(+): Listeria chloramphenicol transferase; Ori Lm: replication origin for Listeria; Ori Ec: p15 origin of replication for E. coli; prfA: Listeria pathogenicity regulating factor A; LLO: C-terminally truncated listeriolysin O, including its promoter; E7: HPV E7; p60-dal; expression cassette of p60 promoter and Listeria dal gene. Selected restriction sites are also depicted.
FIG. 2: Plasmid preparation of pTV3 from E. coli strain MB2159. Qiagen® midi-preparation of nucleic acids was following the manufacturer's protocol. Lanes from left to right: Lanes 1 and 7: Molecular Weight Marker, 100 Bp ladder (Invitrogen). Lane 2: pTV3, clone #15. Lane 3: pTV3, clone #16. Lane 4: pTV3C, clone #22. Lane 5: pTV3C, clone #24. Lane 6: pGG55 control.
FIG. 3. Plasmid maintenance in vitro (A) and in vivo (B). To determine in vitro stability, strains were cultured with (GG55-Chl) and without (GG55-no Chl) chloramphenicol (LM-LLO-E7) or with and without D-alanine [Lmdd(pTV3)]. The cultures were diluted 1:1000 daily into fresh LB. The CFU of the cultures were determined daily on BHI (BHI) and on BHI with chloramphenicol (BHI-Chl) for LM-LLO-E7 or on BHI with D-alanine (BHI-Ala) for Lmdd(pTV3). All liquid medium and plates contained an additional 50 μg of streptomycin per ml, to which Listeria monocytogenes (LM) strain 10403S is naturally resistant. To determine in vivo plasmid maintenance, LM was injected intraperitoneally at a dose of 1/10 the LD50 in50 C57BL/6 mice. Spleens were harvested at different time points post-injection and homogenized in phosphate-buffered saline (PBS). CFU counts were prepared on BHI plates with and without D-alanine for Lmdd(pTV3), on BHI plates with and without chloramphenicol for LM-LLO-E7, and on BHI plates only for wild-type 10403S.
FIG. 4 depicts growth on Luria-Bertoni (LB) agar plates of E. coli strain MB2159 (alanine racemace negative) transformed with the pTV3 vector. Bacteria were plated on different media. Upper left: agar alone. MB2159-TV3 is able to grow. Upper right: agar with alanine. MB2159-TV3 is able to grow. Lower left: agar with chloramphenicol. MB2159-TV3 does not grow because the CAT gene is missing. Lower right: agar with chloramphenicol and alanine. MB2159-TV3 does not grow because the CAT gene is missing.
FIG. 5 depicts growth on LB-agar plates of E. coli strain MB2159 without the pTV3 vector. Agar plates are arranged as in FIG. 4. Upper left: MB2159 does not grow. Upper right: agar with alanine. MB2159 is able to grow. Lower left: agar with chloramphenicol. MB2159 does not grow. Lower right. MB2159 does not grow.
FIG. 6 depicts growth on LB-agar plates of LM strain Lmdd(−) transformed with the pTV3 vector. Bacteria were plated on different media: Top: agar with streptomycin, no added alanine. Lmdd-pTV3 is able to grow (the host strain 10403s is streptomycin resistant). Lower left (agar with chloramphenicol) and lower right (agar with chloramphenicol and alanine): Lmdd-pTV3 does not grow because the CAT gene is not present in pTV3.
FIG. 7 depicts growth on LB-agar plates of LM strain Lmdd(−) without the pTV3 vector. Upper left: agar with streptomycin. Lmdd (−) cannot grow in the absence of d-alanine. Upper right: agar with alanine. Lmdd (−) grows. Lower left (agar with chloramphenicol and alanine) and lower right (agar with chloramphenicol): Lmdd(−) is sensitve to chloramphenicol and does not grow.
FIG. 8 depicts bacterial growth as measured by optical density (600 nanometers [nm]) plotted vs. time. +Ala: media contains D-alanine; +Chl: media contains chloramphenicol.
FIG. 9 depicts tumor regression in response to administration of LM vaccine strains (A). Circles represent naive mice, inverted triangles represent mice administered Lmdd-TV3, and crosses represent mice administered Lm-LLOE7.
FIG. 10 A. Map of pTV6. B. Map of pTV7.
FIG. 11 Map of pTV8.
FIG. 12 Map of pTV9.
FIG. 13 Map of pTV10.
FIG. 14 Map of pTV11.



DETAILED DESCRIPTION OF THE INVENTION
The present invention provides Listeria strains that express a heterologous antigen and a metabolic enzyme, and methods of generating same.
In one embodiment, the present invention provides a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises a protein antigen, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant Listeria strain. In another embodiment, the strain is a Listeria vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of inducing an immune response against a protein antigen of interest in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby inducing an immune response against a protein antigen of interest in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of inducing an immune response against a tumor of interest in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, whereby said tumor expresses said antigen, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby inducing an immune response against a protein antigen of interest in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of treating a cancer in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, the cancer expresses the protein antigen of interest, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby treating a cancer in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of reducing an incidence of a cancer in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, the cancer expresses the protein antigen of interest, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby reducing an incidence of a cancer in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of treating an infectious disease in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, the infectious disease organism expresses the protein antigen of interest, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby treating an infectious disease in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of reducing an incidence of an infectious disease in a subject, comprising the step of administering to the subject a recombinant bacterial strain, comprising an integrated nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding a polypeptide, wherein the polypeptide comprises the protein antigen of interest, the infectious disease organism expresses the protein antigen of interest, and the nucleic acid molecule further comprises a second open reading frame encoding a metabolic enzyme, thereby reducing an incidence of an infectious disease in a subject. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant bacterial strain. In another embodiment, the strain is a bacterial vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
“Nucleic acid molecule” refers, in another embodiment, to a plasmid. In another embodiment, the term refers to an integration vector. In another embodiment, the term refers to a plasmid comprising an integration vector. In another embodiment, the integration vector is a site-specific integration vector. In another embodiment, a nucleic acid molecule of methods and compositions of the present invention can be composed of any type of nucleotide known in the art. Each possibility represents a separate embodiment of the present invention. Each possibility represents a separate embodiment of the present invention.
In another embodiment of the present invention, “nucleic acids” or “nucleotide” refers to a string of at least two base-sugar-phosphate combinations. The term includes, in one embodiment, DNA and RNA. “Nucleotides” refers, in one embodiment, to the monomeric units of nucleic acid polymers. RNA may be, in one embodiment, in the form of a tRNA (transfer RNA), snRNA (small nuclear RNA), rRNA (ribosomal RNA), mRNA (messenger RNA), anti-sense RNA, small inhibitory RNA (siRNA), micro RNA (miRNA) and ribozymes. The use of siRNA and miRNA has been described (Caudy A A et al, Genes & Devel 16: 2491-96 and references cited therein). DNA may be in form of plasmid DNA, viral DNA, linear DNA, or chromosomal DNA or derivatives of these groups. In addition, these forms of DNA and RNA may be single, double, triple, or quadruple stranded. The term also includes, in another embodiment, artificial nucleic acids that may contain other types of backbones but the same bases. In one embodiment, the artificial nucleic acid is a PNA (peptide nucleic acid). PNA contain peptide backbones and nucleotide bases and are able to bind, in one embodiment, to both DNA and RNA molecules. In another embodiment, the nucleotide is oxetane modified. In another embodiment, the nucleotide is modified by replacement of one or more phosphodiester bonds with a phosphorothioate bond. In another embodiment, the artificial nucleic acid contains any other variant of the phosphate backbone of native nucleic acids known in the art. The use of phosphothiorate nucleic acids and PNA are known to those skilled in the art, and are described in, for example, Neilsen P E, Curr Opin Struct Biol 9:353-57; and Raz N K et al Biochem Biophys Res Commun. 297:1075-84. The production and use of nucleic acids is known to those skilled in art and is described, for example, in Molecular Cloning, (2001), Sambrook and Russell, eds. and Methods in Enzymology: Methods for molecular cloning in eukaryotic cells (2003) Purchio and G. C. Fareed. Each nucleic acid derivative represents a separate embodiment of the present invention.
“Stably maintained” refers, in another embodiment, to maintenance of a nucleic acid molecule or plasmid in the absence of selection (e.g. antibiotic selection) for 10 generations, without detectable loss. In another embodiment, the period is 15 generations. In another embodiment, the period is 20 generations. In another embodiment, the period is 25 generations. In another embodiment, the period is 30 generations. In another embodiment, the period is 40 generations. In another embodiment, the period is 50 generations. In another embodiment, the period is 60 generations. In another embodiment, the period is 80 generations. In another embodiment, the period is 100 generations. In another embodiment, the period is 150 generations. In another embodiment, the period is 200 generations. In another embodiment, the period is 300 generations. In another embodiment, the period is 500 generations. In another embodiment, the period is more than generations. In another embodiment, the nucleic acid molecule or plasmid is maintained stably in vitro (e.g. in culture). In another embodiment, the nucleic acid molecule or plasmid is maintained stably in vivo. In another embodiment, the nucleic acid molecule or plasmid is maintained stably both in vitro and in vitro. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of engineering an auxotrophic bacterial strain to express a heterologous antigen, the method comprising the step of contacting the auxotrophic bacterial strain with a nucleic acid molecule, the nucleic acid construct comprising a first nucleic acid sequence encoding a polypeptide that comprises the heterologous antigen, and the nucleic acid construct further comprising a second nucleic acid sequence encoding a metabolic enzyme, thereby engineering an auxotrophic bacterial strain to express a heterologous antigen. In another embodiment, the integrated nucleic acid molecule is integrated into the chromosome. In another embodiment, the recombinant bacterial strain is a recombinant Listeria strain. In another embodiment, the strain is a Listeria vaccine strain. In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In another embodiment, the nucleic acid molecule is stably maintained in the recombinant bacterial strain in the absence of an antibiotic selection. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of engineering a Listeria vaccine strain to express a heterologous antigen, the method comprising contacting an auxotrophic Listeria strain with a plasmid, the plasmid comprising a first nucleic acid sequence encoding a polypeptide that comprises the heterologous antigen, and the plasmid further comprising a second nucleic acid sequence encoding a metabolic enzyme, whereby the auxotrophic Listeria strain takes up the plasmid, and whereby the metabolic enzyme complements a metabolic deficiency of the auxotrophic Listeria strain, thereby engineering a Listeria vaccine strain to express a heterologous antigen.
In another embodiment, the present invention provides a method of engineering a Listeria vaccine strain to express a heterologous antigen, the method comprising transforming an auxotrophic Listeria strain with a plasmid comprising a first nucleic acid encoding the heterologous antigen and a second nucleic acid encoding a metabolic enzyme, whereby the metabolic enzyme complements a metabolic deficiency of the auxotrophic Listeria strain, thereby engineering a Listeria vaccine strain to express a heterologous antigen.
“Transforming,” in one embodiment, is used identically with the term “transfecting,” and refers to engineering a bacterial cell to take up a plasmid or other heterologous DNA molecule. In another embodiment, “transforming” refers to engineering a bacterial cell to express a gene of a plasmid or other heterologous DNA molecule. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the plasmid or nucleic acid molecule of methods and compositions of the present invention further comprises a gene encoding a transcription factor. In another embodiment, the transcription factor is lacking in the auxotrophic Listeria strain or in the bacteria chromosome of a Listeria strain of the present invention. In one embodiment, the transcription factor is prfA (Examples herein). In another embodiment, the transcription factor is any other transcription factor known in the art. Each possibility represents a separate embodiment of the present invention.
In one embodiment, the metabolic gene, transcription factor-encoding gene, etc. is lacking in a chromosome of the bacterial strain. In another embodiment, the metabolic gene, transcription factor, etc. is lacking in all the chromosomes of the bacterial strain. In another embodiment, the metabolic gene, transcription factor, etc. is lacking in the genome of the bacterial strain.
In one embodiment, the gene encoding a transcription factor is mutated in the chromosome. In another embodiment, the gene is deleted from the chromosome. Each possibility represents a separate embodiment of the present invention.
In one embodiment, the transcription factor is mutated in the chromosome. In another embodiment, the transcription factor is deleted from the chromosome. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the integration vector or plasmid of methods and compositions of the present invention does not confer antibiotic resistance to the Listeria vaccine strain. In another embodiment, the integration vector or plasmid does not contain an antibiotic resistance gene. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the first nucleic acid sequence of methods and compositions of the present invention is operably linked to a promoter/regulatory sequence. In another embodiment, the second nucleic acid sequence is operably linked to a promoter/regulatory sequence. In another embodiment, each of the nucleic acid sequences is operably linked to a promoter/regulatory sequence. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the promoter/regulatory sequence of the second nucleic acid sequence functions in E. coli, thereby enabling stable maintenance of the plasmid or nucleic acid molecule in the E. coli strain. In another embodiment, the second nucleic acid sequence is expressed in an E. coli strain upon transfecting the E. coli strain with a plasmid or nucleic acid molecule of the present invention, thereby enabling stable maintenance thereof in the E. coli strain.
Methods for introducing a prophage into LM are well known in the art. In another embodiment, conjugation is utilized. In another embodiment, electroporation is utilized. In another embodiment, any other method known in the art is utilized. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a Listeria vaccine strain, comprising a plasmid, wherein the plasmid comprises a first nucleic acid sequence encoding a polypeptide, wherein the polypeptide comprises a protein antigen, and the plasmid further comprises a second nucleic acid sequence encoding a metabolic enzyme, whereby the metabolic enzyme complements an endogenous metabolic gene that is lacking in a chromosome of the Listeria vaccine strain, and whereby the plasmid is stably maintained in the Listeria vaccine strain in the absence of an antibiotic selection.
In one embodiment, the endogenous metabolic gene is mutated in the chromosome. In another embodiment, the endogenous metabolic gene is deleted from the chromosome. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of engineering a Listeria vaccine strain to express a heterologous antigen, the method comprising contacting an auxotrophic Listeria strain with a nucleic acid construct, the nucleic acid construct comprising a first nucleic acid sequence encoding a polypeptide that comprises the heterologous antigen, and the nucleic acid construct further comprising a second nucleic acid sequence encoding a metabolic enzyme, whereby the nucleic acid construct is incorporated into a genome of the auxotrophic Listeria strain, and whereby the metabolic enzyme complements a metabolic deficiency of the auxotrophic Listeria strain, thereby engineering a Listeria vaccine strain to express a heterologous antigen.
In one embodiment, the nucleic acid construct lacks a Listeria replication region. In another embodiment, only Listeria that contain a copy of the nucleic acid construct that is integrated into the genome are selected upon growth in LB media. In another embodiment, the nucleic acid construct contains a Listeria replication region. Each possibility represents a separate embodiment of the present invention.
In one embodiment, the nucleic acid construct contains an integration site. In one embodiment, the site is a PSA attPP′ integration site. In another embodiment, the site is any another integration site known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the nucleic acid construct contains an integrase gene. In another embodiment, the integrase gene is a PSA integrase gene. In another embodiment, the integrase gene is any other integrase gene known in the art. Each possibility represents a separate embodiment of the present invention.
In one embodiment, the nucleic acid construct is a plasmid. In another embodiment, the nucleic acid construct is a shuttle plasmid. In another embodiment, the nucleic acid construct is an integration vector. In another embodiment, the nucleic acid construct is a site-specific integration vector. In another embodiment, the nucleic acid construct is any other type of nucleic acid construct known in the art. Each possibility represents a separate embodiment of the present invention.
The integration vector of methods and compositions of the present invention is, in another embodiment, a phage vector. In another embodiment, the integration vector is a site-specific integration vector. In another embodiment, the vector further comprises an integrase gene. In another embodiment, the vector further comprises an attPP′ site. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the integration vector is a U153 vector. In another embodiment, the integration vector is an A118 vector. In another embodiment, the integration vector is a PSA vector.
In another embodiment, the vector is an A511 vector (e.g. GenBank Accession No: X91069). In another embodiment, the vector is an A006 vector. In another embodiment, the vector is a B545 vector. In another embodiment, the vector is a B053 vector. In another embodiment, the vector is an A020 vector. In another embodiment, the vector is an A500 vector (e.g. GenBank Accession No: X85009). In another embodiment, the vector is a B051 vector. In another embodiment, the vector is a B052 vector. In another embodiment, the vector is a B054 vector. In another embodiment, the vector is a B055 vector. In another embodiment, the vector is a B056 vector. In another embodiment, the vector is a B101 vector. In another embodiment, the vector is a B110 vector. In another embodiment, the vector is a B111 vector. In another embodiment, the vector is an A153 vector. In another embodiment, the vector is a D441 vector. In another embodiment, the vector is an A538 vector. In another embodiment, the vector is a B653 vector. In another embodiment, the vector is an A513 vector. In another embodiment, the vector is an A507 vector. In another embodiment, the vector is an A502 vector. In another embodiment, the vector is an A505 vector. In another embodiment, the vector is an A519 vector. In another embodiment, the vector is a B604 vector. In another embodiment, the vector is a C703 vector. In another embodiment, the vector is a B025 vector. In another embodiment, the vector is an A528 vector. In another embodiment, the vector is a B024 vector. In another embodiment, the vector is a B012 vector. In another embodiment, the vector is a B035 vector. In another embodiment, the vector is a C707 vector.
In another embodiment, the vector is an A005 vector. In another embodiment, the vector is an A620 vector. In another embodiment, the vector is an A640 vector. In another embodiment, the vector is a B021 vector. In another embodiment, the vector is an HSO47 vector. In another embodiment, the vector is an H10G vector. In another embodiment, the vector is an H8/73 vector. In another embodiment, the vector is an H19 vector. In another embodiment, the vector is an H21 vector. In another embodiment, the vector is an H43 vector. In another embodiment, the vector is an H46 vector. In another embodiment, the vector is an H107 vector. In another embodiment, the vector is an H108 vector. In another embodiment, the vector is an H110 vector. In another embodiment, the vector is an H163/84 vector. In another embodiment, the vector is an H312 vector. In another embodiment, the vector is an H340 vector. In another embodiment, the vector is an H387 vector. In another embodiment, the vector is an H391/73 vector. In another embodiment, the vector is an H684/74 vector. In another embodiment, the vector is an H924A vector. In another embodiment, the vector is an fMLUP5 vector. In another embodiment, the vector is a syn (=P35) vector. In another embodiment, the vector is a 00241 vector. In another embodiment, the vector is a 00611 vector. In another embodiment, the vector is a 02971A vector. In another embodiment, the vector is a 02971C vector. In another embodiment, the vector is a 5/476 vector. In another embodiment, the vector is a 5/911 vector. In another embodiment, the vector is a 5/939 vector. In another embodiment, the vector is a 5/11302 vector. In another embodiment, the vector is a 5/11605 vector. In another embodiment, the vector is a 5/11704 vector. In another embodiment, the vector is a 184 vector. In another embodiment, the vector is a 575 vector. In another embodiment, the vector is a 633 vector. In another embodiment, the vector is a 699/694 vector. In another embodiment, the vector is a 744 vector. In another embodiment, the vector is a 900 vector. In another embodiment, the vector is a 1090 vector. In another embodiment, the vector is a 1317 vector. In another embodiment, the vector is a 1444 vector. In another embodiment, the vector is a 1652 vector. In another embodiment, the vector is a 1806 vector. In another embodiment, the vector is a 1807 vector. In another embodiment, the vector is a 1921/959 vector. In another embodiment, the vector is a 1921/11367 vector. In another embodiment, the vector is a 1921/11500 vector. In another embodiment, the vector is a 1921/11566 vector. In another embodiment, the vector is a 1921/12460 vector. In another embodiment, the vector is a 1921/12582 vector. In another embodiment, the vector is a 1967 vector. In another embodiment, the vector is a 2389 vector. In another embodiment, the vector is a 2425 vector. In another embodiment, the vector is a 2671 vector. In another embodiment, the vector is a 2685 vector. In another embodiment, the vector is a 3274 vector. In another embodiment, the vector is a 3550 vector. In another embodiment, the vector is a 3551 vector. In another embodiment, the vector is a 3552 vector. In another embodiment, the vector is a 4276 vector. In another embodiment, the vector is a 4277 vector. In another embodiment, the vector is a 4292 vector. In another embodiment, the vector is a 4477 vector. In another embodiment, the vector is a 5337 vector. In another embodiment, the vector is a 5348/11363 vector. In another embodiment, the vector is a 5348/11646 vector. In another embodiment, the vector is a 5348/12430 vector. In another embodiment, the vector is a 5348/12434 vector. In another embodiment, the vector is a 10072 vector. In another embodiment, the vector is a 11355C vector. In another embodiment, the vector is a 11711A vector. In another embodiment, the vector is a 12029 vector. In another embodiment, the vector is a 12981 vector. In another embodiment, the vector is a 13441 vector. In another embodiment, the vector is a 90666 vector. In another embodiment, the vector is a 90816 vector. In another embodiment, the vector is a 93253 vector. In another embodiment, the vector is a 907515 vector. In another embodiment, the vector is a 910716 vector. In another embodiment, the vector is a NN-Listeria vector. In another embodiment, the vector is a O1761 vector. In another embodiment, the vector is a 4211 vector. In another embodiment, the vector is a 4286 vector.
In another embodiment, the integration vector is any other site-specific integration vector known in the art that is capable of infecting Listeria. Each possibility represents a separate embodiment of the present invention.
The metabolic enzyme of methods and compositions of the present invention is, in another embodiment, an amino acid metabolism enzyme. In another embodiment, the metabolic enzyme is an alanine racemase (dal) enzyme. In another embodiment, the metabolic enzyme is a D-amino acid transferase enzyme (dat). The LM dal and dat genes were cloned and isolated from LM as described in Thompson et al (Infec Immun 66: 3552-3561, 1998).
In another embodiment, the metabolic enzyme metabolizes an amino acid (AA) that is used for a bacterial growth process. In another embodiment, the product AA is used for a replication process. In another embodiment, the product AA is used for cell wall synthesis. In another embodiment, the product AA is used for protein synthesis. In another embodiment, the product AA is used for metabolism of a fatty acid. In another embodiment, the product AA is used for any other growth or replication process known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the metabolic enzyme catalyzes the formation of an AA used in cell wall synthesis. In another embodiment, the metabolic enzyme catalyzes synthesis of an AA used in cell wall synthesis. In another embodiment, the metabolic enzyme is involved in synthesis of an AA used in cell wall synthesis. In another embodiment, the AA is used in cell wall biogenesis. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the metabolic enzyme is a synthetic enzyme for D-glutamic acid, a cell wall component.
In another embodiment, the metabolic enzyme is encoded by an alanine racemase gene (dal) gene. D-glutamic acid synthesis is controlled in part by the dal gene, which is involved in the conversion of D-glu+pyr to alpha-ketoglutarate+D-ala, and the reverse reaction.
The dal gene of methods and compositions of the present invention is encoded, in another embodiment, by the sequence:







atggtgacaggctggcatcgtccaacatggattgaaatagaccgcgcagc


 


aattcgcgaaaatataaaaaatgaacaaaataaactcccggaaagtgtcg


 


acttatgggcagtagtcaaagctaatgcatatggtcacggaattatcgaa


 


gttgctaggacggcgaaagaagctggagcaaaaggtttctgcgtagccat


 


tttagatgaggcactggctcttagagaagctggatttcaagatgacttta


 


ttcttgtgcttggtgcaaccagaaaagaagatgctaatctggcagccaaa


 


aaccacatttcacttactgtttttagagaagattggctagagaatctaac


 


gctagaagcaacacttcgaattcatttaaaagtagatagcggtatggggc


 


gtctcggtattcgtacgactgaagaagcacggcgaattgaagcaaccagt


 


actaatgatcaccaattacaactggaaggtatttacacgcattttgcaac


 


agccgaccagctagaaactagttattttgaacaacaattagctaagttcc


 


aaacgattttaacgagtttaaaaaaacgaccaacttatgttcatacagcc


 


aattcagctgcttcattgttacagccacaaatcgggtttgatgcgattcg


 


ctttggtatttcgatgtatggattaactccctccacagaaatcaaaacta


 


gcttgccgtttgagcttaaacctgcacttgcactctataccgagatggtt


 


catgtgaaagaacttgcaccaggcgatagcgttagctacggagcaactta


 


tacagcaacagagcgagaatgggttgcgacattaccaattggctatgcgg


 


atggattgattcgtcattacagtggtttccatgttttagtagacggtgaa


 


ccagctccaatcattggtcgagtttgtatggatcaaaccatcataaaact


 


accacgtgaatttcaaactggttcaaaagtaacgataattggcaaagatc


 


atggtaacacggtaacagcagatgatgccgctcaatatttagatacaatt


 


aattatgaggtaacttgtttgttaaatgagcgcatacctagaaaatacat


 


ccattag






(SEQ ID No: 50; GenBank Accession No: AF038438). In another embodiment, the nucleotide encoding dal is homologous to SEQ ID No: 50. In another embodiment, the nucleotide encoding dal is a variant of SEQ ID No: 50. In another embodiment, the nucleotide encoding dal is a fragment of SEQ ID No: 50. In another embodiment, the dal protein is encoded by any other dal gene known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the dal protein has the sequence:







MVTGWHRPTWIEIDRAAIRENIKNEQNKLPESVDLWAVVKANAYGHGIIE


 


VARTAKEAGAKGFCVAILDEALALREAGFQDDFILVLGATRKEDANLAAK


 


NHISLTVFREDWLENLTLEATLRIHLKVDSGMGRLGIRTTEEARRIEATS


 


TNDHQLQLEGIYTHFATADQLETSYFEQQLAKFQTILTSLKKRPTYVHTA


 


NSAASLLQPQIGFDA1RFGISMYGLTPSTEIKTSLPFELKPALALYTEMV


 


HVKELAPGDSVSYGATYTATEREWVATLPIGYADGLIRHYSGFHVLVDGE


 


PAPIIGRVCMDQTIIKLPREFQTGSKVTIIGKDHGNTVTADDAAQYLDTI


 


NYEVTCLLNERIPRKYIH






(SEQ ID No: 51; GenBank Accession No: AF038438). In another embodiment, the dal protein is homologous to SEQ ID No: δ 1. In another embodiment, the dal protein is a variant of SEQ ID No: δ 1. In another embodiment, the dal protein is an isomer of SEQ ID No: 51. In another embodiment, the dal protein is a fragment of SEQ ID No: 51. In another embodiment, the dal protein is a fragment of a homologue of SEQ ID No: 51. In another embodiment, the dal protein is a fragment of a variant of SEQ ID No: 51. In another embodiment, the dal protein is a fragment of an isomer of SEQ ID No: 51.

In another embodiment, the dal protein any other dal protein known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the dal protein of methods and compositions of the present invention retains its enzymatic activity. In another embodiment, the dal protein retains 90% of wild-type activity. In another embodiment, the dal protein retains 80% of wild-type activity. In another embodiment, the dal protein retains 70% of wild-type activity. In another embodiment, the dal protein retains 60% of wild-type activity. In another embodiment, the dal protein retains 50% of wild-type activity. In another embodiment, the dal protein retains 40% of wild-type activity. In another embodiment, the dal protein retains 30% of wild-type activity. In another embodiment, the dal protein retains 20% of wild-type activity. In another embodiment, the dal protein retains 10% of wild-type activity. In another embodiment, the dal protein retains 5% of wild-type activity. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the metabolic enzyme is encoded by a D-amino acid aminotransferase gene (dat). D-glutamic acid synthesis is controlled in part by the dat gene, which is involved in the conversion of D-glu+pyr to alpha-ketoglutarate+D-ala, and the reverse reaction.
In another embodiment, a dat gene utilized in the present invention has the sequence set forth in GenBank Accession Number AF038439. In another embodiment, the dat gene is any another dat gene known in the art. Each possibility represents a separate embodiment of the present invention.
The dat gene of methods and compositions of the present invention is encoded, in another embodiment, by the sequence:







atgaaagtattagtaaataaccatttagttgaaagagaagatgccacagt


 


tgacattgaagaccgcggatatcagtttggtgatggtgtatatgaagtag


 


ttcgtctatataatggaaaattctttacttataatgaacacattgatcgc


 


ttatatgctagtgcagcaaaaattgacttagttattccttattccaaaga


 


agagctacgtgaattacttgaaaaattagttgccgaaaataatatcaata


 


cagggaatgtctatttacaagtgactcgtggtgttcaaaacccacgtaat


 


catgtaatccctgatgatttccctctagaaggcgttttaacagcagcagc


 


tcgtgaagtacctagaaacgagcgtcaattcgttgaaggtggaacggcga


 


ttacagaagaagatgtgcgctggttacgctgtgatattaagagcttaaac


 


cttttaggaaatattctagcaaaaaataaagcacatcaacaaaatgcttt


 


ggaagctattttacatcgcggggaacaagtaacagaatgttctgcttcaa


 


acgtttctattattaaagatggtgtattatggacgcatgcggcagataac


 


ttaatcttaaatggtatcactcgtcaagttatcattgatgttgcgaaaaa


 


gaatggcattcctgttaaagaagcggatttcactttaacagaccttcgtg


 


aagcggatgaagtgttcatttcaagtacaactattgaaattacacctatt


 


acgcatattgacggagttcaagtagctgacggaaaacgtggaccaattac


 


agcgcaacttcatcaatattttgtagaagaaatcactcgtgcatgtggcg


 


aattagagtttgcaaaataa






(SEQ ID No: 52; GenBank Accession No: AF038439). In another embodiment, the nucleotide encoding dat is homologous to SEQ ID No: 52. In another embodiment, the nucleotide encoding dat is a variant of SEQ ID No: 52. In another embodiment, the nucleotide encoding dat is a fragment of SEQ ID No: 52. In another embodiment, the dat protein is encoded by any other dat gene known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the dat protein has the sequence:







MKVLVNNHLVEREDATVDIEDRGYQFGDGVYEVVRLYNGKFFTYNEHIDR


 


LYASAAKIDLVIPYSKEELRELLEKLVAENNINTGNVYLQVTRGVQNPRN


 


HVIPDDFPLEGVLTAAAREVPRNERQFVEGGTAITEEDVRWLRCDIKSLN


 


LLGNILAKN1CAHQQNALEAILHRGEQVTECSASNVSIIKDGVLWTHAAD


 


NLILNGITRQVIIDVAKKNGIPVICEADFTLTDLREADEVFISSTTIEIT


 


PITHIDGVQVADGKRGPITAQLHQYFVEEITRACGELEFAK






(SEQ ID No: 53; GenBank Accession No: AF038439). In another embodiment, the dat protein is homologous to SEQ ID No: 53. In another embodiment, the dat protein is a variant of SEQ ID No: 53. In another embodiment, the dat protein is an isomer of SEQ ID No: 53. In another embodiment, the dat protein is a fragment of SEQ ID No: 53. In another embodiment, the dat protein is a fragment of a homologue of SEQ ID No: 53. In another embodiment, the dat protein is a fragment of a variant of SEQ ID No: 53. In another embodiment, the dat protein is a fragment of an isomer of SEQ ID No: 53.

In another embodiment, the dat protein any other dat protein known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the dat protein of methods and compositions of the present invention retains its enzymatic activity. In another embodiment, the dat protein retains 90% of wild-type activity. In another embodiment, the dat protein retains 80% of wild-type activity. In another embodiment, the dat protein retains 70% of wild-type activity. In another embodiment, the dat protein retains 60% of wild-type activity. In another embodiment, the dat protein retains 50% of wild-type activity. In another embodiment, the dat protein retains 40% of wild-type activity. In another embodiment, the dat protein retains 30% of wild-type activity. In another embodiment, the dat protein retains 20% of wild-type activity. In another embodiment, the dat protein retains 10% of wild-type activity. In another embodiment, the dat protein retains 5% of wild-type activity. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the metabolic enzyme is encoded by dga. D-glutamic acid synthesis is also controlled in part by the dga gene, and an auxotrophic mutant for D-glutamic acid synthesis will not grow in the absence of D-glutamic acid (Pucci et al, 1995, J. Bacteriol. 177: 336-342). A further example includes a gene involved in the synthesis of diaminopimelic acid. Such synthesis genes encode beta-semialdehyde dehydrogenase, and when inactivated, renders a mutant auxotrophic for this synthesis pathway (Sizemore et al, 1995, Science 270: 299-302).
In another embodiment, the metabolic enzyme is encoded by an alr (alanine racemase) gene. In another embodiment, the metabolic enzyme is any other enzyme known in the art that is involved in alanine synthesis. In another embodiment, the metabolic enzyme is any other enzyme known in the art that is involved in L-alanine synthesis. In another embodiment, the metabolic enzyme is any other enzyme known in the art that is involved in D-alanine synthesis. Bacteria auxotrophic for alanine synthesis are well known in the art, and are described in, for example, E. coli (Strych et al, 2002, J. Bacteriol. 184:4321-4325), Corynebacterium glutamicum (Tauch et al, 2002, J. Biotechnol 99:79-91), and Listeria monocytogenes (Frankel et al, U.S. Pat. No. 6,099,848), Lactococcus species, and Lactobacillus species, (Bron et al, 2002, Appl Environ Microbiol, 68: 5663-70). In another embodiment, any D-alanine synthesis gene known in the art is inactivated. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the metabolic enzyme is an amino acid aminotransferase.
In another embodiment, the metabolic enzyme is encoded by serC, a phosphoserine aminotransferase. In another embodiment, the metabolic enzyme is encoded by asd (aspartate beta-semialdehyde dehydrogenase), involved in synthesis of the cell wall constituent diaminopimelic acid. In another embodiment, the metabolic enzyme is encoded by gsaB-glutamate-1-semialdehyde aminotransferase, which catalyzes the formation of 5-aminolevulinate from (S)-4-amino-5-oxopentanoate. In another embodiment, the metabolic enzyme is encoded by HemL, which catalyzes the formation of 5-aminolevulinate from (S)-4-amino-5-oxopentanoate. In another embodiment, the metabolic enzyme is encoded by aspB, an aspartate aminotransferase that catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate. In another embodiment, the metabolic enzyme is encoded by argF-1, involved in arginine biosynthesis. In another embodiment, the metabolic enzyme is encoded by aroE, involved in amino acid biosynthesis. In another embodiment, the metabolic enzyme is encoded by aroD, involved in amino acid biosynthesis. In another embodiment, the metabolic enzyme is encoded by aroC, involved in amino acid biosynthesis. In another embodiment, the metabolic enzyme is encoded by hisB, involved in histidine biosynthesis. In another embodiment, the metabolic enzyme is encoded by hisD, involved in histidine biosynthesis. In another embodiment, the metabolic enzyme is encoded by hisG, involved in histidine biosynthesis. In another embodiment, the metabolic enzyme is encoded by metX, involved in methionine biosynthesis. In another embodiment, the metabolic enzyme is encoded by proB, involved in proline biosynthesis. In another embodiment, the metabolic enzyme is encoded by argR, involved in arginine biosynthesis. In another embodiment, the metabolic enzyme is encoded by argj, involved in arginine biosynthesis. In another embodiment, the metabolic enzyme is encoded by thil, involved in thiamine biosynthesis. In another embodiment, the metabolic enzyme is encoded by LMOf2365—1652, involved in tryptophan biosynthesis. In another embodiment, the metabolic enzyme is encoded by aroA, involved in tryptophan biosynthesis. In another embodiment, the metabolic enzyme is encoded by ilvD, involved in valine and isoleucine biosynthesis. In another embodiment, the metabolic enzyme is encoded by ilvC, involved in valine and isoleucine biosynthesis. In another embodiment, the metabolic enzyme is encoded by leuA, involved in leucine biosynthesis. In another embodiment, the metabolic enzyme is encoded by dapF, involved in lysine biosynthesis. In another embodiment, the metabolic enzyme is encoded by thrB, involved in threonine biosynthesis (all GenBank Accession No. NC—002973).
In another embodiment, the metabolic enzyme is encoded by murE, involved in synthesis of diaminopimelic acid (GenBank Accession No: NC—003485).
In another embodiment, the metabolic enzyme is encoded by LMOf2365-2494, involved in teichoic acid biosynthesis.
In another embodiment, the metabolic enzyme is encoded by WecE (Lipopolysaccharide biosynthesis protein rffA; GenBank Accession No: AE014075.1). In another embodiment, the metabolic enzyme is encoded by amiA, an N-acetylmuramoyl-L-alanine amidase. In another embodiment, the metabolic enzyme is aspartate aminotransferase. In another embodiment, the metabolic enzyme is histidinol-phosphate aminotransferase (GenBank Accession No. NP—466347). In another embodiment, the metabolic enzyme is the cell wall teichoic acid glycosylation protein GtcA.
In another embodiment, the metabolic enzyme is a synthetic enzyme for a peptidoglycan component or precursor. In another embodiment, the component is UDP-N-acetylmuramyl-pentapeptide. In another embodiment, the component is UDP-N-acetylglucosamine. In another embodiment, the component is MurNAc-(pentapeptide)-pyrophosphoryl-undecaprenol. In another embodiment, the component is GlcNAc-β-(1,4)-MurNAc-(pentapeptide)-pyrophosphoryl-undecaprenol. In another embodiment, the component is any other peptidoglycan component or precursor known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the metabolic enzyme is encoded by murG. In another embodiment, the metabolic enzyme is encoded by murD. In another embodiment, the metabolic enzyme is encoded by murA-1. In another embodiment, the metabolic enzyme is encoded by murA-2 (all set forth in GenBank Accession No. NC—002973). In another embodiment, the metabolic enzyme is any other synthetic enzyme for a peptidoglycan component or precursor. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the metabolic enzyme is a trans-glycosylase. In another embodiment, the metabolic enzyme is trans-peptidase. In another embodiment, the metabolic enzyme is a carboxy-peptidase. In another embodiment, the metabolic enzyme is any other class of metabolic enzyme known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the metabolic enzyme is any other Listeria monocytogenes metabolic enzyme known in the art.
In another embodiment, the metabolic enzyme is any other Listeria metabolic enzyme known in the art.
In another embodiment, the metabolic enzyme is any other metabolic enzyme known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the gene encoding the metabolic enzyme is expressed under the control of the Listeria p60 promoter. In another embodiment, the inlA (encodes internalin) promoter is used. In another embodiment, the hly promoter is used. In another embodiment, the ActA promoter is used. In another embodiment, the integrase gene is expressed under the control of any other gram positive promoter. In another embodiment, the gene encoding the metabolic enzyme is expressed under the control of any other promoter that functions in Listeria. The skilled artisan will appreciate that other promoters or polycistronic expression cassettes may be used to drive the expression of the gene. Each possibility represents a separate embodiment of the present invention.
The gene expressed on a plasmid of the present invention comprises, in one embodiment, an isolated nucleic acid encoding a protein that complements the auxotrophic mutant. In another embodiment, if the auxotrophic bacteria is deficient in a gene encoding a vitamin synthesis gene (e.g. pantothenic acid) necessary for bacterial growth, the plasmid DNA comprises a gene encoding a protein for pantothenic acid synthesis. Thus, the auxotrophic bacteria, when expressing the gene on the plasmid, can grow in the absence of pantothenic acid, whereas an auxotrophic bacteria not expressing the gene on the plasmid cannot grow in the absence of pantothenic acid.
In another embodiment, an auxotrophic bacterium utilized in methods and compositions of the present invention is deficient in the metabolic enzyme of methods and compositions of the present invention. In another embodiment, the gene encoding the metabolic enzyme is mutated in the genome of the bacterium. In another embodiment, the gene encoding the metabolic enzyme is deleted from the genome of the bacterium. Each possibility represents a separate embodiment of the present invention.
The attPP′ of methods and compositions of the present invention is, in another embodiment, a U153 attPP′ site. In another embodiment, the attPP site has a sequence contained in SEQ ID No: 26:








        aagctttaaagaaattcaagaagaaacatcggtaactagccataaattaaccaaagttctaatctcgcttgaagagaacaaactgattgaaaaa



 


attggacaatctagagcaacaaaatacaaattaattgaatctacagaggaatatctaaccaatcttcaacacacatttcgaaaaattgttcaattttatgtt


 


gaaaatgataaataaaaatatgaatgtttttttatttgttagtagtgtaactttccatgcgagaggagaacggaaatgaaggcagctatttatatacgcgta


 


tctactcaagaacaaatagagaattactctatacaagctcaaactgaaaagctaacagccttgtgccgctcgaaggattgggacgtatacgatattttcata


 


gacggcggatacagcggttcaaacatgaatcgccccgcactaaatgaaatgctaagtaaattacatgaaattgatgctgttgttgtatatcgcttagataga


 


ctttcccgctcacaaagagatacgataacgcttattgaagaatacttcttaaaaaacaatgtagaatttgttagtttgtctgaaactcttgacacctctagc


 


ccatttgggcgcgcgatgattggtatattatccgtatttgctcaattagagcgcgaaactatacgtgatcgtatggtgatggggaaaattnagcgtattgaa


 


gcaggtcttcctttaacgactgcaaaaggtagaacattcggctatgatgttatagatactaaattatatattaatgaagaagaagcaaaacaattacaaatg


 


atttatgatatttttgaggaagaaaaaagcattaccactttacagaagagactaaaaaaattaggattcaaagtgaaatcatatagcagttacaacaattgg


 


ctaactaatgatttatactgtggttatgtatcttatgcggataaagtgcatacaaaaggtgttcatgagcctattatttcagaggaacaattttatcgagtt


 


caagaaattttttctcgcatgggtaaaaatccaaatatgaatagagattcagcatcgttgctaaataatttggtagtgtgtggaaaatgtgggttgggtttt


 


gttcatcggagaaaagatactgtttcccgcggaaaaaaatatcattatagatattatagttgcaagacttacaaacatactcatgaactagaaaaatgtgga


 


aataaaatttggagagctgacaaactcgaggaattaattattgatcgcgtgaataactatagtttcgcttctaggaatgtagataaagaagacgaattagat


 


agcttaaatgaaaaacttaaaacagaacacgtaaaaaagaaacggctatttgatttatatatcagcggttcttacgaagtttcagaacttgatgctatgatg


 


gctgatatcgatgctcaaattaattattatgaagcacaaatagaagctaacgaagaattgaagaaaaataaaaagatacaagaaaatttagctgatttagca


 


acagttgattttgactctttagagttccgagaaaagcaactttatttaaaatcactaattaataaaatttatattgacggtgaacaagttactattgaatgg


 


ctctagtagcttgtttatttagattgtttagttcctcgttttctctcgttggacggaaacgaatcgagaaactaaaattataaataaaaagtaacctgtttt


 


tctatagattgctttttatcaattatatagaagaaagccgctttttattagattataattgatgttttttgatttatatttcactccctgtgcaaataatga


 


tataacagcaacctcgaactttttagttcggggtatttttttgaaattaatttataaaaacacttgcaattatataatacatgtattataatataaatatag


 


aaaggagttgagaaagtgaaagacatcttagaggaaataaaaacagtccttgaaattgtaactcttgcagtagcgctgataacattacgcaagatagacaaa


 


aacaaggacaagtaaccagaggggtgaaactcccctccctctataaaagtatatcacgtctttcataaattatgaataaatatatctgggttatattaattg


 


ttatatgcgttaacggactcgctagttactttcagaacacagcattgaccatcattgctatactgactacattagcttgtttagtatatttaataaaaaata


 


ggaagtgattaattatgacgaaaaaaacgacctctgacgcgcagttgaaagcaaataaggaatggcaaagcaagaacaaagaacatgcaaactatttaaaat


 


ctcgttcagctgcgcgttcttttataaagaataaagctacgttggaagatttgaaggaacttgaaaaattaattatagagggaaaaattaatcataagggaa


 


tgattaaggataaatgatgcacgctaagcacatgcttggcgttttttgcataaaaaaagccctaacgttgaagttagggactgacatatataaaaaatagaa


 


gttgacaactttaaggcgactaccacgacaggcagcttacaagctatgactagccttgactaatcatttatgcgacactcaaagaattattatctaacttct


 


taatcaagaataacaaaaatcaaacaagttagcaagtatttcaggcattttatttataacaaatatctagatcacaaaaatgtcgcggaaaataatggtcac


 


aaccaatattacataaacttaaaagttctctatttctcttatcaggtttatgtgctgttacgtgatttctacatactctaaaaactgtattagcgaataagt


 


ctacaacttgaattaaatctttattttgtgaatccttatatgatgtttcaacagaagagaaaattggatgttccattgtaaatttaatagttaaatattctt


 


gtaagctatttaatgattcaattgcggtatttctatcatctatttgcattttcaaatagttatttgctgggttaattggtattttagaaatttcatttaccg


 


ttagataaataaaataattaaaagacaaagatgtattattcaaaagatgattgactagttggtggttatcgactatcttaaaatgaaatttagcatctgatt


 


ttgttgaaagcattattaaatattaattttttcatttcaaaaggcatctccgaaccttttatctcttttgtaatatctaacttactagatggatacctttaa


 


gatattttaattttgcatctctgaactgtctaattacattatatggtttctctgtttctaaaaaagcaataacaaaatatctgttattaaaatttttatttt


 


tagttatagttcctgattcatctacaaaaagtctcatcccagttcctccacttttttacttaaattatattatactaattaagtttgaggaagtggaacgta


 


tgtacttataattcgaagttatgaaaaatccccccatcaatataaaacaaaaaagcccccgaaataataatcgagggcattaaactaaatctttttaacaaa


 


cttcggtgttagcagtgagatagtaaccagatttcgttttcaagcgaggtgttccgccttttgttttcgccattcctgtaatcgtgaagatagtgcctaccg


 


gatatgtgccaccggttttatgcttctcagtaaagtctactgaattgtatagatcacactgtactagtgttttaacttttcgcggattttctgtgtagtatg


 


tgtttttgcttgctggtgtgtgtggttttcctgcttttaacttcgctaataatgttgtgttctgcgttgctgttcctttataatccttaattccgtattgat


 


ttgctagttttttacgattcgcaaagctt






(SEQ ID No: 26; att site is underlined). In another embodiment, the attPP′ site, core integration site, and/or surrounding sequence are homologous to SEQ ID No: 26. In another embodiment, the attPP′ site, core integration site, and/or surrounding sequence are a variant of SEQ ID No: 26. In another embodiment, the attPP′ site is any other U153 attPP′ site known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the attPP′ site is an A118 attPP′ site. In another embodiment, the sequence of the site is:







tttagtttctcgtttcttcttcttccaacgagagaaaacgaggaactaaa






(SEQ ID No: 42; att site is underlined; GenBank Accession No: AJ242593). In another embodiment, the attPP′ site, core integration site, and/or surrounding sequence are homologous to SEQ ID No: 42. In another embodiment, the attPP′ site, core integration site, and/or surrounding sequence are a variant of SEQ ID No: 42. In another embodiment, the attPP′ site is a site set forth GenBank Accession No. NC—003216. In another embodiment, the attPP′ site is any other A118 attPP′ site known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the attPP′ site is a PSA attPP′ site. In another embodiment, the sequence of the site is:







ttacataaaatgtttgtggtattatttgtggtatatatatcctaaatggc


 


tttatatcagtgtgtgttaatccctctcaggacgttaaatagtaa






(SEQ ID No: 43; att site is underlined; GenBank Accession No: AJ312240). In another embodiment, the attPP′ site, core integration site, and/or surrounding sequence are homologous to SEQ ID No: 43. In another embodiment, the attPP′ site, core integration site, and/or surrounding sequence are a variant of SEQ ID No: 43. In another embodiment, the attPP′ site is any other PSA attPP′ site known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the attPP′ site is any other attPP′ site known in the art. Each possibility represents a separate embodiment of the present invention.
The attBB′ site of methods and compositions of the present invention is, in another embodiment, an attBB′ site for A118. In another embodiment, the attBB′ site has the sequence:







ttacataaaatgtttgtggtattatttgtggtattccaaaaaaacttaaga


 


aggttcttacnattcttagtttttcatatattcttactccaaaaagctagg


 


catttccctgtgaatatattcattUttctgtaagtttcataaattccgcat


 


gttcctattatcgagagctttatcaatttcagctctaagttgttctaattt


 


tctctcttctaggagcatcgtcaggaagcattcgataaaaacgtttgttaa


 


ttctttttcacccttaaggacacccacctgattcatcaacgaattagaaaa


 


atcacgcatttccacgactaccactccttcactcatatttattacaatctt


 


aaaaaattgtaatatgccaagaaaaaacagaaaacagcttgaaaatacaac


 


tttactaatatctaatgacttgcaaattaccatgtgctataatgacaaaaa


 


ataactcataactaactttgatgcttagtcgttacttagaagttttgctta


 


ttaggcaataactctaggtttcttcttagacataaatacaaacatagagga


 


gttgaatgaaatgaaaaaagaacaaatcagtactcagttttatgaagtaaa


 


cccgcacacgatgattatttttccaaaaaaatctggaagtatagtctattc


 


agaaatttatgaagttgattctcattatacttctaaatttaccccgtttga


 


gctaattaaaaccagctgtaacttttcggatcaagctatgaaggacgcaaa


 


gagggaactaaacacttaattggtgttacccataagccacccattatcatt


 


gacccagtcacttctacttatgtatttccaactgtagcaccaagttcaaca


 


gaatgcatttggattttcccacaacatattaaagattatcatgcaattgga


 


tttaaccacactttaataacattttctaatatggaaacctttgagattgat


 


atgtctttagcatcttttaataatcagattgccagaacctccatgttacat


 


atgaaattttctcaaaaaatgcgtatgatggagagtaatttcccttcaatg


 


aataggtttttcccaccaaccactcttgctgctgaacctaagacgttatta


 


cagcaccatgcttccaaataatgaagaacctaatgatcctcaagatcccga


 


gcaataaatttaaaactaaataaaagccagctacgtaatagtagctggctt


 


ttccttaaaatcattttttattctcaatcgcatctgcaattcgttttaaca


 


ttaataactcatcctctgagtatgtataaggtagttctaaataccatttct


 


cgagttcaggatttccaattaaaggaaaggcgtttaccgaattcttttctc


 


gcaaaccagctacatcatctaataagaaatcggttgttgttccaagaattt


 


ctgctaatttagccaaaataaaaattggcggtcggtggttatcattttcat


 


acttgcttattgtggatgcagttgtcccgattttcgccgccagttgttttn


 


tgtgttaacctatttttctttcgtaaatgaattaatttttctccaaattcc


 


aatacgcccacctcacttcatccagtatagcaatttttcggaaagaattcg


 


agaaattctaaaaagaaatcgctttttaggtttcaaaagacattttcccgt


 


atttatacag






(SEQ ID No: 44; att site is underlined; GenBank Accession No: AF174588). In another embodiment, the attBB′ site is homologous to SEQ ID No: 44. In another embodiment, the attBB′ site is a variant of SEQ ID No: 44. In another embodiment, the attBB′ site is any other A118 attBB′ site known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the attBB′ site is an attBB′ site for PSA. In another embodiment, the attBB′ site has the sequence:







tgtcctgatagctcagctggatagagcaacggccttctaagccgtcggtcg


 


ggggttcgaatccctctcaggacgtaaatagctatatta






(SEQ ID No: 45; att site is underlined; GenBank Accession No: AJ314913). In another embodiment, the attBB′ site is homologous to SEQ ID No: 45. In another embodiment, the attBB′ site is a variant of SEQ ID No: 45. In another embodiment, the attBB′ site is any other PSA attBB′ site known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the attBB′ site is an attBB′ site for U153.
In another embodiment, the attBB′ site is within the gene for tRNAArg. In another embodiment, the attBB′ site is near the gene for tRNAArg. In another embodiment, the attBB′ site is within the gene for comK. In another embodiment, the attBB′ site is near the gene for comK. In another embodiment, the attBB′ site is within any other LM gene known in the art. In another embodiment, the attBB′ site is near any other LM gene known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the attBB′ site is any other attBB′ site known in the art. Each possibility represents a separate embodiment of the present invention.
The integrase protein of methods and compositions of the present invention is, in another embodiment, a U153 integrase. In another embodiment, the integrase protein is encoded by a nucleotide molecule having the sequence set forth in residues 272-1630 of SEQ ID No: 26. In another embodiment, the nucleotide encoding the integrase is homologous to SEQ ID No: 26. In another embodiment, the nucleotide encoding the integrase is a variant of SEQ ID No: 26. In another embodiment, the nucleotide encoding the integrase is a fragment of SEQ ID No: 26. In another embodiment, the integrase protein is encoded by any other U153 integrase gene known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the integrase protein has the sequence:







 


MKAAIYIRVSTQEQIENYSIQAQTEKLTALCRSKDWDVYDIFIDGGYSGSN


 


MNRPALNEMLSKLHEIDAVVVYRLDRLSRSQRDTITLIEEYFLKNNVEFVS


 


LSETLDTSSPFGRAMIGILSVFAQLERETIRDRMVMGKIXRIEAGLPLTTA


 


KGRTFGYDVIDTKLYINEEEAKQLQMIYDIFEEEKSITTLQICRLKKLGFK


 


VKSYSSYNNWLINDLYCGYVSYADKVHTKGVHEPIISEEQFYRVQEIFSRM


 


GKNPNMNRDSASLLNNLVVCGKCGLGFVHRRKDTVSRGKKYHYRYYSCKTY


 


KHTHELEKCGNKIWRADKLEELIIDRVNNYSFASRNVDKEDELDSLNEKLK


 


TEHVKKKRLFDLYISGSYEVSELDAMMADIDAQINYYEAQIEANEELKKNK


 


KIQENLADLATVDFDSLEFREKQLYLKSLINKIYIDGEQVTIEWL (SEQ


 


ID No: 27).






In another embodiment, the integrase is homologous to SEQ ID No: 27. In another embodiment, the integrase is a variant of SEQ ID No: 27. In another embodiment, the integrase is an isoform of SEQ ID No: 27. In another embodiment, the integrase is a fragment of SEQ ID No: 27. In another embodiment, the integrase is any other U153 integrase known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the integrase is a PSA integrase. In another embodiment, the integrase is encoded by a gene having the sequence:








        ttattccgttgtttttgtggcatttgtggtaaaatttgtggtattttcatctgtttttagtgtgaaaaaagcatctactttggactgattatgt



 


tgtcttaaattagagcttagatgactatagtattttaatgttgtattaatgtcatcatgaccaagcctatcagctacataaataatatccatacccgcttct


 


acacataagcctgtatgcgtatgtcgtagcttgtgtaatgtcactggttcagaattgattgtactacatatcttcttcaaagctttattacaagacgcgttg


 


tctactggcttattgtggtaagtgatgaataataacatcaatggattcttaatagcatgttccttcatataatcagtatgccaatttaaatacgaatgtaaa


 


tattgagcggtagagttatcaatatagatcactcgtgatttttttgttttggtatcaatgaatgtattagtgtacttgtaatcccaagctttattcacagtt


 


attgaacgtttagtgaaattaatatccttctttgttagtgcaataatttcttcgaacctcatgcctgtctggacagctagaaagataactgctcgtgatata


 


gaatgaaattttgcaagttcttctaatagtaaatgaactttgtctgtttccataaattgtgctttatttttcgctacgtcctgtccgcttatatgagcccct


 


atagtggggtttttcttcatgtaacctaaatgaacagccttgttaaaaatcgctctaattttgcggtgtctggtgtctacagtggatattgcatagtctaca


 


gataaatgattaataaattgttgatattgaaccgcatcaatcgaattaagtttaattttttcatcgaaataatcaacgaattgattataagcaagatcgtat


 


aaattaatagtagattgactacttttcccatctttaaatgttttcatgaatagcgtataaaattctttgaagttccattctttcagagaactactatcatgc


 


tgaacttgttttaataatttagatgctttatacattaagtttgtttcacttgtatctgtcaaacgcttttctttccattcaccatcgacttttatacgtagg


 


cgaacacaatatttaccgtttgctaatttttttatcttcat






(SEQ ID No: 46; GenBank Accession No: AJ312240). In another embodiment, the nucleotide encoding the integrase is homologous to SEQ ID No: 46. In another embodiment, the nucleotide encoding the integrase is a variant of SEQ ID No: 46. In another embodiment, the nucleotide encoding the integrase is a fragment of SEQ ID No: 46. In another embodiment, the integrase protein is encoded by any other PSA integrase gene known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the sequence of the integrase is:







MKIKKLANGKYCVRLRIKVDGEWKEKRLTDTSETNLMYKASKLLKQVQHDS


 


SSLKEWNFICEFYTLFMKTFKDGKSSQSTINLYDLAYNQFVDYFDEKIKLN


 


SIDAVQYQQFINHLSVDYAISTVDTRHRKIRAIFNICAVHLGYMKKNPTIG


 


AHISGQDVAKNKAQFMETDKVHLLLEELAKFHSISRAVIFLAVQTGMRFEE


 


HALTKKDINFTICRSITVNICAWDYKYTNTFIDTKTKKSRVIYIDNSTAQY


 


LHSYLNWHTDYMKEHAIKNPLMLLFITYHNKPVDNASCNKALKKICSTINS


 


EPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTLKYYSHLSSNLRQ


 


HNQSKVDAFFTLKTDENTTNFTTNATKTTE






(SEQ ID No: 47; GenBank Accession No: AJ312240). In another embodiment, the integrase is homologous to SEQ ID No: 47. In another embodiment, the integrase is a variant of SEQ ID No: 47. In another embodiment, the integrase is an isoform of SEQ ID No: 47. In another embodiment, the integrase is a fragment of SEQ ID No: 47. In another embodiment, the integrase is any other PSA integrase known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the integrase is an A118 integrase. In another embodiment, the integrase is encoded by a gene having the sequence:







caagctactagagccattcaatagtaacttgttcaccatcaatataaattt


 


tgtttattagtgattttaaataaagttgcttttctctgaactctaaagagt


 


caaaatcaactgttgctaaatcagctaaattacttgtatcatttgtattct


 


tcaattcttcgttagatctatttgtgattcataataattaatttgagcatc


 


aatatcattcatcatagaatcaagttctgaaacttcatacgagccatttat


 


atataaatcaaataatcgttttttctttgcatgttctattttaagcttttc


 


atttaagctatctaattcatcttctttatctacatttctggaagcgaaact


 


ataattattcacacgattaataattaattcttcaagtttgtcagctctcca


 


aattttattcccgcatttacgagttcatgagtatgtttataagtcttgcaa


 


ctataatatctataatgatatatttaccacgcgacattgtatctatctacg


 


atgaacaaagcctaacccgcatttactacaaactactaaattatttagcaa


 


cgatgctgaatctctattcatgttcggatttttacccatacgagtaaatat


 


ttcttgaactctatagaattgctcttcactgatgataggttcatgaatacc


 


ttttacatgaactttatctttatatgaaacataaccacaatacaaatcatt


 


agttagccagttgttatagcgattatatgttctaactttaaagcctaattt


 


ttttagtcttttctgtaaaaaagttatactttgttcttcttcgaaaatatc


 


ataaatcagttgtaactgttttgcttcttcttcattaatgtataattttgt


 


atctataacatcatagccgaacgttctacctttcgcagttgttaacggaag


 


acctgcttcaatacgcttaattttccccatcaccatacgatctcggattgt


 


ttcgcgctctagctgtgcgaatactgataatataccaatcattgcacgacc


 


gaaaggggaactagtatcaagcgtttcagacaaactaacaaactctacatt


 


gttttttaagaagtattcttcaataagcgttattgtgtctctttgtgagcg


 


ggatagtctgtctaatcgatatacgactacagcatcaatttcgtgtagttt


 


acttagcatttcatttaatgcgggacgattcatatttgagccggagtatcc


 


gccgtcaatgaaaatatcgtatacgtcccagtccttcgagcggcacaatgc


 


tgttagtttttcagtttgagcttgtattgaataattttctacttgctcttg


 


agtagaaacacgtatataaatagctgccttcatttcc






(SEQ ID No: 48; GenBank Accession No: AJ242593). In another embodiment, the nucleotide encoding the integrase is homologous to SEQ ID No: 48. In another embodiment, the nucleotide encoding the integrase is a variant of SEQ ID No: 48. In another embodiment, the nucleotide encoding the integrase is a fragment of SEQ ID No: 48. In another embodiment, the integrase protein is encoded by any other A118 integrase gene known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the sequence of the integrase is:







MKAAIYIRVSTQEQVENYSIQAQTEKLTALCRSKDWDVYDIFIDGGYSGSN


 


MNRPALNEMLSKLHEIDAVVVYRLDRLSRSQRDTITL1EEYFLKNNVEFVS


 


LSETLDTSSPFGRAMIGILSVFAQLERETIRDRMVMGKIKRIEAGLPLTTA


 


KGRTFGYDVIDTKLYINEEEAKQLQLIYDIFEEEQSITFLQKRLKKLGFKV


 


RTYNRYNNWLTNDLYCGYVSYKDKVHVKGIHEPIISEEQFYRVQEIFTRMG


 


KNPNMNRDSASLLNNLVVCSKCGLGFVHRRKDTMSRGKKYHYRYYSCKTYK


 


HTHELEKCGNKIWRADKLEELIINRVNNYSFASRNVDKEDELDSLNEKLKI


 


EHAKKKRLFDLYINGSYEVSELDSMMNDIDAQINYYESQIEANEELKKNKK


 


IQENLADLATVDFDSLEFREKQLYLKSLINKIYIDGEQVTIEWL






(SEQ ID No: 49; GenBank Accession No: AJ242593). In another embodiment, the integrase is homologous to SEQ ID No: 49. In another embodiment, the integrase is a variant of SEQ ID No: 49. In another embodiment, the integrase is an isoform of SEQ ID No: 49. In another embodiment, the integrase is a fragment of SEQ ID No: 49. In another embodiment, the integrase is any other A118 integrase known in the art. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the integrase gene is any other integrase gene known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the integrase gene is expressed under the control of the Listeria p60 promoter. In another embodiment, the inlA (encodes internalin) promoter is used. In another embodiment, the hly promoter is used. In another embodiment, the ActA promoter is used. In another embodiment, the integrase gene is expressed under the control of any other gram positive promoter. In another embodiment, the integrase gene is expressed under the control of any other promoter that functions in Listeria. The skilled artisan will appreciate that other promoters or polycistronic expression cassettes may be used to drive the expression of the gene. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the step of incorporating the nucleic acid construct of the present invention into the genome of the auxotrophic Listeria strain utilizes two-step allelic exchange. In another embodiment, the step of incorporating utilizes a phage-based integration vector. In another embodiment, the step of incorporating utilizes any other integration method known in the art.
In another embodiment, the step of incorporating the nucleic acid construct utilizes a prophage integration site of the auxotrophic Listeria strain. In another embodiment, the step of incorporating utilizes any other integration site known in the art. Each possibility represents a separate embodiment of the present invention.
Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a Listeria monocytogenes-Escherichia coli shuttle plasmid that is retained by complementation of mutant strains deficient in a metabolic gene both in vitro and in vivo. In one embodiment, the metabolic gene is a D-alanine racemase gene. In another embodiment, the metabolic gene is any other metabolic gene of known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of attenuating a bacterial vaccine strain, comprising the steps of (a) introducing into the strain a mutation in a gene encoding a metabolic enzyme; and (b) transfecting the strain with a plasmid containing a nucleotide sequence encoding the metabolic enzyme, thereby attenuating a bacterial vaccine strain.
In another embodiment, the present invention provides a method of attenuating a Listeria vaccine strain, comprising the steps of (a) introducing into the strain a mutation in a gene encoding a metabolic enzyme; (b) and transfecting the strain with an integration vector containing a nucleotide sequence encoding the metabolic enzyme, thereby attenuating a metabolic enzyme vaccine strain.
In one embodiment, a metabolic gene of methods and compositions of the present invention are expressed under an inducible promoter. In another embodiment, the promoter is a constitutive promoter. In another embodiment, the promoter is any other type of promoter known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a bacterial vaccine strain constructed by the method of the present invention.
In another embodiment, the present invention provides a Listeria vaccine strain constructed by the method of the present invention.
In various embodiments, the antigen of methods and compositions of the present invention includes but is not limited to antigens from the following infectious diseases, measles, mumps, rubella, poliomyelitis, hepatitis A, B (e.g., GenBank Accession No. E02707), and C (e.g., GenBank Accession No. E06890), as well as other hepatitis viruses, influenza, adenovirus (e.g., types 4 and 7), rabies (e.g., GenBank Accession No. M34678), yellow fever, Japanese encephalitis (e.g., GenBank Accession No. E07883), dengue (e.g., GenBank Accession No. M24444), hantavirus, and AIDS (e.g., GenBank Accession No. U18552). Bacterial and parasitic antigens will be derived from known causative agents responsible for diseases including, but not limited to, diphtheria, pertussis (e.g., GenBank Accession No. M35274), tetanus (e.g., GenBank Accession No. M64353), tuberculosis, bacterial and fungal pneumonias (e.g., Haemophilus influenzae, Pneumocystis carinii, etc.), cholera, typhoid, plague, shigellosis, salmonellosis (e.g., GenBank Accession No. L03833), Legionnaire's Disease, Lyme disease (e.g., GenBank Accession No. U59487), malaria (e.g., GenBank Accession No. X53832), hookworm, onchocerciasis (e.g., GenBank Accession No. M27807), schistosomiasis (e.g., GenBank Accession No. L08198), trypanosomiasis, leshmaniasis, giardiasis (e.g., GenBank Accession No. M33641), amoebiasis, filariasis (e.g., GenBank Accession No. J03266), borreliosis, and trichinosis.
In other embodiments, the antigen is one of the following tumor antigens: any of the various MAGEs (Melanoma-Associated Antigen E), including MAGE 1 (e.g., GenBank Accession No. M77481), MAGE 2 (e.g., GenBank Accession No. U03735), MAGE 3, MAGE 4, etc.; any of the various tyrosinases; mutant ras; mutant p53 (e.g., GenBank Accession No. X54156 and AA494311); and p97 melanoma antigen (e.g., GenBank Accession No. M12154). Other tumor-specific antigens include the Ras peptide and p53 peptide associated with advanced cancers, the HPV 16/18 and E6/E7 antigens associated with cervical cancers, MUC 1-KLH antigen associated with breast carcinoma (e.g., GenBank Accession No. J0365 1), CEA (carcinoembryonic antigen) associated with colorectal cancer (e.g., GenBank Accession No. X983 11), gp100 (e.g., GenBank Accession No. S73003) or MARTI antigens associated with melanoma, and the PSA antigen associated with prostate cancer (e.g., GenBank Accession No. X14810). The p53 gene sequence is known (See e.g., Harris et al. (1986) Mol. Cell. Biol., 6:4650-4656) and is deposited with GenBank under Accession No. M14694. Tumor antigens encompassed by the present invention further include, but are not limited to, Her-2/Neu (e.g. GenBank Accession Nos. M16789.1, M16790.1, M16791.1, M16792.1), NY-ESO-1 (e.g. GenBank Accession No. U87459), hTERT (aka telomerase) (GenBank Accession. Nos. NM003219 (variant 1), NM198255 (variant 2), NM 198253 (variant 3), and NM 198254 (variant 4), proteinase 3 (e.g. GenBank Accession Nos. M29142, M75154, M96839, X55668, NM 00277, M96628 and X56606) HPV E6 and E7 (e.g. GenBank Accession No. NC 001526) and WT-1 (e.g. GenBank Accession Nos. NM000378 (variant A), NM024424 (variant B), NM 024425 (variant C), and NM024426 (variant D)), Her-2/Neu (e.g. GenBank Accession Nos. M16789.1, M16790.1, M16791.1, M16792.1), NY-ESO-1 (e.g. GenBank Accession No. U87459), hTERT (aka telomerase) (GenBank Accession. Nos. NM003219 (variant 1), NM198255 (variant 2), NM 198253 (variant 3), and NM 198254 (variant 4), proteinase 3 (e.g. GenBank Accession Nos. M29142, M75154, M96839, X55668, NM 00277, M96628 and X56606) HPV E6 and E7 (e.g. GenBank Accession No. NC 001526) and WT-1 (e.g. GenBank Accession Nos. NM000378 (variant A), NM024424 (variant B), NM 024425 (variant C), and NM024426 (variant D)). Thus, the present invention can be used as immunotherapeutics for cancers including, but not limited to, cervical, breast, colorectal, prostate, lung cancers, and for melanomas.
Each of the above antigens represents a separate embodiment of the present invention.
In another embodiment, the antigen-encoding gene is expressed under the control of the Listeria p60 promoter. In another embodiment, the inlA (encodes internalin) promoter is used. In another embodiment, the hly promoter is used. In another embodiment, the ActA promoter is used. In another embodiment, the integrase gene is expressed under the control of any other gram positive promoter. In another embodiment, the antigen-encoding gene is expressed under the control of any other promoter that functions in Listeria. The skilled artisan will appreciate that other promoters or polycistronic expression cassettes may be used to drive the expression of the gene. Each possibility represents a separate embodiment of the present invention.
In another embodiment of methods and compositions of the present invention, a polypeptide encoded by a nucleic acid sequence thereof is a fusion protein comprising the heterologous antigen and an additional polypeptide. In one embodiment, the additional polypeptide is a non-hemolytic LLO protein or fragment thereof (Examples herein). In another embodiment, the additional polypeptide is a PEST sequence. In another embodiment, the additional polypeptide is an ActA protein or a fragment thereof. ActA proteins and fragments thereof augment antigen presentation and immunity in a similar fashion to LLO.
The additional polypeptide of methods and compositions of the present invention is, in another embodiment, a listeriolysin (LLO) peptide. In another embodiment, the additional polypeptide is an ActA peptide. In another embodiment, the additional polypeptide is a PEST-like sequence peptide. In another embodiment, the additional polypeptide is any other peptide capable of enhancing the immunogenicity of an antigen peptide. Each possibility represents a separate embodiment of the present invention.
The LLO protein utilized to construct vaccines of the present invention has, in another embodiment, the sequence:







MKKIMLVFITLILVSLPIAQQTEAKDASAFNKENSISSMAPPASPPASP


 


KTPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEY


 


IVVEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPV


 


KRDSLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQA


 


YPNVSAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQ


 


EEVISFKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYIS


 


SVAYGRQVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSF


 


KAVIYGGSAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFL


 


KDNELAVIKNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYD


 


PEGNEIVQHKNWSENNKSKLAHFTSSIYLPGNARNINVYAKECTGLAWE


 


WWRTVIDDRNLPLVKNRNISIWGTTLYPKYSNKVDNPIE






(GenBank Accession No. P13128; SEQ ID NO: 56; nucleic acid sequence is set forth in GenBank Accession No. X15127). The first 25 amino acids of the proprotein corresponding to this sequence are the signal sequence and are cleaved from LLO when it is secreted by the bacterium. Thus, in this embodiment, the full length active LLO protein is 504 residues long. In another embodiment, the LLO protein is a homologue of SEQ ID No: 56. In another embodiment, the LLO protein is a variant of SEQ ID No: 56. In another embodiment, the LLO protein is an isomer of SEQ ID No: 56. In another embodiment, the LLO protein is a fragment of SEQ ID No: 56. Each possibility represents a separate embodiment of the present invention.

In another embodiment, “LLO peptide” and “LLO fragment” refer to an N-terminal fragment of an LLO protein. In another embodiment, the terms refer to a full-length but non-hemolytic LLO protein. In another embodiment, the terms refer to a non-hemolytic protein containing a point mutation in cysteine 484 of sequence ID No: 56 or a corresponding residue thereof in a homologous LLO protein. In another embodiment, the LLO fragment contains about the first 400-441 AA of the 529 AA full-length LLO protein. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the N-terminal fragment of an LLO protein utilized in compositions and methods of the present invention has the sequence:







MKKIMLVFITLILVSLPIAQQTEAKDASAFNKENSISSVAPPASPPASP


 


KTPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEY


 


IVVEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPV


 


KRDSLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQA


 


YSNVSAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQ


 


EEVISFKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYIS


 


SVAYGRQVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSF


 


KAVIYGGSAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFL


 


KDNELAVIKNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYD


 


(SEQ ID NO: 57).






In another embodiment, the LLO fragment is a homologue of SEQ ID No: 57. In another embodiment, the LLO fragment is a variant of SEQ ID No: 57. In another embodiment, the LLO fragment is an isomer of SEQ ID No: 57. In another embodiment, the LLO fragment is a fragment of SEQ ID No: 57. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the LLO fragment has the sequence:







MKKIMLVFITLILVSLPIAQQTEAKDASAFNKENSISSVAPPASPPASPK


 


TPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEYIV


 


VEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPVKRD


 


SLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQAYSNV


 


SAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQEEVIS


 


FKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYISSVAYGR


 


QVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSFKAVIYGG


 


SAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFLKDNELAVI


 


KNNSEYIETTSKAYTD (SEQ ID NO: 58).






In another embodiment, the LLO fragment is a homologue of SEQ ID No: 58. In another embodiment, the LLO fragment is a variant of SEQ ID No: 58. In another embodiment, the LLO fragment is an isomer of SEQ ID No: 58. In another embodiment, the LLO fragment is a fragment of SEQ ID No: 58. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the LLO fragment is any other LLO fragment known in the art. Each possibility represents a separate embodiment of the present invention.
“ActA peptide” refers, in another embodiment, to a full-length ActA protein. In another embodiment, the term refers to an ActA fragment. Each possibility represents a separate embodiment of the present invention.
The ActA fragment of methods and compositions of the present invention is, in another embodiment, an N-terminal ActA fragment. In another embodiment, the fragment is any other type of ActA fragment known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the N-terminal fragment of an ActA protein has the sequence:







MRAMMVVFITANCITINPDIIFAATDSEDSSLNTDEWEEEKTEEQPSEVN


 


TGPRYETAREVSSRDIKELEKSNKVRNTNKADLIAMLKEKAEKGPNINNN


 


NSEQTENAAINEEASGADRPAIQVERRHPGLPSDSAAEIKKRRKAIASSD


 


SELESLTYPDKPTKVNKKKVAKESVADASESDLDSSMQSADESSPQPLKA


 


NQQPFFPKVFKKIKDAGKWVRDKIDENPEVKKAIVDKSAGLIDQLLTKKK


 


SEEVNASDFPPPPTDEELRLALPETPMLLGFNAPATSEPSSFEFPPPPTD


 


EELRLALPETPMLLGFNAPATSEPSSFEFPPPPTEDELEIIRETASSLDS


 


SFTRGDLASLRNAINRHSQNFSDFPPIPTEEELNGRGGRP (SEQ ID


 


 No: 59).






In another embodiment, the ActA fragment comprises SEQ ID No: 59. In another embodiment, the ActA fragment is a homologue of SEQ ID No: 59. In another embodiment, the ActA fragment is a variant of SEQ ID No: 59. In another embodiment, the ActA fragment is an isomer of SEQ ID No: 59. In another embodiment, the ActA fragment is a fragment of SEQ ID No: 59. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the N-terminal fragment of an ActA protein has the sequence:







MRAMMVVFITANCITINPDIIFAATDSEDSSLNTDEWEEEKTEEQPSEVN


 


TGPRYETAREVSSRDIKELEKSNKVRNTNKADLIAMLKEKAEKGPNINNN


 


(SEQ ID No: 60).






In another embodiment, the ActA fragment is a homologue of SEQ ID No: 60. In another embodiment, the ActA fragment is a variant of SEQ ID No: 60. In another embodiment, the ActA fragment is an isomer of SEQ ID No: 60. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the ActA fragment of methods and compositions of the present invention comprises a PEST-like sequence. In another embodiment, the PEST-like sequence contained in the ActA fragment is selected from SEQ ID No: 64-67. In another embodiment, the ActA fragment comprises at least 2 of the PEST-like sequences set forth in SEQ ID No: 64-67. In another embodiment, the ActA fragment comprises at least 3 of the PEST-like sequences set forth in SEQ ID No: 64-67. In another embodiment, the ActA fragment comprises the 4 PEST-like sequences set forth in SEQ ID No: 64-67. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the N-terminal ActA fragment is encoded by a nucleotide molecule having the sequence:







atgcgtgcgatgatggtggttttcattactgccaattgcattacgattaa


 


ccccgacataatatttgcagcgacagatagcgaacattctagtctaaaca


 


cagatgaatgggaagaagaaaaaacagaagagcaaccaagcgaggtaaat


 


acgggaccaagatacgaaactgcacgtgaagtaagttcacgtgatattaa


 


agaactagaaaaatcgaataaagtgagaaatacgaacaaagcagacctaa


 


tagcaatgttgaaagaaaaagcagaaaaaggtccaaatatcaataataac


 


aacagtgaacaaactgagaatgcggctataaatgaagaggcttcaggagc


 


cgaccgaccagctatacaagtggagcgtcgtcatccaggattgccatcgg


 


atagcgc agcggaaattaaaaaaagaaggaaagccatagcatcatcgga


 


tagtgagcttgaaagccttacttatccggataaaccaacaaaagtaaata


 


agaaaaaagtggcgaaagagtcagttgcggatgcttctgaaagtgactta


 


gattctagcatgcagtcagcagatgagtcttcaccacaacctttaaaagc


 


aaaccaacaaccatttttccctaaagtatttaaaaaaataaaagatgcgg


 


ggaaatgggtacgtgataaaatcgacgaaaatcctgaagtaaagaaagcg


 


attgttgataaaagtgcagggttaattgaccaattattaaccaaaaagaa


 


aagtgaagaggtaaatgcttcggacttcccgccaccacctacggatgaag


 


agttaagacttgctttgccagagacaccaatgcttcttggttttaatgct


 


cctgctacatcagaaccgagctcattcgaatttccaccaccacctacgga


 


tgaagagttaagacttgctttgccagagacgccaatgcttcttggtttta


 


atgctcctgctacatcggaaccgagctcgttcgaatttccaccgcctcca


 


acagaagatgaactagaaatcatccgggaaacagcatcctcgctagattc


 


tagttttacaagaggggatttagctagtttgagaaatgctattaatcgcc


 


atagtcaaaatttctctgatttcccaccaatcccaacagaagaagagttg


 


aacgggagaggcggtagacca (SEQ No: 61).






In another embodiment, the ActA fragment is encoded by a nucleotide molecule that comprises SEQ ID No: 61. In another embodiment, the ActA fragment is encoded by a nucleotide molecule that is a homologue of SEQ ID No: 61. In another embodiment, the ActA fragment is encoded by a nucleotide molecule that is a variant of SEQ ID No: 61. In another embodiment, the ActA fragment is encoded by a nucleotide molecule that is an isomer of SEQ ID No: 61. In another embodiment, the ActA fragment is encoded by a nucleotide molecule that is a fragment of SEQ ID No: 61. Each possibility represents a separate embodiment of the present invention.

In another embodiment, a recombinant nucleotide of the present invention comprises any other sequence that encodes a fragment of an ActA protein. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the ActA fragment is any other ActA fragment known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment of methods and compositions of the present invention, aPEST-like AA sequence is fused to the antigen peptide. In another embodiment, the PEST-like AA sequence has a sequence selected from SEQ ID No: 62-70. In another embodiment, the PEST-like sequence is any other PEST-like sequence known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the PEST-like AA sequence is








KENSISSMAPPASPPASPKTPIEKKHADEIDK
SEQ ID NO: 62).






In another embodiment, the PEST-like sequence is











KENSISSMAPPASPPASPK
(SEQ ID No: 63).






In another embodiment, fusion of an antigen peptide to any LLO sequence that includes the 1 of the PEST-like AA sequences enumerated herein is efficacious for enhancing cell-mediated immunity against an antigen.

The present invention also provides methods for enhancing cell mediated and anti-tumor immunity and compositions with enhanced immunogenicity which comprise a PEST-like amino acid sequence derived from a prokaryotic organism fused to an antigen. In another embodiment, the PEST-like sequence is embedded within an antigen. In another embodiment, the PEST-like sequence is fused to either the amino terminus of the antigen. In another embodiment, the PEST-like sequence is fused to the carboxy terminus. As demonstrated herein, fusion of an antigen to the PEST-like sequence of LM enhanced cell mediated and anti-tumor immunity of the antigen. Thus, fusion of an antigen to other PEST-like sequences derived from other prokaryotic organisms will also enhance immunogenicity of an antigen. PEST-like sequence of other prokaryotic organism can be identified routinely in accordance with methods such as described by, for example Rechsteiner and Rogers (1996, Trends Biochem. Sci. 21:267-271) for LM. In another embodiment, PEST-like AA sequences from other prokaryotic organisms are identified based by this method. In another embodiment, the PEST-like AA sequence is from another Listeria species. For example, the LM protein ActA contains 4 such sequences.
In another embodiment, the PEST-like AA sequence is a PEST-like sequence from a Listeria ActA protein. In another embodiment, the PEST-like sequence is KTEEQPSEVNTGPR (SEQ ID NO: 64), KASVTDTSEGDLDSSMQSADESTPQPLK (SEQ ID NO: 65), KNEEVNASDFPPPPTDEELR (SEQ ID NO: 66), or RGGIPTSEEFSSLNSGDFTDDENSETTEEEIDR (SEQ ID NO: 67). In another embodiment, the PEST-like sequence is from Listeria seeligeri cytolysin, encoded by the lso gene. In another embodiment, the PEST-like sequence is RSEVTISPAETPESPPATP (SEQ ID NO: 68). In another embodiment, the PEST-like sequence is from Streptolysin O protein of Streptococcus sp. In another embodiment, the PEST-like sequence is from Streptococcus pyogenes Streptolysin O, e.g. KQNTASTETTTTNEQPK (SEQ ID NO: 69) at AA 35-51. In another embodiment, the PEST-like sequence is from Streptococcus equisimilis Streptolysin O, e.g. KQNTANTETTTTNEQPK (SEQ ID NO: 70) at AA 38-54. In another embodiment, the PEST-like sequence has a sequence selected from SEQ ID No: 62-70. In another embodiment, the PEST-like sequence has a sequence selected from SEQ ID No: 64-70. In another embodiment, the PEST-like sequence is another PEST-like AA sequence derived from a prokaryotic organism.
PEST-like sequences of other prokaryotic organism are identified, in another embodiment, in accordance with methods such as described by, for example Rechsteiner and Rogers (1996, Trends Biochem. Sci. 21:267-271) for LM. Alternatively, PEST-like AA sequences from other prokaryotic organisms can also be identified based by this method. Other prokaryotic organisms wherein PEST-like AA sequences would be expected to include, but are not limited to, other Listeria species. In another embodiment, the PEST-like sequence is embedded within the antigenic protein. Thus, in another embodiment, “fusion” refers to an antigenic protein comprising both the antigen peptide and the PEST-like amino acid sequence either linked at one end of the antigen peptide or embedded within the antigen peptide.
In another embodiment, the PEST-like sequence is identified using the PEST-find program. In another embodiment, a PEST-like sequence is defined as a hydrophilic stretch of at least 12 AA in length with a high local concentration of proline (P), aspartate (D), glutamate (E), serine (S), and/or threonine(T) residues. In another embodiment, a PEST-like sequence contains no positively charged AA, namely arginine (R), histidine (H) and lysine (K).
In another embodiment, identification of PEST motifs is achieved by an initial scan for positively charged AA R, H, and K within the specified protein sequence. All AA between the positively charged flanks are counted and only those motifs are considered further, which contain a number of AA equal to or higher than the window-size parameter. In another embodiment, a PEST-like sequence must contain at least 1 P, 1 D or E, and at least 1 S or T.
In another embodiment, the quality of a PEST motif is refined by means of a scoring parameter based on the local enrichment of critical AA as well as the motifs hydrophobicity. Enrichment of D, E, P, S and T is expressed in mass percent (w/w) and corrected for 1 equivalent of D or E, 1 of P and 1 of S or T. In another embodiment, calculation of hydrophobicity follows in principle the method of J. Kyte and R. F. Doolittle (Kyte, J and Doolittle, R F. J. Mol. Biol. 157, 105 (1982). For simplified calculations, Kyte-Doolittle hydropathy indices, which originally ranged from −4.5 for arginine to +4.5 for isoleucine, are converted to positive integers, using the following linear transformation, which yielded values from 0 for arginine to 90 for isoleucine.

Hydropathy index=10*Kyte-Doolittle hydropathy index+45

In another embodiment, a potential PEST motif's hydrophobicity is calculated as the sum over the products of mole percent and hydrophobicity index for each AA species. The desired PEST score is obtained as combination of local enrichment term and hydrophobicity term as expressed by the following equation:

PEST score=0.55*DEPST−0.5*hydrophobicity index.

In another embodiment, “PEST-like sequence” or “PEST-like sequence peptide” refers to a peptide having a score of at least +5, using the above algorithm. In another embodiment, the term refers to a peptide having a score of at least 6. In another embodiment, the peptide has a score of at least 7. In another embodiment, the score is at least 8. In another embodiment, the score is at least 9. In another embodiment, the score is at least 10. In another embodiment, the score is at least 11. In another embodiment, the score is at least 12. In another embodiment, the score is at least 13. In another embodiment, the score is at least 14. In another embodiment, the score is at least 15. In another embodiment, the score is at least 16. In another embodiment, the score is at least 17. In another embodiment, the score is at least 18. In another embodiment, the score is at least 19. In another embodiment, the score is at least 20. In another embodiment, the score is at least 21. In another embodiment, the score is at least 22. In another embodiment, the score is at least 22. In another embodiment, the score is at least 24. In another embodiment, the score is at least 24. In another embodiment, the score is at least 25. In another embodiment, the score is at least 26. In another embodiment, the score is at least 27. In another embodiment, the score is at least 28. In another embodiment, the score is at least 29. In another embodiment, the score is at least 30. In another embodiment, the score is at least 32. In another embodiment, the score is at least 35. In another embodiment, the score is at least 38. In another embodiment, the score is at least 40. In another embodiment, the score is at least 45. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the PEST-like sequence is identified using any other method or algorithm known in the art, e.g the CaSPredictor (Garay-Malpartida H M, Occhiucci J M, Alves J, Belizario J. E. Bioinformatics. 2005 June; 21 Suppl 1:i69-76). In another embodiment, the following method is used:
A PEST index is calculated for each stretch of appropriate length (e.g. a 30-35 AA stretch) by assigning a value of 1 to the AA Ser, Thr, Pro, Glu, Asp, Asn, or Gln. The coefficient value (CV) for each of the PEST residue is 1 and for each of the other AA (non-PEST) is 0.
Each method for identifying a PEST-like sequence represents a separate embodiment of the present invention.
“Fusion to a PEST-like sequence” refers, in another embodiment, to fusion to a protein fragment comprising a PEST-like sequence. In another embodiment, the term includes cases wherein the protein fragment comprises surrounding sequence other than the PEST-like sequence. In another embodiment, the protein fragment consists of the PEST-like sequence. Each possibility represents a separate embodiment of the present invention.
In one embodiment, a vector of the present invention provides the benefits of a Listeria vaccine vector without the risk of increasing antibiotic resistance in bacterial organisms.
In another embodiment, an advantage of vaccine strains of the present invention is that the recombinant nucleic acid molecules or plasmids contained therein are not likely to be retained upon potential transfer to other bacteria in the gut. In another embodiment, the advantage is that the nucleic acid molecules or plasmids do not confer an evolutionary advantage on normal cells. In another embodiment, the advantage is that the nucleic acid molecules or plasmids do not contain active retention systems such as partition sequences. Thus, outside their deficient host cells, the nucleic acid molecules or plasmids will most likely be diluted out of the population and ultimately be eliminated over time. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a kit comprising an antibiotic resistance free bacterial strain of the present invention, a pharmaceutically-acceptable carrier, an applicator, and an instructional material for use thereof.
In another embodiment, the present invention provides a kit comprising an antibiotic resistance free Listeria strain of the present invention, an applicator, and an instructional material for use thereof.
“Alanine racemase” refers, in one embodiment, to an enzyme that converts the L-isomer of the amino acid alanine into its D-isomer. In another embodiment, such enzymes are known by the EC number 5.1.1.1.
“Amino acid metabolism enzyme” refers, in one embodiment, to a peptide or protein that has a functional role in converting an amino acid from one form to another, such as, but not limited to, altering the stereochemistry of the amino acid, hydrolyzing or adding groups to an amino acid, cleaving amino acids, and the like. Each possibility represents a separate embodiment of the present invention.
The term “auxotrophic bacteria” refers, in one embodiment, to a bacteria strain that is not capable of growing or replicating without supplementation of a factor that will permit such growth or replication. Each factor represents a separate embodiment of the present invention.
“Fusion protein” refers, in one embodiment, to a protein that comprises two or more proteins linked together. In one embodiment, the proteins are linked by peptide bonds. In another embodiment, the proteins are linked by other chemical bonds. In another embodiment, the proteins are linked by with one or more amino acids between the two or more proteins, which may be referred to as a spacer. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the tumor targeted by methods and compositions of the present invention is a breast cancer. In another embodiment, the cancer is a melanoma. In another embodiment, the cancer is a glioma tumor. In another embodiment, the cancer is an ovarian neoplasm. In another embodiment, the cancer is a mammary carcinoma. In another embodiment, the cancer is an ependymoma.
In another embodiment, the cancer is a melanoma. In another embodiment, the cancer is a sarcoma. In another embodiment, the cancer is a carcinoma. In another embodiment, the cancer is a lymphoma. In another embodiment, the cancer is a leukemia. In another embodiment, the cancer is mesothelioma. In another embodiment, the cancer is a glioma. In another embodiment, the cancer is a germ cell tumor. In another embodiment, the cancer is a choriocarcinoma. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the cancer is pancreatic cancer. In another embodiment, the cancer is ovarian cancer. In another embodiment, the cancer is gastric cancer. In another embodiment, the cancer is a carcinomatous lesion of the pancreas. In another embodiment, the cancer is pulmonary adenocarcinoma. In another embodiment, the cancer is colorectal adenocarcinoma. In another embodiment, the cancer is pulmonary squamous adenocarcinoma. In another embodiment, the cancer is gastric adenocarcinoma. In another embodiment, the cancer is an ovarian surface epithelial neoplasm (e.g. a benign, proliferative or malignant variety thereof). In another embodiment, the cancer is an oral squamous cell carcinoma. In another embodiment, the cancer is non small-cell lung carcinoma. In another embodiment, the cancer is an endometrial carcinoma. In another embodiment, the cancer is a bladder cancer. In another embodiment, the cancer is a head and neck cancer. In another embodiment, the cancer is a prostate carcinoma.
In another embodiment, the cancer is an acute myelogenous leukemia (AML). In another embodiment, the cancer is a myelodysplastic syndrome (MDS). In another embodiment, the cancer is a non-small cell lung cancer (NSCLC). In another embodiment, the cancer is a Wilms' tumor. In another embodiment, the cancer is a leukemia. In another embodiment, the cancer is a lymphoma. In another embodiment, the cancer is a desmoplastic small round cell tumor. In another embodiment, the cancer is a mesothelioma (e.g. malignant mesothelioma). In another embodiment, the cancer is a gastric cancer. In another embodiment, the cancer is a colon cancer. In another embodiment, the cancer is a lung cancer. In another embodiment, the cancer is a breast cancer. In another embodiment, the cancer is a germ cell tumor. In another embodiment, the cancer is an ovarian cancer. In another embodiment, the cancer is a uterine cancer. In another embodiment, the cancer is a thyroid cancer. In another embodiment, the cancer is a hepatocellular carcinoma. In another embodiment, the cancer is a thyroid cancer. In another embodiment, the cancer is a liver cancer. In another embodiment, the cancer is a renal cancer. In another embodiment, the cancer is a kaposis. In another embodiment, the cancer is a sarcoma. In another embodiment, the cancer is another carcinoma or sarcoma. Each possibility represents a separate embodiment of the present invention.
In other embodiments, the antigen of methods and compositions of the present invention is associated with one of the above cancers.
In another embodiment, the cancer is any other cancer known in the art. Each type of cancer represents a separate embodiment of the present invention.
In other embodiments, the antigen of methods and compositions of the present invention is derived from a fungal pathogen, bacteria, parasite, helminth, or viruses. In other embodiments, the antigen is selected from tetanus toxoid, hemagglutinin molecules from influenza virus, diphtheria toxoid, HIV gp120, HIV gag protein, IgA protease, insulin peptide B, Spongospora subterranea antigen, vibriose antigens, Salmonella antigens, pneumococcus antigens, respiratory syncytial virus antigens, Haemophilus influenza outer membrane proteins, Helicobacter pylori urease, Neisseria meningitidis pilins, N. gonorrhoeae pilins, or human papilloma virus antigens E1 and E2 from type HPV-16, -18, -31, -33, -35 or -45 human papilloma viruses.
In other embodiments, the antigen is associated with one of the following diseases; cholera, diphtheria, Haemophilus, hepatitis A, hepatitis B, influenza, measles, meningitis, mumps, pertussis, small pox, pneumococcal pneumonia, polio, rabies, rubella, tetanus, tuberculosis, typhoid, Varicella-zoster, whooping cough3 yellow fever, the immunogens and antigens from Addison's disease, allergies, anaphylaxis, Bruton's syndrome, cancer, including solid and blood borne tumors, eczema, Hashimoto's thyroiditis, polymyositis, dermatomyositis, type 1 diabetes mellitus, acquired immune deficiency syndrome, transplant rejection, such as kidney, heart, pancreas, lung, bone, and liver transplants, Graves' disease, polyendocrine autoimmune disease, hepatitis, microscopic polyarteritis, polyarteritis nodosa, pemphigus, primary biliary cirrhosis, pernicious anemia, coeliac disease, antibody-mediated nephritis, glomerulonephritis, rheumatic diseases, systemic lupus erthematosus, rheumatoid arthritis, seronegative spondylarthritides, rhinitis, sjogren's syndrome, systemic sclerosis, sclerosing cholangitis, Wegener's granulomatosis, dermatitis herpetiformis, psoriasis, vitiligo, multiple sclerosis, encephalomyelitis, Guillain-Barre syndrome, myasthenia gravis, Lambert-Eaton syndrome, sclera, episclera, uveitis, chronic mucocutaneous candidiasis, urticaria, transient hypogammaglobulinemia of infancy, myeloma, X-linked hyper IgM syndrome, Wiskott-Aldrich syndrome, ataxia telangiectasia, autoimmune hemolytic anemia, autoimmune thrombocytopenia, autoimmune neutropenia, Waldenstrom's macroglobulinemia, amyloidosis, chronic lymphocytic leukemia, non-Hodgkin's lymphoma, malarial circumsporozite protein, microbial antigens, viral antigens, autoantigens, and lesteriosis.
In another embodiment, the infectious disease of targeted by a method of the present invention is one of the above diseases.
In another embodiment, a sequence of the present invention is homologous to a sequence disclosed herein. The terms “homology,” “homologous,” etc, when in reference to any protein, peptide, or nucleotide sequence, refer, in one embodiment, to a percentage of amino acid residues in the candidate sequence that are identical with the residues of a corresponding native polypeptide, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent homology In another embodiment, conservative substitutions are not considered as part of the sequence identity. In another embodiment, conservative substitutions are considered. Methods and computer programs for the alignment are well known in the art.
Homology is, in another embodiment, determined by computer algorithm for sequence alignment, by methods well described in the art. For example, computer algorithm analysis of nucleic acid sequence homology can include the utilization of any number of software packages available, such as, for example, the BLAST, DOMAIN, BEAUTY (BLAST Enhanced Alignment Utility), GENPEPT and TREMBL packages.
In another embodiment, “homology” refers to identity to a sequence selected from SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 70%. In another embodiment, “homology” refers to identity to a sequence selected from SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 72%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 75%. In another embodiment, “homology” refers to identity to a sequence selected from SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 78%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 80%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 82%. In another embodiment, “homology” refers to identity to a sequence selected from SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 83%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 85%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 87%. In another embodiment, “homology” refers to identity to a sequence selected from SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 88%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 90%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, 43 and 42-70 of greater than 92%. In another embodiment, “homology” refers to identity to a sequence selected from SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 93%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 95%. In another embodiment, “homology” refers to identity to a sequence selected from SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 96%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 97%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 98%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, and 42-70 of greater than 99%. In another embodiment, “homology” refers to identity to one of SEQ ID No: 19, 26-27, 32, and 42-70 of 100%. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the terms “gene” and “recombinant gene” refer to nucleic acid molecules comprising an open reading frame encoding a polypeptide of the invention. Such natural allelic variations can typically result in 1-5% variance in the nucleotide sequence of a given gene. Alternative alleles can be identified by sequencing the gene of interest in a number of different individuals or organisms. This can be readily carried out by using hybridization probes to identify the same genetic locus in a variety of individuals or organisms. Any and all such nucleotide variations and resulting amino acid polymorphisms or variations that are the result of natural allelic variation and that do not alter the functional activity are intended to be within the scope of the invention.
Describing two polynucleotides as “operably linked” means, in another embodiment, that a single-stranded or double-stranded nucleic acid moiety comprises the two polynucleotides arranged within the nucleic acid moiety in such a manner that at least one of the two polynucleotides is able to exert a physiological effect by which it is characterized upon the other. By way of example, a promoter operably linked to the coding region of a gene is able to promote transcription of the coding region.
“Promoter/regulatory sequence” refers, in one embodiment, to a nucleic acid sequence which is required for, or enhances, expression of a gene product operably linked to the promoter/regulatory sequence. In another embodiment, this sequence is the core promoter sequence. In another embodiment, this sequence also includes an enhancer sequence and other regulatory elements that are required for expression of the gene product.
Listeria Vaccine Strains
The Listeria strain of methods and compositions of the present invention is, in another embodiment, Listeria monocytogenes (ATCC No. 15313). In another embodiment, the Listeria strain is a recombinant Listeria seeligeri strain. In another embodiment, the Listeria strain is a recombinant Listeria grayi strain. In another embodiment, the Listeria strain is a recombinant Listeria ivanovii strain. In another embodiment, the Listeria strain is a recombinant Listeria murrayi strain. In another embodiment, the Listeria strain is a recombinant Listeria welshimeri strain. In another embodiment, the Listeria strain is a recombinant strain of any other Listeria species known in the art.
In other embodiments, attenuated Listeria strains, such as LM delta-acta mutant (Brundage et al, 1993, Proc. Natl. Acad. Sci., USA, 90:11890-11894), or L. monocytogenes delta-plcA (Camilli et al, 1991, J. Exp. Med., 173:751-754) are used in the present invention. In another embodiment, new attenuated Listeria strains are constructed by introducing one or more attenuating mutations, as will be understood by one of average skill in the art when equipped with the disclosure herein. Examples of such strains include, but are not limited to Listeria strains auxotrophic for aromatic amino acids (Alexander et al, 1993, Infection and Immunity 61:2245-2248) and mutant for the formation of lipoteichoic acids (Abachin et al, 2002, Mol. Microbiol. 43:1-14).
In another embodiment, a recombinant Listeria strain of the present invention has been passaged through an animal host. In another embodiment, the passaging maximizes efficacy of the strain as a vaccine vector. In another embodiment, the passaging stabilizes the immunogenicity of the Listeria strain. In another embodiment, the passaging stabilizes the virulence of the Listeria strain. In another embodiment, the passaging increases the immunogenicity of the Listeria strain. In another embodiment, the passaging increases the virulence of the Listeria strain. In another embodiment, the passaging removes unstable sub-strains of the Listeria strain. In another embodiment, the passaging reduces the prevalence of unstable sub-strains of the Listeria strain. In another embodiment, the Listeria strain contains a genomic insertion of the gene encoding the antigen-containing recombinant peptide. In another embodiment, the Listeria strain carries a plasmid comprising the gene encoding the antigen-containing recombinant peptide. In another embodiment, the passaging is performed as described herein (e.g. in Example 1). In another embodiment, the passaging is performed by any other method known in the art. Each possibility represents a separate embodiment of the present invention.
The skilled artisan, when equipped with the present disclosure and the methods herein, will readily understand that different transcriptional promoters, terminators, carrier vectors or specific gene sequences (e.g. those in commercially available cloning vectors) can be used successfully in methods and compostions of the present invention. As is contemplated in the present invention, these functionalities are provided in, for example, the commercially available vectors known as the pUC series. In another embodiment, non-essential DNA sequences (e.g. antibiotic resistance genes) are removed.
In another embodiment, a commercially available plasmid is used in the present invention. Such plasmids are available from a variety of sources, for example, Invitrogen (La Jolla, Calif.), Stratagene (La Jolla, Calif.), Clontech (Palo Alto, Calif.), or can be constructed using methods well known in the art. Another embodiment is a plasmid such as pCR2.1 (Invitrogen, La Jolla, Calif.), which is a prokaryotic expression vector with a prokaryotic origin of replication and promoter/regulatory elements to facilitate expression in a prokaryotic organism. In another embodiment, extraneous nucleotide sequences are removed to decrease the size of the plasmid and increase the size of the cassette that can be placed therein.
Such methods are well known in the art, and are described in, for example, Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York) and Ausubei et al. (1997, Current Protocols in Molecular Biology, Green & Wiley, New York).
Antibiotic resistance genes are used in the conventional selection and cloning processes commonly employed in molecular biology and vaccine preparation. Antibiotic resistance genes contemplated in the present invention include, but are not limited to, gene products that confer resistance to ampicillin, penicillin, methicillin, I streptomycin, erythromycin, kanamycin, tetracycline, cloramphenicol (CAT), neomycin, hygromycin, gentamicin and others well known in the art. Each gene represents a separate embodiment of the present invention.
Methods for transforming bacteria are well known in the art, and include calcium-chloride competent cell-based methods, electroporation methods, bacteriophage-mediated transduction, chemical, and physical transformation techniques (de Boer et al, 1989, Cell 56:641-649; Miller et al, 1995, FASEB J., 9:190-199; Sambrook et al. 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York; Ausubel et al., 1997, Current Protocols in Molecular Biology, John Wiley & Sons, New York; Gerhardt et al., eds., 1994, Methods for General and Molecular Bacteriology, American Society for Microbiology, Washington, D.C.; Miller, 1992, A Short Course in Bacterial Genetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.) In another embodiment, the Listeria vaccine strain of the present invention is transformed by electroporation. Each method represents a separate embodiment of the present invention.
Plasmids and other expression vectors useful in the present invention are described elsewhere herein, and can include such features as a promoter/regulatory sequence, an origin of replication for gram negative and gram positive bacteria, an isolated nucleic acid encoding a fusion protein and an isolated nucleic acid encoding an amino acid metabolism gene. Further, an isolated nucleic acid encoding a fusion protein and an amino acid metabolism gene will have a promoter suitable for driving expression of such an isolated nucleic acid. Promoters useful for driving expression in a bacterial system are well known in the art, and include bacteriophage lambda, the bla promoter of the beta-lactamase gene of pBR322, and the CAT promoter of the chloramphenicol acetyl transferase gene of pBR325. Further examples of prokaryotic promoters include the major right and left promoters of bacteriophage lambda (PL and PR), the trp, recA, lacZ, lad, and gal promoters of E. coli, the alpha-amylase (Ulmanen et al, 1985. J. Bacteriol. 162:176-182) and the S28-specific promoters of B. subtilis (Gilman et al, 1984 Gene 32:11-20), the promoters of the bacteriophages of Bacillus (Gryczan, 1982, In: The Molecular Biology of the Bacilli, Academic Press, Inc., New York), and Streptomyces promoters (Ward et al, 1986, Mol. Gen. Genet. 203:468-478). Additional prokaryotic promoters contemplated in the present invention are reviewed in, for example, Glick (1987, J. Ind. Microbiol. 1:277-282); Cenatiempo, (1986, Biochimie, 68:505-516); and Gottesman, (1984, Ann. Rev. Genet. 18:415-442). Further examples of promoter/regulatory elements contemplated in the present invention include, but are not limited to the Listerial prfA promoter, the Listerial hly promoter, the Listerial p60 promoter and the Listerial ActA promoter (GenBank Acc. No. NC—003210) or fragments thereof.
In another embodiment, a plasmid of methods and compositions of the present invention comprises a gene encoding a fusion protein. In another embodiment, subsequences are cloned and the appropriate subsequences cleaved using appropriate restriction enzymes. The fragments are then, in another embodiment, ligated to produce the desired DNA sequence. In another embodiment, DNA encoding the antigen is produced using DNA amplification methods, for example polymerase chain reaction (PCR). First, the segments of the native DNA on either side of the new terminus are amplified separately. The 5′ end of the one amplified sequence encodes the peptide linker, while the 3′ end of the other amplified sequence also encodes the peptide linker. Since the 5′ end of the first fragment is complementary to the 3′ end of the second fragment, the two fragments (after partial purification, e.g. on LMP agarose) can be used as an overlapping template in a third PCR reaction. The amplified sequence will contain codons, the segment on the carboxy side of the opening site (now forming the amino sequence), the linker, and the sequence on the amino side of the opening site (now forming the carboxyl sequence). The antigen is ligated into a plasmid. Each method represents a separate embodiment of the present invention.
In another embodiment, the present invention further comprises a phage based chromosomal integration system for clinical applications. A host strain that is auxotrophic for essential enzymes, including, but not limited to, d-alanine racemase will be used, for example Lmdal(−)dat(−). In another embodiment, in order to avoid a “phage curing step,” a phage integration system based on PSA is used (Lauer, et al., 2002 J Bacteriol, 184:4177-4186). This requires, in another embodiment, continuous selection by antibiotics to maintain the integrated gene. Thus, in another embodiment, the current invention enables the establishment of a phage based chromosomal integration system that does not require selection with antibiotics. Instead, an auxotrophic host strain will be complemented.
The recombinant proteins of the present invention are synthesized, in another embodiment, using recombinant DNA methodology. This involves, in one embodiment, creating a DNA sequence that encodes the fusion protein, placing the DNA in an expression cassette, such as the plasmid of the present invention, under the control of a particular promoter/regulatory element, and expressing the protein. DNA encoding the fusion protein (e.g. non-hemolytic LLO/antigen) of the present invention is prepared, in another embodiment, by any suitable method, including, for example, cloning and restriction of appropriate sequences or direct chemical synthesis by methods such as the phosphotriester method of Narang et al. (1979, Meth. Enzymol. 68: 90-99); the phosphodiester method of Brown et al. (1979, Meth. Enzymol 68: 109-151); the diethylphosphoramidite method of Beaucage et al. (1981, Tetra. Lett., 22: 1859-1862); and the solid support method of U.S. Pat. No. 4,458,066.
In another embodiment, chemical synthesis is used to produce a single stranded oligonucleotide. This single stranded oligonucleotide is converted, in various embodiments, into double stranded DNA by hybridization with a complementary sequence, or by polymerization with a DNA polymerase using the single strand as a template. One of skill in the art would recognize that while chemical synthesis of DNA is limited to sequences of about 100 bases, longer sequences can be obtained by the ligation of shorter sequences. In another embodiment, subsequences are cloned and the appropriate subsequences cleaved using appropriate restriction enzymes. The fragments are then be ligated to produce the desired DNA sequence.
In another embodiment, DNA encoding the fusion protein or the recombinant protein of the present invention is cloned using DNA amplification methods such as polymerase chain reaction (PCR). Thus, the gene for non-hemolytic LLO is PCR amplified, using a sense primer comprising a suitable restriction site and an antisense primer comprising another restriction site, e.g. a non-identical restriction site to facilitate cloning. The same is repeated for the isolated nucleic acid encoding an antigen. Ligation of the non-hemolytic LLO and antigen sequences and insertion into a plasmid or vector produces a vector encoding non-hemolytic LLO joined to a terminus of the antigen. The two molecules are joined either directly or by a short spacer introduced by the restriction site.
In another embodiment, the molecules are separated by a peptide spacer consisting of one or more amino acids, generally the spacer will have no specific biological activity other than to join the proteins or to preserve some minimum distance or other spatial relationship between them. In another embodiment, the constituent AA of the spacer are selected to influence some property of the molecule such as the folding, net charge, or hydrophobicity. In another embodiment, the nucleic acid sequences encoding the fusion or recombinant proteins are transformed into a variety of host cells, including E. coli, other bacterial hosts, such as Listeria, yeast, and various higher eukaryotic cells such as the COS, CHO and HeLa cells lines and myeloma cell lines. The recombinant fusion protein gene will be operably linked to appropriate expression control sequences for each host. Promoter/regulatory sequences are described in detail elsewhere herein. In another embodiment, the plasmid further comprises additional promoter regulatory elements, as well as a ribosome binding site and a transcription termination signal. For eukaryotic cells, the control sequences will include a promoter and an enhancer derived from e.g. immunoglobulin genes, SV40, cytomegalovirus, etc., and a polyadenylation sequence. In another embodiment, the sequences include splice donor and acceptor sequences.
The antigens of these and other diseases are well known in the art, and the skilled artisan, when equipped with the present disclosure and the methods and techniques described herein will readily be able to construct a fusion protein comprising a non-hemolytic LLO protein and an antigen for use in the present invention. In another embodiment, in order to select for an auxotrophic bacteria comprising the plasmid, transformed auxotrophic bacteria are grown on a media that will select for expression of the amino acid metabolism gene. In another embodiment, a bacteria auxotrophic for D-glutamic acid synthesis is transformed with a plasmid comprising a gene for D-glutamic acid synthesis, and the auxotrophic bacteria will grow in the absence of D-glutamic acid, whereas auxotrophic bacteria that have not been transformed with the plasmid, or are not expressing the plasmid encoding a protein for D-glutamic acid synthesis, will not grow. In another embodiment, a bacterium auxotrophic for D-alanine synthesis will grow in the absence of D-alanine when transformed and expressing the plasmid of the present invention if the plasmid comprises an isolated nucleic acid encoding an amino acid metabolism enzyme for D-alanine synthesis. Such methods for making appropriate media comprising or lacking necessary growth factors, supplements, amino acids, vitamins, antibiotics, and the like are well known in the art, and are available commercially (Becton-Dickinson, Franklin Lakes, N.J.). Each method represents a separate embodiment of the present invention.
In another embodiment, once the auxotrophic bacteria comprising the plasmid of the present invention have been selected on appropriate media, the bacteria are propagated in the presence of a selective pressure. Such propagation comprises growing the bacteria in media without the auxotrophic factor. The presence of the plasmid expressing an amino acid metabolism enzyme in the auxotrophic bacteria ensures that the plasmid will replicate along with the bacteria, thus continually selecting for bacteria harboring the plasmid. The skilled artisan, when equipped with the present disclosure and methods herein will be readily able to scale-up the production of the Listeria vaccine vector by adjusting the volume of the media in which the auxotrophic bacteria comprising the plasmid are growing.
The skilled artisan will appreciate that, in another embodiment, other auxotroph strains and complementation systems may be adopted for the use with this invention.
Experimental Details Section
EXAMPLE 1
A Plasmid Containing an Amino Acid Metabolism Enzyme Instead of an Antibiotic Resistance Gene is Retained in E. Coli and LM Both In Vitro and In Vivo
Materials and Experimental Methods
Bacterial Strains, Transformation and Selection
E. coli strain MB2159 was used for transformations, using standard protocols. Bacterial cells were prepared for electroporation by washing with H2O.
E. coli strain MB2159 (Strych U et al, FEMS Microbiol Lett. 2001 Mar. 15; 196(2):93-8) is an air (−)/dadX (−) deficient mutant that is not able to synthesize D-alanine racemase. Listeria strain Lm dal(−)/dat(−) (Lmdd) similarly is not able to synthesize D-alanine racemase due to partial deletions of the dal and the dat genes.
Construction of Lmdd
The dal gene was initially inactivated by means of a double-allelic exchange between the chromosomal gene and the temperature-sensitive shuttle plasmid pKSV7 (Smith K et al, Biochimie. 1992 July-August;74(7-8):705-11) carrying an erythromycin resistance gene between a 450-bp fragment from the 5′ end of the original 850-bp dal gene PCR product and a 450-bp fragment from the 3′ end of the dal gene PCR product. Subsequently, a dal deletion mutant covering 82% of the gene was constructed by a similar exchange reaction with pKSV7 carrying homology regions from the 5′ and 3′ ends of the intact gene (including sequences upstream and downstream of the gene) surrounding the desired deletion. PCR analysis was used to confirm the structure of this chromosomal deletion.
The chromosomal dat gene was inactivated by a similar allelic exchange reaction. pKSV7 was modified to carry 450-bp fragments derived by PCR from both the 5′ and 3′ ends of the intact dat gene (including sequences upstream and downstream of the gene). These two fragments were ligated by appropriate PCR. Exchange of this construct into the chromosome resulted in the deletion of 30% of the central bases of the dat gene, which was confirmed by PCR analysis.
Bacterial Culture and In Vivo Passaging of Listeria 
E. coli were cultured following standard methods. Listeria were grown at 37° C., 250 rpm shaking in LB media (Difco, Detroit, Mich.). +50 μg/ml streptomycin, and harvested during exponential growth phase. For Lm-LLOE7, 37 μg/ml chloramphenicol was added to the media. For growth kinetics determinations, bacteria were grown for 16 hours in 10 ml of LB+ antibiotics. The OD600 nm was measured and culture densities were normalized between the strains. The culture was diluted 1:50 into LB+ suitable antibiotics and D-alanine if applicable.
Passaging of Lm in Mice
1×108 CFU were injected intraperitoneally (ip.) into C57BL/6 mice. On day three, spleens were isolated and homogenized in PBS. An aliquot of the spleen suspension was plated on LB plates with antibiotics as applicable. Several colonies were expanded and mixed to establish an injection stock.
Construction of Antibiotic Resistance Factor Free Plasmid pTV3
Construction of p60-dal cassette. The first step in the construction of the antibiotic resistance gene-free vector was construction of a fusion of a truncated p60 promoter to the dal gene. The LM alanine racemase (dal) gene (forward primer: 5′-CCA TGG TGA CAG GCT GGC ATC-3′; SEQ ID NO: 1) (reverse primer: 5′-GCT AGC CTA ATG GAT GTA TTT TCT AGG-3′; SEQ ID NO: 2) and a minimal p60 promoter sequence (forward primer: 5′-TTA ATT AAC AAA TAG TTG GTA TAG TCC-3′; SEQ ID No: 3) (reverse primer: 5′-GAC GAT GCC AGC CTG TCA CCA TGG AAA ACT CCT CTC-3′; SEQ ID No: 4) were isolated by PCR amplification from the genome of LM strain 10403S. The primers introduced a PacI site upstream of the p60 sequence, an NheI site downstream of the dal sequence (restriction sites in bold type), and an overlapping dal sequence (the first 18 bp) downstream of the p60 promoter for subsequent fusion of p60 and dal by splice overlap extension (SOE)-PCR. The sequence of the truncated p60 promoter was: CAAATAGTTGGTATAGTCCTCTTTAGCCTTTGGAGTATTATCTCATCATTTGTTTTTTAGGTGAAAACTGGGTAAACTTAGTATTATCAATATAAAATTAATTCTCAAATACTTAATTACGTACTGGGATTTTCTGAAAAAAGAGAGGAGTTTTCC (SEQ ID NO: 5, Kohler et al, J Bacteriol 173: 4668-74, 1991). Using SOE-PCR, the p60 and dal PCR products were fused and cloned into cloning vector pCR2.1 (Invitrogen, La Jolla, Calif.).
Removal of antibiotic resistance genes from pGG55. The subsequent cloning strategy for removing the Chloramphenicol acetyltransferase (CAT) genes from pGG55 and introducing the p60-dal cassette also intermittently resulted in the removal of the gram-positive replication region (oriRep; Brantl et al, Nucleic Acid Res 18: 4783-4790, 1990). In order to re-introduce the gram-positive oriRep, the oriRep was PCR-amplified from pGG55, using a 5′-primer that added a NarI/EheI site upstream of the sequence (GGCGCCACTAACTCAACGCTAGTAG, SEQ ID NO: 6) and a 3′-primer that added a NheI site downstream of the sequence (GCTAGCCAGCAAAGAAAAACAAACACG, SEQ ID NO: 7). The PCR product was cloned into cloning vector pCR2.1 and sequence verified.
In order to incorporate the p60-dal sequence into the pGG55 vector, the p60-dal expression cassette was excised from pCR-p60dal by PacI/NheI double digestion. The replication region for gram-positive bacteria in. pGG55 was amplified from pCR-oriRep by PCR (primer 1,5′-GTC GAC GGT CAC CGG CGC CAC TAA CTC AAC GCT AGT AG-3′; SEQ ID No: 8); (primer 2, 5′-TTA ATT AAG CTA GCC AGC AAA GAA AAA CAA ACA CG-3′; SEQ ID No: 9) to introduce additional restriction sites for EheI and NheI. The PCR product was ligated into pCR2.1-TOPO (Invitrogen, Carlsbad, Calif.), and the sequence was verified. The replication region was excised by EheI/NheI digestion, and vector pGG55 was double digested with EbeI and NheI, removing both CAT genes from the plasmid simultaneously. The two inserts, p60-dal and oriRep, and the pGG55 fragment were ligated together, yielding pTV3. pTV3 also contains a prfA (pathogenicity regulating factor A) gene. This gene is not necessary for the function of pTV3, but can be used in situations wherein an additional selected marker is required or desired.
Preparation of DNA for Real-Time PCR
Total Listeria DNA was prepared using the Masterpure® Total DNA kit (Epicentre, Madison, Wis.). Listeria were cultured for 24 hours at 37° C. and shaken at 250 rpm in 25 ml of Luria-Bertoni broth (LB). Bacterial cells were pelleted by centrifugation, resuspended in PBS supplemented with 5 mg/ml of lysozyme and incubated for 20 minutes at 37° C., after which DNA was isolated.
In order to obtain standard target DNA for real-time PCR, the LL0-E7 gene was PCR amplified from pGG55 (5′-ATGAAAAAAATAATGCTAGTTTTTATTAC-3′ (SEQ ID NO: 10); 5′-GCGGCCGCTTAATGATGATGATGATGATGTGGTTTCTGAGAACAGATG-3′ (SEQ ID NO: 11)) and cloned into vector pETbluel (Novagen, San Diego, Calif.). Similarly, the plcA amplicon was cloned into pCR2.1. E. coli were transformed with pET-LLOE7 and pCR-plcA, respectively, and purified plasmid DNA was prepared for use in real-time PCR.
Real-Time PCR
Taqman primer-probe sets (Applied Biosystems, Foster City, Calif.) were designed using the ABI PrimerExpress software (Applied Biosystems) with E7 as a plasmid target, using the following primers: 5′-GCAAGTGTGACTCTACGCTTCG-3′ (SEQ ID NO: 12); 5′-TGCCCATTAACAGGTCTTCCA-3′ (SEQ ID NO: 13); 5′-FAM-TGCGTA CAAAGCACACACGTAGACATTCGTAC-TAMRA-3′ (SEQ ID NO: 14) and the one-copy gene picA (TGACATCGTTTGTGTTTGAGCTAG-3′ (SEQ ID NO: 15), 5′-GCAGCGCTCTCTATACCAGGTAC-3′ (SEQ ID NO: 16); 5′-TET-TTAATGTCCATGTTA TGTCTCCGTTATAGCTCATCGTA-TAMRA-3′; SEQ ID NO: 17) as a Listeria genome target.
0.4 μM primer and 0.05 mM probe were mixed with PuRE Taq RTG PCR beads (Amersham, Piscataway, N.J.) as recommended by the manufacturer. Standard curves were prepared for each target with purified plasmid DNA, pET-LLOE7 and pCR-plcA (internal standard) and used to calculate gene copy numbers in unknown samples. Mean ratios of E7 copies/picA copies were calculated based on the standard curves and calibrated by dividing the results for Lmdd-TV3 and Lm-LLOE7 with the results from Lm-E7, a Listeria strain with a single copy of the E7 gene integrated into the genome. All samples were run in triplicate in each qPCR assay which was repeated three times. Variation between samples was analyzed by Two-Way ANOVA using the KyPlot software. Results were deemed statistically significant if p<0.05.
Growth Measurements
Bacteria were grown at 37° C., 250 rpm shaking in Luria Bertani (LB) Medium +/−100 micrograms (μg)/ml D-alanine and/or 37 μg/ml chloramphenicol. The starting inoculum was adjusted based on OD600 nm measurements to be the same for all strains.
Results
An auxotroph complementation system based on D-alanine racemase was utilized to mediate plasmid retention in LM without the use of an antibiotic resistance gene. E. coli strain MB2159 is an alr (−)/dadX (−) deficient mutant that is not able to synthesize D-alanine racemase. Listeria strain Lm dal(−)/dat(−) (Lmdd) similarly is not able to synthesize D-alanine racemase due to partial deletions of the dal and the dat genes. Plasmid pGG55, which is based on E. coli-Listeria shuttle vector pAM401, was modified by removing both CAT genes and replacing them with a p60-dal expression cassette under control of the Listeria p60 promoter to generate pTV3 (FIG. 1). DNA was purified from several colonies (FIG. 2).
To determine plasmid stability in vitro, LM-LLO-E7 and Lmdd(pTV3) were cultured for 70 generations in the presence and absence of selective pressure. CFU were determined daily on selective and nonselective plates for each culture. In this system, plasmid loss results in a greater number of colonies growing on nonselective plates (BHI plus D-alanine for Lmdd(pTV3), BHI only for LM-LL0-E7) versus selective plates (BHI only for Lmdd(pTV3), BHI plus chloramphenicol for LM-LLO-E7). No difference in CFU was detected between nonselective and selective plates (FIG. 3A), indicating stable maintenance of the plasmid throughout the culture for at least 70 generations, when the experiment was terminated.
In addition, plasmid stability in vivo was tested in C57BL/6 mice by isolating viable bacteria at different time points after injection. Again, CFU counts on selective and nonselective plates were used to determine plasmid maintenance among the isolated bacteria (FIG. 3B). No differences in CFU were detected on selective and nonselective plates for each construct, indicating the stable presence of the recombinant plasmid in all bacteria isolated. Since viable Lmdd(pTV3) bacteria were isolated at least until day 5, plasmid loss in vivo followed by early clearance of injected bacteria could be excluded as explaining the level of virulence observed for Lmdd(pTV3) bacteria (Example 2).
In summary, pTV3 was stably maintained in E. coli as well as in Listeria, both in vitro and in vivo. Bacterial growth on LB media that was not supplemented with additional D-alanine indicated that the dal expression cassette was active also in gram-negative E. coli. Both E. coli-pTV3 and Lmdd-pTV3 remained sensitive to chloramphenicol, indicating the successful removal of both CAT genes from the plasmid. Representative plates are depicted in FIGS. 4-7.
The pTV3 copy number per cell was compared between Lm-LLOE7 in the presence of chloramphenicol and Lmdd-TV3 in the absence of chloramphenicol by real-time PCR of the E7 sequences, in both Listeria and E. coli. Lm-LLOE7 expresses LLO/E7 fusion protein from pGG55. Plasmid copy numbers of Lmdd-TV3 and Lm-LLOE7 did not significantly differ from one another, showing stable retention of plasmid pTV3 in both Listeria and E. coli. 
In order to verify the complementation of bacterial functions, in vitro growth kinetics were compared among Lmdd, Lmdd-TV3 and Lm-LLOE7. Lmdd-TV3, but not non-complemented Lmdd was able to grow in alanine-free media (FIG. 8). In fact, Lmdd-TV3 reached logarithmic growth phase sooner than both Lm-LLOE7 and Lmdd complemented with exogenous D-alanine. This growth attenuation of Lm-LLOE7 was partially due to the metabolic burden of CAT expression. However, even in the absence of chloramphenicol, Lm-LLOE7 still grew more slowly in vitro than Lmdd-TV3.
EXAMPLE 2
Plasmids Containing a Metabolic Enzyme do not Increase The Virulence of Bacteria
Materials and Experimental Methods
Hemolytic Lysis Assay
4×109 CFU of Listeria were thawed, pelleted by centrifugation (1 minute, 14000 rpm) and resuspended in 100 μl PBS, pH 5.5 with 1 M cysteine. Bacteria were serially diluted 1:2 and incubated for 45 minutes at 37° C. in order to activate secreted LLO. Defibrinated total sheep blood (Cedarlane, Hornby, Ontario, Canada) was washed twice with 5 volumes of PBS and three to four times with 6 volumes of PBS-Cysteine until the supernatant remained clear, pelleting cells at 3000×g for 8 minutes between wash steps, then resuspended to a final concentration of 10% (v/v) in PBS-Cysteine. 100 μl of 10% washed blood cells were mixed with 100 μl of Listeria suspension and incubated for additional 45 minutes at 37° C. Un-lysed blood cells were then pelleted by centrifugation (10 minutes, 1000×g). 100 μl of supernatant was transferred into a new plate and the OD530 nm was determined and plotted against the sample dilution.
Results
As virulence is linked to LLO function, the hemolytic lysis activity between Lmdd-TV3 and Lm-LLOE7 was compared. This assay tests LLO function by lysis of red blood cells and can be performed with culture supernatant, purified LLO or bacterial cells. Lmdd-TV3 displayed higher hemolytic lysis activity than Lm-LLOE7.
In vivo virulence was also measured by determining LD50 values, a more direct, and therefore accurate, means of measuring virulence. The LD50 of Lmdd-TV3 (0.75×109) was very close to that of Lm-LLOE7 (1×109), showing that plasmids containing a metabolic enzyme do not increase the virulence of bacteria.
EXAMPLE 3
Vaccine Strains Carrying Plasmids Containing a Metabolic Enzyme Mediate Antigen Expression
Antigen expression from the metabolic enzyme-containing plasmid was tested in vitro by Western blot. When analyzing equal amounts of total protein from bacterial culture supernatants, Lmdd-TV3 cultures contained approximately double the amount of total antigen than Lm-LLOE7 cultures. This difference may be a result of a higher overall metabolic load in Lm-LLOE7, due to the larger size of the plasmid (12.8 kB) compared to Lmdd-TV3 (7.6 kB).
Thus, metabolic enzymes can be used instead of antibiotic resistance genes to mediate plasmid retention in auxtrophic bacteria. Further, such plasmids have utility in expression of heterologous proteins in bacteria.
EXAMPLE 4
Induction of Anti-Tumor Immunity by Plasmids Containing a Metabolic Enzyme
Materials and Experimental Methods
Experimental Design
105 TC-1 (ATCC, Manassas, Va.) were implanted subcutaneously in C57BL/6 mice (n=8) and allowed to grow for about 7 days, after which tumors were palpable. TC-1 is a C57BL/6 epithelial cell line that was immortalized with HPV E6 and E7 and transformed with activated ras, which forms tumors upon subcutaneous implantation. Mice were immunized with 0.1 LD50 of the appropriate Listeria strain on days 7 and 14 following implantation of tumor cells. A non-immunized control group (naïve) was also included. Tumor growth was measured with electronic calipers.
Results
Efficacy of the metabolic enzyme-containing plasmid as a cancer vaccine was determined in a tumor regression model. The TC-1 cell line model, which is well characterized for HPV vaccine development and which allowed for a controlled comparison of the regression of established tumors of similar size after immunization with Lmdd-TV3 or Lm-LLOE7, was used. In two separate experiments, immunization of mice with Lmdd-TV3 and Lm-LLOE7 resulted in similar tumor regression (FIG. 9) with no statistically significant difference (p<0.05) between vaccinated groups. All immunized mice were still alive after 63 days, whereas non-immunized mice had to be sacrificed when their tumors reached 20 mm diameter. Cured mice remained tumor-free until the termination of the experiment.
Thus, metabolic enzyme-containing plasmids are efficacious as a therapeutic cancer vaccine. Because immune responses required for a therapeutic cancer vaccine are stronger than those required for a prophylactic cancer vaccine, these results demonstrate utility as well for a prophylactic cancer vaccine.
EXAMPLE 5
Plasmids Containing a Metabolic Enzyme Induce Antigen-Specific, Tumor Infiltrating T-Cells
Materials and Experimental Methods
T-Cell Analysis
T-cells from spleen and tumor infiltrating T-cells were analyzed for CD8 and CD4 surface markers and E7 specificity according to standard protocols (Gunn et al. (2001, J. Immunol, 167: 6471-6479). C57BL/6 mice were immunized ip. 7 and 14 days after tumor implantation with Lmdd-TV3 or Lm-LLOE7. Splenocytes and tumors were harvested 5 days after the second injection, and were stained at room temperature with H-2Db tetramers loaded with the E7 peptide (RAHYNIVTF, SEQ ID NO: 18) or a control (HIV-Gag) peptide at a 1:200 dilution. Tetramers were provided by the National Institute of Allergy and Infectious Diseases Tetramer Core Facility and the National Institutes of Health AIDS Research and Reference Reagent Program.
Three-color flow cytometry for CD8 (53-6.7, PE conjugated), and E7H-2 Db tetramer was performed using a FACSCalibur® flow cytometer with CellQuest® software (Becton Dickinson, Mountain View, Calif.). Intracellular gamma interferon (IFN-) staining was performed on a second subset of cells. Before staining for the cell surface antigens and IFN-production, lymphocytes were stimulated in vitro by culturing in the presence of monensin (BD Biosciences) to accumulate intracellular IFN-γ in the Golgi apparatus. After culture for 5 hr in RP-10 supplemented with interleukin-2 (50 U/ml) and 1 μl of brefeldin A (monensin) per ml, the cells were surface stained for effector markers at 4° C. for 20 min with phycoerythrin-conjugated anti-CD8 (PharMingen) and antigen-presenting cell-conjugated MEL-14 (anti-CD62 ligand). Cells were gated on (selected for) CD62 ligand low to select activated cells before being analyzed for CD8+ IFN-gamma+ populations.
Results
Anti-tumor efficacy of a vaccine is often linked to its ability to induce antigen-specific, tumor-infiltrating lymphocytes. To further characterize Lmdd-TV3 efficacy, the tumor-infiltrating cytotoxic T-cells (CTL) for E7 antigen specificity were therefore analyzed. Both Lmdd-TV3 and Lm-LLOE7 induce a significant percentage of E7 tetramer specific T-cells infiltrating the tumor (Table 1). No significant differences were observed in the percentages of IFN-γ-producing CD8+ T cells in L. monocytogenes LLO-E7-immunized mice versus Lmdd(pTV3)-treated mice. Thus, both Lmdd-TV3 and Lm-LLOE7 induced tumor infiltrating, antigen-specific CTL that controlled tumor growth.







TABLE 1







Cells were stained with anti-CD8- antibody and E7-tetramer and


subjected to FACS analysis. After gating on (selecting) CD8+/E7-


tetramer+/CD62−, the percentage of CD8+/E7-tetramer+/CD62− cells


from total live cells was calculated.











CD8+, E7-tetamer+, CD62−



Experiment A
Experiment B














CD8+, E7-
CD8+, IFN-
CD8+, E7-
CD8+, IFN-


Group
Dose
tetamer+
gamma+
tetamer+
gamma+















Naïve
0
8.81
1.33
4.86
0.01


Lmdd-
0.75 ×
20.72
7.06
14.86
5.5


TV3
108






Lm-
  1 ×
27.43
5.55
20.82
7.93


LLOE7
108









EXAMPLE 6
Generation of a Listeria Vaccine Vector Containing an Integrated Heterologous Gene, without the Use of an Antibiotic Resistance Gene
Materials and Experimental Methods
Generation of GG-L74
GG-L74 was created from Listeria strain 10403S by double allelic exchange at the orfZ domain, using a temperature-sensitive shuttle plasmid, as described in Gunn et al. (2001, J. Immunology 167: 6471-6479). GG-L74 was generated by introducing an expression cassette containing the hly-E7 fusion gene into the orfZ domain of the L. monocytogenes genome. The hly promoter drives the expression of the first 441 AA of the hly gene product, which is joined by the Xho1 site to the E7 gene. The result is a hly-E7 fusion gene that was transcribed and secreted as LLO-E7. The hly-E7 gene was ligated into the pKSV7 shuttle vector in the reverse orientation to avoid integration into the hly gene. The resulting plasmid, GG-L74, is an expression system that includes the previously described expression cassette inserted in the middle of a 1.6 Kb sequence that corresponds to the orfX, Y, Z domain of the L. monocytogenes genome. L. monocytogenes strain 10403S was transformed with pGG-74. The homology domains allow for insertion of the LL0-E7 gene cassette into the or orfZ domain by homologous recombination as described in Gunn et al. (2001, J. Immunology 167: 6471-6479). Clones were screened for integration of the LL0-E7 gene cassette into the orfZ domain.
Results
A Listeria vaccine vector, GG-L74, expressing a fusion of a non-hemolytic LLO fragment to the E7 antigen of human papilloma virus from the Listeria chromosome was produced by transfecting Lmdd with an hly-E7 fusion expression cassette, using p60-dal as the selectable marker. GGL74 has an LD50 in mice of 106 CFU.
EXAMPLE 7
Chromosomal Integration of Recombinant Genes Based on Phage Integration System
Materials and Experimental Methods
Construction of pTV6-11
pTV6-1 are constructed from pPL1 or pPL2 as follows:
First, pPL1 and pPL2 will be described:
pPL1
pPL1 has the sequence:








(SEQ ID No: 19; GenBank Accession No. AJ417488)









gacgtcattaaccctcactaaagggaacaaaagctgggtaccgggccccccctcgaggtcgacggtatcgataagcttgatatcgaattcctgcagcccggg



 


ggatccactagttctagagcggccgccaccgcggtggagctccaattcgccctatagtgagtcgtattgacgtcgctatttaacgaccctgccctgaaccga


 


cgaccgggtcgaatttgctttcgaatttctgccattcatccgcttattatcacttattcaggcgtagcaccaggcgtttaagggcaccaataactgccttaa


 


aaaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacagacggcatgatgaacctgaatc


 


gccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactg


 


gtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaa


 


tatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacacta


 


tcccatatcaccagctcaccgtctttcattgccatacggaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgc


 


ttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttcttta


 


cgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgccc


 


ggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgccgatcaacgtctcattttcgccaaaagttggcccagggcttcccggtatcaaca


 


gggacaccaggatttatttattctgcgaagtgatcttccgtcacaggtatttattcggcgcaaagtgcgtcgggtgatgctgccaacttactgatttagtgt


 


atgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccgg


 


acatcagcgctagcggagtgtatactggcttactatgttggcactgatgagggtgtcagtgaagtgcttcatgtggcaggagaaaaaaggctgcaccggtgc


 


gtcagcagaatatgtgatacaggatatattccgcttcctcgctcactgactcgctacgctcggtcgttcgactgcggcgagcggaaatggcttacgaacggg


 


gcggagatttcctggaagatgccaggaagatacttaacagggaagtgagagggccgcggcaaagccgtttttccataggctccgcccccctgacaagcatca


 


cgaaatctgacgctcaaatcagtggtggcgaaacccgacaggactataaagataccaggcgtttccccctggcggctccctcgtgcgctctcctgttcctgc


 


ctttcggtttaccggtgtcattccgctgttatggccgcgtttgtctcattccacgcctgacactcagttccgggtaggcagttcgctccaagctggactgta


 


tgcacgaaccccccgttcagtccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggaaagacatgcaaaagcaccactggcagcagcca


 


ctggtaattgatttagaggagttagtcttgaagtcatgcgccggttaaggctaaactgaaaggacaagttttggtgactgcgctcctccaagccagttacct


 


cggttcaaagagttggtagctcagagaaccttcgaaaaaccgccctgcaaggcggttttttcgttttcagagcaagagattacgcgcagaccaaaacgatct


 


caagaagatcatcttattaatcagataaaatatttctagatttcagtgcaatttatctcttcaaatgtagcacctgaagtcagccccatacgatataagttg


 


taattctccgccgcttgccctcatctgttacgccggcggtagccggccagcctcgcagagcaggattcccgttgagcaccgccaggtgcgaataagggacag


 


tgaagaaggaacacccgctcgcgggtgggcctacttcacctatcctgcccggctgacgccgttggatacaccaaggaaagtctacacgaaccctttggcaaa


 


atcctgtatatcgtgcgaaaaaggatggatattccgaaaaaatcgctataatgaccccgaagcagggttatgcagcggaaaagcgctgcttccctgctgttt


 


tgtggaatatctaccgactggaaacaggcaaatgcaggaaattactgaactgaggggacaggcgagaggcatgcgataaaaagcaatctatagaaaaacagg


 


ttactttttatttataattttagtttctcgattcgtttccgtccaacgagagaaaacgaggaactaaacaatctaaataaacaagctactagagccattcaa


 


tagtaacttgttcaccgtcaatataaattttattaattagtgattttaaataaagttgcttttctcggaactctaaagagtcaaaatcaactgttgctaaat


 


cagctaaattttcttgtatctttttatttttcttcaattcttcgttagcttctatttgtgcttcataataattaatttgagcatcgatatcagccatcatag


 


catcaagttctgaaacttcgtaagaaccgctgatatataaatcaaatagccgtttcttttttacgtgttctgttttaagtttttcatttaagctatctaatt


 


cgtcttctttatctacattcctagaagcgaaactatagttattcacgcgatcaataattaattcctcgagtttgtcagctctccaaattttatttccacatt


 


tttctagttcatgagtatgtttgtaagtcttgcaactataatatctataatgatatttttttccgcgggaaacagtatcttttctccgatgaacaaaaccca


 


acccacattttccacacactaccaaattatttagcaacgatgctgaatctctattcatatttggatttttacccatgcgagaaaaaatttcttgaactcgat


 


aaaattgttcctctgaaataataggctcatgaacaccttttgtatgcactttatccgcataagatacataaccacagtataaatcattagttagccaattgt


 


tgtaactgctatatgatttcactttgaatcctaatttttttagtctcttctgtaaagtggtaatgcttttttcttcctcaaaaatatcataaatcatttgta


 


attgttttgcttcttcttcattaatatataatttagtatctataacatcatagccgaatgttctaccttttgcagtcgttaaaggaagacctgcttcaatac


 


gcttaattttccccatcaccatacgatcacgtatagtttcgcgctctaattgagcaaatacggataatataccaatcatcgcgcgcccaaatgggctagagg


 


tgtcaagagtttcagacaaactaacaaattctacattgttttttaagaagtattcttcaataagcgttatcgtatctctttgtgagcgggaaagtctatcta


 


agcgatatacaacaacagcatcaatttcatgtaatttacttagcatttcatttagtgcggggcgattcatgtttgaaccgctgtatccgccgtctatgaaaa


 


tatcgtatacgtcccaatccttcgagcggcacaaggctgttagcttttcagtttgagcttgtatagagtaattctctatttgttcttgagtagatacgcgta


 


tataaatagctgccttcatttccgttctcctctcgcatggaaagttaagatctttttttcagaaaatcccagtacgtaattaagtatttgagaattaatttt


 


atattgattaatactaagtttacccagttttcacctaaaaaacaaatgatgagataatagctccaaaggctaaagaggactataccaactatttgtaataat


 


tctgtaacagttgaaaagcgaacgtgtattcttagggcttgagatgtattgctgggtaaacctttatagtgtaagtgggatgtgaacgttaatcaacaactt


 


tcgctatgggaaacctattgttttttgttaatagaaaaacttaatacatttgtaatataaaaaccggcagtttttccgttcttcgtgactcgaaatgaattg


 


ccagatgagtttatggtattctataatagaaggtatggaggatgttatataatgagacagaattatgatgatcgaaagctagcttggcactggccgtcgttt


 


tacaacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaagaggcccgcaccg


 


atcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcctgatgcggtattttctccttacgcatctgtgcggtatttcacaccgcatatgatccc


 


ggatctggagctgtaatataaaaaccttcttcaactaacggggcaggttagtgacattagaaaaccgactgtaaaaagtacagtcggcattatctcatatta


 


taaaagccagtcattaggcctatctgacaattcctgaatagagttcataaacaatcctgcatgataaccatcacaaacagaatgatgtacctgtaaagatag


 


cggtaaatatattgaattacctttattaatgaattttcctgctgtaataatgggtagaaggtaattactattattattgatattttaagttaaacccataaa


 


tgaagtccatggaataatagaaagagaaaaagcattttcaggtataggtgttttgggaaacaatttccccgaaccattatatttctctacatcagaaaggta


 


taaatcataaaactctttgaagtcattctttacaggagtccaaataccagagaatgttttagatacaccatcaaaaattgtataaagtggctctaacttatc


 


ccaataacctaactctccgtcgctattgtaaccagttctaaaagctgtatttgagtttatcacccttgtcactaagaaaataaatgcagggtaaaatttata


 


tccttcttgttttatgtttcggtataaaacactaatatcaatttctgtggttatactaaaagtcgtttgttggttcaaataatgattaaatatctcttttct


 


cttccaattgtctaaatcaattttattaaagttcatttgatatgcctcctaaatttttatctaaagtgaatttaggaggcttacttgtctgctttcttcatt


 


agaatcaatccttttttaaaagtcaatattactgtaacataaatatatattttaaaaatatcccactttatccaattttcgtttgttgaactaatgggtgct


 


ttagttgaagaataaaagaccacattaaaaaatgtggtcttttgtgtttttttaaaggatttgagcgtagcgaaaaatccttttctttcttatcttgataat


 


aagggtaactattgcccagatccgggatcatatggtgcactctcagtacaatctgctctgatgccgcatagttaagccagccccgacacccgccaacacccg


 


ctgacgcgccctgacgggcttgtctgctcccggcatccgcttacagacaagctgtgaccgtctccgggagctgcatgtgtcagaggttttcaccgtcatcac


 


cgaaacgcgcgagacgaaagggcctcgtgatacgcctatttttataggttaatgtcatgataataatggtttctta.






bp 1 to 171 of pPL1 contain the multiple cloning site from pBluescript KS (Alting-Mees, M A, and Short J M. 1989. pBluescript II: gene mapping vectors. Nucleic Acids Res. 17: 9494), and were subcloned using the primers 5′-GGACGTCATTAACCCTCACTAAAGG-3′ (SEQ ID No: 20) and 5′-GGACGTCAATACGACTCACTATAGG-3′ (SEQ ID No: 21).
bp 172 to 2253 contain the low-copy-number gram-negative origin of replication and chloramphenicol acetyltransferase (CAT) gene from pACYC 184 (Chang, A C et al, 1978. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134:1141-1156), and were cloned after PCR with primers 5′-GGACGTCGCTATTTAACGACCCTGC-3′ (SEQ ID No: 22) and 5′-GAGCTGCAGGAGAATTACAACTTATATCGTATGGGG-3′ (SEQ ID No: 23).
bp 2254 to 2624 contain the RP4 origin of transfer (oriT) (Pansegrau, W E et al, 1994. Complete nucleotide sequence of Birmingham IncP alpha plasmids. Compilation and comparative analysis. J. Mol. Biol. 239:623-663) (for use in direct conjugation from E. coli to L. monocytogenes), and was cloned from plasmid pCTC3 (Williams, D R et al, 1990. Conjugative plasmid transfer from Escherichia coli to Clostridium acetobutylicum. J. Gen. Microbiol. 136:819-826) after PCR with primers 5′-GCACTGCAGCCGCTTGCCCTCATCTGTTACGCC-3′ (SEQ ID No: 24) and 5′-CATGCATGCCTCTCGCCTGTCCCCTCAGTTCAG-3′ (SEQ ID No: 25).
bp 2629 to 4127 contain the listeriophage U153 integrase gene and attachment site (attPP′) (Gen Bank Accession Number AJ417489) that direct the site-specific integration of the plasmid, and were cloned after PCR with primers 5′-GTAGATCTTAACTTTCCATGCGAGAGGAG-3′ (SEQ ID No: 28) and 5′-GGGCATGCGATAAAAAGCAATCTATAGAAAAACAGG-3′ (SEQ ID No: 29).
bp 4134 to 4563 contain the LM p60 promoter, used to drive expression of the U153 integrase gene, (Kohler, S M et al, 1990. The gene coding for protein p60 of Listeria monocytogenes and its use as a specific probe for Listeria monocytogenes. Infect. Immun. 58:1943-1950), and were PCR amplified with primers 5′-CCTAAGCTTTCGATCATCATAATTCTGTC-3′ (SEQ ID No: 30) and 5′-GGGCATGCAGATCTTTTTTTCAGAAAATCCCAGTACG-3′ (SEQ ID No: 31) and cloned upstream of the integrase gene.
bp 4570 to 6101 contain a HindIII-AatII restriction fragment subcloned from pUC18-Cat (obtained from Nancy Freitag, University of Washington), which in turn contains (bp 4788 to 5850) the inducible gram-positive CAT gene from pC194 (Horinouchi, S, and Weisbium, B, 1982. Nucleotide sequence and functional map of pC194, a plasmid that specifies inducible chloramphenicol resistance. J. Bacteriol. 150:815-825).
Cloning of the hly and actA Genes into pPL1
The hly gene was subcloned from plasmid pDP-906 (Jones, S et al. 1994. Characterization of Listeria monocytogenes pathogenesis in a strain expressing perfringolysin O in place of listeriolysin O. Infect. lmmun. 62: 5608-5613) by restriction digestion with BamHI and XbaI, gel purifying a 2.9-kb fragment, and ligating it into pPL1 cut with BamHI and SpeI (pPL24). The actA gene was PCR amplified from 10403S genomic DNA with primers 5′-GGTCTAGATCAAGCACATACCTAG-3′ (SEQ ID No: 54) and 5′-CGGGATCCTGAAGCTTGGGAAGCAG-3′ (SEQ ID No: 55). The 2220 by PCR product was gel purified, cut with BamHI and XbaI, and clonedinto pPL1 cut with BamHI and SpeI (pPL25).
pPL2
pPL2 (FIG. 10B) has the sequence:








(SEQ ID No: 32)









gacgtcattaaccctcactaaagggaacaaaagctggtaccgggccccccctcgaggtcgacggtatcgataagcttgatatcgaattcctgcagcccgggg



 


gatccactagttctagagcggccgccaccgcggtggagctccaattcgccctatagtgagtcgtattgacgtcgctatttaacgaccctgccctgaaccgac


 


gaccgggtcgaatttgctttcgaatttctgccattcatccgcttattatcacttattcaggcgtagcaaccaggcgtttaagggcaccaataactgccttaa


 


aaaaattacgccccgccctgccactcatcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatc


 


gccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactg


 


gtgaaactcacccagggattggctgagacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaa


 


tatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagcgatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacacta


 


tcccatatcaccagctcaccgtctttcattgccatacggaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgc


 


ttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttcttta


 


cgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgccc


 


ggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgccgatcaacgtctcattttcgccaaaagttggcccagggcttcccggtatcaaca


 


gggacaccaggatttatttattctgcgaagtgatcttccgtcacaggtatttattcggcgcaaagtgcgtcgggtgatgctgccaacttactgatttagtgt


 


atgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccgg


 


acatcagcgctagcggagtgtatactggcttactatgttggcactgatgagggtgtcagtgaagtgcttcatgtggcaggagaaaaaaggctgcaccggtgc


 


gtcagcagaatatgtgatacaggatatattccgcttcctcgctcactgactcgctacgctcggtcgttcgactgcggcgagcggaaatggcttacgaacggg


 


gcggagatttcctggaagatgccaggaagatacttaacagggaagtgagagggccgcggcaaagccgtttttccataggctccgcccccctgacaagcatca


 


cgaaatctgacgctcaaatcagtggtggcgaaacccgacaggactataaagataccaggcgtttccccctggcggctccctcgtgcgctctcctgttcctgc


 


ctttcggtttaccggtgtcattccgctgttatggccgcgtttgtctcattccacgcctgacactcagttccgggtaggcagttcgctccaagctggactgta


 


tgcacgaaccccccgttcagtccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggaaagacatgcaaaagcaccactggcagcagcca


 


ctggtaattgatttagaggagttagtcttgaagtcatgcgccggttaaggctaaactgaaaggacaagttttggtgactgcgctcctccaagccagttacct


 


cggttcaaagagttggtagctcagagaaccttcgaaaaaccgccctgcaaggcggttttttcgttttcagagcaagagattacgcgcagaccaaaacgatct


 


caagaagatcatcttattaatcagataaaatatttctagatttcagtgcaatttatctcttcaaatgtagcacctgaagtcagccccatacgatataagttg


 


taattctccgccgcttgccctcatctgttacgccggcggtagccggccagcctcgcagagcaggattcccgttgagcaccgccaggtgcgaataagggacag


 


tgaagaaggaacacccgctcgcgggtgggcctacttcacctatcctgcccggctgacgccgttggatacaccaaggaaagtctacacgaaccctttggcaaa


 


atcctgtatatcgtgcgaaaaaggatggatataccgaaaaaatcgctataatgaccccgaagcagggttatgcagcggaaaagcgctgcttccctgctgttt


 


tgtggaatatctaccgactggaaacaggcaaatgcaggaaattactgaactgaggggacaggcgagaggcatgcgtggagggaaagaagaacgctgttgaaa


 


aaatcttctctggactacttgaaacaaaagaattaaagtcattttataaaaaccttgagaaaaaacatcttgatataaaaactatttataacgaatatttat


 


ttcaatgtaataataaataatatttattattacataaaatgtttgtggtattatttgtggtatatatatcctaaatggctttatatcagtgtgtgttaatcc


 


ctctcaggacgttaaatagtaatgtaaagaaatctctaaaacgttgaaaagccttgatattaaagggcggatgaatgttttggagttttttttatatcgtat


 


aatacccgttttattccgttgtttttgtggcatttgtggtaaaatttgtggtattttcatctgtttttagtgtgaaaaaagcatctactttggactgattat


 


gttgtcttaaattagagcttagatgactatagtattttaatgttgtattaatgtcatcatgaccaagcctatcagctacataaataatatccatacccgctt


 


ctacacataagcctgtatgcgtatgtcgtagcttgtgtaatgtcactggttcagaattgattgtactacatatcttcttcaaagctttattacaagacgcgt


 


tgtctactggcttattgtggtaagtgatgaataataacatcaatggattcttaatagcatgttccttcatatattcagtatgccaatttaaatacgaatgta


 


aatattgagcggtagagttatcaatatagatcactcgtgatttttttgttttggtatcaatgaatgtattagtgtacttgtaatcccaagctttattcacag


 


ttattgaacgtttagtgaaattaatatccttctttgttagtgcaataatttcttcgaacctcatgcctgtctggacagctagaaagataactgctcgtgata


 


tagaatgaaattttgcaagttcttctaatagtaaatgaactttgtctgtttccataaattgtgctttatttttcgctacgtcctgtccgcttatatgagccc


 


ctatagtggggtttttcttcatgtaacctaaatgaacagccttgttaaaaatcgctctaattttgcggtgtctggtgtctacagtggatattgcatagtcta


 


cagataaatgattaataaattgttgatattgaaccgcatcaatcgaattaaatttaattttttcatcgaaataatcaacgaattgattataagcaagatcgt


 


ataaattaatagtagattgactacttttcccatctttaaatgttttcatgaatagcgtataaaattctttgaagttccattctttcagagaactactatcat


 


gctgaacttgttttaataatttagatgctttatacattaagtttgtttcacttgtatctgtcaaacgcttttctttccattcaccatcgacttttatacgta


 


ggcgaacacaatatttaccgtttgctaatttttttatcttcattaataccaccacctgtttatttttggagatctttttttcagaaaatcccagtacgtaat


 


taagtatttgagaattaattttatattgattaatactaagtttacccagttttcacctaaaaaacaaatgatgatataatagctccaaaggctaaagaggac


 


tataccaactatttgtaataattctgtaacagttgaaaagcgaacgtgtattcttagggcttgagatgtattgctgggtaaacctttatagtgtaagtggga


 


tgtgaacgttaatcaacaactttcgctatgggaaacctattgttttttgttaatagaaaaacttaatacatttgtaatataaaaaccggcagtttttccgtt


 


cttcgtgactcgaaatgaattgccagatgagtttatggtattctataatagaaggtatggaggatgttatataatgagacagaattatgatgatcgaaagct


 


agcttggcactggccgtcgttttacaacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgt


 


aatagcgaagaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcctgatgcggtattttctccttacgcatctgtgcggt


 


atttcacaccgcatatgatcccggatctggagctgtaatataaaaaccttcttcaactaacggggcaggttagtgacattagaaaaccgactgtaaaaagta


 


cagtcggcattatctcatattataaaagccagtcattaggcctatctgacaattcctgaatagagttcataaacaatcctgcatgataaccatcacaaacag


 


aatgatgtacctgtaaagatagcggtaaatatattgaattacctttattaatgaattttcctgctgtaataatgggtagaaggtaattactattattattga


 


tatttaagttaaacccagtaaatgaagtccatggaataatagaaagagaaaaagcattttcaggtataggtgttttgggaaacaatttccccgaaccattat


 


atttctctacatcagaaaggtataaatcataaaactctttgaagtcattctttacaggagtccaaataccagagaatgttttagatacaccatcaaaaattg


 


tataaagtggctctaacttatcccaataacctaactctccgtcgctattgtaaccagttctaaaagctgtatttgagtttatcacccttgtcactaagaaaa


 


taaatgcagggtaaaatttatatccttcttgttttatgtttcggtataaaacactaatatcaatttctgtggttatactaaaagtcgtttgttggttcaaat


 


aatgattaaatatctcttttctcttccaattgtctaaatcaattttattaaagttcatttgatatgcctcctaaatttttatctaaagtgaatttaggaggc


 


ttacttgtctgctttcttcattagaatcaatccttttttaaaagtcaatattactgtaacataaatatatattttaaaaatatcccactttatccaattttc


 


gtttgttgaactaatgggtgctttagttgaagaataaaagaccacattaaaaaatgtggtcttttgtgtttttttaaaggatttgagcgtagcgaaaaatcc


 


ttttctttcttatcttgataataagggtaactattgcccagatccgggatcatatggtgcactctcagtacaatctgctctgatgccgcatagttaagccag


 


ccccgacacccgccaacacccgctgacgcgccctgacgggcttgtctgctcccggcatccgcttacagacaagctgtgaccgtctccgggagctgcatgtgt


 


cagaggttttcaccgtcatcaccgaaacgcgcgagacgaaagggcctcgtgatacgcctatttttataggttaatgtcatgataataatggtttctta.






To construct pPL2, the PSA attachment site (tRNAarg-attBB′) DNA sequence was obtained through a combination of inverse PCR and genome walking. Inverse PCR was performed on Sau3AI-digested DP-L4061 DNA (WSLC 1042, lysogenic for PSA; GenBank Accession No: AJ314913) with the divergent primers PL95 (5′-ACATAATCAGTCCAAAGTAGATGC; SEQ ID No: 33) and PL97 (5′-ACGAATGTAAATATTGAGCGG; SEQ ID No: 34), which anneal within the PSA int gene. The resulting DNA sequence was used to design further oligonucleotides, and these were used with the Genome Walker® kit (Clontech).
pPL1 was modified to utilize a different attachment site on the L. monocytogenes chromosome by replacing the U153 integrase gene and attachment site in the plasmid. The PSA int and attPP′ were PCR amplified from PSA genomic DNA (GenBank Accession No: AJ312240) with primers PL100 (5′-GAAGATCTCCAAAAATAAACAGGTGGTGG; SEQ ID No: 71) and PL101 (5′-CATGCATGCGTGGAGGGAAAGAAGAACGC; SEQ ID No: 35) with Vent DNA polymerase, digested with Bg1II and SphI, and ligated to pPL1 that had been digested with the same enzymes, generating pPL2.
The DNA sequence of the PSA tRNAArg-attBB′ from serotype 1/2 L. monocytogenes strains was obtained by a plasmid trap strategy. DP-L4211 (pPL2 integrated in 10403S) genomic DNA was digested with Nsi I and NheI, which do not cleave in the vector, and ligated under dilute conditions to promote self-ligation. The ligations were transformed into E. coli XL1-Blue, and chloramphenicol-resistant colonies were selected. The plasmids obtained were sequenced with the convergent primers PL94 (5′-GGAGGGAAAGAAGAACGC; SEQ ID No: 36) and PL95 (SEQ ID No: 33) for attPB′ and attBP′, respectively, which flank attPP′ in the PSA genomic DNA sequence. A serotype 1⁄2-specific PCR assay across tRNAArg-attBB′ was developed from the 10403S DNA sequence and used to determine the prophage status of various LM strains. Primers PL102 (5′-TATCAGACCTAACCCAAACCTTCC; SEQ ID No: 37) and PL103 (5′-AATCGCAAAATAAAAATCTTCTCG; SEQ ID No: 38) specifically amplify a 533-bp PCR product in nonlysogenic serotype 1⁄2 strains. The primer pair NC16 (5′-GTCAAAACATACGCTCTTATC; SEQ ID No: 39) and PL95 specifically amplify a 499-bp PCR product in strains that either are lysogenic or contain an integration vector at tRNAArg-attBB′.
Construction of pTV6-7
The U153 integrase gene and the U153 attPP' integration site from pPL1 are modified by PCR to contain restriction sites at the 5′-end and the 3′-end that are compatible with cloning these nucleic acids into shuttle plasmid pTV3. The Listeria replication region from pTV3 is removed, resulting in plasmid pTV6 (FIG. 11A). This plasmid contains replication functions for its amplification in E. coli, a dal gene for complementation of dal auxotroph E. coli and Listeria, and integration functions (U153 integrase, attPP′ site) for integration of the plasmid into the Listeria genome. pTV6 also contains a prfA (pathogenicity regulating factor A) gene. This gene is not necessary for the function of pTV6, but can be used in situations wherein an additional selected marker in the plasmid or the integration vector is required or desired. In other experiments, a similar plasmid lacking the prfA gene is utilized (pTV7; FIG. 11B).
Construction of pTV8-9
The PSA integrase gene and attPP′ integration site from pPL2 are modified by PCR to contain restriction sites at the 5′-end and the 3′-end that are compatible with cloning these nucleic acids into shuttle plasmid pTV3 and the Listeria replication region from pTV3 is removed, resulting in plasmid pTV8 (FIG. 11). pTV8 is similar to pTV6, except that it contains the PSA sequences instead of the U153 sequences. pTV8 also contains a prfA gene, which is not necessary for function, as described above for pTV6, and can be removed (pTV9; FIG. 12).
Construction of pTV10-11
The A118 integrase gene and attPP′ integration site from A118 DNA (GenBank Accession No. NC—003216) are modified by PCR to contain restriction sites at the 5′-end and the 3′-end that are compatible with cloning these nucleic acids into shuttle plasmid pTV3 and the Listeria replication region from pTV3 is removed, resulting in plasmid pTV10 (FIG. 13). pTV10 is similar to pTV6, except that it contains the A118 sequences instead of the U153 sequences. pTV10 also contains a prfA gene, which is not necessary for function, as described above for pTV6, and can be removed (pTV11; FIG. 14).
Phage Curing, Conjugation, and Molecular Confirmation of Plasmid Integration.
For phage curing, L. monocytogenes (LM) 10403S derivatives carrying a prophage at comK-attBB′ (integrated in the comk open reading frame) are grown in BHI at 37° C. to 108 CFU/ml and infected with listeriophage U153 at a multiplicity of infection of 20:1 in the presence of 5 mM CaCl2. Cultures are incubated with shaking at 37° C. for 75 min, and inhibition of growth is monitored by comparison of the optical density at 600 nm (OD600) of the infected culture with an uninfected control culture. The infected culture is diluted 10−2 and 10−4 in BHI, and both dilutions are grown at 37° C. until the 10−2 dilution culture increases 100-fold in optical density. The 104-fold dilution culture is then diluted 10−2, and 3 microliter (mcl) is plated on BHI.
Fifty colonies are tested for phage release initially by transferring colonies into 0.25 ml of LB broth and replica plating at 30° C. on a lawn of Mack-4R (DP-L862), a non-lysogenic rough strain of L. monocytogenes particularly susceptible to forming plaques. Candidates are then tested for ability to form plaques by spotting 10 mcl of culture on a lawn of Mack-4R. Colonies that do not form plaques are tested for ability to support plaque formation by the phage from the parent 10403S strain (Φ10403 [Hodgson, D A. 2000. Generalized transduction of serotype 1⁄2 and serotype 4b strains of Listeria monocytogenes. Mol. Microbiol. 35:312-323]). Curing is confirmed molecularly by PCR with the comK-attBB-specific primer pair PL60 and PL61 (sequences follow) for the absence of a phage at comK-attBB. Approximately 10% of colonies are cured by using this procedure.
Recipient LM strains are made streptomycin resistant for counterselection in conjugation experiments by plate selection on BHI supplemented with 200 microgram (mcg) of antibiotic per ml.
pPL1 plasmid constructs were electroporated into E. coli strain MB2159, and bacterial strains are grown to mid-log phase (OD600 of 0.55) with shaking at 30° C. E. coli donor strains are grown in LB containing 25 mcg of chloramphenicol/ml, and LM recipient strains are grown in BHI. Donor culture (2.5 ml) is mixed with 1.5 ml of recipient culture and filtered onto washed 0.45-micron-pore-size HA-type filters (47 mm; Millipore). The filter is washed once with 10 ml of BHI, transferred to a BHI plate with no antibiotics, and incubated for 2 h at 30° C. Bacterial cells are gently resuspended in 2.5 ml of BHI, and 25- and 50-mcl aliquots are plated in 3 ml of LB top agar on BHI plates supplemented with 7.5 mcg chloramphenicol and 200 mcg streptomycin per ml. Plates are incubated at 30° C. overnight and shifted to 37° C. for 2 to 3 days.
Individual colonies are picked and screened by PCR for integration at the phage attachment, using 2 pairs of primers: The first primer pair specifically amplifies attBP′, thereby detecting integrated strains (but not those containing the vector as an episomal plasmid). The second primer pair specifically amplifies comK-attBB′, thereby detecting nonlysogenic strains. PCR assays are performed in a Hybaid Omn-ETM thermocycler with an annealing temperature of 55° C. for 30 cycles; integrants arise at a frequency of approximately 104 per donor cell.
Results
In a first experiment, a shuttle plasmid is constructed containing (1) a replication gene for E. coli, (2) a U153 attPP′ integration site, (3) a Listeria dal gene under the control of its natural promoter, and (4) a U153 integrase gene under the control of the Listeria p60 promoter. The U153 integrase gene and attPP′ integration site are subcloned into shuttle plasmid pTV3, and the Listeria replication region from pTV3 is removed, generating plasmid pTV6. The plasmid is amplified in dal auxotroph E. coli strain MB2159 (Example 1), isolated, and subsequently conjugated into Listeria. Because the plasmid does not contain a Listeria replication region, only Listeria that contain a copy that is integrated into the genome are selected upon growth in LB media. In other experiments, as a further selective measure, alanine-free media is utilized.
In other experiments, to facilitate prophage integration, phage curing is performed prior to conjugation. In other experiments, an integration vector not requiring phage curing (e.g. a PSA vector) is utilized.
In another experiment, a similar shuttle plasmid, pTV8, is constructed, but using instead a PSA attPP′ integration site and integrase gene. The plasmid is amplified and conjugated into Listeria, as described for pTV6.
In another experiment, a similar shuttle plasmid, pTV10, is constructed, but using instead a A118 attPP′ integration site and integrase gene. The plasmid is amplified and conjugated into Listeria, as described for pTV6.
EXAMPLE 8
Creation of General Shuttle Integration Vectors Based on pTV6, 8, and 11
pTV6, 8, and 11 are digested with KasI or EheI and AatII, and/or other appropriate restriction enzymes, removing the prfA gene, the LL0-E7 fusion gene, and most of the LLO promoter. A multiple cloning site consisting of BamHI, XhoI, XbaI, NotI, SpeI, SmaI, and SacI is introduced by ligating the following paired oligonucleotides to the vector backbone:
5′-CGG ATC CCT CGA GCT CAG AGC GGC CGC ACT AGT CCC GGG GAG CTC G (SEQ ID No: 40).
5′-TCG ACG AGC TCC CCG GGA CTA GTG CGG CCG CTC TGA GCT CGA GGG ATC CGA CGT (SEQ ID No: 41; overhanging ends that are compatible with the vector sites restricted with AatI and SalI are in italics).
An antigen cassette of interest is then ligated into the multiple cloning site. The plasmid is then used to create a vaccine strain expressing the antigen encoded therein.

## Claims

1. A recombinant Listeria strain comprising an integrated nucleic acid molecule, wherein said integrated nucleic acid molecule comprises a) a first open reading frame encoding a polypeptide comprising a protein antigen, and b) a second open reading frame encoding a metabolic enzyme, wherein said nucleic acid molecule does not comprise an antibiotic resistance gene, and further wherein said nucleic acid is stably retained in said recombinant Listeria under in vitro and in vivo conditions.

2. The recombinant Listeria strain of claim 1, wherein said nucleic acid molecule further comprises a gene encoding a transcription factor.

3. The recombinant Listeria strain of claim 2, wherein the chromosome of said recombinant Listeria a strain lacks said gene encoding a transcription factor.

4. The recombinant Listeria strain of claim 1, wherein said polypeptide is a fusion protein comprising said protein antigen and an additional polypeptide, wherein said additional peptide enhances the immunogenicity of said protein antigen.

5. The recombinant Listeria strain of claim 2, wherein said additional polypeptide is a non-hemolytic LLO protein or fragment thereof, a PEST- amino acid sequence, or an ActA fragment.

6. The recombinant Listeria strain of claim 1, wherein said nucleic acid molecule is a phage integration vector.

7. The recombinant Listeria strain of claim 1, wherein said metabolic enzyme is an amino acid metabolism enzyme.

8. The recombinant Listeria strain of claim 1, wherein said metabolic enzyme catalyzes a formation of an amino acid used for a cell wall synthesis in said recombinant Listeria strain.

9. The recombinant Listeria strain of claim 1, wherein said metabolic enzyme is an alanine racemase enzyme.

10. The recombinant Listeria strain of claim 1, wherein said metabolic enzyme is a D-amino acid transferase enzyme.

11. The recombinant Listeria strain of claim 1, wherein said recombinant Listeria strain has been passaged through an animal host.

12. The recombinant Listeria of claim 1, wherein said nucleic acid comprises a third open reading frame encoding an additional metabolic enzyme.

13. The recombinant Listeria strain of claim 12, wherein said metabolic enzyme catalyzes a formation of an amino acid used for a cell wall synthesis in said recombinant Listeria strain.

14. The recombinant Listeria strain of claim 12, wherein said metabolic enzyme is an alanine racemase enzyme.

15. The recombinant Listeria strain of claim 12, wherein said metabolic enzyme is a D-amino acid transferase enzyme.