WO1993019603A1

WO1993019603A1 - Prokaryotes including dna encoding bacteriophage immunity

Info

Publication number: WO1993019603A1
Application number: PCT/US1993/002655
Authority: WO
Inventors: William R. Jacobs; Graham Hatfull
Original assignee: Albert Einstein College Of Medicine; University Of Pittsburgh
Priority date: 1992-03-31
Filing date: 1993-03-12
Publication date: 1993-10-14
Also published as: AU3929793A

Abstract

A prokaryote which is transformed with DNA which includes at least one DNA sequence which encodes immunity to a lytic bacteriophage. The prokaryote can be a bacterium, and in particular a mycobacterium. Such transformed mycobacteria may be employed in vaccines, and thereby eliminating the need for vaccines including mycobacteria having antibiotic resistance markers.

Description

'it

PROKARYO ES INCLUDING DNA ENCODING BACTERIOPHAGE IMMDNITT

This invention relates to prokaryotes, such as bacteria, an in particular to mycobacteria. More particularly, this inventio relates to prokaryotes which have been transformed with DN encoding immunity to a lytic bacteriophage.

Certain mycobacteria represent major pathogens of man an animals. For example, tuberculosis is generally caused in human by Mycobacterium tuberculosis, and in cattle by Mycobacteriu bovis. which may also be transmitted to humans and other animals Mycobacteria leprae is the causative agent of leprosy. M tuberculosis and mycobacteria of the avium-intracellulare scrofulaceum group (MAIS group) represent major opportunisti pathogens of patients with acquired immune deficiency syndrom (AIDS). M. pseudotuberculosis is a major pathogen of cattle.

On the other hand, Bacille Calmette-Guerin, or BCG, a avirulent strain of M. bovis, is widely used in human vaccines and in particular is used as a live vaccine, which is protectiv against tuberculosis. BCG is the only childhood vaccine which i currently given at birth, has a very low incidence of advers effects, and can be used repeatedly in an individual (eg., i multiple forms). In addition, BCG and other mycobacteria (eg. M. smeαmatis) . employed in vaccines, have adjuvant propertie among the best currently known and, therefore, stimulate

SUBSTITUTE SHEET recipient's immune system to respond to antigens with great effectiveness.

It has been suggested by Jacobs, et al, Nature, Vol. 327, No. 6122, pgs. 532-535 (June 11, 1987) that BCG could be used as a host for the construction of recombinant vaccines. In other words, it was suggested to take an existing vaccine (in this case against tuberculosis) and expand its protective repetoire through the introduction of one or more genes from other pathogens. Because BCG vaccines are administered as live bacteria, it is essential that any foreign antigens, polypeptides, or proteins expressed by the bacteria are not lost from the bacteria subsequent to vaccination.

Transformation, the process whereby naked DNA is introduced into bacterial cells, has been carried out successfully in mycobacteria. Jacobs, et al (1987), hereinabove cited, have described transformation of mycobacteria through chemical methods, and Snapper, et al. PNAS, Vol. 85, pgs. 6987-6991

(September 1988) have described transformation of mycobacteria by electroporation. Electroporation can give from 10 5 to 106 transformants per μg of plasmid DNA and such plasmid DNA's may carry genes for resistance to antibiotic markers such as kanamycin (Snapper, et al 1988) to allow for selection of transformed cells from non-transformed cells.

Jacobs, et al (1987) and Snapper, et al (1988) have also described the use of cloning vehicles, such as plasmids and bacteriophageε, for carrying genes of interest into mycobacteria.

Combination of the above-mentioned techniques, along with standard tools of molecular cloning (e.g., use of restriction enzymes, etc.) allows the cloning of genes of interest into vectors and introduction of such genes into mycobacteria. To express these genes, it is important to have available signals for gene expression, in particular, transcription promoter elements. Such promoter elements have been isolated from

SUBSTITUTESHEET mycobacterial heat shock genes, and used to express foreig antigens in mycobacteria.

There are, however, relatively few selectable markers fo the transformation of mycobacteria and many of the antibioti resistance methods that are useful for the fast-growin mycobacteria, such as, for example, M. smeσmatis. are unsuitabl for the slow-growing mycobacteria, such as M. bovis BCG, becaus many of the antibiotics themselves are not stable for the lon periods of incubation required for growth of the organisms. I addition, the presence of antibiotic resistance genes in live bacterial vaccines, such as BCG vaccines, is undesirable becaus these genes may be transmitted to other bacteria present in the host, whereby such bacteria become resistant to the antibiotic.

It is therefore an object of the present invention to provide transformed prokaryotes, such as transforme mycobacteria, that do not use antibiotic resistance genes as selectable markers, and to provide vaccines employing such organisms.

In accordance with an aspect of the present invention, there is provided a prokaryote transformed with DNA which includes at least one DNA sequence which encodes immunity to a lytic bacteriophage.

Prokaryotes which may be transformed with DNA which includes at least one DNA sequence which encodes immunity to a lytic bacteriophage include, but are not limited to, bacteria. Bacteria which may be transformed include, but are not limited to, mycobacteria, Actinomyces species, Norcardia species, Streptomyces species, Corynebacteria species. Salmonella species. Vibrio species, and E. coli. In one embodiment, the bacterium is a mycobacterium. Mycobacteria which may be transformed include, but are not limited to, Mycobacterium bovis-BCG. M. smeσmatis, M. avium. M. phlei, M. fortiutum. M. lufu, M. paratuberculosis, M. habana, M. scrofalaceum, M. leprae, and M. intracellulare. In one embodiment, the mycobacterium is M. bovis-BCG. In another embodiment, the mycobacterium is M. smeσmatis.

As hereinabove stated, the prokaryote is transformed with DNA which includes at least one DNA sequence which encodes immunity to a lytic bacteriophage. Temperate bacteriophages can adopt two different life cycles. The lytic cycle involves simple reproduction of viral particles within a bacterial cell, followed by lysis of the cell and release of the particles. Alternatively, temperate phages enter a lysogenic state in which most of the viral functions are inactivated, and the phage genome becomes integrated into the bacterial chromosome. The lytic functions of the phage are inactivated by a transcriptional repressor. The repressor regulates the genes of the resident prophage, and also prevents the lytic cycles of any superinfecting phages, thereby conferring immunity to a lytic bacteriophage.

In one embodiment, the at least one DNA sequence encodes immunity to a lytic mycobacteriophage. As an illustrative example, mycobacteriophage L5 is a temperate phage that infects and lysogenizes M. smegmatis. In accord with the temperate nature of L5, it not only infects M. smeσmatis but also forms stable lysogens in which the bacteriophage genome is integrated into the bacterial chromosome and the lytic functions have been inactivated (Snapper, et al., Proc. Nat. Acad. Sci.. Vol. 85, pgs. 6987-6991, 1988, and Lee, et al., Proc. Nat. Acad. Sci., Vol. 88, pgs. 3111-3115, 1991). L5 lysogens of M. smegmatis are immune to superinfection by L5, and also to superinfection by another mycobacteriophage known as mycobacteriophage D29. Mycobacteriophage D29, however, is not a temperate phage and does not itself form lysogens.

A gene has been isolated from the L5 genome, which encodes a 183 amino acid protein, which confers immunity to L5 superinfection. This gene, which is approximately 0.6kb in

SHEET length, is designated gene 71. As further described hereinbelow, this gene has been placed into an E. coli mycobacteria shuttle vector. The vector was then electroporated into M. smeσmatis. Transformants were then selected by infection with bacteriophage L5c(dl), which is a variant of L5 that does not lysogenize. Therefore, the M. smeσmatis organisms which have been transformed with the shuttle vector will survive the L5c(dl) infection. It is to be understood, however, that the scope of the present invention is not to be limited to immunity to L5 or any other mycobacteriophage superinfection, or to any specific genes which encode mycobacteriophage immunity, such as gene 71 of L5.

In one embodiment, the DNA which transforms the mycobacterium includes a first DNA sequence which is a phage DNA portion encoding bacteriophage integration, preferably mycobacteriophage integration, into a mycobacterium chromosome, and the at least one DNA sequence which encodes immunity to a lytic bacteriophage.

The term "phage DNA portion", as used herein, means that the DNA sequence is derived from a phage and lacks the DNA which is required for phage replication.

Bacteriophages from which the phage DNA portion may be derived include, but are not limited to, mycobacteriophages, such as but not limited to the L5, LI, Bxbl and TM4 mycobacteriophages; the lambda phage of E.coli; the toxin phages of Corynebacteria; phages of Actinomycetes and Norcadia, the 0 C31 phage of Streptomyces; and the P22 phage of Salmonella. Preferably, the phage DNA portion encodes mycobacteriophage integration into a mycobacterium chromosome.

In a preferred embodiment, the first DNA sequence includes DNA encoding integrase, which is a protein that provides for integration of the DNA into the ycobacterial chromosome. Most preferably, the first DNA sequence also includes DNA which encodes an AttP site. The DNA sequence encoding the AttP site and the integrase provides for an integration event which is referred to as site-specific integration. DNA containing the AttP site and the integrase gene is capable of integration into a corresponding AttB site of a mycobacterium chromosome.

It is to be understood that the exact DNA sequence encoding the attP site may vary among different phages, and that the exact DNA sequence encoding the attB site may vary among different mycobacteria.

The integration event results in the formation of two new junction sites called AttL and AttR, each of which contain part of each of AttP and AttB. The inserted and integrated DNA which includes the first DNA sequence and the DNA which encodes immunity to a lytic bacteriophage, is flanked by the AttL and AttR sites. The insertion and integration of the phage DNA portion results in the formation of a transformed mycobacterium.

The DNA may further include a DNA sequence encoding a protein or polypepetide heterlogous to the mycobacterium into which the DNA is to be integrated.

The DNA which encodes a protein heterologous to mycobacteria may be DNA which is all or a portion of a gene encoding protein(s) or polypeptide(s) of interest; DNA encoding a selectable marker or markers; or DNA encoding both a selectable marker or markers and at least one protein or polypeptide of interest.

Proteins or polypeptides of interest, which may be encoded by such DNA include, but are not limited to, antigens, anti-tumor agents, enzymes, lymphokines, pharmacologic agents, immunopotentiators, and reporter molecules of interest in a diagnostic context.

Antigens for which such DNA sequence may encode include, but are not limited to, Mycobacterium leprae antigens; Mycobacterium tuberculosis antigens; Rickettsia antigens; malaria sporozoites

SUBSTITUTESHEET and merozoites; diphtheria toxoids; tetanus toxoids; Clostridium antigens; Leishmania antigens; Salmonella antigens; Borrelia antigens; Mycobacterium africanu antigens; Mycobacterium intracellulare antigens; Mycobacterium aviu antigens; Treponema antigens; Pertussis antigens; Schistosoma antigens; Filaria antigens; Herpes virus antigens; influenza and parainfluenza virus antigens; measles virus antigens; mumps virus antigens; hepatitis virus antigens; Shigella antigens; Neisseria antigens; rabies antigens, polio virus antigens; Rift Valley Fever virus antigens; dengue virus antigens; measles virus antigens; Human Immunodeficiency Virus (HIV) antigens; respiratory syncytial virus (RSV) antigens; snake venom antigens; and Vibrio cholera antigens. Enzymes which may be encoded include, but are not limited to, steroid enzymes.

Anti-tumor agents which may be encoded by such DNA include, but are not limited to, interferon-α, interferon-β, or interferon- , and tumor necrosis factor, or TNF. Lymphokines which may be encoded include, but are not limited to, interleukins 1 through 8.

Reporter molecules which may be encoded include, but are not limited to, luciferase, B-galactosidase, B-glucuronidase, and catechol dehydrogenase.

Other peptides or proteins which may be encoded by such DNA sequence include, but are not limited to, those which encode for stress proteins, which can be administered to evoke an immune response or to induce tolerance in an autoimmune disease (eg., rheumatoid arthritis) .

The phage DNA portion of the present invention, which includes the first DNA sequence encoding mycobacterium phage integration into a mycobacterium chromosome, the at least one DNA sequence encoding immunity to a lytic bacteriophage; and the DNA encoding at least one protein or polypeptide heterologous to mycobacteria, may be constructed through genetic engineering

BSTITUTE SHEET techniques known to those skilled in the art. In a preferred embodiment, the phage DNA portion may be a plasmid including, in addition to the DNA encoding integration and the DNA encoding a heterologous protein, an origin of replication for any of a wide variety of organisms, which includes, but is not limited to, E.coli, Streptomyces species. Bacillus species, Staphylococcus species, Shigella species. Salmonella species and various species of pneumococci. Most preferably, the plasmid includes an origin of replication for E.coli.

The phage DNA portion also may include a suitable promoter for controlling expression of the at least one DNA sequence encoding a protein or polypeptide heterologous to the mycobacterium. Suitable promoters include, but are not limited to, mycobacterial promoters such as the BCG HSP60 and HSP70 promoters; mycobactin promoters of M. tuberculosis and BCG, the superoxide dismutase promoter, the α-antigen promoter of M. tuberculosis and BCG, the MBP-70 promoter, the 45 kda antigen promoter of M. tuberculosis and BCG; and the mycobacterial asd promoter; the mycobacterial 14 kda and 12 kda antigen promoters; mycobacteriophage promoters such as the Bxbl promoter, the LI, L5, and D29 promoters, and the TM4 promoters; E.coli promoters; or any other suitable promoter. The selection of a suitable promoter is deemed to be within the scope of those of ordinary skill in the art from the teachings contained herein.

The promoter sequence may, in one embodiment, be part of an expression cassette which also includes a portion of the gene normally under the control of the promoter. For example, when a mycobacterial HSP60 or HSP70 promoter is employed, the expression cassette may include, in addition to the promoter, a portion of the gene for the HSP60 or HSP70 protein. When the expression cassette and the at least one DNA sequence encoding a protein or polypeptide heterologous to the mycobacterium such as hereinabove described, are expressed, the protein expressed by the cassette and the DNA encoding a protein or poplypeptide heterologous to the mycobacterium is a fusion protein of a fragment of a mycobacterial protein (eg., the HSP60 or HSP70 protein), and the protein or polypeptide heterologous to the mycobacterium.

In a preferred embodiment, the transcription initiation site, the ribosomal binding site, and the start codon, which provides for the initiation of the translation of mRNA, are each of mycobacterial origin. The stop codon, which stops translation of mRNA, thereby terminating synthesis of the protein or peptide heterologous to the mycobacterium, and the transcription termination site, may be of mycobacterial origin, or of other bacterial origin, or such stop codon and transcription termination site may be those of the at least one DNA sequence encoding a protein or polypeptide heterologous to the mycobacterium.

In accordance with another embodiment, the mycobacterium is transformed with an expression vector including the at least one DNA sequence which encodes immunity to a bacteriophage, and a promoter selected from the class consisting of mycobacterial promoters and mycobacteriophage promoters for controlling expression of at least one DNA sequence encoding a protein or polypeptide heterologous to the mycobaterium. The mycobacterial and mycobacteriophage promoters and heterologous proteins and polypeptides may be selected from those hereinabove described.

The promoter sequence may also be part of an expression cassette which also includes a portion of the gene normally under the control of the promoter, as hereinabove described. When the expression cassette and the at least one DNA sequence encoding a protein or polypeptide heterologous to the mycobacterium, are expressed, the protein expressed by the cassette and the at least one DNA sequence is a fusion protein of a fragment of a mycobacterial protein and the protein or polypeptide heterologous to the mycobacterium. Also as hereinabove described, the transcription initiation site, the ribosomal binding site, and the start codon, which provides for the initiation of the translation of mRNA, may each be of mycobacterial origin. The stop codon, may, as hereinabove described, be of mycobacterial origin, or of other bacterial origin, or such stop codon and transcription termination site may be those of the DΝA encoding the at least one protein or polypeptide heterologous to the mycobacterium.

In accordance with one embodiment, the vector further includes a mycobacterial origin of replication.

In accordance with another embodiment, the vector may be a plasmid. The plasmid may be a non-shuttle plasmid, or may be a shuttle plasmid which further includes a bacterial origin of replication such as an E. coli origin of replication, a Bacillus origin of replication, a Staphylococcus origin of replication, a Streptomyces origin of replication, or a pneumococcal origin of replication. In one embodiment, the shuttle plasmid includes an E. coli origin of replication.

In accordance with yet another embodiment, the vector may further include a multiple cloning site, and the at least one DΝA encoding a protein or polypeptide heterologous to the mycobacterium sequence is inserted in the multiple cloning site.

In addition to the DΝA encoding immunity to a lytic bacteriophage, DΝA encoding a heterlogous protein or polypeptide, and the mycobacterial promoter for controlling expression of the at least one DΝA sequence encoding a heterologous protein or polypeptide, the expression vector may, in one embodiment, further include a DΝA sequence encoding bacteriophage integration into a mycobacterium chromosome. Bacteriophages from which the DΝA sequence encoding bacteriophage integration into a mycobacterium chromosome may be derived include, but are not limited to, those hereinabove described. Preferably, the DΝA sequence encodes mycobacteriophage integration into a mycobacterium chromosome. The DNA sequence which encodes bacteriophage integration into a mycobacterium chromosome may include DNA which encodes integrase, which is a protein that provides for integration of the vector into the mycobacterial chromosome. Preferably, the DNA sequence encoding mycobacteriophage integration also includes DNA which encodes an attP site.

The DNA encoding the attP site and the integrase provides for an integration event which is referred to as- site-specific integration. DNA containing the attP site and the integrase gene is capable of integrating into a corresponding attB site of a mycobacterium chromosome, as hereinabove described.

The transformed mycobacteria, which include DNA which includes at least one DNA sequence which encodes immunity to a lytic bacteriophage, and preferably a DNA sequence which encodes a protein or polypeptide which is heterologous to mycobacteria, may be utilized in the production of a vaccine or a therapeutic agent, depending upon the protein(s) or polypeptide expressed by the transformed mycobacteria.

To form such a vaccine or therapeutic agent, the transformed mycobacteria are administered in conjunction with a suitable pharmaceutical carrier. As representative examples of suitable carriers there may be mentioned: mineral oil, alum, synthetic polymers, etc. Vehicles for vaccines and therapeutic agents are well known in the art and the selection of a suitable vehicle is deemed to be within the scope of those skilled in the art from the teachings contained herein. The selection of a suitable vehicle is also dependent upon the manner in which the vaccine or therapeutic agent is to be administered. The vaccine or therapeutic agent may be in the form of an injectable dose and may be administered intramuscularly, intravenously, orally, intradermally, or by subcutaneous administration.

Other means for administering the vaccine or therapeutic agent should be apparent to those skilled in the art from the teachings herein; accordingly, the scope of the invention is not to be limited to a particular delivery form.

When the transformed mycobacteria are employed as a vaccine, such a vaccine has important advantages over other presently available vaccines. Mycobacteria have, as hereinabove indicated, adjuvant properties among the best currently known and, therefore, stimulate a recipient's immune system to respond with great effectiveness. This aspect of the vaccine induces cell-mediated immunity and thus is especially useful in providing immunity against pathogens in cases where cell-mediated immunity appears to be critical for resistance. Also, mycobacteria may stimulate long-term memory or immunity. It thus may be possible to prime long-lasting T cell memory, which stimulates secondary antibody responses neutralizing to the infectious agent or the toxin. Such priming of T cell memory is useful, for example, against tetanus and diphtheria toxins, pertussis, malaria, influenza virus. Herpes virus, rabies. Rift Valley fever virus, dengue virus, measles virus. Human Immunodeficiency Virus (HIV), respiratory syncytial virus, human tumors, and snake venoms. Another advantage in employing mycobacteria transformed with the phage DNA portion of the present invention as a vaccine or a therapeutic agent is that mycobacteria in general have a large genome (i.e., approximately 3 x 10 base pairs in length). Because the genome is large, it is able to accommodate a large amount of DNA from other source(s), and may possibly be employed to make a vaccine and/or therapeutic agent containing DNA sequences encoding more than one antigen and/or therapeutic agent. As hereinabove stated, it is desired that antibiotiβ markers be removed from the transformed mycobacteria prior to utilization of the mycobacteria in a vaccine, in one embodiment, a vector is constructed which includes an attP site, DNA encoding immunity to a bacteriophage, DNA encoding integrase, an antibiotic resistance marker, and directly oriented copies of a site which may be recognized by a resolvase protein. An in vitro reaction using purified resolvase protein resolves the vector into a catenane which comprises two daughter molecules which are topologically linked as singly-linked circular DNA molecules. One circle includes the attP site and the DNA which encodes immunity to a lytic bacteriophage. The other circle includes the gene encoding integrase as well as the antibiotic resistance marker. This circle does not include a mycobacterial origin of replication. When the singly-linked circles are transformed into a mycobacterium, the circle containing the attP site and the gene encoding immunity to a lytic bacteriophage will integrate into the mycobacterial chromosome. The circle which includes the gene encoding integrase and the antibiotic resistance marker does not integrate into the mycobacterial chromosome. When the catenane is transfected into the mycobacterium, the catenane becomes a substrate for cellular DNA topoisomerase II enzyme. The action of the enzyme upon the catenane results in the separation of the two circular DNA molecules from each other. Although the integrase and the antibiotic resistance marker are expressed when the circular DNA molecules are first transfected into the mycobacterium, the circle which includes the antibiotic resistance marker will eventually be lost because such circle cannot integrate, nor can the circular DNA molecule replicate within the mycobacterium. Thus, there are provided transformed mycobacteria which do not include antibiotic resistance markers, and may be selected through bacteriophage infection.

TE SHEET Although the present invention has been described in detail with respect to mycobacteria, it is to be understood that within the scope of the present invention that prokaryotes other than mycobacteria may be transformed with DNA encoding immunity to a lytic bacteriophage, and preferably also with DNA encoding a protein or polypeptide which is heterologous to the prokaryote.

The invention will now be described with respect to the following examples; however, the scope of the present invention is not intended to be limited thereby.

Example 1 - Mappinσ the determinants of L5 superimmunity

Recombinant plasmids were constructed that contained segments of the mycobacteriophage L5 genome inserted into an E. coli-mycobacterial shuttle vector known as pMD30. pMD30 is a derivative of pϋC119 modified such that it may replicate in both E. coli and mycobacteria, and it contains the aph kanamycin resistance gene. pMD30 was constructed by inserting the 1 kb Hindlll fragment from pKD43 (Derbyshire, et al., Proc. Nat. Acad. Sci.. Vol. 84, pgs. 8049-8053, (1987)) containing the aph gene into the Seal site of pUC119 (Figure 1) to make pMD02. (Figure 2). pMD02 was then cleaved with XmnI and the Hpal-EcoRV fragment containing ori M from pYUB12 (Figure 3, obtained from Dr. William Jacobs) was inserted. The resulting plasmid is pMD30 (Figure 4). One recombinant plasmid, which contained a 9.5kb Kpnl fragment (Figure 5), conferred immuity to L5 superinfection by wild-type L5 phage in M. smegmatis. Further analysis of this 9.5kb Kpnl fragment showed that a smaller segment, about 1.3kb in length (Figure 6), and including a gene encoding a 183 amino acid protein, conferred this phenotype, and that the 183 amino acid protein expressed by this 1.3kb fragment was responsible. The gene encoding this 183 amino acid protein is referred to as gene 71. Gene 71 is located from nucleotide position 44,882 to nucleotide position 44,331 in the L5 genome. Example 2 - Isolation of clear plaque derivatives of L5

Clear plaque derivatives were isolated as spontaneous mutants that formed clear plaques on bacterial lawns, as opposed to the turbid plaques of the wild-type mycobacteriophage L5. Clear plaques indicate those cells which were killed by L5 infection and therefore cannot form lysogens. One of these derivatives, designated L5c(dl), was found to contain a small deletion of the L5 genome, including part of gene 71 , by restriction enzyme digestion with Bgl II. Bacterial survivors of an L5c(dl) infection of M. smegmatis occur at a frequency of about 10 .

Example 3

A. Construction of plasmids including gene 71

Recombinant plasmids were constructed in which the 1.3kb fragment of the L5 genome which contains gene 71 is inserted into an E. coli-mycornycobacterial shuttle vector. The construction of plasmids containing smaller segments of the 9.5kb Kpnl fragment until a plasmid was constructed which included the 1.3kb fragment of the L5 genome containing gene 71 was as follows: pMD04 (Figure 7) was made by inserting the Hindlll fragment (with blunt ends generated by Klenow) from pKD43 containing the kanamycin resistance gene and inserting such fragment into the Seal site of pUCllδ. (Figure 8). pMD31 (Figure 9) was then constructed by isolating the Hpal-EcoRV fragment from pYUB12 (Figure 3 provided by Dr. William Jacobs), and inserting it into the XmnI site of pMD04. pMD31 is a shuttle vector which may replicate in both E. coli and M. smegmatis. and contains a kanamycin resistance gene for selection in both bacterial species. pZS24 (Figure 10) contains the 9.5kb Kpnl fragment of phage L5 inserted into the Kpnl site of pUC119 (Figure 1). pZS24 was constructed by gel purification of the 9.5kb fragment and ligating into the Kpnl site of pUC119. The 9.5kb Kpnl fragment of pZS24 was then isolated; and inserted into the Kpnl site of pMD31 to make pMD40 (Figure 11). The SnaBI-PstI 2kb fragment of pMD40 was then isolated with blunt ends and inserted into the blunted Xbal site of pMD31 to form pMD70 (Figure 12). The BamHI-PstI 2kb fragment is isolated from pMD70 and inserted into pϋCllδ cut with BamHI and PstI to form pMD90 (Figure 13). pMD90 is digested with Sail, which cuts twice, and then religated to form pMD131. (Figure 14). A 1.3kb BamHI-PstI fragment is removed from pMD131, and inserted into the BamHI-PstI site of pMD30 to make pMD132 (Figure 15). These plasmids also carry the aph gene from Tn903 (provided by K. Derbyshire and Nigel Grindley of Yale University) that confers resistance to kanamycin, and an E. coli origin of replication.

B. Phage selection of σene 71 transformants Plasmid DNA's from pYUB12 or pMD70 were then electroporated into M. smegmatis. according to the procedure of Snapper, et al. (1988), and transformants were selected either by kanamycin selection (Snapper, et al., 1988), or as survivors of a phage infection. Phage infection with L5c(dl) with a multiplicity of infection (m.o.i.) of about 10 according to the procedure of Snapper, et al. (1988) (i.e., 10 phage particles to each bacterial cell. ) after a period of recovery from electroporation, efficiently killed non-transformed cells, but not plas id-transformed cells. The phage-selected transformants also were determined to be resistant to kanamycin, thus indicating that they are true transformants.

M. smegmatis strain mc 2 155 cells (approximately 4 x 108 cells prior to electroporation) were electroporated with pYUB12, pMD70, or without DNA, and incubated for 1 hour in broth to allow expression of the selectable genes. Transformants were selected either with kanamycin (Snapper, et al., 1988) or by phage D29 infection.

TUTE SHEET The procedure for D29 phage infection was as follows: D29 phages were added to M. smegmatis cells such that the multiplicity of infection was about 10. This is typically about g

4 x 10 plaque forming units (pfu) of phage. The phages were allowed to adsorb to . the bacteria by incubation at 37°C for 30 minutes. The entire sample was then plated onto solid media.

From several independent experiments carried out as hereinabove described, it was found that spontaneous D29 resistant mutants (from non-transformed mycobacteria or mycobacteria transformed with pYUB12) occur at a higher frequency (about 1-10 transformants/ug DNA) than nontransformed kamamycin resistant mutants wherein almost no transformants were detected. Such spontaneous D29 resistant mutants were found, after purification, to be resistant to both D29 and L5 but sensitive to heteroimmune mycobacteriophages such as TM4, thus indicating that such colonies are true D29 resistant derivatives. Also, as expected, the majority of pMD70 D29-selected transformants are also kanamycin resistant (of 148 colonies in one experiment and 37 in another, all were kanamycin resistant). Example 4 - Phage selection of integrated gene 71 transformants

In this example, the integrating vector containing gene 71 is pMH35, the construction of which is detailed as follows: pNG199 (obtained from Dr. Nigel Grindley) is a plasmid that contains multiple copies of a res site of transposon inserted into a pUC vector. When two res sites are directly oriented, such sites encode an active site for resolvase which resolves plasmids into singly-linked catenanes. A PvuII (130 bp) fragment of pNG199, containing the res site, was purified and inserted into the vector pUCllβ (Fig. 8) at the Smal site. The resulting plasmid is pGH513 (Figure 16). pMH5 (Figure 17), which contains the mycobacteriophage L5 attP site was digested with BamHI and Sail, and the 613 bp fragment containing the L5 attP site was inserted between the BamHI and Sail sites of pGH513 to form pGH515 (Figure 18). pGH515 thus contains a single res site and an attP site. pGH515 was digested with BamHI and PvuII (Figure 18), and a 1.2 kb fragment containing the int gene of mycobacteriophage L5 was inserted into the Asp718 site of pGH515 to form pGH516. (Figure 19). pGH516 contains the attP site and int gene of L5, which are separated by a single res site. pGH318 (obtained from Dr. Nigel Grindley), like pNG199 is a plasmid that contains multiple copies of a res site of transposon δ inserted into a pUC vector. pGH318 was digested with EcoRI, and a 130 bp fragment containing the res site was inserted into the EcoRI site of pGH516 to form pGH519. (Figure 20). pGH519 contains the attP site and int gene of L5 plus two res sites which are in direct orientation. It was found that the segment of DNA in pGH519 that contains the int gene is not expressed in mycobacteria. Therefore, it was necessary to replace the upstream sequences with the sequence (i.e., the promoter sequence) required for int expression. This was achieved as follows: pLP2 (Figure 21) was derived from pMH9.4 (Figure 22 - Lee, et al., PNASv Vol. 88, pgs. 3111-3115, April 1991) by cutting with Ndel and Xbal, blunt ending the ends with Klenow, and religation. pLP2 thus has a defective attP site, but has a functional int gene. pGH529 (Figure 23) was derived by digesting pMH9.4 (Figure 22) by cutting with SphI, and religating. pGH529 has a functional attP site, but the int gene is non-functional. pGH531 (Figure 24) was then constructed by ligating the 1680 bp Asp718-Sall fragment from pLP2 (Figure 21) to the 5062 bp Asp718-Sall fragment from pGH529 (Figure 23). pGH531 was then digested with Bglll and Sad, and a 728 bp Bglll-SacI fragment from pGH531 was inserted into the Bglll-SacI piece of pGH519 to form pMH27 (Figure 25). pMH27 was then opened at the Smal site and an aph kanamycin resistance cassette from pKD43 was inserted. The resulting plasmid is called pMH33 (Figure 26). pMH33 was then cut with Dral, and a Hindi11 - Bam HI fragment (1.3 kb) from pMD131 (Figure 14) that contains gene 71 was inserted to form pMH35 (Figure 27).

Thus, pMH35 includes an attP site, an integrase (int) gene, σene 71, and a gene encoding kanamycin resistance (aph gene). pMH35 is efficiently transformed through electroporation into M. smegmatis, and transformants can be selected by either L5c(dl) infection or by kanamycin selection.

Because it is desirable in the final construction step of vaccine development that antibiotic resistance markers be removed, a method for removing such markers was developed. A cointegrate molecule was constructed which contains two directly oriented copies of the res site derived from transposon 6 (Hatfull, et al., "Resolvases and DNA-invertases: A Family of Enzymes Active in Site-Specific Recombination, " Genetic Recombination, Kucherlapatti and Smith, eds., ASM Press (1988)). Such directly oriented copies of the res site are contained in pMH35. An in vitro reaction using purified resolvase protein resolves the cointegrate pMH35 into two daughter molecules which are topologically linked as singly-linked circular DNA molecules (Figure 28.) (according to the procedure of Hatfull, et al., Proc. Nat. Acad. Sci., Vol. 83, pgs. 5429-5433 (1986)). One of the daughter molecules contains the L5 attP site and σene 71, and the other daughter molecule contains the int gene and the aph (kanamycin resistance) gene.

M. smeσmatis was then transformed by electroporation (Snapper, et al. (1988)) with pMH35 which had been resolved into the circular DNA molecules as hereinabove described. Transformants selected by L5c(dl) infection occurred at an approximately 10-fold higher frequency than those selected with kanamycin according to the procedure of Snapper, et al. (1988).

Also, 83% of the phage-selected transformants containing the resolved pMH35 were kanamycin sensitive, thus indicating that the circular DNA molecules carrying the int gene and aph gene, but lacking an attP site and a mycobacterial origin of replication had been lost. This was determined by the following hybridization study:

2 M.smeσmatis strain mc 155 was transformed with pMH9.4 (as a control), pMH35 (unresolved), or pMH35 resolved with purified resolvase in vitro.

Organisms transformed with pMH9.4 were selected with kanamycin, and organisms transformed with pMH35 (either resolved or unresolved) were selected for L5c(dl) resistance.

Transformants were then selected for sensitivity or resistance to kanamycin by patch plating. All pMH9.4 and unresolved pMH35 transformants were resistant to kanamycin. 83% of the transformants which were transformed with resolved pMH35 were sensitive to kanamycin and the remainder were resistant. The kanamycin resistant transformants (17% of the population) may be a small population of organisms transformed with pMH35 which had not been resolved. DNA from: (a) two separate M. smeσmatis mc 2155 non-transformed organisms; (b) two separate M. smegmatis mc 2155 organisms transformed with pMH9.4; (c) two separate M. smeσmatis mc 2155 organisms transformed with unresolved pMH35; (d) two separate M. smeσmatis mc 155 organisms transformed with resolved

2 pMH35; and (e) two separate M. smegmatis mc 155 organisms from the 17% of the transformed cell culture hereinabove described which included transformants that were transformed with resolved pMH35; however, these organisms were transformed with pMH35 DNA which was not resolved.

The DNA's were cut with BamHI and Sspl, and electrophoresed on a standard 1% agarose gel. The DNA's were then transferred to nitrocellulose and hybridized with radiolabelled DNA. The autoradiograph of the nitrocellulose filter (Figure 29) indicates that the pattern of bands seen with the kanamycin-sensitive transformants which were transformed with resolved pMH35 DNA (lanes 8 and 9) is consistent with these transformants arising from the expected products of in vitro resolution of pMH35. Additional bands are also present in the DNA from the organisms that were selected with L5c(dl), as shown in lanes 6 through 11. The sizes of these bands are consistent with their arising from a resident L5c(dl) prophage. Thus such organisms are L5 lysogens.

Lanes 6, 7, 10, and 11 include five bands which are not present in lanes 8 and 9. These bands may correspond to elements present (such as kanamycin resistance) in unresolved pMH35, but are lost after resolution of pMH35 into two singly-linked circular DNA portions.

Example 5

Selection of pMH35 in BCG using D29 as a selecting phage.

BCG organisms were electroporated with pMH35. Following a 3 hr. expression period, the organisms were plated on 7H9 media containing ADC enrichment and 10 D29 phages. After 3 weeks incubation, BCG colonies immune to D29 infection were found in an

4 amount of 10 colony forming units per μg of DNA. No colonies were found for BCG transformed with a control vector pMV261,

(Stover, et al.. Nature. Vol. 351, pgs. 456-460 (June 6, 1991)) which does not include DNA encoding phage immunity.

It is to be understood, however, that the scope of the present invention is not to be limited to the specific embodiments described above. The invention may be practiced other than as particularly described and still be within the scope of the accompanying claims.

Claims

WHAT IS CLAIMED IS:

1. A prokaryote transformed with DNA which includes at least one DNA sequence which encodes immunity to a lytic bacteriophage.

2. The prokaryote of Claim 1 wherein said prokaryote is a bacterium.

3. The prokaryote of Claim 2 wherein said bacterium is a mycobacterium.

4. The mycobacterium of Claim 3 wherein said mycobacterium is selected from the group consisting of Mycobacterium bovis-BCG. M. smegmatis, M. avium, M. phlei. M. fortuitum, M. lufu. M. paratuberculosis. M. habana, M. scrofalaceum, M. leprae. and M. intracellulare.

5. The mycobacterium of Claim 4 wherein said mycomycobacterium is M. smeσmatis.

6. The mycobacterium of Claim 4 wherein said mycobacterium is M. bovis-BCG.

7. The mycobaterium of Claim 3 wherein said at least one DNA sequence encodes immunity to a lytic mycobacteriophage.

8. The mycobacterium of Claim 7 wherein said lytic mycobacteriophage is mycobacteriophage L5c(dl).

9. The mycobacterium of Claim 3 wherein said DNA includes a first DNA sequence which is a phage DNA portion encoding bacteriophage integration into a mycobacterium chromosome and said at least one DNA sequence which encodes immunity to a lytic bacteriophage.

10. The mycobacterium of Claim 9 wherein said phage DNA portion encodes mycobacteriophage integration into a mycobacterium chromosome.

11. The mycobacterium of Claim 10 wherein said first DNA sequence includes DNA encoding integrase.

12. The mycobacterium of Claim 11 wherein said first DNA sequence includes DNA encoding an attP site.

13. The mycobacterium of Claim 9 wherein said DNA further includes a DNA sequence encoding a protein or polypeptide which is heterologous to the mycobacterium into which said DNA is to be integrated.

14. The mycobacterium of Claim 3 wherein said mycobacterium is transformed with an expression vector including said at least one DNA sequence which encodes immunity to a bacteriophage and a promoter selected from the class consisting of mycobacterial promoters and mycobacteriophage promoters for controlling expression of said at least one DNA sequence.

15. The mycobacterium of Claim 14 wherein said expression vector further includes DNA encoding a protein or polypeptide heterologous to the mycobacterium which expresses the protein or polypeptide.

16. The mycobacterium of Claim 14 wherein said expression vector further includes a mycobacterial origin of replication.

17. The mycobacterium of Claim 14 wherein said mycobacterium is selected from the class consisting of Mycobacterium- bovis-BCG, M. smegmatis, M. avium, M. phlei. M. fortuitum. M. lufu, M. paratuberculosis, M. habana. M. scrofalaceum. M. leprae, and M. intracellulare.

18. The mycobacterium of Claim 17 wherein said mycobacterium is M. smeσmatis.

19. The mycobacterium of Claim 17 wherein said mycobacterium is M. bovis-BCG.

20. A vaccine, comprising: the transformed mycobacterium of Claim 13, and an acceptable pharmaceutical carrier.

21. A vaccine, comprising: the transformed mycobacterium of Claim 14, and an acceptable pharmaceutical carrier.

SUBSTITUTE SHEET