EP0303668A1 - Stable expression vectors - Google Patents

Abstract

Le vecteur sert au clonage et à l'expression d'ADN hétérologue dans des cellules hôtes d'un type donné (en particulier gram positif, y compris des cellules hôtes Bacillus et notamment B.subtilis, B.pumilis ou B.amyloliquefaciens). Un procédé permettant d'obtenir ce type de vecteur est également décrit. Lesdits vecteurs sont obtenus à partir de plasmides qui sont normalement conservés à l'état stable dans les cellules hôtes données par clonage d'une cassette d'ADN hétérologue comprenant un marqueur sélectionnable, au moins un site de restriction unique qui ne se trouve pas dans le plasmide et éventuellement une terminaison de transcription et un promoteur dans un site non unique du plasmide, suivi par une sélection des vecteurs résultants pour la conservation stable dans les cellules hôtes données. Cette approche augmente au maximum les chances d'obtenir un vecteur stable ainsi que la possibilité de trouver une position sur le plasmide où l'insertion d'ADN n'interrompt pas une région essentielle ou importante pour la réplication et où la conservation stable est grandement accrue. La présente invention décrit des vecteurs de Bacillus spécifiques (pPOD2152, pPOD2154, pPOD2158, pPOD2161, pPOD2167 et pPOD2168), dont on a découvert qu'ils conservent l'ADN hétérologue cloné avec une stabilité de 100 % pendant au moins 70 générations.The vector is used for cloning and expression of heterologous DNA in host cells of a given type (in particular gram positive, including Bacillus host cells and in particular B.subtilis, B.pumilis or B.amyloliquefaciens). A method for obtaining this type of vector is also described. Said vectors are obtained from plasmids which are normally conserved in the stable state in the given host cells by cloning of a heterologous DNA cassette comprising a selectable marker, at least one unique restriction site which is not found in the plasmid and optionally a transcription termination and a promoter in a non-unique site of the plasmid, followed by selection of the resulting vectors for stable conservation in the given host cells. This approach maximizes the chances of obtaining a stable vector as well as the possibility of finding a position on the plasmid where the insertion of DNA does not interrupt an essential or important region for replication and where stable conservation is greatly increased. The present invention describes specific Bacillus vectors (pPOD2152, pPOD2154, pPOD2158, pPOD2161, pPOD2167 and pPOD2168), which have been found to retain cloned heterologous DNA with 100% stability for at least 70 generations.

Description

Stable expression vectors

Field of Invention

This invention relates to recombinant DNA technology and in particular to expression vectors for expression of foreign genes in microorganisms, especially gram positive microorganisms, and to methods by which such vectors may be obtained.

Background of the Invention

The gram positive microorganisms of species Bacillus subtilis are potentially very useful for the cloning and expression of heterologous genes. This species has a significant advantage over the commonly used gram negative bacterial host, Escherichia coli, in that it is able to efficiently secrete many proteins into the medium, thus simplifying the extraction and purification of the desired protein. Additionally, B. subtilis is non-pathogenic with respect to humans. In view of these advantages a number of attempts have been made to develop recombinant DNA expression vector systems for use in B. subtilis.

The presence of extrachromosomal DNA in bacteria of the genus Bacillus was first demonstrated in the species Bacillus pumilis (Lovett, P.S. (1973) J. Bacteriol 115, 291-298; Lovett and Burdick (1973) Biochem. Biophys. Res. Comm. 54 365-370) and since then plasmids have been found in other species such as Bacillus subtilis (Tanaka et al (1977) J. Bacteriol 129. (3) 1487-1494). The major problem associated with development of these endogenous plasmids as cloning vectors is the lack of naturally occurring markers such as antibiotic resistance markers which are essential for the identification of transformants. In order to overcome this problem, derivatives of an endogenous B. subtilis plasmid have been constructed carrying a leu gene as marker (Tanaka and Sakaguchi (1978) Molec. Gen. Genet. 165 269-276). These leu⁺ plasmids were further modified by the addition of an antibiotic resistance marker (Tanaka and Kawano (1980) Gene 10131-136). This particular line of research does not appear, however, to have resulted in the production of vectors suitable for cloning and efficiently expressing foreign genes. This apparent lack of success may be attributed to the use of an antibiotic resistance marker derived from B. subtilis i.e. the same source with which the plasmids are naturally associated and from which they were isolated. The use of fragments from a homologous source greatly increases the chance of chromosomal integration of the plasmid and it may be that the addition of the antibiotic resistance markers adversely affected the stability of the plasmid. Chromosomal integration is an extremely undesirable event if the aim is to produce vectors containing multiple copies of heterologous DNA sequences to obtain high level expression of foreign genes. If the plasmid becomes integrated into the chromosome the copy number of the heterologous DNA becomes that of the chromosome.

The finding that Staphylococcus aureus plasmids could replicate in B. subtilis led to investigations of the suitability of such plasmids as expression vectors for use in B. subtilis. Use of such vectors to express cloned DNA in B. subtilis has been found to be associated with instability problems. S. aureus replicons carrying cloned DNA are stably maintained in B. subtilis host cells only in the presence of selection pressure, e.g. antibiotics. This renders such vectors unsuitable for use in large scale industrial processes, in view of the requirement to use costly procedures to remove the antibiotic or other selection pressure.

Other attempts at-;deriving suitable vectors for cloning heterologous DNA in Bacillus strains have focussed on the development of shuttle plasmids such as for example S.aureus/B. subtilis, E .coli/B.cereus, and E.coli/B. subtilis shuttle plasmids. These shuttle plasmids are incapable of stably maintaining cloned DNA in the absence of selection and, when carrying foreign DNA, undergo deletions under selection pressure. They are therefore unsuitable for expression of foreign genes. We have now prepared vectors useful for cloning and expressing heterologous DNA in B. subtilis. In contrast to prior art vectors, the vectors of the invention have been found to stably maintain cloned DNA in the absence of selection over many generations thereby making them extremely useful as vectors for expressing DNA coding for commercially important products in large scale fermentations.

Summary of the Invention

Accordingly in a first aspect the invention provides a vector suitable for cloning and expressing heterologous DNA in host cells of a given type comprising:

plasmid DNA derived from a plasmid which is normally stably maintained in said host cells

and, ligated with said plasmid DNA, heterologous DNA comprising at least one restriction site which is unique in said heterologous DNA and which does not occur in said plasmid DNA, and DNA coding for at least one selectable marker;

characterised in that,

said heterologous DNA is ligated within a non-unique restriction site of said plasmid and the vector is normally stably maintained in said host cells.

The invention also includes methods for obtaining vectors according to the first aspect.

Thus in a second aspect the invention provides a method for obtaining vectors according to the first aspect of the invention comprising: providing (a) a plasmid which is normally stably maintained in host cells of a given type, and

(b)a cassette of heterologous DNA comprising at least one restriction site which is unique in said cassette and which does not occur in said plasmid, at either end thereof linkers ligatable with a non-unique restriction site of said plasmid, and DNA coding for at least one selectable marker;

partially digesting said plasmid with a restriction enzyme which cleaves at said non unique restriction site to provide a plurality of linear digested plasmid DNA molecules;

ligating said cassette with said linear DNA molecules to provide a plurality of vectors, and

selecting from said vectors one or more vectors for stable maintenance in the absence of selection in said host cells

In the context of the present description the vectors (or plasmids) are "normally stably maintained" in the host cells and selected for stable maintenance if the vectors are present in substantially 100% of host cells after growth for at least 50 generations in the absence of selection

Partial digestion cleaves the plasmid at one or more of the non-unique restriction sites to give a plurality of. linear DNA molecules.

Ligation of the cassette of the heterologous DNA with these linear DNA molecules produces a number of different vectors since the cassette of heterologous DNA becomes inserted at or between the various non-unique restriction enzyme cleavage sites in the plasmid. The vectors so produced are then selected for stability in the host cells. Stability is indicative that the cassette has been inserted at the optimum site(s) for insertion. The stability of the vectors may be tested in small scale serial subculture experiments.

This approach maximises the chance of obtaining a stable vector as opposed to the customary prior art methods which simply choose a unique site which is present in the plasmid for cloning and expression of foreign DNA. By digesting the plasmid and then inserting the cassette at a variety of positions, the likelihood of finding a position on the plasmid where insertion of DNA does not interrupt a region essential or important for replication and stable maintenance functions is greatly increased. Once a suitable site has been identified i.e. one at which addition of heterologous DNA has substantially no effect on plasmid stability, it is then possible to add the desired foreign gene by means of a unique site provided by the heterologous DNA in the cassette.

The use of heterologous DNA for the cassette decreases the chance of recombination occurring and of the foreign gene becoming integrated into the chromosome. The term 'heterologous' is used herein to indicate that the DNA is derived from a source(s) which differs from the species of microorganism used as the host for expression.

The selectable marker may be any gene conferring a phenotype which enables selection of transformants. Commonly used selectable markers include genes coding for antibiotic resistance or sensitivity, or a characteristic selectable by the removal or addition of a specific metabolite.

The method of the invention is generally applicable and is particularly useful in the provision of vectors suitable for cloning and expressing genes in bacterial host cells especially in gram positive bacteria. Particularly preferred bacterial host cells are members of the genus Bacillus, e.g. B. lichenformis , B. brevis, B. sphaericus, B. megaterium, B.polymyxa, B. circulans, and most especially in B.pumilis, B. subtilis and B. amyloliquefaciens hosts.

Preferably the plasmid used for preparation of the vectors is an endogenous plasmid, i.e. one which occurs or is found naturally in the host used for cloning and expression. Thus the plasmid may be a Bacillus plasmid, and is preferably a Bacillus pumilis. Bacillus amyloliquefaciens or a Bacillus subtilis plasmid. Examples of suitable plasmids are pLS11, pLS12 ρLS13 , pLS14 as described by Tanaka et al (J. Bacteriol. 129, 1487 - 1494 (1977)) These plasmids are available from the Bacillus Genetic Stock Centre, at the Ohio State University, Ohio, USA. The 8.5kb plasmid found in Bacillus strain 1E2 or substantially similar variants or mutants of the said plasmid are especially preferred. This plasmid is believed to be identical to pLS14 and for convenience has been designated ρPOD2000 hereinafter in the present description. A restriction map of pPOD2000 is provided hereinafter at Figure 1.

In preferred embodiments of the invention the heterologous DNA of the vector (the cassette) additionally comprises at least one transcription terminator.

The transcription terminator may be derived from either Gram positive or Gram negative microorganisms. For example, the transcription terminator may be that of the B. amyloliquefaciens ∝ - amylase gene. We have found the use of transcription terminators derived from E. coli to be particularly suitable, such as the phage λto, or the rrnBT1T2 transcription terminator.

The vectors of the invention may be used for cloning and expressing foreign genes. The foreign genes may be cloned into the vector using the at least one unique restriction enzyme recognition site present in the cassette of heterologous DNA.. If desired, additional unique restriction sites may be added to the cassette by adding a further li nker to the cassette to the at least one enzyme recognition site. As used herein the term 'foreign gene' means a heterologous DNA sequence coding for a desired gene product.

In order to effect expression of the foreign gene it is necessary that the vector contains a suitable promoter, such as a heterologous promoter. Thus advantageously the heterologous DNA of the vector of the invention may include a promoter suitably positioned in relation to the at least unique restriction to promote expression of a foreign gene inserted at the site. Alternatively the natural promoter of the foreign gene may be used and conveniently may be inserted into the vector with the foreign gene.

Two criteria are of importance in relation to the choice of the heterologous promoter. The promoter preferably allows high level expression of the desired foreign gene and does not destabilise the system resulting in plasmid loss. The promoter further preferably does not allow high level expression during the growth phase of the culture of microorganism containing the hybrid plasmid.

Advantageously the promoter may be a promoter expression from which is regulatable or otherwise controllable.

The natural promoter of the foreign gene may be used and, if desired, production of the RNA species may be made controllable by incorporating a regulating circuit such as an operator sequence and repressor gene into the system. The promoter may be derived from a strain of Bacillus and if desired may be made controllable . Suitable promoters, which may if desired be made controllable, include, for example, subtilisin promoters, e.g. derived from B. amyloliquefaciens, amylase promoters e.g. derived from B. amyloliquefaciens, E. coli promoters e.g. phage T5 promoters, and where the microorganism host for expression is a non-lysogenic strain of bacteriuιh«the SP02 and Φ105 promoters may be used. Promoter sequences are typically derived from natural sources, though may be synthesized, in whole or in part, by oligonucleotide synthesis techniques. Thus in a third aspect the invention further provides an expression vector for expression of a foreign gene product comprising a vector according to the first aspect of the invention having the foreign gene inserted at the at least one unique restriction site of the heterologous DNA of the said vector.

The invention also includes transformed host cells.

Thus in a fourth aspect the invention further provides host cells of a given type transformed with a vector according to the first aspect of the invention or expression vector according to the third aspect of the invention.

Preferably the host cells are the endogenous host cells of the plasmid from which the vectors are derived. In particular the host cells are gram positive bacterial host cells, especially of the genus Bacillus, most especially of species B subtilis.

The cassette of heterologous DNA and the vectors of the invention may be prepared using methods well known in the recombinant DNA art.

Thus the cassette comprising the desired heterologous DNA may be initially assembled conveniently on a plasmid. The optimal plasmid for cassette assembly will vary depending on the required components of the cassette. E. coli vectors containing multi-purpose cloning sites are particularly suitable for assembling the cassette prior feo insertion into the endogenous plasmid. We have found the pUC series of plasmids, especially the plasmid pUC8, to be particularly suitable for cassette assembly.

It is believed that the overall size of the cassette may affect the stability of the vector. It is believed that it is advantageous to keep the cassette as small as possible, e.g. - a maximum size of less than about 2KB. The selectable marker may be isolated as a restriction fragment and may be inserted at an appropriate point in the cassette. Where it is desired to add a transcription terminator to the cassette this must be positioned and oriented appropriately to prevent readthrough transcription from the foreign gene. The ends of the cassette may be modified by adding linkers of the desired sequence thereby creating the desired restriction enzyme recognition sites.

A particularly preferred cassette is the 1.5KB HIND III cassette fragment as hereinafter described and shown in Figure 3.

In preferred embodiments, the plasmid is partially digested and then purified prior to ligation with the cassette of heterologous DNA. The linearised form of the plasmid, i.e. the plasmid cleaved at only one of the multiple restriction sites, may be identified by size. For example, gel electrophoresis techniques may be used in which a complete digest of the plasmid using a restriction enzyme which cleaves the plasmid only once is run in an adjacent track and the linearised form of the plasmid is identified by its similarity of mobility. The linearised form is then purified and ligated with the cassette. Where the host is a gram positive microorganism such as a Bacillus host this may be then transformed by, for example, a protoplast method. Where the host is a gram-negative microorganism transformation may be carried out using methods well known in the art. Transformants are selected using the selectable marker.

The desired promoter and/or the transcription terminator and foreign gene may be added to the cassette as one unit where for example the promoter and/or transcription terminator may be those naturally associated with the foreign gene.

The heterologous promoter and foreign gene are cloned into an appropriate site of the cassette contained in the plasmid as described above. Transformants are selected and theirnability to express the foreign gene is examined. Stability of the transformants may then be investigated. In a preferred embodiment the foreign gene is added to the cassette and oriented in the vector such that transcription of the gene is in the direction of the transcription terminator.

We have found that vectors according to the present invention maintain cloned DNA with 100% stability for at least 70 generations.

Particularly preferred vectors according to the invention are ρPOD2152, pPOD2154, pPOD2158, pPOD2161, pPOD2167 and pPOD2168 as hereinafter specifically described.

Brief Description of the Drawings

The invention is further illustrated in the following non-limiting examples which refer to the accompanying diagrams Figures 1 - 6, in which:

Figure 1 shows a restriction map of plasmid pPOD2000 Figure 2 is a diagram showing plasmid restriction maps and a scheme indicating the mode of construction of plasmid pPOD2132 Figure 3 is a similar diagram indicating the mode of construction of plasmid pPOD2145 Figure 4 shows vector restriction maps of the various classes of vector arising from the insertion of the cassette Figure 5 shows a restriction map of ρPOD2180 Figure 6 shows restriction maps of the various vectors resulting from the insertion of the ∝-amylase gene into the vectors of the invention. Description of the Specific Embodiments

Example 1

The Endogenous Plasmid pPOD2000

Bacillus strain 1E2 was used as the source of the endogenous plasmid (a strain maintained by the Bacillus Genetic Stock Centre, The Ohio State University, 484 West, 12th Avenue, Columbus, Ohio 43210, USA). This strain was grown in Penassay broth (Difco Antibiotic Medium No. 3) and the cells harvested in late logarithmic growth phase (0.D600nm of 1.0). Plasmid DNA was then isolated from the cells by the method of Birnboim & Doly, 1979 (Nucl. Acid. Res. 7 : 1513). Agarose gel electrophoresis of such preparations revealed a single plasmid species 8.5kb in size, which was designated pPOD2000. Plasmid copy number determinations were performed for pPOD2000 by the method of Projan et al, 1983 (Plasmid 9: 182-190) using 1E2 cells in early, mid and late logarithmic growth phase and at several time points in stationary phase. The plasmid was found to maintain a copy number of 10 per chromosome irrespective of growth phase. A restriction map of pPOD2000 was generated by standard techniques, (described in Maniatis et al, 1982 - Molecular Cloning, A Laboratory Manual, Cold Spring Harbor

Laboratory) and is presented in Figure 1. The plasmid contains five HindIII sites distributed fairly evenly around the map. A cassette was therefore constructed with Hindlll ends suitable for insertion into pPOD2000 in five different positions. pPOD2000 contains no recognition sites for the enzymes BamHl and Sma1, and the cassette was constructed with unique sites for these two enzymes to facilitate the cloning of foreign genes as described below. Example 2

Construction of plasmid pPOD2145 (Cassette construction)

Starting plasmids. The well-known high copy number plasmid pUC8

(Vierra and Messing, 1982, Gene 19: 259) was chosen as the vector in which to assemble most of the cassette because it contains a suitable series of adjacent restriction sites. pUC8 can be purchased from Bethesda Research Laboratories, Cambridge, UK. The well known Staphylococcus aureus plasmid pC194 (lordanescu, S et al 1978, Plasmid 1: 468-479) was chosen as the source of the antibiotic resistance marker for three reasons: (a) because its chloramphenicol resistance gene is known to be suitable for selection of B. subtilis transformants using the protoplast transformation procedure (Chang and Cohen, 1979, Molec. Gen. Genet. 168: 111); (b) because the promoter of that gene is relatively inefficient in B. subtilis (A. Mountain & M. Nugent, unpublished) and therefore unlikely to destabilise plasmids in that host by readthrough transcription or metabolic load effects and (c) because pC194 has been fully sequenced and partially characterised

(Horinouchi & Weisblum, 1982, J. Bacteriol 150: 815) such that restriction fragments have been identified which contain the Cm^r gene but not intact replication functions. pCPP3 (Band et al,

1983, Gene 26: 313-315) was the source of the λto transcription terminator, which has been shown to function efficiently in B. subtilis (Peschke et al, 1985, J. Molec. Biol 186, 547-555). Restriction maps of these starting plasmids are given in Figure 2. Strains containing each of pC194 and pCPP3 are maintained by the American Type Culture Collection, Rockville, Maryland, USA (ATCC strains 37034 and 37278). Routine media and conditions for restriction enzyme digestions, DNA ligations, agarose gel electrophoresis and preparation of E. coli competent cells were as described in Maniatis et al 1982. (a) Construction of plasmid pPOD2103. 2μg of pC194 DNA was digested to completion first with HpaII, then with Clal, and the digest subjected to agarose gel electrophoresis. The 1310bp fragment containing the Cm^r gene was excised from the gel, purified by the electroelution procedure of McDonell et al (1982, J. Molec.

Biol. 110, 119-146), subjected to phenol extraction and ethanol precipitation, and resuspended in TE buffer (comprising 5mM

Tris/HCl, pH 7.5 and 0.5mM EDTA) . 0.5μg of pUC8 was digested with

Accl and treated with calf intestinal phosphatase. Following phenol extraction, ethanol precipitation and resuspension in TE the digest was ligated with 0.5μg of the Cm^r fragment. The ligation mixture was used to transform competent cells of E. coli s trai n

JM101 (ATCC strain 33876) with selection for ampicillin resistant transformants. Several transformants were identified which were also resistant to chloramphenicol. Among these one was identified by restriction analysis in which the Cm^r gene was oriented with its

3' end adjacent to the BamHl site of the pUC8 vector (see Figure

2). This plasmid was designated pPOD2103.

(b) Construction of plasmid pPOD2104. 5ug of pCPP3 was digested to completion with EcoRl, and then with BamHl. The double digest was subjected to agarose gel electrophoresis and the 950bρ fragment carrying the Cm^r gene and λto was purified by electroelution, phenol extraction and ethanol precipitation, and resuspended in TE buffer. The fragment was digested to completion with Sau3A and agarose gel electrophoresis performed on the digest. The 189bp fragment carrying λto was purified by electroelution, phenol extraction and ethanol precipitation, and resuspended in TE buffer. 0.5μg of plasmid pPOD2103 was digested with BamHl and treated with calf intestinal phosphatase, followed by phenol extraction and ethanol precipitation. Following resuspension in TE the digest was ligated with 0.1μg of the 189bp λto fragment. The ligation mixture was used to transform competent cells of E. coli strain DH1 (ATCCH-strain 33849), with selection for ampicillin resistant transformants. Plasmid minipreparations were performed on 12 such transformants by the method of Birnboim & Doly, 1979 (Nucl. Acid. Res. 7: 1513). Agarose gel electrophoresis of double EcoRl/Hindlll digests of these plasmids revealed that five possessed the approximately 1.5kb fragment expected from a single insert of the λto fragment in pPOD2103. The approximately 1.5kb fragment was purified following agarose gel electrophoresis of preparative double EcoRl/HindIII digests on these five plasmids. Agarose gel electrophoresis of Hinfl digests on the purified fragments was used to identify a clone in which the 189bp λto fragment was oriented appropriately to terminate transcripts initiated at the promoter of the Cm gene (see Figure 3). This plasmid was designated pPOD2104.

(c). Construction of plasmid pPOD2132. Agarose gel electrophoresis of a complete BamHl digest of ρPOD2104 showed that cloning the 189bp Sau3A fragment carrying λto into the BamHl site of pPOD2103 had reconsituted BamHl sites at each end of the terminator. In order to leave the BamHl site adjacent to the 3' end of the Cm^r gene

(BamHl site 1, Figure 1) as a unique site to facilitate further cloning it was necessary to remove the other BamHl site, adjacent to the Smal site (BamHl site 2, Figure 1). This was accomplished by using the DNA polymerising activity of the Klenow fragment of E. coli DNA polymerase to fill in the recessed 3' ends of a partial

BamHl digest of pPOD2104. 3μg aliquots of pPOD2104 DNA were incubated with 0.1 units of BamHl at 37ºC for 5, 10 and 20 minutes respectively. 1/10th of each digest was subjected to agarose gel electrophoresis and the remaining 9/10 stored at -20ºC. The 5 minute digest was adjudged to be the most suitable since it contained the greatest proportion of the linearised partial digestion product, i.e. cleaved at only one of the two BamHl sites. Following phenol extraction to inactivate the restriction enzyme, and ethanol precipitation, the remaining 9/10 of the 5 minute digest was resuspended in TE buffer. Recessed 3' ends in the digest were then filled in by using the Klenow fragment of DNA polymerase in the presence of all four deoxyribonucleotide triphosphates as described in Maniatis et al, 1982 (Molecular Cloning, A Laboratory Manual). Following a further phenol extraction and ethanol precipitation the digest was resuspended in TE buffer and electrophoresed on a preparative agarose gel. The linear form was purified from the gel by electroelution and phenol extraction. Following ethanol precipitation the approximately 0.2 μg of linear pPOD2104 recovered was resuspended in 10μl of TE buffer and ligated in a volume of 100μl to effect circularisation. The ligation mixture was transformed into E . coli strain DH1 with selection for ampicillin resistant transformants. Plasmid minipreparations were performed on 20 such transformants. Complete BamHI digests on these plasmids showed that all possessed only a single BamHI site, and BamHI/Stul double digests were performed to distinguish clones lacking BamHI site 1 from those lacking site 2. Agarose gel electrophoresis of these double digests revealed that 17/20 clones had a 590bp fragment indicating removal of site 1, with the remaining 3 showing a 400bρ fragment consistent with the loss of site 2. Complete BamHl, Smal and Stul single digests, and complete Stul/BamHl and Smal/BamHl double digests were performed on the three clones apparently lacking site 2 and subjected to agarose gel electrophoresis to confirm this interpretation. All three were linearised by the single digests and gave the 395bρ and 190bρ fragments expected from the Stul/BamHl and Smal/BamHl double digests respectively. One of the three plasmids was designated pPOD2132 (see Figure 2).

(d) Construction of plasmid pPOD2145. 2μg of plasmid pPOD2132 was linearised by complete digestion with EcoRl, phenol extracted and ethanol precipitated. Following resuspension of the digest the recessed 3' ends were filled in using the Klenow fragment of DNA polymerase in the presence of dATP and dTTP . Following phenol extraction and ethanol precipitation 0.7μg of this DNA was ligated with 2.0μg of synthetic HindIII linkers. Following phenol extraction and ethanol precipitation the ligation mixture was resuspended in Hindlll buffer and twice treated with 50 units of Hindlll to cleave off excess linkers. The Hindlll digest was then subjected to preparative agarose gel electrophoresis and the 1.5 kb Hindlll fragment containing the Cm^r gene and λto was purified by electroelution and phenol extraction, and resuspended in TE buffer. 1μg of pBR322 DNA (Bolivar et al, 1977, Gene 2: 95-113) was digested to completion with HindIII and treated with calf intestinal phosphatase. Following phenol extraction, ethanol precipitation and resuspension in TE, 0.1μg of this DNA was ligated with 0.1μg of the 1.5kb HindIII fragment. The ligation mixture was transformed into competent cells of E. coli strain DH1 with selection for ampicillin resistant transformants. Among these several were identified which also displayed resistance to chloramphenicol up to 20μg per ml. Complete single digests with HindIII, EcoRl, Clal and BamHl, and complete double digests with BamHl/Smal and BamHl/EcoRl were performed on plasmid preparations of two of these clones. Agarose gel electrophoresis of these digests showed all were consistent with both plasmids comprising pBR322 carrying a single insert of the 1.5kb HindIII fragment in the HindIII site. One of the two hybrid plasmids was designated pPOD2145 (see Figure 3). A restriction map of the 1.5kb HindIII fragment, hereafter referred to as the HindIII cassette fragment, is given in Figure 3.

Example 3

Insertion of the cassette into pPOD2000

Partial HindIII digests were performed on pPOD2000 by incubating 5μg of pPOD2000 DNA at 37ºC with 1 unit of HindIII for 5, 10 and 20 minutes respectively. 1/10th of each digest was subjected to agarose gel electrophoresis and the remaining 9/10this stored at -20ºC. The 10 minute digest was adjudged to be the most suitable since it contained the greatest proportion of the required partial digestion product, i.e. pPOD2000 linearised by cleavage at only one of the five HindIII sites, the linearised form being identified by electrophoresing on the same gel a complete Sall digest of pPOD2000. (As indicated in Figure 1, pPOD2000 contains only a single Sail site). The remaining 9/10 of the 10 minute partial HindIII digest was phenol extracted and ethanol precipitated. Following resuspension in TE the digest was treated with calf intestinal phosphatase, then electrophoresed on a preparative agarose gel. The linearised form was purified from the gal by electroelution and phenol extraction. Following ethanol precipitation the DNA was resuspended in TE.

2μg of pPOD2145 DNA was digested to completion with HindIII, and the digest electrophoresed on a preparative agarose gel. The 1.5kb HindIII cassette fragment was purified from the gel by electroelution and phenol extraction. Following ethanol precipitation the fragment was resuspended in TE. 0.2μg of the cassette fragment was ligated with 0.2μg of the purified linearised form from the partial HindIII digest of pPOD2000, and the ligation mixture used to transform protoplasts of B. subtilis strain PSLl, a strain maintained by the Bacillus Genetic Stock Centre, Colombia, Ohio (BGSC strain IA510). The protoplasts were prepared and transformation effected by the procedure of Chang & Cohen (1979, Molec. Gen. Genet. 168: 111). Transformants were selected on DM3 medium containing (in addition to the ingredients described by Chang

& Cohen) 0.9% soluble starch, 0.4% gelatin, 0.04% BSA, and 5μg per ml of chloramphenicol. 15 such Cm^r transformants were isolated and preparations of the plasmids they carried were performed using the procedure described in Example 1 for pPOD2000. A series of restriction digests was performed on these plasmids to determine the position and orientation of the HindIII cassette. The results are summarised in Table 1. 11 of the 15 plasmids were found to comprise intact pPOD2000 with the cassette cloned into one of three HindIII sites, sites 1, 4 or 5 (see Figure 1). In the remaining 4 plasmids the smallest HindIII fragment of pPOD2000 (extending from HindIII site 1 to site 2, see Figure 1) had been replaced by the HindIII cassette. These 4 plasmids were presumed to result from the presence - in the gel-purified preparation of pPOD2000 linearised by partial digestion with Hindlll to which the cassette was ligated - of pPOD2000 DNA extending from HindIII site 1 round in the clockwise direction to Hindlll site 2, this being due to the very similar mobility of the two DNA species, of sizes 8.5kb and 8.0kb, in the preparative agarose gel. No cassette insertions were found to be located in Hindlll site 3, suggesting the presence of essential plasmid functions in this region. Seven different classes of cassette insertions were identified, distinguished by differences in the location and orientation of the cassette (see Figure 4 and Table 1).

Table 1

Isolation and Mutation of the HindIII cassette in the cassette insertants

Plasmid Insertion Location Orientation of Cm^r gene

Class of with respect to pPOD2000 Cassette Map in Figure 1

pPOD2159, 2162 2168 1 HindIII Site 1 Clockwise

pPOD2161 2 HindIII S i te 1 Anticlockwise

ρPOD2167 3 HindIII Site 4 Clockwise

pPOD2154, 2169, 2171 4 HindIII Site 4 Anticlockwise

PPOD2155, 2164,

2165 5 HindIII Site 5 Anticlockwise

pPOD2158, 2170 6 HindIII Sites 1 - 2 Clockwise

pPOD2152, 2166 7 HindIII Sites 1 - 2 Anticlockwise Example 4

Stability tests on the cassette insertants

Small scale serial subculture experiments were performed on

PSLl carrying one representative of each of the seven classes of cassette insertant listed in Table 1 and PSLl carrying ρC194, to determine the segregational stability of the plasmids in the absence of selection. A single colony of each strain was inoculated into 4ml L-broth containing 5μg per ml chloramphenicol in a 30ml

Universal container (Sterilin), and incubated in an orbital shaker (37ºC, 240rpm) until stationary phase was reached. 4μl of this culture was then inoculated into 4ml L-broth without antibiotic, and grown again to stationary phase. This 1/1000 dilution and subculturing in the absence of antibiotic selection was repeated four times, at which point it was estimated that the strains had been grown for approximately 50 generations in the absence of selection. Dilutions of the final stationary phase cultures were plated onto L-agar and 100 single colonies picked onto both L-agar and L-agar containing chloramphenicol at 5μg per ml. The number of colonies resistant to the antibiotic was expressed as a percentage of the number growing on the L-agar plate, and taken as representing the proportion of the population carrying the plasmid. The results are given in Table 2. They show that insertion of the cassette in either orientation into pPOD2000 at HindIII sites 1 or 4, or replacing the smallest pPOD2000 HindIII fragment between sites 1 and 2, gives hybrid plasmids which are maintained with 100% stability in the absence of selection. In the same experiment pC194, the Staphyloccoccus aureus plasmid from which is taken the Cm^r gene contained in the cassette, is maintained with only 90% stability. Table 2

Stability Tests on representative cassette insertants

Plasmid Insertion Class % Cells retaining plasmid after 50 generations without selection

pPOD2168 1 100

pPOD2161 2 100

pPOD2167 3 100

pPOD2154 4 100

pPOD2155 5 97

pPOD2158 6 100

pPOD2152 7 100

pC194 - 90 Example 5

Construction of hybrid plasmids carrying an ∝-amylase gene

The usefulness of the vectors derived from pPOD2000 and described in Example 4 was examined by cloning into one representative of four (out of the seven) classes an ∝-amylase gene originating in a Bacillus species closely related to B. subtilis. The ∝-amylase gene was subcloned from a hybrid plasmid designated pPOD2180 which comprised the vector pBD64 (Gryczan et al., 1980, J. Bacteriol. 141: 246-253) with a 2.5kb partial Sau3A fragment of the closely related Bacillus species cloned into the BglII site. A restriction map of pPOD2180 is given in Figure 5. The ∝-amylase gene is efficiently transcribed and translated in B. subtilis using the natural gene expression signals of that gene.

2μg of ρPOD2180 DNA was digested to completion with first Bglll, then BamHl, and the digest electrophoresed on a preparative agarose gel. The 2kb fragment which contains the entire ∝-amylase gene was purified from the gel by electroelution and phenol extraction. Following ethanol precipitation the fragment was resuspended in TE. 1μg of each of the plasmids pPOD2152, pPOD2158, pPOD2168, and pPOD2154 was digested to completion with BamHl, and treated with calf intestinal phosphatase. Following phenol extraction and ethanol precipitation the digests were resuspended in TE. 0.2μg of each of these four DNA's was ligated with 0.2μg of the 2kb BglII/BamHl fragment carrying the amylase gene. The ligation mixtures were used to transform the amylase-defective B. subtilis strain 1A289 (BGSC strain 1A289) with selection for chloramphenicol resistant transformants using the protoplast transformation procedure and selective medium described in Example 3. Since this selective medium contained starch transformants containing the cloned amylase gene could be directly identified by the appearance of clearing zones surrounding the transformant colony. The appearance of such zones also demonstrated the expression of the cloned amylase gene in the B. subtilis host and the secretion from it of the ∝-amylase enzyme.

Plasmid preparations were performed on several transformants resulting from ligation of the 2kb fragment carrying the amylase gene with each of the vectors derived from pPOD2000. A series of restriction digests were performed on these plasmids, with results which confirmed that they comprised the intact vectors with the intact 2kb insert carrying the amylase gene. The digests also showed that for each of the four vectors hybrids were recovered in which the cloned 2kb fragment was oriented such that the amylase gene was transcribed towards the λto terminator. For two of the vectors only, pPOD2158 and pPOD2168, hybrids were also recovered in which the 2kb fragment was in the opposite orientation, i.e. such that the amylase gene was transcribed towards the Cm^r gene. A total of six different types of hybrid clone were therefore identified, all of which comprised intact vector + insert, and in all of which the cloned amylase gene was expressed with secretion of the amylase. A restriction map for one representative of each of the six different types of hybrid plasmid, pPOD2191, 2192, 2193,

2194, 2195 and 2196, is given in Figure 6.

Example 6

Stability tests on the hybrids carrying the amylase gene

Experiments were performed to determine the segregational stability in strain 1A289 of the following plasmids: pPOD2152, 2158, 2168, 2154 (the four endogenous plasmid-based cloning vectors into which the amylase gene was cloned, as described in Example 5); pPOD2191, 2192, 2193, 2194, 2195, 2196 (representing the six different types of hybrid carrying the amylase gene); pBD64 (the conventional high copy number vector into which the amylase gene was initially cloned) and pPOD2180 (comprising the amylase gene cloned into pBD64). A single colony of each strain was inoculated into

4mls L-broth containing 5μg per ml of chloramphenicol in a 30ml Universal container and incubated in an orbital shaker (37ºC,

240rpm) until stationary phase was reached. 20μl of these cultures were inoculated into 21 shake flasks containing 200mls of HB medium, which comprised the following ingredients (adjusted to pH 7.5):

7g/l (NH₄)₂SO₄; 6.24g/l NaH₂PO₄.2H₂O; 5g/l Yeastex (Bovril Foods Limited, Burton on Trent); 40g/l glycerol; 10ml/l trace elements (Pirt et. al, 1975, Principles of microbe and cell cultivation, p.134, Oxford Blackwell Scientific Publications). HB medium permits much higher biomass to be achieved for strain 1A289 than L-broth or other conventional complex media, and it was therefore used in the stability tests to prolong the growth phase. These cultures were incubated in an orbital shaker until stationary phase was reached, at which point 20μl of each was then inoculated into a further 200ml of HB medium, and the cultures grown again until stationary phase was reached. This 1/10,000 dilution and subculturing in the absence of selection was repeated a further four times, at which point it was estimated that each strain had been grown for at least 70 generations in the absence of selection. Dilutions of the final stationary phase cultures were platedes out on L-agar and 100 single colonies picked onto both L-agar and L-agar containing chloramphenicol at 5μg/ml. The number of colonies resistant to the antibiotic was expressed as a percentage of the number growing on the L-agar plate, and taken as representing the proportion of the population carrying the plasmid. For plasmids pPOD2180, 2191, 2192, 2193, 2194, 2195 and 2196 the 100 colonies were also picked onto L-agar containing 1% starch to test for retention and expression of the cloned amylase gene: for each plasmid a 100% correlation was observed between growth on chloramphenicol and production of clearing zones on plates containing starch, suggesting the results were not complicated by structural instabilities. The results are presented in Table 3. All six hybrids comprising the amylase gene cloned into the endogenous plasmid-based vectors showed dramatically greater stability than the high copy number hybrid pPOD2180, this plasmid being totally lost from the population after about 50 generations. The four hybrid plasmids (pPOD2191, 2193, 2194 and 2196) in which the cloned amylase gene was oriented such that transcripts initiated at the amylase promoter would terminate at λto were all maintained with 100% stability in this experiment. Amylase assays and analysis of proteins secreted from these strains by SDS/polyacrylamide gel electrophoresis revealed approximately 3 grams per litre of amylase in the culture supernatants. The high degree of stable maintenance of these hybrids and high yields of amylase demonstrate the potential usefulnes of the vectors for production of enzymes and other products. The two hybrid plasmids (pPOD2192 and 2195) in which the cloned amylase gene was in the opposite orientation, i.e. transcribed away from λ to were somewhat less stably maintained, suggesting the terminator is important in preventing destabilisation by readthrough transcription.

The vector pPOD2152 and one of the hybrids derived from it which was maintained with 100% stability in strain 1A289, namely pPOD2191, were transferred by the protoplast transformation procedure described in Example 3 into the hypersecretion mutant B. subtilis strain 1A199 (Bacillus Genetic Stock Centre strain 1A199). This strain contains a mutation, sacU^h, which leads to increased production of the B. subtilis ∝-amylase, levansucrase and proteases, and also to increased instability of a number of hybrid plasmids, including a high copy number hybrid comprising the α-amylase gene of B. amyloliquefaciens cloned into pUB110 (Vehmaanpera and Korhola, 1986, Appl. Microbiol. Biotechnol. 23:456-461). Segregational stability tests were performed on 1A199 carrying pPOD2152 and pPOD2191 using the procedure described above for 1A289 carrying pPOD2191. In contrast to the results described in the literature for hybrid plasmids which use vectors derived from Staphylococcus aureus plasmid replicons, pPOD2191 was found to be maintained with 100% stability after 50 generations in the absence of selection in this sacU mutant, as was pPOD2152.

Example 7

The usefulness of one of the vectors derived from pPOD2000 and described in Example 4, pPOD2152, was further demonstrated by cloning into it a gene 'encoding another example of a commercially important enzyme, namely subtilisin from B. amyloliquefaciens. The gene was taken from plasmid pPT30, which comprises a 3.4Kb EcoRl fragment containing the entire subtilisin gene cloned into pUB110 (Thomas et al, 1985, Nature 318:375-376). 3ug of pPT30 DNA was digested with EcoRl, electrophoresed on an agarose gel and the 3.4Kb EcoRl fragment containing the subtilisin gene purified as described in Example 2a. The recessed 3' ends of this fragment were filled in as described in Example 2c. lug of pPOD2152 was digested with BamHl and the recessed 3' ends filled in as described in Example 2c. 0.5ug of this pPOD2152 DNA was ligated with 0.5ug of the subtilisin fragment and the mixture transformed into B. subtilis strain 1A289 as described in Example 3. Colonies carrying the subtilisin gene cloned into pPOD2152 were identified by their production of a large clearing zone on L-agar plates containing chloramphenicol and 1% skimmed milk. The presence of the cloned subtilisin fragment in these clones, and the orientation of the subtilisin gene with respect to the λto transcription terminator was established by perfroming restriction digests on purified plasmid DNA. Similarly the same fragment carrying the subtilisin gene was cloned into the BamHl site of the Staphylococcus aureus plasmid pUB110, the replicon from which cloning vectors and expression vectors for use in B. subtilis are most commonly derived (Gryczan, 1982, in "The Molecular Biology of the Bacilli", Ed. D.A. Dubnau, Academic Press, pp 307-329). Segregational stability tests were then performed on representative clones as described in Example 6, except that the presence or absence of the hybrid plasmids carrying the subtilisin gene was scored both by antibiotic restistance (chloramphenicol for pPOD2152 hybrids, and kanamycin for pUB110 hybrids) and the presence or absence of large clearing zones on L-agar plates containing 1% skimmed milk. pPOD2380 was chosen as a representative pP0D2152 clone in which the subtilisin gene was oriented such that it was transcribed from its own promoter towards λto, and was identical to pPOD2191 shown in Figure 6 except with the amylase gene replaced by the sutilisin gene. pPOD2390 and pPOD2391 were chosen as representative pUB110 clones with the subtilisin gene in opposite orentations in the BamHl site. The results are presented in Table 4. and show that pPOD2380 was maintained with 100% stability after 50 generations in the absence of selection, while the pUB110 hybrids proved segregationally unstable.

Table 4

Stability tests on pPOD2152, pUB110, pPOD2380, pPOD2390 and pPOD2391

%cells retaining plasmid

Plasmid Vector Insert after 50 generations

pUB110 pUB110 None 100

ρPOD2390 pUB110 subtilisin gene 49

pPOD2391 pUB110 subtilisin gene 19

pPOD2152 pPOD2152 None 100

ρPOD2380 pPOD2152 subtilisin gene 100

Example 8

Further evidence for the usefulness of one of the vectors derived from pPOD20O0, pPOD2152, was obtained by demostrating its ability to stably maintain a hybrid gene encoding another heterologous secreted product, namely an E. coli β-lactamase. A translational fusion was made in which the truncated E. coli β-lactamase described by Palva et al, 1982, Proc. Natl. Acad. Sci. USA 79:5582-5586, which lacks its own signal sequence was fused in-frame to the end of the signal sequence of the ∝-amylase gene described in Example 5. A 2Kb BamHl fragment carrying this amylase/β-lactamase fusion - expressing β-lactamase using the amylase promoter, translation initiation region and signal sequence coding region - was ligated with pPOD2152 digested with BamHl, and the mixture transformed into 1A289 protoplasts. Chloramphenicol resistant transformants were screened for ampicillin resistance to identify hybrids carrying the amylase/β-lactamase fusion fragment. Plasmid pPOD2395 was identified by restiction digests as a hybrid comprising pPOD2152 carrying the 2Kb amylase/β-lactmase fusion oriented such that transcription of the β-lactamase gene from the amylase promoter was towards λto. Segregational stability tests were performed on 1A289 carrying pPOD2395 and pPOD2152 as described in Example 6, except that presence or absence of the plasmids was scored by resistance to both chloramphenicol and ampicillin for pPOD2395, and to chloramphenicol only for pPOD2152. Both plasmids proved to be maintained with 100% stability after 70 generations in the absence of selection.

Table 3

Stability tests on pPOD2191, 2, 3, 4, 5, & 6 and pPOD2180

Plasmid Vector Insert Direction of %Cells of g-Amylase retaining gene with plasmid respect to after 70 λto generations

pPOD2168 None 100

pPOD2152 None 100

pPOD2158 None 100

pPOD2154 None 100

pBD64 None 95

pPOD2191 pPOD2152 ∝-amylase gene towards λto 100

pPOD2192 pPOD2158 ∝-amylase gene away from λto 96

pPOD2193 ρPOD2168 ∝-amylase gene towards λto 100

pPOD2194 pPOD2154 ∝-amylase gene towards λto 100

pPOD2195 pPOD2168 ∝-amylase gene away from λto 25

pP0D2196 pPOD2158 ∝-amylas e gene towards λ to 100

pPOD2180 pBD64 ∝-amylase gene λto not present 0

Claims

1. A vector suitable for cloning and expressing heterologous DNA in host cells of a given type comprising:

plasmid DNA derived from a plasmid which is normally stably maintained in said host cells, and

ligated with said plasmid DNA, heterologous DNA comprising at least one restriction site which is unique in said heterologous DNA and which does not occur in said plasmid DNA, and DNA coding for at least one selectable marker;

characterised in that, said heterologous DNA is ligated within a non-unique restriction site of said plasmid and the vector is normally stably maintained in said host cells.

2. An expression vector comprising a vector according to claim 1 in which a foreign gene has been inserted at the at least one unique restriction site of the heterologous DNA of the vector.

3. A vector according to claim 1 or 2, in which the plasmid is a Bacillus plasmid.

4. A vector according to any of the preceeding claims in which the heterologous DNA additionally comprises at least one transcription terminator.

5. A vector according to any of the preceeding claims in which the heterologous DNA of the vector includes a promoter.

6. A vector according to any one of claims 2 to 4, in which the natural promoter of the foreign gene is included therewith.

7. A vector according to any of claims 2-6 in which the heterologous DNA comprises at least one transcription terminator and in which the foreign gene is oriented in the vector such that transcription of the gene is in the direction of the at least one transcription terminator.

8. Vectors ρPOD2152, ρPOD2154 , pPOD2158, ρPOD2161 and pPOD2168 as hereinafter specifically described.

9. Host cells transformed with a vector according to any of the preceeding claims.

10. Transformed host cells according to claim 9 which are gram positive bacterial host cells.

11. Transformed host cells according to claim 10 of genus Bacillus.

12. Transformed host cells according to claim 11 of species B . subtilis, B. pumilis or B. amyloliquefaciens.

13. A method for obtaining vectors suitable for cloning and expression of heterologous DNA in host cells of a given type comprising:

providing (a) a plasmid which is normally stably maintained in said host cells, and

(b) a cassette of heterologous DNA comprising at least one restriction site which is unique in said cassette and which does not occur in said plasmid, at either and thereof linkers ligatable with a non-unique restriction site of said plasmid, and DNA coding for at least one selectable marker; partially digesting said plasmid with a restriction enzyme which cleaves at said non-unique restriction site to provide a plurality of linear digested plasmid DNA molecules;

ligating said cassette with said linear DNA molecules to provide a plurality of vectors, and

selecting from said vectors one or more vectors for stable maintenance in the absence of selection in said host cells.

14. A method according to claim 13, in which the plasmid is a Bacillus plasmid.

15. A method according to claim 13 or 14, in which after partial digestion of the plasmid the linearised form of the plasmid is purified and ligated with the cassette.

16. A method according to any one of claims 13, 14 or 15, in which the vectors are selected for stable maintenance by serial subculture in the host cells.

17. A method for the preparation of an expression vector according to claim 2 in which a foreign gene is ligated into the at least one unique restriction site of the heterologous DNA of a vector according to claim 1.

18. A method for the preparation of host cells according to claim 9 comprising transforming host cells with a vector according to claim 1 or an expression vector according to claim 2.

19. A process for the production of a foreign gene product comprising culturing host cells transformed with an expression vector according to claim 2 to express the foreign gene product.