# Patent

## Title
2-micron family plasmid and use thereof

## Abstract

The present invention provides a 2 μm-family plasmid comprising a polynucleotide sequence insertion, deletion and/or substitution between the first base after the last functional codon of at least one of either a REP2 gene or an FLP gene and the last base before the FRT site in an inverted repeat adjacent to said gene.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a National Stage application based on International Application No. PCT/GB2004/005435, filed Dec. 23, 2004, which claims priority to Great Britain Application No. 0329722.3, filed Dec. 23, 2003, the disclosures of which are incorporated herein by reference.
FIELD OF THE INVENTION
The present application relates to modified plasmids and uses thereof.
BACKGROUND OF THE INVENTION
Certain closely related species of budding yeast have been shown to contain naturally occurring circular double stranded DNA plasmids. These plasmids, collectively termed 2 μm-family plasmids, include pSR1, pSB3 and pSB4 from Zygosaccharomyces rouxii (formerly classified as Zygosaccharomyces bisporus), plasmids pSB1 and pSB2 from Zygosaccharomyces bailii, plasmid pSM1 from Zygosaccharomyces fermentati, plasmid pKD1 from Kluyveromyces drosphilarum, an un-named plasmid from Pichia membranaefaciens (hereinafter referred to as “pPM1”) and the 2 μm plasmid and variants (such as Scp1, Scp2 and Scp3) from Saccharomyces cerevisiae (Volkert, et al., 1989, Microbiological Reviews, 53, 299; Painting, et al., 1984, J. Applied Bacteriology, 56, 331) and other Saccharomyces species, such as S. carlsbergensis. As a family of plasmids these molecules share a series of common features in that they possess two inverted repeats on opposite sides of the plasmid, have a similar size around 6-kbp (range 4757 to 6615-bp), at least three open reading frames, one of which encodes for a site specific recombinase (such as FLP in 2 μm) and an autonomously replicating sequence (ARS), also known as an origin of replication (ori), located close to the end of one of the inverted repeats. (Futcher, 1988, Yeast, 4, 27; Murray et al., 1988, J. Mol. Biol. 200, 601 and Toh-e et al., 1986, Basic Life Sci. 40, 425). Despite their lack of discernible DNA sequence homology, their shared molecular architecture and the conservation of function of the open reading frames have demonstrated a common link between the family members.
The 2 μm plasmid (FIG. 1) is a 6,318-bp double-stranded DNA plasmid, endogenous in most Saccharomyces cerevisiae strains at 60-100 copies per haploid genome. The 2 μm plasmid comprises a small-unique (US) region and a large unique (UL) region, separated by two 599-bp inverted repeat sequences. Site-specific recombination of the inverted repeat sequences results in inter-conversion between the A-form and B-form of the plasmid in vivo (Volkert & Broach, 1986, Cell, 46, 541). The two forms of 2 μm differ only in the relative orientation of their unique regions.
While DNA sequencing of a cloned 2 μm plasmid (also known as Scp1) from Saccharomyces cerevisiae gave a size of 6,318-bp (Hartley and Donelson, 1980, Nature, 286, 860), other slightly smaller variants of 2 μm, Scp2 and Scp3, are known to exist as a result of small deletions of 125-bp and 220-bp, respectively, in a region known as STB (Cameron et al., 1977, Nucl. Acids Res., 4, 1429: Kikuchi, 1983, Cell, 35, 487 and Livingston & Hahne, 1979, Proc. Natl. Acad. Sci. USA, 76, 3727). In one study about 80% of natural Saccharomyces strains from around the world contained DNA homologous to 2 μm (by Southern blot analysis) (Hollenberg, 1982, Current Topics in Microbiology and Immunobiology, 96, 119). Furthermore, variation (genetic polymorphism) occurs within the natural population of 2 μm plasmids found in S. cerevisiae and S. carlsbergensis, with the NCBI sequence (accession number NC—001398) being one example.
The 2 μm plasmid has a nuclear localisation and displays a high level of mitotic stability (Mead et al, 1986, Molecular & General Genetics, 205, 417). The inherent stability of the 2 μm plasmid results from a plasmid-encoded copy number amplification and partitioning mechanism, which is easily compromised during the development of chimeric vectors (Futcher & Cox, 1984, J. Bacteriol., 157, 283; Bachmair & Ruis, 1984, Monatshefte für Chemie, 115, 1229). A yeast strain, which contains a 2 μm plasmid is known as [cir+], while a yeast strain which does not contain a 2 μm plasmid is known as [cir0].
The US-region contains the REP2 and FLP genes, and the UL-region contains the REP1 and D (also known as RAF) genes, the STB-locus and the origin of replication (Broach & Hicks, 1980, Cell, 21, 501; Sutton & Broach, 1985, Mol. Cell. Biol., 5, 2770). The Flp recombinase binds to FRT-sites (Flp Recognition Target) within the inverted repeats to mediate site-specific recombination, which is essential for natural plasmid amplification and control of plasmid copy number in vivo (Senecoff et al, 1985, Proc. Natl. Acad. Sci. U.S.A., 82, 7270; Jayaramn, 1985, Proc. Natl. Acad. Sci. U.S.A., 82, 5875). The copy number of 2 μm-family plasmids can be significantly affected by changes in Flp recombinase activity (Sleep et al, 2001, Yeast, 18, 403; Rose & Broach, 1990, Methods Enzymol., 185, 234). The Rep1 and Rep2 proteins mediate plasmid segregation, although their mode of action is unclear (Sengupta et al, 2001, J. Bacteriol., 183, 2306). They also repress transcription of the FLP gene (Reynolds et al, 1987, Mol. Cell. Biol., 7, 3566).
The FLP and REP2 genes are transcribed from divergent promoters, with apparently no intervening sequence defined between them. The FLP and REP2 transcripts both terminate at the same sequence motifs within the inverted repeat sequences, at 24-bp and 178-bp respectively after their translation termination codons (Sutton & Broach, 1985, Mol. Cell. Biol., 5, 2770).
In the case of FLP, the C-terminal coding sequence also lies within the inverted repeat sequence. Furthermore, the two inverted repeat sequences are highly conserved over 599-bp, a feature considered advantageous to efficient plasmid replication and amplification in vivo, although only the FRT-sites (less than 65-bp) are essential for site-specific recombination in vitro (Senecoff et al, 1985, Proc. Natl. Acad. Sci. U.S.A., 82, 7270; Jayararm, 1985, Proc. Natl. Acad. Sci. U.S.A., 82, 5875; Meyer-Leon et al, 1984, Cold Spring Harbor Symposia On Quantitative Biology, 49, 797). The key catalytic residues of Flp are arginine-308 and tyrosine-343 (which is essential) with strand-cutting facilitated by histidine-309 and histidine 345 (Prasad et al, 1987, Proc. Natl. Acad. Sci. U.S.A., 84, 2189; Chen et al, 1992, Cell, 69, 647; Grainge et al, 2001, J. Mol. Biol., 314, 717).
Two functional domains are described in Rep2. Residues 15-58 form a Rep1-binding domain, and residues 59-296 contain a self-association and STB-binding region (Sengupta et al, 2001, J. Bacteriol., 183, 2306).
Chimeric or large deletion mutant derivatives of 2 μm which lack many of the essential functional regions of the 2 μm plasmid but retain functional the cis element ARS and STB, cannot effectively partition between mother and daughter cells at cell division. Such plasmids can do so if these functions are supplied in traces, by for instance the provision of a functional 2 μm plasmid within the host, a so called [cir+] host.
Genes of interest have previously been inserted into the UL-region of the 2 μm plasmid. For example, see plasmid pSAC3U1 in EP 0 286 424. However, there is likely to be a limit to the amount of DNA that can usefully be inserted into the UL-region of the 2 μm plasmid without generating excessive asymmetry between the US and UL-regions. Therefore, the US-region of the 2 μm plasmid is particularly attractive for the insertion of additional DNA sequences, as this would tend to equalise the length of DNA fragments either side of the inverted repeats.
This is especially true for expression vectors, such as that shown in FIG. 2, in which the plasmid is already crowded by the introduction of a yeast selectable marker and adjacent DNA sequences. For example, the plasmid shown in FIG. 2 includes a β-lactamase gene (for ampicillin resistance), a LEU2 selectable marker and an oligonucleotide linker, the latter two of which are inserted into a unique SnaBI-site within the UL-region of the 2 μm-family disintegration vector, pSAC3 (see EP 0 286 424). The E. coli DNA between the XbaI-sites that contains the ampicillin resistance gene is lost from the plasmid shown in FIG. 2 after transformation into yeast. This is described in Chinery & Hinchliffe, 1989, Curr. Genet., 16, 21 and EP 0 286 424, where these types of vectors are designated “disintegration vectors”. In the crowded state shown in FIG. 2, it is not readily apparent where further polynucleotide insertions can be made. A NotI-site within the linker has been used for the insertion of additional DNA fragments, but this contributes to further asymmetry between the UL and US regions (Sleep et al, 1991, Biotechnology (N Y), 9, 183).
We had previously attempted to insert additional DNA into the US-region of the 2 μm plasmid and maintain its high inherent plasmid stability. In the 2 μm-family disintegration plasmid pSAC300, a 1.1-kb DNA fragment containing the URA3 gene was inserted into EagI-site between REP2 and FLP in US-region in such a way that transcription from the URA3 gene was in same direction as REP2 transcription (see EP 0 286 424). When S150-2B [cir0] was transformed to uracil prototrophy by pSAC300, it was shown to be considerably less stable (50% plasmid loss in under 30 generations) than comparable vectors with URA3 inserted into the UL-region of 2 μm (0-10% plasmid loss in under 30 generations) (Chinery & Hinchliffe, 1989, Curr. Genet., 16, 21; EP 0 286 424). Thus, insertion at the EagI site may have interfered with FLP expression and it was concluded that the insertion position could have a profound effect upon the stability of the resultant plasmid, a conclusion confirmed by Bijvoet et al., 1991, Yeast, 7, 347.
It is desirable to insert further polynucleotide sequences into 2 μm-family plasmids. For example, the insertion of polynucleotide sequences that encode host derived proteins, recombinant proteins, or non-coding antisense or RNA interference (RNAi) transcripts may be desirable. Moreover, it is desirable to introduce multiple further polynucleotide sequences into 2 μm-family plasmids, thereby to provide a plasmid which encodes, for example, multiple separately encoded multi-subunit proteins, different members of the same metabolic pathway, additional selective markers or a recombinant protein (single or multi-subunit) and a chaperone to aid the expression of the recombinant protein.
However, the 6,318-bp 2 μm plasmid, and other 2 μm-family plasmids, are crowded with functional genetic elements (Sutton & Broach, 1985, Mol. Cell. Biol., 5, 2770; Broach et al, 1979, Cell, 16, 827), with no obvious positions existing for the insertion of additional DNA sequences without a concomitant loss in plasmid stability. In fact, except for the region between the origin of replication and the D gene locus, the entire 2 μm plasmid genome is transcribed into at least one poly(A)+ species and often more (Sutton & Broach, 1985, Mol. Cell. Biol., 5, 2770). Consequently, most insertions might be expected to have a detrimental impact on plasmid function in vivo.
Indeed, persons skilled in the art have given up on inserting heterologous polynucleotide sequences into 2 μm-family plasmids.
Robinson et al, 1994, Bio/Technology, 12, 381-384 reported that a recombinant additional PDI gene copy in Saccharomyces cerevisiae could be used to increase the recombinant expression of human platelet derived growth factor (PDGF) B homodimer by ten-fold and Schizosacharomyces pombe acid phosphatase by four-fold. Robinson obtained the observed increases in expression of PDGF and S. pombe acid phosphatase using an additional chromosomally integrated PDI gene copy. Robinson reported that attempts to use the multi-copy 2 μm expression vector to increase PDI protein levels had had a detrimental effect on heterologous protein secretion.
Shusta et al, 1998, Nature Biotechnology), 16, 773-777 described the recombinant expression of single-chain antibody fragments (scFv) in Saccharomyces cerevisiae. Shusta reported that in yeast systems, the choice between integration of a transgene into the host chromosome versus the use of episomal expression vectors can greatly affect secretion and, with reference to Parekh & Wittrup, 1997, Biotechnol. Prog., 13, 117-122, that stable integration of the scFv gene into the host chromosome using a δ integration vector was superior to the use of a 2 μm-based expression plasmid. Parekh & Wittrup, op. cit., had previously taught that the expression of bovine pancreatic trypsin inhibitor (BPTI) was increased by an order of magnitude using a δ integration vector rather than a 2 μm-based expression plasmid. The 2 μm-based expression plasmid was said to be counter-productive for the production of heterologous secreted protein.
Bao et al, 2000, Yeast, 16, 329-341, reported that the KlPDI1 gene had been introduced into K. lactis on a multi-copy plasmid, pKan707, and that the presence of the plasmid caused the strain to grow poorly. In the light of the earlier findings in Bao et al, 2000, Bao & Fukuhara, 2001, Gene, 272, 103-110, chose to introduce a single duplication of KlPDI1 on the host chromosome.
Accordingly, the art teaches the skilled person to integrate transgenes into the yeast chromosome, rather than into a multicopy vector. There is, therefore, a need for alternative ways of transforming yeast.
DESCRIPTION OF THE INVENTION
The present invention relates to recombinantly modified versions of 2 μm-family plasmids.
A 2 μm-family plasmid is a circular, double stranded, DNA plasmid. It is typically small, such as between 3,000 to 10,000 bp, preferably between 4,500 to 7000 bp, excluding recombinantly inserted sequences. Preferred 2 μm-family plasmids for use in the present invention comprise sequences derived from one or more of plasmids pSR1, pSB3, or pSB4 as obtained from Zygosaccharomyces rouxii, pSB1 or pSB2 both as obtained from Zygosaccharomyces bailli, pSM1 as obtained from Zygosaccharomyces fermentati, pKD1 as obtained from Kluyveromyces drosophilarum, pPM1 as obtained from Pichia membranaefaciens and the 2 μm plasmid and variants (such as Scp1, Scp2 and Scp3) as obtained from Saccharomyces cerevisiae, for example as described in Volkert et al, 1989, Microbiological Reviews, 53 (3), 299-317, Murray et al, 1988, Mol. Biol., 200, 601-607 and Painting, et al., 1984, J. Applied Bacteriology, 56, 331.
A 2 μm-family plasmid is capable of stable multicopy maintenance within a yeast population, although not necessarily all 2 μm-family plasmids will be capable of stable multicopy maintenance within all types of yeast population. For example, the 2 μm plasmid is capable of stable multicopy maintenance, inter alia, within Saccharomyces cerevisiae and Saccharomyces carlsbergensis. 
By “multicopy maintenance” we mean that the plasmid is present in multiple copies within each yeast cell. A yeast cell comprising 2 μm-family plasmid is designated [cir+], whereas a yeast cell that does not comprise 2 μm-family plasmid is designated [cir0]. A [cir+] yeast cell typically comprises 10-100 copies of 2 μm-family plasmid per haploid genome, such as 20-90, more typically 30-80, preferably 40-70, more preferably 50-60 copies per haploid genome. Moreover, the plasmid copy number can be affected by the genetic background of the host which can increase the plasmid copy number of 2 μm-like plasmid to above 100 per haploid genome (Gerbaud and Guerineau, 1980, Curr. Genetics, 1, 219, Holm, 1982, Cell, 29, 585, Sleep et al., 2001, Yeast, 18, 403 and WO99/00504). Multicopy stability is defined below.
A 2 μm-family plasmid typically comprises at least three open reading frames (“ORFs”) that each encode a protein that functions in the stable maintenance of the 2 μm-family plasmid as a multicopy plasmid. The proteins encoded by the three ORFs can be designated FLP, REP1 and REP2. Where a 2 μm-family plasmid comprises not all three of the ORFs encoding FLP, REP1 and REP2 then ORFs encoding the missing protein(s) should be supplied in trans, either on another plasmid or by chromosomal integration.
A “FLP” protein is a protein capable of catalysing the site-specific recombination between inverted repeat sequences recognised by FLP. The inverted repeat sequences are termed FLP recombination target (FRT) sites and each is typically present as part of a larger inverted repeat (see below). Preferred FLP proteins comprise the sequence of the FLP proteins encoded by one of plasmids pSR1, pSB1, pSB2, pSB3, pSB4, pSM1, pKD1, pPM1 and the 2 μm plasmid, for example as described in Volkert et al, op. cit., Murray et al, op. cit and Painting et al, op. cit. Variants and fragments of these FLP proteins are also included in the present invention. “Fragments” and “variants” are those which retain the ability of the native protein to catalyse the site-specific recombination between the same FRT sequences. Such variants and fragments will usually have at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or more, homology with an FLP protein encoded by one of plasmids pSR1, pSB1, pSB2, pSB3, pSM1, pKD1 and the 2 μm plasmid. Different FLP proteins can have different FRT sequence specificities. A typical FRT site may comprise a core nucleotide sequence flanked by inverted repeat sequences. In the 2 μm plasmid, the FRT core sequence is 8 nucleotides in length and the flanking inverted repeat sequences are 13 nucleotides in length (Volkert et al, op. cit.). However the FRT site recognised by any given FLP protein may be different to the 2 μm plasmid FRT site.
REP1 and REP2 are proteins involved in the partitioning of plasmid copies during cell division, and may also have a role in the regulation of FLP expression. Considerable sequence divergence has been observed between REP1 proteins from different 2 μm-family plasmids, whereas no sequence alignment is currently possible between REP2 proteins derived from different 2 μm-family plasmids. Preferred REP1 and REP2 proteins comprise the sequence of the REP1 and REP2 proteins encoded by one of plasmids pSR1, pSB1, pSB2, pSB3, pSB4, pSM1, pKD1, pPM1 and the 2 μm plasmid, for example as described in Volkert et al, op. cit., Murray et al, op. cit. and Painting et al, op. cit. Variants and fragments of these REP1 and REP2 proteins are also included in the present invention. “Fragments” and “variants” of REP1 and REP2 are those which, when encoded by the plasmid in place of the native ORF, do not disrupt the stable multicopy maintenance of the plasmid within a suitable yeast population. Such variants and fragments of REP1 and REP2 will usually have at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or more, homology with a REP1 and REP2 protein, respectively, as encoded by one of plasmids pSR1, pSB1, pSB2, pSB3, pSB4, pSM1, pKD1, pPM1 and the 2 μm plasmid.
The REP1 and REP2 proteins encoded by the ORFs on the plasmid must be compatible. REP1 and REP2 are compatible if they contribute, in combination with the other functional elements of the plasmid, towards the stable multicopy maintenance of the plasmid which encodes them. Whether or not a REP1 and REP2 ORF contributes towards the stable multicopy maintenance of the plasmid which encodes them can be determined by preparing mutants of the plasmid in which each of the REP1 and REP2 ORFs are specifically disrupted. If the disruption of an ORF impairs the stable multicopy maintenance of the plasmid then the ORF can be concluded to contribute towards the stable multicopy maintenance of the plasmid in the non-mutated version. It is preferred that the REP1 and REP2 proteins have the sequences of REP1 and REP2 proteins encoded by the same naturally occurring 2 μm-family plasmid, such as pSR1, pSB1, pSB2, pSB3, pSB4, pSM1, pKD1, pPM1 and the 2 μm plasmid, or variant or fragments thereof.
A 2 μm-family plasmid comprises two inverted repeat sequences. The inverted repeats may be any size, so long as they each contain an FRT site (see above). The inverted repeats are typically highly homologous. They may share greater than 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5% or more sequence identity. In a preferred embodiment they are identical. Typically the inverted repeats are each between 200 to 1000 bp in length. Preferred inverted repeat sequences may each have a length of from 200 to 300 bp, 300 to 400 bp, 400 to 500 bp, 500 to 600 bp, 600 to 700 bp, 700 to 800 bp, 800 to 900 bp, or 900 to 1000 bp. Particularly preferred inverted repeats are those of the plasmids pSR1 (959 bp), pSB1 (675 bp), pSB2 (477 bp), pSB3 (391 bp), pSM1 (352 bp), pKD1 (346 bp), the 2 μm plasmid (599 bp), pSB4 and pPM1.
The sequences of the inverted repeats may be varied. However, the sequences of the FRT site in each inverted repeat should be compatible with the specificity of the FLP protein encoded by the plasmid, thereby to enable the encoded FLP protein to act to catalyse the site-specific recombination between the inverted repeat sequences of the plasmid. Recombination between inverted repeat sequences (and thus the ability of the FLP protein to recognise the FRT sites with the plasmid) can be determined by methods known in the art. For example, a plasmid in a yeast cell under conditions that favour FLP expression can be assayed for changes in the restriction profile of the plasmid which would result from a change in the orientation of a region of the plasmid relative to another region of the plasmid. The detection of changes in restriction profile indicate that the FLP protein is able to recognise the FRT sites in the plasmid and therefore that the FRT site in each inverted repeat are compatible with the specificity of the FLP protein encoded by the plasmid.
In a particularly preferred embodiment, the sequences of inverted repeats, including the FRT sites, are derived from the same 2 μm-family plasmid as the ORF encoding the FLP protein, such as pSR1, pSB1, pSB2, pSB3, pSB4, pSM1, pKD1, pPM1 or the 2 μm plasmid.
The inverted repeats are typically positioned within the 2 μm-family plasmid such that the two regions defined between the inverted repeats (e.g. such as defined as UL and US in the 2 μm plasmid) are of approximately similar size, excluding exogenously introduced sequences such as transgenes. For example, one of the two regions may have a length equivalent to at least 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, up to 100%, of the length of the other region.
A 2 μm-family plasmid comprises the ORF that encodes FLP and one inverted repeat (arbitrarily termed “IR1” to distinguish it from the other inverted repeat mentioned in the next paragraph) juxtaposed in such a manner that IR1 occurs at the distal end of the FLP ORF, without any intervening coding sequence, for example as seen in the 2 μm plasmid. By “distal end” in this context we mean the end of the FLP ORF opposite to the end from which the promoter initiates its transcription. In a preferred embodiment, the distal end of the FLP ORF overlaps with IR1.
A 2 μm-family plasmid comprises the ORF that encodes REP2 and the other inverted repeat (arbitrarily termed “IR2” to distinguish it from IR1 mentioned in the previous paragraph) juxtaposed in such a manner that IR2 occurs at the distal end of the REP2 ORF, without any intervening coding sequence, for example as seen in the 2 μm plasmid. By “distal end” in this context we mean the end of the REP2 ORF opposite to the end from which the promoter initiates its transcription.
In one embodiment, the ORFs encoding REP2 and FLP may be present on the same region of the two regions defined between the inverted repeats of the 2 μm-family plasmid, which region may be the bigger or smaller of the regions (if there is any inequality in size between the two regions).
In one embodiment, the ORFs encoding REP2 and FLP may be transcribed from divergent promoters.
Typically, the regions defined between the inverted repeats (e.g. such as defined as UL and US in the 2 μm plasmid) of a 2 μm-family plasmid may comprise not more than two endogenous genes that encode a protein that functions in the stable maintenance of the 2 μm-family plasmid as a multicopy plasmid. Thus in a preferred embodiment, one region of the plasmid defined between the inverted repeats may comprise not more than the ORFs encoding FLP and REP2; FLP and REP1; or REP1 and REP2, as endogenous coding sequence.
A 2 μm-family plasmid comprises an origin of replication (also known as an autonomously replicating sequence—“ARS”), which is typically bidirectional. Any appropriate ARS sequence can be present. Consensus sequences typical of yeast chromosomal origins of replication may be appropriate (Broach et al, 1982, Cold Spring Harbor Symp. Quant. Biol., 47, 1165-1174; Williamson, Yeast, 1985, 1, 1-14). Preferred ARSs include those isolated from pSR1, pSB1, pSB2, pSB3, pSB4, pSM1, pKD1, pPM1 and the 2 μm plasmid.
Thus, a 2 μm-family plasmid typically comprises at least ORFs encoding FLP and REP2, two inverted repeat sequences each inverted repeat comprising an FRT site compatible with FLP protein, and an ARS sequence. Preferably the plasmid also comprises an ORF encoding REP1, although it may be supplied in trans, as discussed above. Preferably the FRT sites are derived from the same 2 μm-family plasmid as the sequence of the encoded FLP protein. Preferably the sequences of the encoded REP1 and REP2 proteins are derived from the same 2 μm-family plasmid as each other. More preferably, the FRT sites are derived from the same 2 μm-family plasmid as the sequence of the encoded FLP, REP1 and REP2 proteins. Even more preferably, the sequences of the ORFs encoding FLP, REP1 and REP2, and the sequence of the inverted repeats (including the FRT sites) are derived from the same 2 μm-family plasmid. Yet more preferably, the ARS site is obtained from the same 2 μm-family plasmid as one or more of the ORFs of FLP, REP1 and REP2, and the sequence of the inverted repeats (including the FRT sites). Preferred plasmids include plasmids pSR1, pSB3 and pSB4 as obtained from Zygosaccharomyces rouxii, pSB1 or pSB2 both as obtained from Zygosaccharomyces bailli, pSM1 as obtained from Zygosaccharomyces fermentati, pKD1 as obtained from Kluyveromyces drosophilarum, pPM1 as obtained from Pichia membranaefaciens, and the 2 μm plasmid as obtained from Saccharomyces cerevisiae, for example as described in Volkert et al, 1989, op. cit., Murray et al, op. cit. and Painting et al, op. cit.
Optionally, a 2 μm-family plasmid may comprise a region equivalent to the STB region (also known as REP3) of the 2 μm plasmid, as defined in Volkert et al, op. cit. The STB region in a 2 μm-family plasmid of the invention may comprise two or more tandem repeat sequences, such as three, four, five or more. Alternatively, no tandem repeat sequences may be present. The tandem repeats may be any size, such as 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 bp or more in length. The tandem repeats in the STB region of the 2 μm plasmid are 62 bp in length. It is not essential for the sequences of the tandem repeats to be identical. Slight sequence variation can be tolerated. It may be preferable to select an STB region from the same plasmid as either or both of the REP1 and REP2 ORFs. The STB region is thought to be a cis-acting element and preferably is not transcribed.
Optionally, a 2 μm-family plasmid may comprise an additional ORF that encodes a protein that functions in the stable maintenance of the 2 μm-family plasmid as a multicopy plasmid. The additional protein can be designated RAF or D. ORFs encoding the RAF or D gene can be seen on, for example, the 2 μm plasmid and pSM1. Thus a RAF or D ORF can comprise a sequence suitable to encode the protein product of the RAF or D gene ORFs encoded by the 2 μm plasmid or pSM1, or variants and fragments thereof. Thus variants and fragments of the protein products of the RAF or D genes of the 2 μm plasmid or pSM1 are also included in the present invention. “Fragments” and “variants” of the protein products of the RAF or D genes of the 2 μm plasmid or pSM1 are those which, when encoded by the 2 μm plasmid or pSM1 in place of the native ORF, do not disrupt the stable multicopy maintenance of the plasmid within a suitable yeast population. Such variants and fragments will usually have at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 950%, 98%, 99%, or more, homology with the protein product of the RAF or D gene ORFs encoded by the 2 μm plasmid or pSM1.
The present invention provides a 2 μm-family plasmid comprising a polynucleotide sequence insertion, deletion and/or substitution between the first base after the last functional codon of at least one of either a REP2 gene or an FLP gene and the last base before the FRT site in an inverted repeat adjacent to said gene.
A polynucleotide sequence insertion is any additional polynucleotide sequence inserted into the plasmid. Preferred polynucleotide sequence insertions are described below. A deletion is removal of one or more base pairs, such as the removal of up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more base pairs, which may be as a single contiguous sequence or from spaced apart regions within a DNA sequence. A substitution is the replacement of one or more base pairs, such as the replacement of up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more base pairs, which may be as a single contiguous sequence or from spaced apart regions within a DNA sequence. It is possible for a region to be modified by any two of insertion, deletion or substitution, or even all three.
The last functional codon of either a REP2 gene or a FLP gene is the codon in the open reading frame of the gene that is furthest downstream from the promoter of the gene whose replacement by a stop codon will lead to an unacceptable loss of multicopy stability of the plasmid, when determined by a test such as defined in Chinery & Hinchliffe (1989, Curr. Genet., 16, 21-25). It may be appropriate to modify the test defined by Chinery & Hinchcliffe, for example to maintain exponential logarithmic growth over the desired number of generations, by introducing modifications to the inocula or sub-culturing regime. This can help to account for differences between the host strain under analysis and S. cerevisiae S150-2B used by Chinery & Hinchcliffe, and/or to optimise the test for the individual characteristics of the plasmid(s) under assay, which can be determined by the identity of the insertion site within the small US-region of the 2 μm-like plasmid, and/or other differences in the 2 μm-like plasmid, such as the size and nature of the inserted sequences within the 2 μm-like plasmid and/or insertions elsewhere in the 2 μm-like plasmid. For yeast that do not grow in the non-selective medium (YPD, also designated YEPD) defined in Chinery & Hinchliffe (1989, Curr. Genet., 16, 21-25) other appropriate non-selective media might be used. A suitable alternative non-selective medium typically permits exponential logarithmic growth over the desired number of generations. For example, sucrose or glucose might be used as alternative carbon sources. Plasmid stability may be defined as the percentage cells remaining prototrophic for the selectable marker after a defined number of generations. The number of generations will preferably be sufficient to show a difference between a control plasmid, such as pSAC35 or pSAC310, or to show comparable stability to such a control plasmid. The number of generations may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100 or more. Higher numbers are preferred. The acceptable plasmid stability might be 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 500%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9% or substantially 100%. Higher percentages are preferred. The skilled person will appreciate that, even though a plasmid may have a stability less than 100% when grown on non-selective media, that plasmid can still be of use when cultured in selective media. For example plasmid pDB2711 as described in the examples is only 10% stable when the stability is determined accordingly to Example 1, but provides a 15-fold increase in recombinant transferrin productivity in shake flask culture under selective growth conditions.
Thus, disruption of the REP2 or FLP genes at any point downstream of the last functional codon in either gene, by insertion of a polynucleotide sequence insertion, deletion or substitution will not lead to an unacceptable loss of multicopy stability of the plasmid. We have surprisingly found that the REP2 gene of the 2 μm plasmid can be disrupted after codon 59 and that the FLP gene of the 2 μm plasmid can be disrupted after codon 344, each without leading to an unacceptable loss of multicopy stability of the plasmid. The last functional codon in equivalent genes in other 2 μm-family plasmids can be determined routinely by modifying the relevant genes and determining stability as described above. Typically, therefore, modified plasmids of the present invention are stable, in the sense that the modifications made thereto do not lead to an unacceptable loss of multicopy stability of the plasmid.
The REP2 and FLP genes in a 2 μm plasmid of the invention each have an inverted repeat adjacent to them. The inverted repeat can be identified because (when reversed) it matches the sequence of another inverted repeat within the same plasmid. By “adjacent” is meant that the FLP or REP2 gene and its inverted repeat are juxtaposed in such a manner that the inverted repeat occurs at the distal end of the gene, without any intervening coding sequence, for example as seen in the 2 μm plasmid. By “distal end” in this context we mean the end of the gene opposite to the end from which the promoter initiates its transcription. In a preferred embodiment, the distal end of the gene overlaps with the inverted repeat.
In a first preferred aspect of the invention, the polynucleotide sequence insertion, deletion and/or substitution occurs between the first base after the last functional codon of the REP2 gene and the last base before the FRT site in an inverted repeat adjacent to said gene, preferably between the first base of the inverted repeat and the last base before the FRT site, even more preferably at a position after the translation termination codon of the REP2 gene and before the last base before the FRT site.
The term “between”, in this context, includes the defined outer limits and so, for example, an insertion, deletion and/or substitution “between the first base after the last functional codon of the REP2 gene and the last base before the FRT site” includes insertions, deletions and/or substitutions at the first base after the last functional codon of the REP2 gene and insertions, deletions and/or substitutions at the last base before the FRT site.
In a second preferred aspect of the invention, the polynucleotide sequence insertion, deletion and/or substitution occurs between the first base after the last functional codon of the FLP gene and the last base before the FRT site in an inverted repeat adjacent to said gene, preferably between the first base of the inverted repeat and the last base before the FRT site, more preferably between the first base after the end of the FLP coding sequence and the last base before the FRT site, such as at the first base after the end of the FLP coding sequence. The polynucleotide sequence insertion, deletion and/or substitution may occur between the last base after the end of FLP and the FspI-site in the inverted repeat, but optionally not within the FspI-site.
In one embodiment, other than the polynucleotide sequence insertion, deletion and/or substitution, the FLP gene and/or the REP2 gene has the sequence of a FLP gene and/or a REP2 gene, respectively, derived from a naturally occurring 2 μm-family plasmid.
The term “derived from” includes sequences having an identical sequence to the sequence from which they are derived. However, variants and fragments thereof, as defined above, are also included. For example, an FLP gene having a sequence derived from the FLP gene of the 2 μm plasmid may have a modified promoter or other regulatory sequence compared to that of the naturally occurring gene. Alternatively, an FLP gene having a sequence derived from the FLP gene of the 2 μm plasmid may have a modified nucleotide sequence in the open reading frame which may encode the same protein as the naturally occurring gene, or may encode a modified FLP protein. The same considerations apply to REP2 genes having a sequence derived from a particular source.
A naturally occurring 2 μm-family plasmid is any plasmid having the features defined above as being essential features for a 2 μm-family plasmid, which plasmid is found to naturally exist in yeast, i.e. has not been recombinantly modified to include heterologous sequence. Preferably the naturally occurring 2 μm-family plasmid is selected from pSR1 (Accession No. X02398), pSB3 (Accession No. X02608) or pSB4 as obtained from Zygosaccharomyces rouxii, pSB1 or pSB2 (Accession No. NC—002055 or M18274) both as obtained from Zygosaccharomyces bailli, pSM1 (Accession No. NC—002054) as obtained from Zygosaccharomyces fermentati, pKD1 (Accession No. X03961) as obtained from Kluyveromyces drosophilarum, pPM1 as obtained from Pichia membranaefaciens, or, most preferably, the 2 μm plasmid (Accession No. NC—001398 or J01347) as obtained from Saccharomyces cerevisiae. Accession numbers refer to deposits at the NCBI.
Preferably, other than the polynucleotide sequence insertion, deletion and/or substitution, the sequence of the inverted repeat adjacent to said FLP and/or REP2 gene is derived from the sequence of the corresponding inverted repeat in the same naturally occurring 2 μm-family plasmid as the sequence from which the gene is derived. Thus, for example, if the FLP gene is derived from the 2 μm plasmid as obtained from S. cerevisiae, then it is preferred that the inverted repeat adjacent to the FLP gene has a sequence derived from the inverted repeat that is adjacent to the FLP gene in the 2 μm plasmid as obtained from S. cerevisiae. If the REP2 gene is derived from the 2 μm plasmid as obtained from S. cerevisiae, then it is preferred that the inverted repeat adjacent to the REP2 gene has a sequence derived from the inverted repeat that is adjacent to the REP2 gene in the 2 μm plasmid as obtained from S. cerevisiae. 
Where, in the first preferred aspect of the invention, other than the polynucleotide sequence insertion, deletion and/or substitution, the REP2 gene and the inverted repeat sequence have sequences derived from the corresponding regions of the 2 μm plasmid as obtained from S. cerevisiae, then it is preferred that the polynucleotide sequence insertion, deletion and/or substitution occurs at a position between the first base of codon 59 of the REP gene and the last base before the FRT site in the adjacent inverted repeat, more preferably at a position between the first base of the inverted repeat and the last base before the FRT site, even more preferably at a position after the translation termination codon of the REP2 gene and before the last base before the FRT site, such as at the first base after the end of the REP2 coding sequence.
Where, other than the polynucleotide sequence insertion, deletion and/or substitution, the REP2 gene and the inverted repeat sequence have sequences derived from the corresponding regions of the 2 μm plasmid as obtained from S. cerevisiae, then in one embodiment, other than the polynucleotide sequence insertion, deletion and/or substitution, the sequence of the REP2 gene and the adjacent inverted repeat is as defined by SEQ ID NO:1 or variant thereof. In SEQ ID NO:1, the first base of codon 59 of the REP2 gene is represented by base number 175 and the last base before the FRT site is represented by base number 1216. The FRT sequence given here is the 55-base-pair sequence from Sadowski et al, 1986, pp 7-10, Mechanisms of Yeast Recombination (Current Communications in Molecular Biology) CSHL. Ed. Klar, A. Strathern, J. N. In SEQ ID NO:1, the first base of the inverted repeat is represented by base number 887 and the first base after the translation termination codon of the REP2 gene is represented by base number 892.
In an even more preferred embodiment of the first aspect of the invention, other than the polynucleotide sequence insertion, deletion and/or substitution, the REP2 gene and the inverted repeat sequence have sequences derived from the corresponding regions of the 2 μm plasmid as obtained from S. cerevisiae and, in the absence of the interruption the polynucleotide sequence insertion, deletion and/or substitution, comprise an XcmI site or an FspI site within the inverted repeat and the polynucleotide sequence insertion, deletion and/or substitution occurs at the XcmI site, or at the FspI site. In SEQ ID NO:1, the XcmI site is represented by base numbers 935-949 and the FspI site is represented by base numbers 1172-1177.
Where, in the second preferred aspect of the invention, other than the polynucleotide sequence insertion, deletion and/or substitution, the FLP gene and the adjacent inverted repeat sequence have sequences derived from the corresponding regions of the 2 μm plasmid as obtained from S. cerevisiae, then it is preferred that the polynucleotide sequence insertion, deletion and/or substitution occurs at a position between the first base of codon 344 of the FLP gene and the last base before the FRET site, more preferably between the first base of the inverted repeat and the last base before the FRT site, yet more preferably between the first base after the end of the FLP coding sequence and the last base before the FRT site, such as at the first base after the end of the FLP coding sequence. The FspI site between the FLP gene and the FRT site can be avoided as an insertion site.
Where, other than the polynucleotide sequence insertion, deletion and/or substitution, the FLP gene and the adjacent inverted repeat sequence have sequences derived from the corresponding regions of the 2 μm plasmid as obtained from S. cerevisiae, then in one embodiment, other than the polynucleotide sequence insertion, deletion and/or substitution, the sequence of the FLP gene and the inverted repeat that follows the FLP gene is as defined by SEQ ID NO:2 or variant thereof. In SEQ ID NO:2, the first base of codon 344 of the FLP gene is represented by base number 1030 and the last base before the FRT site is represented by base number 1419, the first base of the inverted repeat is represented by base number 1090, and the first base after the end of the FLP coding sequence is represented by base number 1273.
In an even more preferred embodiment of the second preferred aspect of the invention, other than the polynucleotide sequence insertion, deletion and/or substitution, the FLP gene and the adjacent inverted repeat sequence have sequences derived from the corresponding regions of the 2 μm plasmid as obtained from S. cerevisiae and, in the absence of the polynucleotide sequence insertion, deletion and/or substitution, comprise an HgaI site or an FspI site within the inverted repeat and the polynucleotide sequence insertion, deletion and/or substitution occurs at the cut formed by the action of HgaI on the HgaI site (HgaI cuts outside the 5 bp sequence that it recognises), or at the FspI. In SEQ ID NO:2, the HgaI site is represented by base numbers 1262-1266 and the FspI site is represented by base numbers 1375-1380.
The skilled person will appreciate that the features of the plasmid defined by the first and second preferred aspects of the present invention are not mutually exclusive. Thus, a plasmid according to a third preferred aspect of the present invention may comprise polynucleotide sequence insertions, deletions and/or substitutions between the first bases after the last functional codons of both of the REP2 gene and the FLP gene and the last bases before the FRT sites in the inverted repeats adjacent to each of said genes, which polynucleotide sequence insertions, deletions and/or substitutions can be the same or different. For example, a plasmid according to a third aspect of the present invention may, other than the polynucleotide sequence insertions, deletions and/or substitutions, comprise the sequence of SEQ ID NO:1 or variant thereof and the sequence of SEQ ID NO:2 or variant thereof, each comprising a polynucleotide sequence insertion, deletion and/or substitution at a position as defined above for the first and second preferred aspects of the invention, respectively.
The skilled person will appreciate that the features of the plasmid defined by the first, second and third preferred aspects of the present invention do not exclude the possibility of the plasmid also having other sequence modifications. Thus, for example, a 2 μm-family plasmid of the first, second and third preferred aspects of the present invention may additionally comprise a polynucleotide sequence insertion, deletion and/or substitution which is not at a position as defined above. Accordingly, the plasmid may additionally carry transgenes at a site other than the insertion sites of the invention.
Alternative insertion sites in 2 μm plasmids are known in the art, but do not provide the advantages of using the insertion sites defined by the present invention. Nevertheless, plasmids which already include a polynucleotide sequence insertion, deletion and/or substitution at a site known in the art can be further modified by making one or more further modifications at one or more of the sites defined by the first, second and third preferred aspects of the present invention. The skilled person will appreciate that, as discussed in the introduction to this application, there are considerable technical limitations placed on the insertion of transgenes at sites of 2 μm-family plasmids other than as defined by the first and second aspects of the invention.
Typical modified 2 μm plasmids known in the art include those described in Rose & Broach (1990, Methods Enzymol., 185, 234-279), such as plasmids pCV19, pCV20, CVneo, which utilise an insertion at EcoRI in FLP, plasmids pCV21, pGT41 and pYE which utilise EcoRI in D as the insertion site, plasmid pHKB52 which utilises PstI in D as the insertion site, plasmid pJDB248 which utilises an insertion at PstI in D and EcoRI in D, plasmid pJDB219 in which PstI in D and EcoRI in FLP are used as insertion sites, plasmid G18, plasmid pAB18 which utilises an insertion at ClaI in FLP, plasmids pGt39 and pA3, plasmids pYT11, pYT14 and pYT11-LEU which use PstI in D as the insertion site, and plasmid PTY39 which uses EcoRI in FLP as the insertion site. Other 2 μm plasmids include pSAC3, pSAC3U1, pSAC3U2, pSAC300, pSAC310, pSAC3C1, pSAC3PL1, pSAC3SL4, and pSAC3SC1 are described in EP 0 286 424 and Chinery & Hinchliffe (1989, Curr. Genet., 16, 21-25) which also described PstI, EagI or SnaBI as appropriate 2 μm insertion sites. Further 2 μm plasmids include pAYE255, pAYE316, pAYE443, pAYE522 (Kerry-Williams et al, 1998, Yeast, 14, 161-169), pDB2244 (WO 00/44772) and pAYE329 (Sleep et al, 2001, Yeast, 18, 403-421).
In one preferred embodiment, a 2 μm-like plasmid as defined by the first, second and third preferred aspects of the present invention additionally comprises a polynucleotide sequence insertion, deletion and/or substitution which occurs within an untranscribed region around the ARS sequence. For example, in the 2 μm plasmid obtained from S. cerevisiae, the untranscribed region around the ARS sequence extends from end of the D gene to the beginning of ARS sequence. Insertion into SnaBI (near the origin of replication sequence ARS) is described in Chinery & Hinchliffe, 1989, Curr. Genet., 16, 21-25. The skilled person will appreciate that an additional polynucleotide sequence insertion, deletion and/or substitution can also occur within the untranscribed region at neighbouring positions to the SnaBI site described by Chinery & Hinchliffe.
A plasmid according to any of the first, second or third aspects of the present invention may be a plasmid capable of autonomous replication in yeast, such as a member of the Saccharomyces, Kluyveromyces, Zygosaccharomyces, or Pichia genus, such Saccharomyces cerevisiae, Saccharomyces carlsbergensis, Kluyveromyces lactis, Pichia pastoris and Pichia membranaefaciens, Zygosaccharomyces rouxii, Zygosaccharomyces bailii, Zygosaccharomyces fermentati, or Kluyveromyces drosphilarum. S. cerevisiae and S. carlsbergensis are thought to provide a suitable host cell for the autonomous replication of all known 2 μm plasmids.
In a preferred embodiment, the, or at least one, polynucleotide sequence insertion, deletion and/or substitution included in a 2 μm-family plasmid of the invention is a polynucleotide sequence insertion. Any polynucleotide sequence insertion may be used, so long as it is not unacceptably detrimental to the stability of the plasmid, by which we mean that the plasmid is at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 40% 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9% or substantially 100% stable on non-selective media such as YEPD media compared to the unmodified plasmid, the latter of which is assigned a stability of 100%. Preferably, the above mentioned level of stability is seen after separately culturing yeast cells comprising the modified and unmodified plasmids in a culture medium for one, two, three, four, five, six, seven, eight, nine ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100 or more generations.
Where the plasmid comprises a selectable marker, higher levels of stability can be obtained when transformants are grown under selective conditions (e.g. in minimal medium), since the medium can place a selective pressure on the host to retain the plasmid.
Stability in non-selective and selective (e.g. minimal) media can be determined using the methods set forth above. Stability in selective media can be demonstrated by the observation that the plasmids can be used to transform yeast to prototrophy.
Typically, the polynucleotide sequence insertion will be at least 4, 6, 8, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500 or more base pairs in length. Usually, the polynucleotide sequence insertion will be up to 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 6 kb, 7 kb, 8 kb, 9 kb, 10 kb or more in length. The skilled person will appreciate that the 2 μm plasmid of the present invention may comprise multiple polynucleotide sequence insertions at different sites within the plasmid. Typically, the total length of polynucleotide sequence insertions is no more than 5 kb, 10 kb, 15 kb, 20 kb, 25 kb or 30 kb although greater total length insertion may be possible.
The polynucleotide sequence may or may not be a linker sequence used to introduce new restriction sites. For example a synthetic linker may or may not be introduced at the FspI site after the FLP gene, such as to introduce a further restriction site (e.g. BamHI).
The polynucleotide sequence insertion may contain a transcribed region or may contain no transcribed region. A transcribed region may encode an open reading frame, or may be non-coding. The polynucleotide sequence insertion may contain both transcribed and non-transcribed regions.
A transcribed region is a region of DNA that can be transcribed by RNA polymerase, typically yeast RNA polymerase. A transcribed region can encode a functional RNA molecule, such as ribosomal or transfer RNA or an RNA molecule that can function as an antisense or RNA interference (“RNAi”) molecule. Alternatively a transcribed region can encode a messenger RNA molecule (mRNA), which mRNA can contain an open reading frame (ORF) which can be translated in vivo to produce a protein. The term “protein” as used herein includes all natural and non-natural proteins, polypeptides and peptides. Preferably, the ORF encodes a heterologous protein. By “heterologous protein” we mean a protein that is not naturally encoded by a 2 μm-family plasmid (i.e. a “non-2 μm-family plasmid protein”). For convenience the terms “heterologous protein” and “non-2 μm-family plasmid protein” are used synonymously throughout this application. Preferably, therefore, the heterologous protein is not a FLP, REP1, REP2, or a RAF/D protein as encoded by any one of pSR1, pSB3 or pSB4 as obtained from Z. rouxii, pSB1 or pSB2 both as obtained from Z. bailli, pSM1 as obtained from Z. fermentati, pKD1 as obtained from K. drosophilarum, pPM1 as obtained from P. membranaefaciens and the 2 μm plasmid as obtained from S. cerevisiae. 
Where the polynucleotide sequence insertion encodes an open reading frame, then it may additionally comprise some polynucleotide sequence that does not encode an open reading frame (termed “non-coding region”).
Non-coding region in the polynucleotide sequence insertion may contain one or more regulatory sequences, operatively linked to the open reading frame, which allow for the transcription of the open reading frame and/or translation of the resultant transcript.
The term “regulatory sequence” refers to a sequence that modulates (i.e., promotes or reduces) the expression (i.e., the transcription and/or translation) of an open reading frame to which it is operably linked. Regulatory regions typically include promoters, terminators, ribosome binding sites and the like. The skilled person will appreciate that the choice of regulatory region will depend upon the intended expression system. For example, promoters may be constitutive or inducible and may be cell- or tissue-type specific or non-specific.
Where the expression system is yeast, such as Saccharomyces cerevisiae, suitable promoters for S. cerevisiae include those associated with the PGK1 gene, GAL1 or GAL10 genes, TEF1, TEF2, PYK1, PMA1, CYC1, PHO5, TRP1, ADH1, ADH2, the genes for glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, triose phosphate isomerase, phosphoglucose isomerase, glucokinase, α-mating factor pheromone, a-mating factor pheromone, the PRB1 promoter, the PRA1 promoter, the GPD1 promoter, and hybrid promoters involving hybrids of parts of 5′ regulatory regions with parts of 5′ regulatory regions of other promoters or with upstream activation sites (e.g. the promoter of EP-A-258 067).
Suitable transcription termination signals are well known in the art. Where the host cell is eukaryotic, the transcription termination signal is preferably derived from the 3′ flanking sequence of a eukaryotic gene, which contains proper signals for transcription termination and polyadenylation. Suitable 3′ flanking sequences may, for example, be those of the gene naturally linked to the expression control sequence used, i.e. may correspond to the promoter. Alternatively, they may be different. In that case, and where the host is a yeast, preferably S. cerevisiae, then the termination signal of the S. cerevisiae ADH1, ADH2, CYC1, or PGK1 genes are preferred.
It may be beneficial for the promoter and open reading frame of the heterologous gene, such as the those of the chaperone PDI1, to be flanked by transcription termination sequences so that the transcription termination sequences are located both upstream and downstream of the promoter and open reading frame, in order to prevent transcriptional read-through into neighbouring genes, such as 2 μm genes, and vice versa.
In one embodiment, the favoured regulatory sequences in yeast, such as Saccharomyces cerevisiae, include: a yeast promoter (e.g. the Saccharomyces cerevisiae PRB1 promoter), as taught in EP 431 880; and a transcription terminator, preferably the terminator from Saccharomyces ADH1, as taught in EP 60 057.
It may be beneficial for the non-coding region to incorporate more than one DNA sequence encoding a translational stop codon, such as UAA, UAG or UGA, in order to minimise translational read-through and thus avoid the production of elongated, non-natural fusion proteins. The translation stop codon UAA is preferred. Preferably, at least two translation stop codons are incorporated.
The term “operably linked” includes within its meaning that a regulatory sequence is positioned within any non-coding region such that it forms a relationship with an open reading frame that permits the regulatory region to exert an effect on the open reading frame in its intended manner. Thus a regulatory region “operably linked” to an open reading frame is positioned in such a way that the regulatory region is able to influence transcription and/or translation of the open reading frame in the intended manner, under conditions compatible with the regulatory sequence.
Where the polynucleotide sequence insertion as defined by the first, second or third aspects of the present invention includes an open reading frame that encodes a protein, then it may be advantageous for the encoded protein to be secreted. In that case, a sequence encoding a secretion leader sequence may be included in the open reading frame.
For production of proteins in eukaryotic species such as the yeasts Saccharomyces cerevisiae, Zygosaccharomyces species, Kluyveromyces lactis and Pichia pastoris, known leader sequences include those from the S. cerevisiae acid phosphatase protein (Pho5p) (see EP 366 400), the invertase protein (Suc2p) (see Smith et al. (1985) Science, 229, 1219-1224) and heat-shock protein-150 (Hsp150p) (see WO 95/33833). Additionally, leader sequences from the S. cerevisiae mating factor alpha-1 protein (MFα-1) and from the human lysozyme and human serum albumin (HSA) protein have been used, the latter having been used especially, although not exclusively, for secreting human albumin. WO 90/01063 discloses a fusion of the MFα-1 and HSA leader sequences, which advantageously reduces the production of a contaminating fragment of human albumin relative to the use of the MFα-1 leader sequence. In addition, the natural transferrin leader sequence may be used to direct secretion of transferrin and other heterologous proteins.
Alternatively, the encoded protein may be intracellular.
In one preferred embodiment, at least one polynucleotide sequence insertion as defined by the first, second or third aspects of the present invention includes an open reading frame comprising a sequence that encodes a yeast protein. In another preferred embodiment, at least one polynucleotide sequence insertion as defined by the first, second or third aspects of the present invention includes an open reading frame comprising a sequence that encodes a yeast protein from the same host from which the 2 μm-like plasmid is derived.
In another preferred embodiment, at least one polynucleotide sequence insertion as defined by the first, second or third aspects of the present invention includes an open reading frame comprising a sequence that encodes a protein involved in protein folding, or which has chaperone activity or is involved in the unfolded protein response (Stanford Genome Database (SGD), http:://db.yeastgenome.org). Preferred proteins may be selected from protein encoded by AHA1, CCT2, CCT3, CCT4, CCT5, CCT6, CCT7, CCT8, CNS1, CPR3, CPR6, ERO1, EUG1, FMO1, HCH1, HSP10, HSP12, HSP104, HSP26, HSP30, HSP42, HSP60, HSP78, HSP82, JEM1, MDJ1, MDJ2, MPD1, MPD2, PDI1, PFD1, ABC1, APJ1, ATP11, ATP12, BTT1, CDC37, CNS1, CPR6, CPR7, HSC82, KAR2, LHS1, MGE1, MRS11, NOB1, ECM10, SSA1, SSA2, SSA3, SSA4, SSC1, SSE2, SIL1, SLS1, ORM1, UBI4, ORM2, PER1, PTC2, PSE1 and HAC1 or a truncated intronless HAC1 (Valkonen et al. 2003, Applied Environ. Micro. 69, 2065).
A preferred protein involved in protein folding, or protein with chaperone activity or a protein involved in the unfolded protein response may be:

    
    
        a heat shock protein, such as a protein that is a member of the hsp70 family of proteins (including Kar2p, SSA and SSB proteins, for example proteins encoded by SSA1, SSA2, SSA3, SSA4, SSB1 and SSB2), a protein that is a member of the HSP90-family, or a protein that is a member of the HSP40-family or proteins involved in their modulation (e.g. Sil1p), including DNA-J and DNA-J-like proteins (e.g. Jem1p, Mdj2p);
        a protein that is a member of the karyopherin/importin family of proteins, such as the alpha or beta families of karyopherin/importin proteins, for example the karyopherin beta protein encoded by PSE1;
        a protein that is a member of the ORMDL family described by Hjelmqvist et al, 2002, Genome Biology, 3 (6), research 0027.1-0027.16, such as Orm2p.
        a protein that is naturally located in the endoplasmic reticulum or elsewhere in the secretory pathway, such as the golgi. For example, a protein that naturally acts in the lumen of the endoplasmic reticulum (ER), particularly in secretory cells, such as PDI
        a protein that is a transmembrane protein anchored in the ER, such as a member of the ORMDL family described by Hjelmqvist et al, 2002, supra, (for example, Orm2p);
        a protein that acts in the cytosol, such as the hsp70 proteins, including SSA and SSB proteins, for example proteins encoded by SSA1, SSA2, SSA3, SSA4, SSB1 and SSB2;
        a protein that acts in the nucleus, the nuclear envelope and/or the cytoplasm, such as Pse1p;
        a protein that is essential to the viability of the cell, such as PDI or an essential karyopherin protein, such as Pse1p;
        a protein that is involved in sulphydryl oxidation or disulphide bond formation, breakage or isomerization, or a protein that catalyses thiol:disulphide interchange reactions in proteins, particularly during the biosynthesis of secretory and cell surface proteins, such as protein disulphide isomerases (e.g. Pdi1p, Mpd1p), homologues (e.g. Eug1p) and/or related proteins (e.g. Mpd2p, Fmo1p, Ero1p);
        a protein that is involved in protein synthesis, assembly or folding, such as PDI and Ssa1p;
        a protein that binds preferentially or exclusively to unfolded, rather than mature protein, such as the hsp70 proteins, including SSA and SSB proteins, for example proteins encoded by SSA1, SSA2, SSA3, SSA4, SSB1 and SSB2;
        a protein that prevents aggregation of precursor proteins in the cytosol, such as the hsp70 proteins, including SSA and SSB proteins, for example proteins encoded by SSA1, SSA2, SSA3, SSA4, SSB1 and SSB2;
        a protein that binds to and stabilises damaged proteins, for example Ssa1p;
        a protein that is involved in the unfolded protein response or provides for increased resistance to agents (such as tunicamycin and dithiothreitol) that induce the unfolded protein response, such as a member of the ORMDL family described by Hjelmqvist et al, 2002, supra (for example, Orm2p) or a protein involved in the response to stress (e.g. Ubi4p);
        a protein that is a co-chaperone and/or a protein indirectly involved in protein folding and/or the unfolded protein response (e.g. hsp104p, Mdj1p);
        a protein that is involved in the nucleocytoplasmic transport of macromolecules, such as Pse1p;
        a protein that mediates the transport of macromolecules across the nuclear membrane by recognising nuclear location sequences and nuclear export sequences and interacting with the nuclear pore complex, such as Pse1p;
        a protein that is able to reactivate ribonuclease activity against RNA of scrambled ribonuclease as described in as described in EP 0 746 611 and Hillson et al, 1984, Methods Enzymol., 107, 281-292, such as PDI;
        a protein that has an acidic pI (for example, 4.0-4.5), such as PDI;
        a protein that is a member of the Hsp70 family, and preferably possesses an N-terminal ATP-binding domain and a C-terminal peptide-binding domain, such as Ssa1p.
        a protein that is a peptidyl-prolyl cis-trans isomerases (e.g. Cpr3p, Cpr6p);
        a protein that is a homologues of known chaperones (e.g. Hsp10p);
        a protein that is a mitochondrial chaperone (e.g. Cpr3p);
        a protein that is a cytoplasmic or nuclear chaperone (e.g. Cns1p);
        a protein that is a membrane-bound chaperone (e.g. Orm2p, Fmo1p);
        a protein that has chaperone activator activity or chaperone regulatory activity (e.g. Aha1p, Hac1p, Hch1p);
        a protein that transiently binds to polypeptides in their immature form to cause proper folding transportation and/or secretion, including proteins required for efficient translocation into the endoplasmic reticulum (e.g. Lhs1p) or their site of action within the cell (e.g. PseIp);
        a protein that is a involved in protein complex assembly and/or ribosome assembly (e.g. Atp11p, PseIp, Nob1p);
        a protein of the chaperonin T-complex (e.g. Cct2p); or
        a protein of the prefoldin complex (e.g. Pfd1p).
    
    


One preferred chaperone is protein disulphide isomerase (PDI) or a fragment or variant thereof having an equivalent ability to catalyse the formation of disulphide bonds within the lumen of the endoplasmic reticulum (ER). By “PDI” we include any protein having the ability to reactivate the ribonuclease activity against RNA of scrambled ribonuclease as described in EP 0 746 611 and Hillson et al, 1984, Methods Enzymol. 107, 281-292.
Protein disulphide isomerase is an enzyme which typically catalyzes thiol:disulphide interchange reactions, and is a major resident protein component of the E.R. lumen in secretory cells. A body of evidence suggests that it plays a role in secretory protein biosynthesis (Freedman, 1984, Trends Biochem. Sci., 9, 438-41) and this is supported by direct cross-linking studies in situ (Roth and Pierce, 1987, Biochemistry, 26, 4179-82). The finding that microsomal membranes deficient in PDI show a specific defect in cotranslational protein disulphide formation (Bulleid and Freedman, 1988, Nature, 335, 649-51) implies that the enzyme functions as a catalyst of native disulphide bond formation during the biosynthesis of secretory and cell surface proteins. This role is consistent with what is known of the enzyme's catalytic properties in vitro; it catalyzes thiol:disulphide interchange reactions leading to net protein disulphide formation, breakage or isomerization, and can typically catalyze protein folding and the formation of native disulphide bonds in a wide variety of reduced, unfolded protein substrates (Freedman et al., 1989, Biochem. Soc. Symp., 55, 167-192). PDI also functions as a chaperone since mutant PDI lacking isomerase activity accelerates protein folding (Hayano et al, 1995, FEBS Letters, 377, 505-511). Recently, sulphydryl oxidation, not disulphide isomerisation was reported to be the principal function of Protein Disulphide Isomerase in S. cerevisiae (Solovyov et al., 2004, J. Biol. Chem., 279 (33) 34095-34100). The DNA and amino acid sequence of the enzyme is known for several species (Scherens et al, 1991, Yeast, 7, 185-193; Farquhar et al, 1991, Gene, 108, 81-89; EP074661; EP0293793; EP0509841) and there is increasing information on the mechanism of action of the enzyme purified to homogeneity from mammalian liver (Creighton et al, 1980, J. Mol. Biol., 142, 43-62; Freedman et al, 1988, Biochem. Soc. Trans., 16, 96-9; Gilbert, 1989, Biochemistry, 28, 7298-7305; Lundstrom and Holmgren, 1990, J. Biol. Chem., 265, 9114-9120; Hawkins and Freedman, 1990, Biochem. J, 275, 335-339). Of the many protein factors currently implicated as mediators of protein folding, assembly and translocation in the cell (Rothman, 1989, Cell, 59, 591-601), PDI has a well-defined catalytic activity.
The deletion or inactivation of the endogenous PDI gene in a host results in the production of an inviable host. In other words, the endogenous PDI gene is an “essential” gene.
PDI is readily isolated from mammalian tissues and the homogeneous enzyme is a homodimer (2×57 kD) with characteristically acidic pI (4.0-4.5) (Hillson et al, 1984, Methods Enzymol., 107, 281-292). The enzyme has also been purified from wheat and from the alga Chlamydomonas reinhardii (Kaska et al, 1990, Biochem. J, 268, 63-68), rat (Edman et al, 1985, Nature, 317, 267-270), bovine (Yamauchi et al, 1987, Biochem. Biophys. Res. Comm., 146, 1485-1492), human (Pihlajaniemi et al, 1987, EMBO. J, 6, 643-9), yeast (Scherens et al, supra; Farquhar et al, supra) and chick (Parkkonen et al, 1988, Biochem. J, 256, 1005-1011). The proteins from these vertebrate species show a high degree of sequence conservation throughout and all show several overall features first noted in the rat PDI sequence (Edman et al., 1985, op. cit.).
A yeast protein disulphide isomerase precursor, PDI1, can be found as Genbank accession no. CAA42373 or BAA00723. It has the following sequence of 522 amino acids (SEQ ID NO: 3):








  1 mkfsagavls wsslllassv faqqeavape dsavvklatd sfneyiqshd lvlaeffapw



 


 61 cghcknmape yvkaaetlve knitlaqidc tenqdlcmeh nipgfpslki fknsdvnnsi


 


121 dyegprtaea ivqfmikqsq pavavvadlp aylanetfvt pvivqsgkid adfnatfysm


 


181 ankhfndydf vsaenadddf kisiylpsam depvvyngkk adiadadvfe kwlqvealpy


 


241 fgeidgsvfa qyvesglplg ylfyndeeel eeykplftel akknrglmnf vsidarkfgr


 


301 hagnlnmkeq fplfaihdmt edlkyglpql seeafdelsd kivleskaie slvkdflkgd


 


361 aspivksqei fengdssvfq lvgknhdeiv ndpkkdvlvl yyapwcghck rlaptyqela


 


421 dtyanatsdv liakldhten dvrgvviegy ptivlypggk ksesvvyqgs rsldslfdfi


 


481 kenghfdvdg kalyeeaqek aaeeadadae ladeedaihd el






An alternative PDI sequence can be found as Genbank accession no. CAA38402. It has the following sequence of 530 amino acids (SEQ ID NO: 4):








  1 mkfsagavls wsslllassv faqqeavape dsavvklatd sfneyiqshd lvlaeffapw



 


 61 cghcknmape yvkaaetlve knitlaqidc tenqdlcmeh nipgfpslki fknrdvnnsi


 


121 dyegprtaea ivqfmikqsq pavavvadlp aylanetfvt pvivqsgkid adfnatfysm


 


181 ankhfndydf vsaenadddf klsiylpsam depvvyngkk adiadadvfe kwlqvealpy


 


241 fgeidgsvfa qyvesglplg ylfyndeeel eeykplftel akknrglmnf vsidarkfgr


 


301 hagnlnmkeq fplfaihdmt edlkyglpql seeafdelsd kivleskaie slvkdflkgd


 


361 aspivksqei fenqdssvfq lvgknhdeiv ndpkkdvlvl yyapwcghck rlaptyqela


 


421 dtyanatsdv liakldhten dvrgvviegy ptivlypggk ksesvvyqgs rsldslfdfi


 


481 kenghfdvdg kalyeeaqek aaeeaeadae aeadadaela deedaihdel






Variants and fragments of the above PDI sequences, and variants of other naturally occurring PDI sequences are also included in the present invention. A “variant”, in the context of PDI, refers to a protein wherein at one or more positions there have been amino acid insertions, deletions, or substitutions, either conservative or non-conservative, provided that such changes result in a protein whose basic properties, for example enzymatic activity (type of and specific activity), thermostability, activity in a certain pH-range (pH-stability) have not significantly been changed. “Significantly” in this context means that one skilled in the art would say that the properties of the variant may still be different but would not be unobvious over the ones of the original protein.
By “conservative substitutions” is intended combinations such as Val, Ile, Leu, Ala, Met; Asp, Glu; Asn, Gln; Ser, Thr, Gly, Ala; Lys, Arg, His; and Phe, Tyr, Trp. Preferred conservative substitutions include Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe, Tyr.
A “variant” typically has at least 25%, at least 50%, at least 60% or at least 70%, preferably at least 80%, more preferably at least 90%, even more preferably at least 95%, yet more preferably at least 99%, most preferably at least 99.5% sequence identity to the polypeptide from which it is derived.
The percent sequence identity between two polypeptides may be determined using suitable computer programs, as discussed below. Such variants may be natural or made using the methods of protein engineering and site-directed mutagenesis as are well known in the art.
A “fragment”, in the context of PDI, refers to a protein wherein at one or more positions there have been deletions. Thus the fragment may comprise at most 5, 10, 20, 30, 40 or 50%, typically up to 60%, more typically up to 70%, preferably up to 80%, more preferably up to 90%, even more preferably up to 95%, yet more preferably up to 99% of the complete sequence of the full mature PDI protein. Particularly preferred fragments of PDI protein comprise one or more whole domains of the desired protein.
A fragment or variant of PDI may be a protein that, when expressed recombinantly in a host cell, such as S. cerevisiae, can complement the deletion of the endogenously encoded PDI gene in the host cell and may, for example, be a naturally occurring homolog of PDI, such as a homolog encoded by another organism, such as another yeast or other fungi, or another eukaryote such as a human or other vertebrate, or animal or by a plant.
Another preferred chaperone is SSA1 or a fragment or variant thereof having an equivalent chaperone-like activity. SSA1, also known as YG100, is located on chromosome I of the S. cerevisiae genome and is 1.93-kbp in size.
One published protein sequence of SSA1 is as follows (SEQ ID NO: 5):







MSKAVGIDLGTTYSCVAHFANDRVDIIANDQGNRTTPSFVAFTDTERLIG


 


DAAKNQAAMNPSNTVFDAKRLIGRNFNDPEVQADMKHFPFKLIDVDGKPQ


 


IQVEFKGETKNFTPEQISSMVLGKMKETAESYLGAKVNDAVVTVPAYFND


 


SQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKGKEEHVLIFDLGGG


 


TFDVSLLFIEDGIFEVKATAGDTHLGGEDFDNRLVNHFIQEFKRKNKKDL


 


STNQRALRRLRTACERAKRTLSSSAQTSVEIDSLFEGIDFYTSITRARFE


 


ELCADLFRSTLDPVEKVLRDAKLDKSQVDEIVLVGGSTRIPKVQKLVTDY


 


FNGKEPNRSINPDEAVAYGAAVQAAILTGDESSKTQDLLLLDVAPLSLGI


 


ETAGGVMTKLIPRNSTISTKKFEIFSTYADNQPGVLIQVFEGERAKTKDN


 


NLLGKFELSGIPPAPRGVPQIEVTFDVDSNGILNVSAVEKGTGKSNKITI


 


TNDKGRLSKEDIEKMVAEAEKFKEEDEKESQRIASKNQLESIAYSLKNTI


 


SEAGDKLEQADKDTVTKKAEETISWLDSNTTASKEEFDDKLKELQDIANP


 


IMSKLYQAGGAPGGAAGGAPGGFPGGAPPAPEAEGPTVEEVD






A published coding sequence for SSA1 is a follows, although it will be appreciated that the sequence can be modified by degenerate substitutions to obtain alternative nucleotide sequences which encode an identical protein product (SEQ ID NO: 6):







ATGTCAAAAGCTGTCGGTATTGATTTAGGTACAACATACTCGTGTGTTGC


 


TCACTTTGCTAATGATCGTGTGGACATTATTGCCAACGATCAAGGTAACA


 


GAACCACTCCATCTTTTGTCGCTTTCACTGACACTGAAAGATTGATTGGT


 


GATGCTGCTAAGAATCAAGCTGCTATGAATCCTTCGAATACCGTTTTCGA


 


CGCTAAGCGTTTGATCGGTAGAAACTTCAACGACCCAGAAGTGCAGGCTG


 


ACATGAAGCACTTCCCATTCAAGTTGATCGATGTTGACGGTAAGCCTCAA


 


ATTCAAGTTGAATTTAAGGGTGAAACCAAGAACTTTACCCCAGAACAAAT


 


CTCCTCCATGGTCTTGGGTAAGATGAAGGAAACTGCCGAATCTTACTTGG


 


GAGCCAAGGTCAATGACGCTGTCGTCACTGTCCCAGCTTACTTCAACGAT


 


TCTCAAAGACAAGCTACCAAGGATGCTGGTACCATTGCTGGTTTGAATGT


 


CTTGCGTATTATTAACGAACCTACCGCCGCTGCCATTGCTTACGGTTTGG


 


ACAAGAAGGGTAAGGAAGAACACGTCTTGATTTTCGACTTGGGTGGTGGT


 


ACTTTCGATGTCTCTTTGTTGTTCATTGAAGACGGTATCTTTGAAGTTAA


 


GGCCACCGCTGGTGACACCCATTTGGGTGGTGAAGATTTTGACAACAGAT


 


TGGTCAACCACTTCATCCAAGAATTCAAGAGAAAGAACAAGAAGGACTTG


 


TCTACCAACCAAAGAGCTTTGAGAAGATTAAGAACCGCTTGTGAAAGAGC


 


CAAGAGAACTTTGTCTTCCTCCGCTCAAACTTCCGTTGAAATTGACTCTT


 


TGTTCGAAGGTATCGATTTCTACACTTCCATCACCAGAGCCAGATTCGAA


 


GAATTGTGTGCTGACTTGTTCAGATCTACTTTGGACCCAGTTGAAAAGGT


 


CTTGAGAGATGCTAAATTGGACAAATCTCAAGTCGATGAAATTGTCTTGG


 


TCGGTGGTTCTACCAGAATTCCAAAGGTCCAAAAATTGGTCACTGACTAC


 


TTCAACGGTAAGGAACCAAACAGATCTATCAACCCAGATGAAGCTGTTGC


 


TTACGGTCCTGCTGTTCAAGCTGCTATTTTGACTGGTGACGAATCTTCCA


 


AGACTCAAGATCTATTGTTGTTGGATGTCGCTCCATTATCCTTGGGTATT


 


GAAACTGCTGGTGGTGTCATGACCAAGTTGATTCCAAGAAACTCTACCAT


 


TTCAACAAAGAAGTTCGAGATCTTTTCCACTTATGCTGATAACCAACCAG


 


GTGTCTTGATTCAAGTCTTTGAAGGTGAAAGAGCCAAGACTAAGGACAAC


 


AACTTGTTGGGTAAGTTCGAATTGAGTGGTATTCCACCAGCTCCAAGAGG


 


TGTCCCACAAATTGAAGTCACTTTCGATGTCGACTCTAACGGTATTTTGA


 


ATGTTTCCGCCGTCGAAAAGGGTACTGGTAAGTCTAACAAGATCACTATT


 


ACCAACGACAAGGGTAGATTGTCCAAGGAAGATATCGAAAAGATGGTTGC


 


TGAAGCCGAAAAATTCAAGGAAGAAGATGAAAAGGAATCTCAAAGAATTG


 


CTTCCAAGAACGAATTGGAATCCATTGCTTACTCTTTGAAGAACACCATT


 


TCTGAAGCTGGTGACAAATTGGAACAAGCTGACAAGGACACCGTCACCAA


 


GAAGGCTGAAGAGACTATTTCTTGGTTAGACAGCAACACCACTGCCAGCA


 


AGGAAGAATTCGATGACAAGTTGAAGGAGTTGCAAGACATTGCCAACCCA


 


ATCATGTCTAAGTTGTACCAAGCTGGTGGTGCTCCAGGTGGCGCTGCAGG


 


TGGTGCTCCAGGCGGTTTCCCAGGTGGTGCTCCTCCAGCTCCAGAGGCTG


 


AAGGTCCAACCGTTGAAGAAGTTGATTAA






The protein Ssa1p belongs to the Hsp70 family of proteins and is resident in the cytosol. Hsp70s possess the ability to perform a number of chaperone activities; aiding protein synthesis, assembly and folding; mediating translocation of polypeptides to various intracellular locations, and resolution of protein aggregates (Becker & Craig, 1994, Eur. J. Biochem. 219, 11-23). Hsp70 genes are highly conserved, possessing an N-terminal ATP-binding domain and a C-terminal peptide-binding domain. Hsp70 proteins interact with the peptide backbone of, mainly unfolded, proteins. The binding and release of peptides by hsp70 proteins is an ATP-dependent process and accompanied by a conformational change in the hsp70 (Becker & Craig, 1994, supra).
Cytosolic hsp70 proteins are particularly involved in the synthesis, folding and secretion of proteins (Becker & Craig, 1994, supra). In S. cerevisiae cytosolic hsp70 proteins have been divided into two groups; SSA (SSA 1-4) and SSB (SSB 1 and 2) proteins, which are functionally distinct from each other. The SSA family is essential in that at least one protein from the group must be active to maintain cell viability (Becker & Craig, 1994, supra). Cytosolic hsp70 proteins bind preferentially to unfolded and not mature proteins. This suggests that they prevent the aggregation of precursor proteins, by maintaining them in an unfolded state prior to being assembled into multimolecular complexes in the cytosol and/or facilitating their translocation to various organelles (Becker & Craig, 1994, supra). SSA proteins are particularly involved in post-translational biogenesis and maintenance of precursors for translocation into the endoplasmic reticulum and mitochondria (Kim et al., 1998, Proc. Natl. Acad. Sci. USA. 95, 12860-12865; Ngosuwan et al., 2003, J. Biol. Chem. 278 (9), 7034-7042). Ssa1p has been shown to bind damaged proteins, stabilising them in a partially unfolded form and allowing refolding or degradation to occur (Becker & Craig, 1994, supra; Glover & Lindquist, 1998, Cell. 94, 73-82).
Variants and fragments of SSA1 are also included in the present invention. A “variant”, in the context of SSA1, refers to a protein having the sequence of native SSA1 other than for at one or more positions where there have been amino acid insertions, deletions, or substitutions, either conservative or non-conservative, provided that such changes result in a protein whose basic properties, for example enzymatic activity (type of and specific activity), thermostability, activity in a certain pH-range (pH-stability) have not significantly been changed. “Significantly” in this context means that one skilled in the art would say that the properties of the variant may still be different but would not be unobvious over the ones of the original protein.
By “conservative substitutions” is intended combinations such as Val, Ile, Leu, Ala, Met; Asp, Glu; Asn, Gln; Ser, Thr, Gly, Ala; Lys, Arg, His; and Phe, Tyr, Trp. Preferred conservative substitutions include Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe, Tyr.
A “variant” of SSA1 typically has at least 25%, at least 50%, at least 60% or at least 70%, preferably at least 80%, more preferably at least 90%, even more preferably at least 95%, yet more preferably at least 99%, most preferably at least 99.5% sequence identity to the sequence of native SSA1.
The percent sequence identity between two polypeptides may be determined using suitable computer programs, as discussed below. Such variants may be natural or made using the methods of protein engineering and site-directed mutagenesis as are well known in the art.
A “fragment”, in the context of SSA1, refers to a protein having the sequence of native SSA1 other than for at one or more positions where there have been deletions. Thus the fragment may comprise at most 5, 10, 20, 30, 40 or 50%, typically up to 60%, more typically up to 70%, preferably up to 80%, more preferably up to 90%, even more preferably up to 95%, yet more preferably up to 99% of the complete sequence of the full mature SSA1 protein. Particularly preferred fragments of SSA1 protein comprise one or more whole domains of the desired protein.
A fragment or variant of SSA1 may be a protein that, when expressed recombinantly in a host cell, such as S. cerevisiae, can complement the deletion of the endogenously encoded SSA1 gene in the host cell and may, for example, be a naturally occurring homolog of SSA1, such as a homolog encoded by another organism, such as another yeast or other fungi, or another eukaryote such as a human or other vertebrate, or animal or by a plant.
Another preferred chaperone is PSE1 or a fragment or variant thereof having equivalent chaperone-like activity.
PSE1, also known as KAP121, is an essential gene, located on chromosome XIII.
A published protein sequence for the protein pse1p is a follows (SEQ ID NO: 7):







MSALPEEVNRTLLQIVQAFASPDNQIRSVAEKALSEEWITENNIEYLLTF


 


LAEQAAFSQDTTVAALSAVLFRKLALKAPPSSKLMIMSKNITHIRKEVLA


 


QIRSSLLKGFLSERADSIRHKLSDAIAECVQDDLPAWPELLQALIESLKS


 


GNPNFRESSFRILTTVPYLITAVDINSILPIFQSGFTDASDNVKIAAVTA


 


FVGYFKQLPKSEWSKLGILLPSLLNSLPRFLDDGKDDALASVFESLIELV


 


ELAPKLFKDMFDQIIQFTDMVIKNKDLEPPARTTALELLTVFSENAPQMC


 


KSNQNYGQTLVMVTLIMMTEVSIDDDDAAEWIESDDTDDEEEVTYDHARQ


 


ALDRVALKLGGEYLAAPLFQYLQQMITSTEWRERFAAMMALSSAAEGCAD


 


VLIGEIPKILDMVIPLINDPHPRVQYGCCNVLGQISTDFSPFIQRTAHDR


 


ILPALISKLTSECTSRVQTHAAAALVNFSEFASKDILEPYLDSLLTNLLV


 


LLQSNKLYVQEQALTTIAFIAEAAKNKFIKYYDTLMPLLLNVLKVNNKDN


 


SVLKGKCMECATLIGFAVGKEKFHEHSQELISILVALQNSDIDEDDALRS


 


YLEQSWSRICRILGDDFVPLLPIVIPPLLITAKATQDVGLIEEEEAANFQ


 


QYPDWDVVQVQGKHIAIHTSVLDDKVSAMELLQSYATLLRGQFAVYVKEV


 


MEEIALPSLDFYLHDGVRAAGATLIPILLSCLLAATGTQNEELVLLWHKA


 


SSKLIGGLMSEPMPEITQVYHNSLVNGIKVMGDNCLSEDQLAAFTKGVSA


 


NLTDTYERMQDRHGDGDEYNENIDEEEDFTDEDLLDEINKSIAAVLKTTN


 


GHYLKNLENIWPMINTFLLDNEPILVIFALVVIGDLIQYGGEQTASMKNA


 


FIPKVTECLISPDARIRQAASYIIGVCAQYAPSTYADVCIPTLDTLVQIV


 


DFPGSKLEENRSSTENASAAIAKILYAYNSNIPNVDTYTANWFKTLPTIT


 


DKEAASFNYQFLSQLIENNSPIVCAQSNISAVVDSVIQALNERSLTEREG


 


QTVISSVKKLLGFLPSSDAMAIFNRYPADIMEKVHKWFA*






A published nucleotide coding sequence of PSE1 is a follows, although it will be appreciated that the sequence can be modified by degenerate substitutions to obtain alternative nucleotide sequences which encode an identical protein product (SEQ ID NO: 8):







ATGTCTGCTTTACCGGAAGAAGTTAATAGAACATTACTTCAGATTGTCCA


 


GGCGTTTGCTTCCCCTGACAATCAAATACGTTCTGTAGCTGAGAAGGCTC


 


TTAGTGAAGAATGGATTACCGAAAACAATATTGAGTATCTTTTAACTTTT


 


TTGGCTGAACAAGCCGCTTTCTCCCAAGATACAACAGTTGCAGCATTATC


 


TGCTGTTCTGTTTAGAAAATTAGCATTAAAAGCTCCCCCTTCTTCGAAGC


 


TTATGATTATGTCCAAAAATATCACACATATTAGGAAAGAAGTTCTTGCA


 


CAAATTCGTTCTTCATTGTTAAAAGGGTTTTTGTCGGAAAGAGCTGATTC


 


AATTAGGCACAAACTATCTGATGCTATTGCTGAGTGTGTTCAAGACGACT


 


TACCAGCATGGCCAGAATTACTACAAGCTTTAATAGAGTCTTTAAAAAGC


 


GGTAACCCAAATTTTAGAGAATCCAGTTTTAGAATTTTGACGACTGTACC


 


TTATTTAATTACCGCTGTTGACATCAACAGTATCTTACCAATTTTTCAAT


 


CAGGCTTTACTGATGCAAGTGATAATGTCAAAATTGCTGCAGTTACGGCT


 


TTCGTGGGTTATTTTAAGCAACTACCAAAATCTGAGTGGTCCAAGTTAGG


 


TATTTTATTACCAAGTCTTTTGAATAGTTTACCAAGATTTTTAGATGATG


 


GTAAGGACGATGCCCTTGCATCAGTTTTTGAATCGTTAATTGAGTTGGTG


 


GAATTGGCACCAAAACTATTCAAGGATATGTTTGACCAAATAATACAATT


 


CACTGATATGGTTATAAAAAATAAGGATTTAGAACCTCCAGCAAGAACCA


 


CAGCACTCGAACTGCTAACCGTTTTCAGCGAGAACGCTCCCCAAATGTGT


 


AAATCGAACCAGAATTACGGGCAAACTTTAGTGATGGTTACTTTAATCAT


 


GATGACGGAGGTATCCATAGATGATGATGATGCAGCAGAATGGATAGAAT


 


CTGACGATACCGATGATGAAGAGGAAGTTACATATGACCACGCTCGTCAA


 


GCTCTTGATCGTGTTGCTTTAAAGCTGGGTGGTGAATATTTGGCTGCACC


 


ATTGTTCCAATATTTACAGCAAATGATCACATCAACCGAATGGAGAGAAA


 


GATTCGCGGCCATGATGGCACTTTCCTCTGCAGCTGAGGGTTGTGCTGAT


 


GTTCTGATCGGCGAGATCCCAAAAATCCTGGATATGGTAATTCCCCTCAT


 


CAACGATCCTCATCCAAGAGTACAGTATGGATGTTGTAATGTTTTGGGTC


 


AAATATCTACTGATTTTTCACCATTCATTCAAGAACTGCACACGATAGAA


 


TTTTGCCGGCTTTAATATCTAAAACTAACGTCAGAATGCACCTCAAGAGT


 


TCAAACGCACGCCGCAGCGGCTCTGGTTAACTTTTCTGAATTCGCTTCGA


 


AGGATATTCTTGAGCCTTACTTGGATAGTCTATTGACAAATTTATTAGTT


 


TTATTACAAAGCAACAAACTTTACGTACAGGAACAGGCCCTAACAACCAT


 


TGCATTTATTGCTGAAGCTGCAAAGAATAAATTTATCAAGTATTACGATA


 


CTCTAATGCCATTATTATTAAATGTTTTGAAGGTTAACAATAAAGATAAT


 


AGTGTTTTGAAAGGTAAATGTATGGAATGTGCAACTCTGATTGGTTTTGC


 


CGTTGGTAAGGAAAAATTTCATGAGCACTCTCAAGAGCTGATTTCTATAT


 


TGGTCGCTTTACAAAACTCAGATATCGATGAAGATGATGCGCTCAGATCA


 


TACTTAGAACAAAGTTGGAGCAGGATTTGCCGAATTCTGGGTGATGATTT


 


TGTTCCGTTGTTACCGATTGTTATACCACCCCTGCTAATTACTGCCAAAG


 


CAACGCAAGACGTCGGTTTAATTGAAGAAGAAGAAGCAGCAAATTTCCAA


 


CAATATCCAGATTGGGATGTTGTTCAAGTTCAGGGAAAACACATTGCTAT


 


TCACACATCCGTCCTTGACGATAAAGTATCAGCAATGGAGCTATTACAAA


 


GCTATGCGACACTTTTAAGAGGCCAATTTGCTGTATATGTTAAAGAAGTA


 


ATGGAAGAAATAGCTCTACCATCGCTTGACTTTTACCTACATGACGGTGT


 


TCGTGCTGCAGGAGCAACTTTAATTCCTATTCTATTATCTTGTTTACTTG


 


CAGCCACCGGTACTCAAAACCGAGGAATTGGTATTGTTGTGGCATAAAGC


 


TTCGTCTAAACTAATCGGAGGCTTAATGTCAGAACCAATGCCAGAAATCA


 


CGCAAGTTTATCACAACTCGTTAGTGAATGGTATTAAAGTCATGGGTGAC


 


AATTGCTTAAGCGAAGACCAATTAGCGGCATTTACTAAGGGTGTCTCCGC


 


CAACTTAACTGACACTTACGAAAGGATGCAGGATCGCCATGGTGATGGTG


 


ATGAATATAATGAAAATATTGATGAAGAGGAAGACTTTACTGACGAAGAT


 


CTTCTCGATGAAATCAACAAGTCTATCGCGGCCGTTTTGAAAACCACAAA


 


TGGTCATTATCTAAAGAATTTGGAGAATATATGGCCTATGATAAACACAT


 


TCCTTTTAGATAATGAACCAATTTTAGTCATTTTTGCATTAGTAGTGATT


 


GGTGACTTGATTCAATATGGTGGCGAACAAACTGCTAGCATGAAGAACGC


 


ATTTATTCCAAAGGTTACCGAGTGCTTGATTTCTCCTGACGCTCGTATTC


 


GCCAAGCTGCTTCTTATATAATCGGTGTTTGTGCCCAATACGCTCCATCT


 


ACATATGCTGACGTTTGCATACCGACTTTAGATACACTTGTTCAGATTGT


 


CGATTTTCCAGGCTCCAAACTGGAAGAAAATCGTTCTTCAACAGAGAATG


 


CCAGTGCAGCCATCGCCAAAATTCTTTATGCATACAATTCCAACATTCCT


 


AACGTAGACACGTACACGGCTAATTGGTTCAAAACGTTACCAACAATAAC


 


TGACAAAGAAGCTGCCTCATTCAACTATCAATTTTTGAGTCAATTGATTG


 


AAAATAATTCGCCAATTGTGTGTGCTCAATCTAATATCTCCGCTGTAGTT


 


GATTCAGTCATACAAGCCTTGAATGAGAGAAGTTTGACCGAAAGGGAAGG


 


CCAAACGGTGATAAGTTCAGTTAAAAAGTTGTTGGGATTTTTGCCTTCTA


 


GTGATGCTATGGCAATTTTCAATAGATATCCAGCTGATATTATGGAGAAA


 


GTACATAAATGGTTTGCATAA






The PSE1 gene is 3.25-kbp in size. Pse1p is involved in the nucleocytoplasmic transport of macromolecules (Seedorf & Silver, 1997, Proc. Natl. Acad. Sci. USA. 94, 8590-8595). This process occurs via the nuclear pore complex (NPC) embedded in the nuclear envelope and made up of nucleoporins (Ryan & Wente, 2000, Curr. Opin. Cell Biol. 12, 361-371). Proteins possess specific sequences that contain the information required for nuclear import, nuclear localisation sequence (NLS) and export, nuclear export sequence (NES) (Pemberton et al., 1998, Curr. Opin. Cell Biol. 10, 392-399). Pse1p is a karyopherin/importin, a group of proteins, which have been divided up into α and β families. Karyopherins are soluble transport factors that mediate the transport of macromolecules across the nuclear membrane by recognising NLS and NES, and interact with and the NPC (Seedorf & Silver, 1997, supra; Pemberton et al., 1998, supra; Ryan & Wente, 2000, supra). Translocation through the nuclear pore is driven by GTP hydrolysis, catalysed by the small GTP-binding protein, Ran (Seedorf & Silver, 1997, supra). Pse1p has been identified as a karyopherin β. 14 karyopherin β proteins have been identified in S. cerevisiae, of which only 4 are essential. This is perhaps because multiple karyopherins may mediate the transport of a single macromolecule (Isoyama et al., 2001, J. Biol. Chem. 276 (24), 21863-21869). Pse1p is localised to the nucleus, at the nuclear envelope, and to a certain extent to the cytoplasm. This suggests the protein moves in and out of the nucleus as part of its transport function (Seedorf & Silver, 1997, supra). Pse1p is involved in the nuclear import of transcription factors (Isoyama et al., 2001, supra; Ueta et al., 2003, J. Biol. Chem. 278 (50), 50120-50127), histones (Mosammaparast et al., 2002, J. Biol. Chem. 277 (1), 862-868), and ribosomal proteins prior to their assembly into ribosomes (Pemberton et al., 1998, supra). It also mediates the export of mRNA from the nucleus. Karyopherins recognise and bind distinct NES found on RNA-binding proteins, which coat the RNA before it is exported from the nucleus (Seedorf & Silver, 1997, Pemberton et al., 1998, Supra).
As nucleocytoplasmic transport of macromolecules is essential for proper progression through the cell cycle, nuclear transport factors, such as pse1p are novel candidate targets for growth control (Seedorf & Silver, 1997, supra).
Overexpression of Pse1p (protein secretion enhancer) on a multicopy plasmid in S. cerevisiae has also been shown to increase protein secretion levels of a repertoire of biologically active proteins (Chow et al., 1992; J. Cell. Sci. 101 (3), 709-719).
Variants and fragments of PSE1 are also included in the present invention. A “variant”, in the context of PSE1, refers to a protein having the sequence of native PSE1 other than for at one or more positions where there have been amino acid insertions, deletions, or substitutions, either conservative or non-conservative, provided that such changes result in a protein whose basic properties, for example enzymatic activity (type of and specific activity), thermostability, activity in a certain pH-range (pH-stability) have not significantly been changed. “Significantly” in this context means that one skilled in the art would say that the properties of the variant may still be different but would not be unobvious over the ones of the original protein.
By “conservative substitutions” is intended combinations such as Val, Ile, Leu, Ala, Met; Asp, Glu; Asn, Gln; Ser, Thr, Gly, Ala; Lys, Arg, His; and Phe, Tyr, Trp. Preferred conservative substitutions include Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe, Tyr.
A “variant” of PSE1 typically has at least 25%, at least 50%, at least 60% or at least 70%, preferably at least 80%, more preferably at least 90%, even more preferably at least 95%, yet more preferably at least 99%, most preferably at least 99.5% sequence identity to the sequence of native PSE1.
The percent sequence identity between two polypeptides may be determined using suitable computer programs, as discussed below. Such variants may be natural or made using the methods of protein engineering and site-directed mutagenesis as are well known in the art.
A “fragment”, in the context of PSE1, refers to a protein having the sequence of native PSE1 other than for at one or more positions where there have been deletions. Thus the fragment may comprise at most 5, 10, 20, 30, 40 or 50%, typically up to 60%, more typically up to 70%, preferably up to 80%, more preferably up to 90%, even more preferably up to 95%, yet more preferably up to 99% of the complete sequence of the full mature PSE1 protein. Particularly preferred fragments of PSE1 protein comprise one or more whole domains of the desired protein.
A fragment or variant of PSE1 may be a protein that, when expressed recombinantly in a host cell, such as S. cerevisiae, can complement the deletion of the endogenous PSE1 gene in the host cell and may, for example, be a naturally occurring homolog of PSE1, such as a homolog encoded by another organism, such as another yeast or other fungi, or another eukaryote such as a human or other vertebrate, or animal or by a plant.
Another preferred chaperone is ORM2 or a fragment or variant thereof having equivalent chaperone-like activity.
ORM2, also known as YLR350W, is located on chromosome XII (positions 828729 to 829379) of the S. cerevisiae genome and encodes an evolutionarily conserved protein with similarity to the yeast protein Orm1p. Hjelmqvist et al, 2002, Genome Biology, 3 (6), research 0027.1-0027.16 reports that ORM2 belongs to gene family comprising three human genes (ORMDL1, ORMDL2 and ORMDL3) as well as homologs in microsporidia, plants, Drosophila, urochordates and vertebrates. The ORMDL genes are reported to encode transmembrane proteins anchored in the proteins endoplasmic reticulum (ER).
The protein Orm2p is required for resistance to agents that induce the unfolded protein response. Hjelmqvist et al, 2002 (supra) reported that a double knockout of the two S. cerevisiae ORMDL homologs (ORM1 and ORM2) leads to a decreased growth rate and greater sensitivity to tunicamycin and dithiothreitol.
One published sequence of Orm2p is as follows (SEQ ID NO: 9):







MIDRTKNESPAFEESPLTPNVSNLKPFPSQSNKISTPVTDHRRRRSSSVI


 


SHVEQETFEDENDQQMLPNMNATWVDQRGAWLIHIVVIVLLRLFYSLFGS


 


TPKWTWTLTNMTYIIGFYIMFHLVKGTPFDFNGGAYDNLTMWEQINDETL


 


YTPTRKFLLIVPIVLFLISNQYYRNDMTLFLSNLAVTVLIGVVPKLGITH


 


RLRISIPGITGRAQIS*






The above protein is encoded in S. cerevisiae by the following coding nucleotide sequence, although it will be appreciated that the sequence can be modified by degenerate substitutions to obtain alternative nucleotide sequences which encode an identical protein product (SEQ ID NO: 10):







ATGATTGACCGCACTAAAAACGAATCTCCAGCTTTTGAAGAGTCTCCGCT


 


TACCCCCAATGTGTCTAACCTGAAACCATTCCCTTCTCAAAGCAACAAAA


 


TATCCACTCCAGTGACCGACCATAGGAGAAGACGGTCATCCAGCGTAATA


 


TCACATGTGGAACAGGAAACCTTCGAAGACGAAAATGACCAGCAGATGCT


 


TCCCAACATGAACGCTACGTGGGTCGACCAGCGAGGCGCGTGGTTGATTC


 


ATATCGTCGTAATAGTACTCTTGAGGCTCTTCTACTCCTTGTTCGGGTCG


 


ACGCCCAAATGGACGTGGACTTTAACAAACATGACCTACATCATCGGATT


 


CTATATCATGTTCCACCTTGTCAAAGGTACGCCCTTCGACTTTAACGGTG


 


GTGCGTACGACAACCTGACCATGTGGGAGCAGATTAACGATGAGACTTTG


 


TACACACCCACTAGAAAATTTCTGCTGATTGTACCCATTGTGTTGTTCCT


 


GATTAGCAACCAGTACTACCGCAACGACATGACACTATTCCTCTCCAACC


 


TCGCCGTGACGGTGCTTATTGGTGTCGTTCCTAAGCTGGGAATTACGCAT


 


AGACTAAGAATATCCATCCCTGGTATTACGGGCCGTGCTCAAATTAGTTA


 


G






Variants and fragments of ORM2 are also included in the present invention. A “variant”, in the context of ORM2, refers to a protein having the sequence of native ORM2 other than for at one or more positions where there have been amino acid insertions, deletions, or substitutions, either conservative or non-conservative, provided that such changes result in a protein whose basic properties, for example enzymatic activity (type of and specific activity), thermostability, activity in a certain pH-range (pH-stability) have not significantly been changed. “Significantly” in this context means that one skilled in the art would say that the properties of the variant may still be different but would not be unobvious over the ones of the original protein.
By “conservative substitutions” is intended combinations such as Val, Ile, Leu, Ala, Met; Asp, Glu; Asn, Gln; Ser, Thr, Gly, Ala; Lys, Arg, His; and Phe, Tyr, Trp. Preferred conservative substitutions include Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe, Tyr.
A “variant” of ORM2 typically has at least 25%, at least 50%, at least 60% or at least 70%, preferably at least 80%, more preferably at least 90%, even more preferably at least 95%, yet more preferably at least 99%, most preferably at least 99.5% sequence identity to the sequence of native ORM2.
The percent sequence identity between two polypeptides may be determined using suitable computer programs, as discussed below. Such variants may be natural or made using the methods of protein engineering and site-directed mutagenesis as are well known in the art.
A “fragment”, in the context of ORM2, refers to a protein having the sequence of native ORM2 other than for at one or more positions where there have been deletions. Thus the fragment may comprise at most 5, 10, 20, 30, 40 or 50%, typically up to 60%, more typically up to 70%, preferably up to 80%, more preferably up to 90%, even more preferably up to 95%, yet more preferably up to 99% of the complete sequence of the full mature ORM2 protein. Particularly preferred fragments of ORM2 protein comprise one or more whole domains of the desired protein.
A fragment or variant of ORM2 may be a protein that, when expressed recombinantly in a host cell, such as S. cerevisiae, can complement the deletion of the endogenous ORM2 gene in the host cell and may, for example, be a naturally occurring homolog of ORM2, such as a homolog encoded by another organism, such as another yeast or other fungi, or another eukaryote such as a human or other vertebrate, or animal or by a plant.
It is particularly preferred that a plasmid according to a first, second or third aspects of the invention includes, either within a polynucleotide sequence insertion, or elsewhere on the plasmid, an open reading frame encoding a protein comprising the sequence of albumin or a fragment or variant thereof. Alternatively, the host cell into which the plasmid is transformed may include within its genome a polynucleotide sequence encoding a protein comprising the sequence of albumin or a fragment or variant thereof, either as an endogenous or heterologous sequence.
By “albumin” we include a protein having the sequence of an albumin protein obtained from any source. Typically the source is mammalian. In one preferred embodiment the serum albumin is human serum albumin (“HSA”). The term “human serum albumin” includes the meaning of a serum albumin having an amino acid sequence naturally occurring in humans, and variants thereof. Preferably the albumin has the amino acid sequence disclosed in WO 90/13653 or a variant thereof. The HSA coding sequence is obtainable by known methods for isolating cDNA corresponding to human genes, and is also disclosed in, for example, EP 73 646 and EP 286 424.
In another preferred embodiment the “albumin” has the sequence of bovine serum albumin. The term “bovine serum albumin” includes the meaning of a serum albumin having an amino acid sequence naturally occurring in cows, for example as taken from Swissprot accession number P02769, and variants thereof as defined below. The term “bovine serum albumin” also includes the meaning of fragments of full-length bovine serum albumin or variants thereof, as defined below.
In another preferred embodiment the albumin is an albumin derived from (i.e. has the sequence of) one of serum albumin from dog (e.g. see Swissprot accession number P49822), pig (e.g. see Swissprot accession number P08835), goat (e.g. as available from Sigma as product no. A2514 or A4164), turkey (e.g. see Swissprot accession number O73860), baboon (e.g. as available from Sigma as product no. A1516), cat (e.g. see Swissprot accession number P49064), chicken (e.g. see Swissprot accession number P19121), ovalbumin (e.g. chicken ovalbumin) (e.g. see Swissprot accession number P01012), donkey (e.g. see Swissprot accession number P39090), guinea pig (e.g. as available from Sigma as product no. A3060, A2639, O5483 or A6539), hamster (e.g. as available from Sigma as product no. A5409), horse (e.g. see Swissprot accession number P35747), rhesus monkey (e.g. see Swissprot accession number Q28522), mouse (e.g. see Swissprot accession number O89020), pigeon (e.g. as defined by Khan et al, 2002, Int. J. Biol. Macromol., 30 (3-4), 171-8), rabbit (e.g. see Swissprot accession number P49065), rat (e.g. see Swissprot accession number P36953) and sheep (e.g. see Swissprot accession number P14639) and includes variants and fragments thereof as defined below.
Many naturally occurring mutant forms of albumin are known. Many are described in Peters, (1996, All About Albumin: Biochemistry Genetics and Medical Applications, Academic Press, Inc., San Diego, Calif., p. 170-181). A variant as defined above may be one of these naturally occurring mutants.
A “variant albumin” refers to an albumin protein wherein at one or more positions there have been amino acid insertions, deletions, or substitutions, either conservative or non-conservative, provided that such changes result in an albumin protein for which at least one basic property, for example binding activity (type of and specific activity e.g. binding to bilirubin), osmolarity (oncotic pressure, colloid osmotic pressure), behaviour in a certain pH-range (pH-stability) has not significantly been changed. “Significantly” in this context means that one skilled in the art would say that the properties of the variant may still be different but would not be unobvious over the ones of the original protein.
By “conservative substitutions” is intended combinations such as Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe, Tyr. Such variants may be made by techniques well known in the art, such as by site-directed mutagenesis as disclosed in U.S. Pat. No. 4,302,386 issued 24 Nov. 1981 to Stevens, incorporated herein by reference.
Typically an albumin variant will have more than 40%, usually at least 50%, more typically at least 60%, preferably at least 70%, more preferably at least 80%, yet more preferably at least 90%, even more preferably at least 95%, most preferably at least 98% or more sequence identity with naturally occurring albumin. The percent sequence identity between two polypeptides may be determined using suitable computer programs, for example the GAP program of the University of Wisconsin Genetic Computing Group and it will be appreciated that percent identity is calculated in relation to polypeptides whose sequence has been aligned optimally. The alignment may alternatively be carried out using the Clustal W program (Thompson et al., 1994). The parameters used may be as follows:
Fast pairwise alignment parameters: K-tuple (word) size; 1, window size; 5, gap penalty; 3, number of top diagonals; 5. Scoring method: x percent. Multiple alignment parameters: gap open penalty; 10, gap extension penalty; 0.05. Scoring matrix: BLOSUM.
The term “fragment” as used above includes any fragment of full-length albumin or a variant thereof, so long as at least one basic property, for example binding activity (type of and specific activity e.g. binding to bilirubin), osmolarity (oncotic pressure, colloid osmotic pressure), behaviour in a certain pH-range (pH-stability) has not significantly been changed.
“Significantly” in this context means that one skilled in the art would say that the properties of the variant may still be different but would not be unobvious over the ones of the original protein. A fragment will typically be at least 50 amino acids long. A fragment may comprise at least one whole sub-domain of albumin. Domains of HSA have been expressed as recombinant proteins (Dockal, M. et al., 1999, J. Biol. Chem., 274, 29303-29310), where domain I was defined as consisting of amino acids 1-197, domain II was defined as consisting of amino acids 189-385 and domain III was defined as consisting of amino acids 381-585. Partial overlap of the domains occurs because of the extended α-helix structure (h10-h1) which exists between domains I and II, and between domains II and III (Peters, 1996, op. cit., Table 2-4). HSA also comprises six sub-domains (sub-domains IA, IB, IIA, IIB, IIIA and IIIB). Sub-domain IA comprises amino acids 6-105, sub-domain IB comprises amino acids 120-177, sub-domain IIA comprises amino acids 200-291, sub-domain IIB comprises amino acids 316-369, sub-domain IIIA comprises amino acids 392-491 and sub-domain IIIB comprises amino acids 512-583. A fragment may comprise a whole or part of one or more domains or sub-domains as defined above, or any combination of those domains and/or sub-domains.
Thus the polynucleotide insertion may comprise an open reading frame that encodes albumin or a variant or fragment thereof.
Alternatively, it is preferred that a plasmid according to a first, second or third aspects of the invention includes, either within a polynucleotide sequence insertion, or elsewhere on the plasmid, an open reading frame encoding a protein comprising the sequence of transferrin or a variant or fragment thereof. Alternatively, the host cell into which the plasmid is transformed may include within its genome a polynucleotide sequence encoding a protein comprising the sequence of transferrin or a variant or fragment thereof, either as an endogenous or heterologous sequence.
The term “transferrin” as used herein includes all members of the transferrin family (Testa, Proteins of iron metabolism, CRC Press, 2002; Harris & Aisen, Iron carriers and iron proteins, Vol. 5, Physical Bioinorganic Chemistry, VCH, 1991) and their derivatives, such as transferrin, mutant transferrins (Mason et al, 1993, Biochemistry, 32, 5472; Mason et al, 1998, Biochem. J., 330 (1), 35), truncated transferring, transferrin lobes (Mason et al, 1996, Protein Expr. Purif., 8, 119; Mason et al, 1991, Protein Expr. Purif., 2, 214), lactoferrin, mutant lactoferrins, truncated lactoferrins, lactoferrin lobes or fusions of any of the above to other peptides, polypeptides or proteins (Shin et al, 1995, Proc. Natl. Acad. Sci. USA, 92, 2820; Ali et al, 1999, J. Biol. Chem., 274, 24066; Mason et al, 2002, Biochemistry, 41, 9448).
The transferrin may be human transferrin. The term “human transferrin” is used herein to denote material which is indistinguishable from transferrin derived from a human or which is a variant or fragment thereof. A “variant” includes insertions, deletions and substitutions, either conservative or non-conservative, where such changes do not substantially alter the useful ligand-binding or immunogenic properties of transferrin.
Mutants of transferrin are included in the invention. Such mutants may have altered immunogenicity. For example, transferrin mutants may display modified (e.g. reduced) glycosylation. The N-linked glycosylation pattern of a transferrin molecule can be modified by adding/removing amino acid glycosylation consensus sequences such as N-X-S/T, at any or all of the N, X, or S/T position. Transferrin mutants may be altered in their natural binding to metal ions and/or other proteins, such as transferrin receptor. An example of a transferrin mutant modified in this manner is exemplified below.
We also include naturally-occurring polymorphic variants of human transferrin or human transferrin analogues. Generally, variants or fragments of human transferrin will have at least 50% (preferably at least 80%, 90% or 95%) of human transferrin's ligand binding activity (for example iron-binding), weight for weight. The iron binding activity of transferrin or a test sample can be determined spectrophotometrically by 470 nm:280 nm absorbance ratios for the proteins in their iron-free and fully iron-loaded states. Reagents should be iron-free unless stated otherwise. Iron can be removed from transferrin or the test sample by dialysis against 0.1M citrate, 0.1M acetate, 10 nm EDTA pH4.5. Protein should be at approximately 20 mg/mL in 100 mM HEPES, 10 mM NaHCO3 pH8.0. Measure the 470 nm:280 nm absorbance ratio of apo-transferrin (Calbiochem, CN Biosciences, Nottingham, UK) diluted in water so that absorbance at 280 nm can be accurately determined spectrophotometrically (0% iron binding). Prepare 20 mM iron-nitrilotriacetate (FeNTA) solution by dissolving 191 mg nitrotriacetic acid in 2 mL 1M NaOH, then add 2 mL 0.5M ferric chloride. Dilute to 50 mL with deionised water. Fully load apo-transferrin with iron (100% iron binding) by adding a sufficient excess of freshly prepared 20 mM FeNTA, then dialyse the holo-transferrin preparation completely against 100 mM HEPES, 10 mM NaHCO3 pH8.0 to remove remaining FeNTA before measuring the absorbance ratio at 470 nm:280 nm. Repeat the procedure using test sample, which should initially be free from iron, and compare final ratios to the control.
Additionally, single or multiple heterologous fusions comprising any of the above; or single or multiple heterologous fusions to albumin, transferrin or immunoglobins or a variant or fragment of any of these may be used. Such fusions include albumin N-terminal fusions, albumin C-terminal fusions and co-N-terminal and C-terminal albumin fusions as exemplified by WO 01/79271, and transferrin N-terminal fusions, transferrin C-terminal fusions, and co-N-terminal and C-terminal transferrin fusions.
The skilled person will also appreciate that the open reading frame of any other gene or variant, or part or either, can be utilised to form a whole or part of an open reading frame in forming a polynucleotide sequence insertion for use with the present invention. For example, the open reading frame may encode a protein comprising any sequence, be it a natural protein (including a zymogen), or a variant, or a fragment (which may, for example, be a domain) of a natural protein; or a totally synthetic protein; or a single or multiple fusion of different proteins (natural or synthetic). Such proteins can be taken, but not exclusively, from the lists provided in WO 01/79258, WO 01/79271, WO 01/79442, WO 01/79443, WO 01/79444 and WO 01/79480, or a variant or fragment thereof, the disclosures of which are incorporated herein by reference. Although these patent applications present the list of proteins in the context of fusion partners for albumin, the present invention is not so limited and, for the purposes of the present invention, any of the proteins listed therein may be presented alone or as fusion partners for albumin, the Fc region of immunoglobulin, transferrin, lactoferrin or any other protein or fragment or variant of any of the above, including fusion proteins comprising any of the above, as a desired polypeptide. Further examples of transferrin fusions are given in US patent applications US2003/0221201 and US2003/0226155.
Preferred other examples of desirable proteins for expression by the present invention includes sequences comprising the sequence of a monoclonal antibody, an etoposide, a serum protein (such as a blood clotting factor), antistasin, a tick anticoagulant peptide, transferrin, lactoferrin, endostatin, angiostatin, collagens, immunoglobulins or immunoglobulin-based molecules or fragment of either (e.g. a Small Modular ImmunoPharmaceuticalTM (“SMIP”) or dAb, Fab′ fragments, F(ab′)2, scAb, scFv or scFv fragment), a Kunitz domain protein (such as those described in WO 03/066824, with or without albumin fusions) interferons, interleukins, IL10, IL11, IL2, interferon α species and sub-species, interferon β species and sub-species, interferon γ species and sub-species, leptin, CNTF, CNTFAx15, IL1-receptor antagonist, erythropoetin (EPO) and EPO mimics, thrombopoetin (TPO) and TPO mimics, prosaptide, cyanovirin-N, 5-helix, T20 peptide, T1249 peptide, HIV gp41, HIV gp120, urokinase, prourokinase, tPA (tissue plasminogen activator), hirudin, platelet derived growth factor, parathyroid hormone, proinsulin, insulin, glucagon, glucagon-like peptides, insulin-like growth factor, calcitonin, growth hormone, transforming growth factor β, tumour necrosis factor, G-CSF, GM-CSF, M-CSF, FGF, coagulation factors in both pre and active forms, including but not limited to plasminogen, fibrinogen, thrombin, pre-thrombin, pro-thrombin, von Willebrand's factor, α1-antitrypsin, plasminogen activators, Factor VII, Factor VIII, Factor IX, Factor X and Factor XIII, nerve growth factor, LACI (lipoprotein associated coagulation inhibitor, also known as tissue factor pathway inhibitor or extrinsic pathway inhibitor), platelet-derived endothelial cell growth factor (PD-ECGF), glucose oxidase, serum cholinesterase, aprotinin, amyloid precursor, inter-alpha trypsin inhibitor, antithrombin III, apo-lipoprotein species, Protein C, Protein S, a variant or fragment or fusion protein of any of the above. The protein may or may not be hirudin.
A “variant”, in the context of the above-listed proteins, refers to a protein wherein at one or more positions there have been amino acid insertions, deletions, or substitutions, either conservative or non-conservative, provided that such changes result in a protein whose basic properties, for example enzymatic activity or receptor binding (type of and specific activity), thermostability, activity in a certain pH-range (pH-stability) have not significantly been changed. “Significantly” in this context means that one skilled in the art would say that the properties of the variant may still be different but would not be unobvious over the ones of the original protein.
By “conservative substitutions” is intended combinations such as Val, Ile, Leu, Ala, Met; Asp, Glu; Asn, Gln; Ser, Thr, Gly, Ala; Lys, Arg, His; and Phe, Tyr, Trp. Preferred conservative substitutions include Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe, Tyr.
A “variant” typically has at least 25%, at least 50%, at least 60% or at least 70%, preferably at least 80%, more preferably at least 90%, even more preferably at least 95%, yet more preferably at least 99%, most preferably at least 99.5% sequence identity to the polypeptide from which it is derived.
The percent sequence identity between two polypeptides may be determined using suitable computer programs, for example the GAP program of the University of Wisconsin Genetic Computing Group and it will be appreciated that percent identity is calculated in relation to polypeptides whose sequence has been aligned optimally.
The alignment may alternatively be carried out using the Clustal W program (Thompson et al., (1994) Nucleic Acids Res., 22 (22), 4673-80). The parameters used may be as follows:

    
    
        Fast pairwise alignment parameters: K-tuple (word) size; 1, window size; 5, gap penalty; 3, number of top diagonals; 5. Scoring method: x percent.
        Multiple alignment parameters: gap open penalty; 10, gap extension penalty; 0.05.
        Scoring matrix: BLOSUM.
    
    


Such variants may be natural or made using the methods of protein engineering and site-directed mutagenesis as are well known in the art.
A “fragment”, in the context of the above-listed proteins, refers to a protein wherein at one or more positions there have been deletions. Thus the fragment may comprise at most 5, 10, 20, 30, 40 or 50% of the complete sequence of the full mature polypeptide. Typically a fragment comprises up to 60%, more typically up to 70%, preferably up to 80%, more preferably up to 90%, even more preferably up to 95%, yet more preferably up to 99% of the complete sequence of the full desired protein. Particularly preferred fragments of a desired protein comprise one or more whole domains of the desired protein.
It is particularly preferred that a plasmid according to a first, second or third aspects of the invention includes, either within a polynucleotide sequence insertion, or elsewhere on the plasmid, an open reading frame encoding a protein comprising the sequence of albumin or a fragment or variant thereof, or any other protein take from the examples above (fused or unfused to a fusion partner) and at least one other heterologous sequence, wherein the at least one other heterologous sequence may contain a transcribed region, such as an open reading frame. In one embodiment, the open reading frame may encode a protein comprising the sequence of a yeast protein. In another embodiment the open reading frame may encode a protein comprising the sequence of a protein involved in protein folding, or which has chaperone activity or is involved in the unfolded protein response, preferably protein disulphide isomerase.
The resulting plasmids may or may not have symmetry between the US and UL regions. For example, a size ratio of 1:1, 5:4, 5:3, 5:2, 5:1 or 5:<1 can be achieved between US and UL or between UL and US regions. The benefits of the present invention do not rely on symmetry being maintained.
The present invention also provides a method of preparing a plasmid of the invention, which method comprises—

    
    
        (a) providing a 2 μm-family plasmid comprising a REP2 gene or an FLP gene and an inverted repeat adjacent to said gene;
        (b) providing a polynucleotide sequence and inserting the polynucleotide sequence into the plasmid at a position according to the first, second or third preferred aspects of the invention; and/or
        (c) additionally or as an alternative to step (b), deleting some or all of the nucleotide bases at the positions according to the first, second or third preferred aspects of the invention; and/or
        (d) additionally or as an alternative to either of steps (b) and (c), substituting some or all of the nucleotide bases at the positions according to the first, second or third preferred aspects of the invention with alternative nucleotide bases.
    
    


Steps (b), (c) and (d) can be achieved using techniques well known in the art, including cloning techniques, site-directed mutagenesis and the like, such as are described in by Sambrook et al., Molecular Cloning: A Laboratory Manual, 2001, 3rd edition, the contents of which are incorporated herein by reference. For example, one such method involves ligation via cohesive ends. Compatible cohesive ends can be generated on a DNA fragment for insertion and plasmid by the action of suitable restriction enzymes. These ends will rapidly anneal through complementary base pairing and remaining nicks can be closed by the action of DNA ligase.
A further method uses synthetic double stranded oligonucleotide linkers and adaptors. DNA fragments with blunt ends are generated by bacteriophage T4 DNA polymerase or E. coli DNA polymerase I which remove protruding 3′ termini and fill in recessed 3′ ends. Synthetic linkers and pieces of blunt-ended double-stranded DNA, which contain recognition sequences for defined restriction enzymes, can be ligated to blunt-ended DNA fragments by T4 DNA ligase. They are subsequently digested with appropriate restriction enzymes to create cohesive ends and ligated to an expression vector with compatible termini. Adaptors are also chemically synthesised DNA fragments which contain one blunt end used for ligation but which also possess one preformed cohesive end. Alternatively a DNA fragment or DNA fragments can be ligated together by the action of DNA ligase in the presence or absence of one or more synthetic double stranded oligonucleotides optionally containing cohesive ends.
Synthetic linkers containing a variety of restriction endonuclease sites are commercially available from a number of sources including Sigma-Genosys Ltd, London Road, Pampisford, Cambridge, United Kingdom.
Accordingly, the present invention also provides a plasmid obtainable by the above method.
The present invention also provides a host cell comprising a plasmid as defined above. The host cell may be any type of cell. Bacterial and yeast host cells are preferred. Bacterial host cells may be useful for cloning purposes. Yeast host cells may be useful for expression of genes present in the plasmid.
In one embodiment the host cell is a cell in which the plasmid is stable as a multicopy plasmid. Plasmids obtained from one yeast type can be maintained in other yeast types (Irie et al, 1991, Gene, 108 (1), 139-144; Irie et al, 1991, Mol. Gen. Genet., 225 (2), 257-265). For example, pSR1 from Zygosaccharomyces rouxii can be maintained in Saccharomyces cerevisiae. Where the plasmid is based on pSR1, pSB3 or pSB4 the host cell may be Zygosaccharomyces rouxii, where the plasmid is based on pSB1 or pSB2 the host cell may be Zygosaccharomyces bailli, where the plasmid is based on pPM1 the host cell may be Pichia membranaefaciens, where the plasmid is based on pSM1 the host cell may be Zygosaccharomyces fermentati, where the plasmid is based on pKD1 the host cell may be Kluyveromyces drosophilarum and where the plasmid is based on the 2 μm plasmid the host cell may be Saccharomyces cerevisiae or Saccharomyces carlsbergensis. A 2 μm-family plasmid of the invention can be said to be “based on” a naturally occurring plasmid if it comprises one, two or preferably three of the genes FLP, REP1 and REP2 having sequences derived from that naturally occurring plasmid.
A plasmid as defined above, may be introduced into a host through standard techniques. With regard to transformation of prokaryotic host cells, see, for example, Cohen et al (1972) Proc. Natl. Acad. Sci. USA 69, 2110 and Sambrook et al (2001) Molecular Cloning, A Laboratory Manual, 3rd Ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. Transformation of yeast cells is described in Sherman et al (1986) Methods In Yeast Genetics, A Laboratory Manual, Cold Spring Harbor, N.Y. The method of Beggs (1978) Nature 275, 104-109 is also useful. Methods for the transformation of S. cerevisiae are taught generally in EP 251 744, EP 258 067 and WO 90/01063, all of which are incorporated herein by reference. With regard to vertebrate cells, reagents useful in transfecting such cells, for example calcium phosphate and DEAE-dextran or liposome formulations, are available from Stratagene Cloning Systems, or Life Technologies Inc., Gaithersburg, Md. 20877, USA.
Electroporation is also useful for transforming cells and is well known in the art for transforming yeast cell, bacterial cells and vertebrate cells. Methods for transformation of yeast by electroporation are disclosed in Becker & Guarente (1990) Methods Enzymol 194, 182.
Generally, the plasmid will transform not all of the hosts and it will therefore be necessary to select for transformed host cells. Thus, a plasmid according to any one of the first, second or third aspects of the present invention may comprise a selectable marker, either within a polynucleotide sequence insertion, or elsewhere on the plasmid, including but not limited to bacterial selectable marker and/or a yeast selectable marker. A typical bacterial selectable marker is the β-lactamase gene although many others are known in the art. Suitable yeast selectable marker include LEU2 (or an equivalent gene encoding a protein with the activity of β-lactamase malate dehydrogenase), TRP1, HIS3, HIS4, URA3, URA5, SFA1, ADE2, MET15, LYS5, LYS2, ILV2, FBA1, PSE1, PDI1 and PGK1. In light of the different options available, the most suitable selectable markers can be chosen. If it is desirable to do so, URA3 and/or LEU2 can be avoided. Those skilled in the art will appreciate that any gene whose chromosomal deletion or inactivation results in an inviable host, so called essential genes, can be used as a selective marker if a functional gene is provided on the plasmid, as demonstrated for PGK1 in a pgk1 yeast strain (Piper and Curran, 1990, Curr. Genet. 17, 119). Suitable essential genes can be found within the Stanford Genome Database (SGD), http:://db.yeastgenome.org).
Additionally, a plasmid according to any one of the first, second or third aspects of the present invention may comprise more than one selectable marker, either within a polynucleotide sequence insertion, or elsewhere on the plasmid.
One selection technique involves incorporating into the expression vector a DNA sequence marker, with any necessary control elements, that codes for a selectable trait in the transformed cell. These markers include dihydrofolate reductase, G418 or neomycin resistance for eukaryotic cell culture, and tetracyclin, kanamycin or ampicillin (i.e. β-lactamase) resistance genes for culturing in E. coli and other bacteria. Alternatively, the gene for such selectable trait can be on another vector, which is used to co-transform the desired host cell.
Another method of identifying successfully transformed cells involves growing the cells resulting from the introduction of a plasmid of the invention, optionally to allow the expression of a recombinant polypeptide (i.e. a polypeptide which is encoded by a polynucleotide sequence on the plasmid and is heterologous to the host cell, in the sense that that polypeptide is not naturally produced by the host). Cells can be harvested and lysed and their DNA or RNA content examined for the presence of the recombinant sequence using a method such as that described by Southern (1975) J. Mol. Biol. 98, 503 or Berent et al (1985) Biotech. 3, 208, or other methods of DNA and RNA analysis common in the art. Alternatively, the presence of a polypeptide in the supernatant of a culture of a transformed cell can be detected using antibodies.
In addition to directly assaying for the presence of recombinant DNA, successful transformation can be confirmed by well known immunological methods when the recombinant DNA is capable of directing the expression of the protein. For example, cells successfully transformed with an expression vector produce proteins displaying appropriate antigenicity. Samples of cells suspected of being transformed are harvested and assayed for the protein using suitable antibodies.
Thus, in addition to the transformed host cells themselves, the present invention also contemplates a culture of those cells, preferably a monoclonal (clonally homogeneous) culture, or a culture derived from a monoclonal culture, in a nutrient medium. Alternatively, transformed cells may themselves represent an industrially/commercially or pharmaceutically useful product and can be purified from a culture medium and optionally formulated with a carrier or diluent in a manner appropriate to their intended industrial/commercial or pharmaceutical use, and optionally packaged and presented in a manner suitable for that use. For example, whole cells could be immobilised; or used to spray a cell culture directly on to/into a process, crop or other desired target. Similarly, whole cell, such as yeast cells can be used as capsules for a huge variety of applications, such as fragrances, flavours and pharmaceuticals.
Transformed host cells may then be cultured for a sufficient time and under appropriate conditions known to those skilled in the art, and in view of the teachings disclosed herein, to permit the expression of any ORF(s) in the one or more polynucleotide sequence insertions within the plasmid.
The present invention thus also provides a method for producing a protein comprising the steps of (a) providing a plasmid according to the first, second or third aspects of the invention as defined above; (b) providing a suitable host cell; (c) transforming the host cell with the plasmid; and (d) culturing the transformed host cell in a culture medium, thereby to produce the protein.
Many expression systems are known, including bacteria (for example E. coli and Bacillus subtilis), yeasts, filamentous fungi (for example Aspergillus), plant cells, whole plants, animal cells and insect cells.
In one embodiment the preferred host cells are the yeasts in which the plasmid is capable of being maintained as a stable multicopy plasmid. Such yeasts include Saccharomyces cerevisiae, Kluyveromyces lactis, Pichia pastoris, Zygosaccharomyces rouxii, Zygosaccharomyces bailli, Zygosaccharomyces fermentati, and Kluyveromyces drosophilarum. 
A plasmid is capable of being maintained as a stable multicopy plasmid in a host, if the plasmid contains, or is modified to contain, a selectable (e.g. LEU2) marker, and stability, as measured by the loss of the marker, is at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9% or substantially 100% after one, two, three, four, five, six, seven, eight, nine ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100 or more generations. Loss of a marker can be assessed as described above, with reference to Chinery & Hinchliffe (1989, Curr. Genet., 16, 21-25).
It is particularly advantageous to use a yeast deficient in one or more protein mannosyl transferases involved in O-glycosylation of proteins, for instance by disruption of the gene coding sequence.
Recombinantly expressed proteins can be subject to undesirable post-translational modifications by the producing host cell. For example, the albumin protein sequence does not contain any sites for N-linked glycosylation and has not been reported to be modified, in nature, by O-linked glycosylation. However, it has been found that recombinant human albumin (“rHA”) produced in a number of yeast species can be modified by O-linked glycosylation, generally involving mannose. The mannosylated albumin is able to bind to the lectin Concanavalin A. The amount of mannosylated albumin produced by the yeast can be reduced by using a yeast strain deficient in one or more of the PMT genes (WO94/04687). The most convenient way of achieving this is to create a yeast which has a defect in its genome such that a reduced level of one of the Pmt proteins is produced. For example, there may be a deletion, insertion or transposition in the coding sequence or the regulatory regions (or in another gene regulating the expression of one of the PMT genes) such that little or no Pmt protein is produced. Alternatively, the yeast could be transformed to produce an anti-Pmt agent, such as an anti-Pmt antibody.
If a yeast other than S. cerevisiae is used, disruption of one or more of the genes equivalent to the PMT genes of S. cerevisiae is also beneficial, e.g. in Pichia pastoris or Kluyveromyces lactis. The sequence of PMT1 (or any other PMT gene) isolated from S. cerevisiae may be used for the identification or disruption of genes encoding similar enzymatic activities in other fungal species. The cloning of the PMT1 homologue of Kluyveromyces lactis is described in WO 94/04687.
The yeast will advantageously have a deletion of the HSP150 and/or YAP3 genes as taught respectively in WO 95/33833 and WO 95/23857.
The present application also provides a method of producing a protein comprising the steps of providing a host cell as defined above, which host cell comprises a plasmid of the present invention and culturing the host cell in a culture medium thereby to produce the protein. The culture medium may be non-selective or place a selective pressure on the stable multicopy maintenance of the plasmid.
A method of producing a protein expressed from a plasmid of the invention preferably further comprise the step of isolating the thus produced protein from the cultured host cell or the culture medium.
The thus produced protein may be present intracellularly or, if secreted, in the culture medium and/or periplasmic space of the host cell. The protein may be isolated from the cell and/or culture medium by many methods known in the art. For example purification techniques for the recovery of recombinantly expressed albumin have been disclosed in: WO 92/04367, removal of matrix-derived dye; EP 464 590, removal of yeast-derived colorants; EP 319 067, alkaline precipitation and subsequent application of the albumin to a lipophilic phase; and WO 96/37515, U.S. Pat. No. 5,728,553 and WO 00/44772, which describe complete purification processes; all of which are incorporated herein by reference. Proteins other than albumin may be purified from the culture medium by any technique that has been found to be useful for purifying such proteins.
Such well-known methods include ammonium sulphate or ethanol precipitation, acid or solvent extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography, lectin chromatography, concentration, dilution, pH adjustment, diafiltration, ultrafiltration, high performance liquid chromatography (“HPLC”), reverse phase HPLC, conductivity adjustment and the like.
In one embodiment, any one or more of the above mentioned techniques may be used to further purifying the thus isolated protein to a commercially acceptable level of purity. By commercially acceptable level of purity, we include the provision of the protein at a concentration of at least 0.01 g·L−1, 0.02 g·L−1, 0.03 g·L−1, 0.04 g·L−1, 0.05 g·L−1, 0.06 g·L−1, 0.07 g·L−1, 0.08 g·L−1, 0.09 g·L−1, 0.1 g·L−1, 0.2 g·L−1, 0.3 g·L−1, 0.4 g·L−1, 0.5 g·L−1, 0.6 g·L−1, 0.7 g·L−1, 0.8 g·L−1, 0.9 g·L−1, 1 g·L−1, 2 g·L−1, 3 g·L−1, 4 g·L−1, 5 g·L−1, 6 g·L−1, 7 g·L−1, 8 g·L−1, 9 g·L−1, 10 g·L−1, 15 g·L−1, 20 g·L−1, 25 g·L−1, 30 g·L−1, 40 g·L−1, 50 g·L−1, 60 g·L−1, 70 g·L−1, 70 g·L−1, 90 g·L−1, 100 g·L−1, 150 g·L−1, 200 g·L−1, 250 g·L−1, 300 g·L−1, 350 g·L−1, 400 g·L−1, 500 g·L−1, 600 g·L−1, 700 g·L−1, 800 g·L−1, 900 g·L−1, 1000 g·L−1, or more.
The thus purified protein may be lyophilised. Alternatively it may be formulated with a carrier or diluent, and optionally presented in a unit form.
It is preferred that the protein is isolated to achieve a pharmaceutically acceptable level of purity. A protein has a pharmaceutically acceptable level of purity if it is essentially pyrogen free and can be administered in a pharmaceutically efficacious amount without causing medical effects not associated with the activity of the protein.
The resulting protein may be used for any of its known utilities, which, in the case of albumin, include i.v. administration to patients to treat severe burns, shock and blood loss, supplementing culture media, and as an excipient in formulations of other proteins.
Although it is possible for a therapeutically useful desired protein obtained by a process of the invention to be administered alone, it is preferable to present it as a pharmaceutical formulation, together with one or more acceptable carriers or diluents. The carrier(s) or diluent(s) must be “acceptable” in the sense of being compatible with the desired protein and not deleterious to the recipients thereof. Typically, the carriers or diluents will be water or saline which will be sterile and pyrogen free.
Optionally the thus formulated protein will be presented in a unit dosage form, such as in the form of a tablet, capsule, injectable solution or the like.
We have also demonstrated that a plasmid-borne gene encoding a protein comprising the sequence of an “essential” protein can be used to stably maintain the plasmid in a host cell that, in the absence of the plasmid, does not produce the essential protein. A preferred essential protein is an essential chaperone, which can provide the further advantage that, as well as acting as a selectable marker to increase plasmid stability, its expression simultaneously increases the expression of a heterologous protein encoded by a recombinant gene within the host cell. This system is advantageous because it allows the user to minimise the number of recombinant genes that need to be carried by a plasmid. For example, typical prior art plasmids carry marker genes (such as those as described above) that enable the plasmid to be stably maintained during host cell culturing process. Such marker genes need to be retained on the plasmid in addition to any further genes that are required to achieve a desired effect. However, the ability of plasmids to incorporate exogenous DNA sequences is limited and it is therefore advantageous to minimise the number of sequence insertions required to achieve a desired effect. Moreover, some marker genes (such as auxotrophic marker genes) require the culturing process to be conducted under specific conditions in order to obtain the effect of the marker gene. Such specific conditions may not be optimal for cell growth or protein production, or may require inefficient or unduly expensive growth systems to be used.
Thus, it is possible to use a gene that recombinantly encodes a protein comprising the sequence of an “essential protein” as a plasmid-borne gene to increase plasmid stability, where the plasmid is present within a cell that, in the absence of the plasmid, is unable to produce the “essential protein”.
It is preferred that the “essential protein” is one that, when its encoding gene(s) in a host cell are deleted or inactivated, does not result in the host cell developing an auxotrophic (biosynthetic) requirement. By “auxotrophic (biosynthetic) requirement” we include a deficiency that can be complemented by additions or modifications to the growth medium. Therefore, an “essential marker gene” which encodes an “essential protein”, in the context of the present invention is one that, when deleted or inactivated in a host cell, results in a deficiency which cannot be complemented by additions or modifications to the growth medium. The advantage of this system is that the “essential marker gene” can be used as a selectable marker on a plasmid in host cell that, in the absence of the plasmid, is unable to produce that gene product, to achieve increased plasmid stability without the disadvantage of requiring the cell to be cultured under specific selective (e.g. selective nutrient) conditions. Therefore, the host cell can be cultured under conditions that do not have to be adapted for any particular marker gene, without losing plasmid stability. For example, host cells produced using this system can be cultured in non-selective media such as complex or rich media, which may be more economical than the minimal media that are commonly used to give auxotrophic marker genes their effect.
The cell may, for example, have its endogenous gene or genes deleted or otherwise inactivated.
It is particularly preferred if the “essential protein” is an “essential” chaperone, as this can provide the dual advantage of improving plasmid stability without the need for selective growth conditions and increasing the production of proteins, such as endogenously encoded or a heterologous proteins, in the host cell. This system also has the advantage that it minimises the number of recombinant genes that need to be carried by the plasmid if one chooses to use over-expression of an essential chaperone to increase protein production by the host cell.
Preferred “essential proteins” for use in this aspect of the invention include the “essential” chaperones PDI1 and PSE1, and other “essential” gene products such as PGK1 or FBA1 which, when the endogenous gene(s) encoding these proteins are deleted or inactivated in a host cell, do not result in the host cell developing an auxotrophic (biosynthetic) requirement.
Accordingly, in a fourth aspect, the present invention also provides a host cell comprising a plasmid (such as a plasmid according to any of the first, second or third aspects of the invention), the plasmid comprising a gene that encodes an essential chaperone wherein, in the absence of the plasmid, the host cell is unable to produce the chaperone. Preferably, in the absence of the plasmid, the host cell is inviable. The host cell may further comprise a recombinant gene encoding a heterologous (or homologous, in the sense that the recombinant gene encodes a protein identical in sequence to a protein encoded by the host cell) protein, such as those described above in respect of earlier aspects of the invention.
The present invention also provides, in a fifth aspect, a plasmid comprising, as the sole selectable marker, a gene encoding an essential chaperone. The plasmid may further comprise a gene encoding a heterologous protein. The plasmid may be a 2 μm-family plasmid and is preferably a plasmid according to any of the first, second or third aspects of the invention.
The present invention also provides, in a sixth aspect, a method for producing a heterologous protein comprising the steps of: providing a host cell comprising a plasmid, the plasmid comprising a gene that encodes an essential chaperone wherein, in the absence of the plasmid, the host cell is unable to produce the chaperone and wherein the host cell further comprises a recombinant gene encoding a heterologous protein; culturing the host cell in a culture medium under conditions that allow the expression of the essential chaperone and the heterologous protein; and optionally purifying the thus expressed heterologous protein from the cultured host cell or the culture medium; and further optionally, lyophilising the thus purified protein.
The method may further comprise the step of formulating the purified heterologous protein with a carrier or diluent and optionally presenting the thus formulated protein in a unit dosage form, in the manner discussed above. In one preferred embodiment, the method involves culturing the host cell in non-selective media, such as a rich media.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 shows a plasmid map of the 2 μm plasmid.
FIG. 2 shows a plasmid map of pSAC35.
FIG. 3 shows some exemplified FLP insertion sites.
FIGS. 4 to 8, 10, 11, 13 to 32, 36 to 42, 44 to 46, 48 to 54 and 57 to 76 show maps of various plasmids.
FIG. 9 shows the DNA fragment from pDB2429 containing the PDI1 gene.
FIG. 12 shows some exemplified REP2 insertion sites.
FIG. 33 shows table 3 as referred to in the Examples.
FIG. 34 shows the sequence of SEQ ID NO: 1.
FIG. 35 shows the sequence of SEQ ID NO: 2.
FIG. 43 shows the sequence of PCR primers DS248 and DS250.
FIG. 47 shows plasmid stabilities with increasing number of generation growth in non-selective liquid culture for S. cerevisiae containing various pSAC35-derived plasmids.
FIG. 55 shows the results of RIE. 10 mL YEPD shale flasks were inoculated with DXY1 trp1Δ [pDB2976], DXY1 trp1Δ [pDB2977], DXY1 trp1Δ [pDB2978], DXY1 trp1Δ [pDB2979], DXY1 trp1Δ [pDB2980] or DXY1 trp1Δ [pDB2981] transformed to tryptophan prototrophy with a 1.41 kb NotI/PstI pdi1::TRP1 disrupting DNA fragment was isolated from pDB3078. Transformants were grown for 4-days at 30° C., 200 rpm. 4 μL culture supernatant loaded per well of a rocket immunoelectrophoresis gel (Weeke, B. 1976. Rocket immunoelectrophoresis. In N. H. Azelsen, J. Kroll, and B. Weeke [eds.], A manual of quantitative immunoelectrophoresis. Methods and applications. Universitetsforlaget, Oslo, Norway). rHA standards concentrations are in μg/mL. 700 μL goat anti-HA (Sigma product A-1151 resuspended in 5 mL water)/50 mL agarose. Precipin was stained with Coomassie blue. Isolates selected for further analysis are indicated (*).
FIG. 56 shows the results of RIE. 10 mL YEPD shake flasks were inoculated with DXY1 [pDB2244], DXY1 [pDB2976], DXY1 trp1Δ pdi1::TRP1 [pDB2976], DXY1 [pDB2978], DXY1 trp1Δ pdi1::TRP1 [pDB2978], DXY1 [pDB2980], DXY1 trp1Δ pdi1::TRP1 [pDB2980], DXY1 [pDB2977], DXY1 trp1Δ pdi1::TRP1 [pDB2977], DXY1 [pDB2979] DXY1 trp1Δ pdi1::TRP1 [pDB2979], DXY1 [pDB2981] and DXY1 trp1Δ pdi1::TRP1 [pDB2981], and were grown for 4-days at 30° C., 200 rpm. 4 μL culture supernatant loaded per well of a rocket immunoelectrophoresis gel. rHA standards concentrations are in μg/mL. 800 μL goat anti-HA (Sigma product A-1151 resuspended in 5 mL water)/50 mL agarose. Precipin was stained with Coomassie blue. Isolates selected for further analysis are indicated (*)



EXAMPLES
These example describes the insertion of additional DNA sequences into a number of positions, defined by restriction endonuclease sites, within the US-region of a 2 μm-family plasmid, of the type shown in FIG. 2 and generally designated pSAC35, which includes a β-lactamase gene (for ampicillin resistance, which is lost from the plasmid following transformation into yeast), a LEU2 selectable marker and an oligonucleotide linker, the latter two of which are inserted into a unique SnaBI-site within the UL-region of the 2 μm-family disintegration vector, pSAC3 (see EP 0 286 424). The sites chosen were towards the 3′-ends of the REP2 and FLP coding regions or in the downstream inverted repeat sequences. Short synthetic DNA linkers were inserted into each site, and the relative stabilities of the modified plasmids were compared during growth on non-selective media. Preferred sites for DNA insertions were identified. Insertion of larger DNA fragments containing “a gene of interest” was demonstrated by inserting a DNA fragment containing the PDI1 gene into the XcmI-site after REP2.
Example 1
Insertion of Synthetic DNA Linker into XcmI-Sites in the Small Unique Region of pSAC35
Sites assessed initially for insertion of additional DNA into the US-region of pSAC35, were the XcmI-sites in the 599-bp inverted repeats. One XcmI-site cuts 51-bp after the REP2 translation termination codon, whereas the other XcmI-site cuts 127-bp before the end of the FLP coding sequence, due to overlap with the inverted repeat (see FIG. 3).
The sequence inserted was a 52-bp linker made by annealing 0.5 mM solutions of oligonucleotides CF86 and CF87. This DNA linker contained a core region “SnaBI-PacI-FseI/SfiI-SmaI-SnaBI”, which encoded restriction sites absent from pSAC35.




Plasmid pSAC35 was partially digested with XcmI, the linear 11-kb fragment was isolated from a 0.7% (w/v) agarose gel, ligated with the CF86/CF87 XcmI linker (neat, 10−1 and 10−2 dilutions) and transformed into E. coli DH5α. Ampicillin resistant transformants were selected and screened for the presence of plasmids that could be linearised by SmaI digestion. Restriction enzyme analysis identified pDB2688 (FIG. 4) with the linker cloned into the XcmI-site after REP2. DNA sequencing using oligonucleotides primers CF88, CF98 and CF99 (Table 1) confirmed the insertion contained the correct lifer sequence.







TABLE 1







Oligonucleotide sequencing printers:









Primer
Description
Sequence





CF88
REP2 primer, 20 mer
5′-ATCACGTAATACTTCTAGGG-3′


(SEQ ID NO: 13)




 


CF98
REP2 primer, 20 mer
5′-AGAGTGAGTTGGAAGGAAGG-3′


(SEQ ID NO: 14)




 


CF99
REP2 primer, 20 mer
5′-AGCTCGTAAGCGTCGTTACC-3′


(SEQ ID NO: 15)




 


CF90
FLP primer, 20 mer
5′-CTAGTTTCTCGGTACTATGC-3′


(SEQ ID NO: 16)




 


CF91
FLP primer, 20 mer
5′-GAGTTGACTAATGTTGTGGG-3′


(SEQ ID NO: 17)




 


CF100
FLP primer, 20 mer
5′-AAAGCTTTGAAGAAAAATGC-3′


(SEQ ID NO: 18)




 


CF101
FLP primer, 20 mer
5′-GCAAGGGGTAGGATCGATCC-3′


(SEQ ID NO: 19)




 


CF123
pDB2783 MCS, 24 mer
5′-ATTCGAGCTCGGTACCTACGTACT-3′


(SEQ ID NO: 20)




 


CF126
pDB2783 MCS, 24 mer
5′-CCCGGGCACGTGGGATCCTCTAGA-3′


(SEQ ID NO: 21)




 


M13-Forward
pDB2783 MCS, 17 mer
5′-GTAAAACGACGGCCAGT-3′


(SEQ ID NO: 22)




 


M13-Reverse
pDB2783 MCS, 16 mer
5′-AACAGCTATGACCATG-3′


(SEQ ID NO: 23)




 


CF129
Inverted repeat primer,
5′-GTGTTTATGCTTAAATGCG-3′


(SEQ ID NO: 24)
19 mer



 


CF130
REP2 primer, 20 mer
5′-TCCTCTTGCATTTGTGTCTC-3′


(SEQ ID NO: 25)




 


CF131
REP2 primer, 19 mer
5′-ATCTTCCTATTATTATAGC-3′


(SEQ ID NO: 26)









Restriction enzyme analysis also identified pDB2689 (FIG. 5), with the linker cloned into the XcmI-site in the FLP gene. However, the linker in pDB2689 was shown by DNA sequencing using primers CF90 and CF91 to have a missing G:C base-pair within the FseI/SfiI site (marked above in bold in the CF86+CF87 linker). This generated a coding sequence for a mutant Flp-protein, with 39 C-terminal amino acid residues replaced by 56 different amino acids before the translation termination codon.
The missing base-pair in the pDB2689 tinker sequence was corrected to produce pDB2786 (FIG. 6). To achieve this, a 31-bp 5′-phosphorylated SnaBI-linker was made from oligonucleotides CF104 and CF105. This was ligated into the SnaBI site of pDB2689, which had previously been treated with calf intestinal alkaline phosphatase. DNA sequencing with primers CF90, CF91, CF100 and CF101 confirmed the correct DNA linker sequence in pDB2786. This generated a coding sequence for a mutant Flp-protein, with 39 C-terminal residues replaced by 14 different residues before translation termination.




An additional plasmid, pDB2798 (FIG. 7), was also produced by ligation of the SnaBI linker in the opposite direction to pDB2786. The linker sequence in pDB2798 was confirmed by DNA sequencing. Plasmid pDB2798 contained a coding sequence for a mutant Flp-protein, with 39 C-terminal residues replaced by 8 different residues before translation termination.
A linker was also cloned into the XcmI-site in the FLP gene to truncate the Flp protein at the site of insertion. The linker used was a 45-bp 5′-phosphorylated XcmI-linker made from oligonucleotides CF120 and CF121.




This CF120/CF121 XcmI linker was ligated with 11-kb pSAC35 fragments produced by partial digestion with XcmI, followed by treatment with calf intestinal alkaline phosphatase. Analysis of ampicillin resistant E. coli DH5α transformants identified clones containing pDB2823 (FIG. 8). DNA sequencing with primers CF90, CF91, CF100 and CF101 confirmed the linker sequence in pDB2823. Translation termination within the linker inserted would result in the production of Flp (1-382), which lacked 41 C-terminal residues.
The impact on plasmid stability from insertion of linker sequences into the XcmI-sites within the US-region of pSAC35 was assessed for pDB2688 and pDB2689. Plasmid stability was determined in a S. cerevisiae strain by loss of the LEU2 marker during non-selective grown on YEPS. The same yeast strain, transformed with pSAC35, which is structurally similar to pSAC3, but contains additional DNA inserted at the SnaBI site that contained a LEU2 selectable marker (Chinery & Hinchliffe, 1989, Curr. Genet., 16, 21), was used as the control.
The yeast strain was transformed to leucine prototrophy using a modified lithium acetate method (Sigma yeast transformation kit, YEAST-1, protocol 2; (Ito et al, 1983, J. Bacteriol., 153, 163; Elble, 1992, Biotechniques, 13, 18)). Transformants were selected on BMMD-agar plates, and were subsequently patched out on BMMD-agar plates. Cryopreserved trehalose stocks were prepared from 10 mL BMMD shake flask cultures (24 hrs, 30° C., 200 rpm).
The composition of YEPD and BMMD is described by Sleep et al., 2002, Yeast 18, 403. YEPS and BMMS are similar in composition to YEPD and BMMD accept that 2% (w/v) sucrose was substituted for the 2% (w/v) glucose as the sole initial carbon source.
For the determination of plasmid stability a 1 mL cryopreserved stock was thawed and inoculated into 100 mL YEPS (initial OD600≈0.04-0.09) in a 250 mL conical flask and grow for approximately 72 hours (70-74 hrs) at 30° C. in an orbital shaker (200 rpm, Innova 4300 incubator shaker, New Brunswick Scientific).
Samples were removed from each flask, diluted in YEPS-broth (10−2 to 10−5 dilution), and 100 μL aliquots plated in duplicate onto YEPS-agar plates. Cells were grown at 30° C. for 3-4 days to allow single colonies to develop. For each yeast stock analysed, 100 random colonies were patched in replica onto BMMS-agar plates followed by YEPS-agar plates. After growth at 30° C. for 3-4 days the percentage of colonies growing on both BMMS-agar plates and YEPS-agar plates was determined as the measure of plasmid stability.
In the above analysis to measure the loss of the LEU2 marker from transformants, pSAC35 and pDB2688 appeared to be 100% stable, whereas pDB2689 was 72% stable. Hence, insertion of the linker into the XcmI-site after REP2 had no apparent effect on plasmid stability, despite altering the transcribed sequence and disrupting the homology between the 599-bp inverted repeats. Insertion of the linker at the XcmI-site in FLP also resulted in a surprisingly stable plasmid, despite both disruption of the inverted repeat and mutation of the Flp protein.
Example 2
Insertion of the PDI1 Gene into the XcmI Linker of pDB2688
The insertion of a large DNA fragment into the US-region of 2 μm-like vectors was demonstrated by cloning the S. cerevisiae PDI1 gene into the XcmI-linker of pDB2688. The PDI1 gene (FIG. 9) was cloned on a 1.9-kb SacI-SpeI fragment from a larger S. cerevisiae SKQ2n genomic DNA fragment containing the PDI1 gene (as provided in the plasmid pMA3a:C7 that is described in U.S. Pat. No. 6,291,205 and also described as Clone C7 in Crouzet & Tuite, 1987, Mol. Gen. Genet., 210, 581-583 and Farquhar et al, 1991, supra), which had been cloned into YIplac211 (Gietz & Sugino, 1988, Gene, 74, 527-534) and had a synthetic DNA linker containing a SacI restriction site inserted at a unique Bsu36I-site in the 3′ untranslated region of the PDI1 gene. The 1.9-kb SacI-SpeI fragment was treated with T4 DNA polymerase to fill the SpeI 5′-overhang and remove the SacI 3′-overhang. This PDI1 fragment included 212-bp of the PDI1 promoter upstream of the translation initiation codon, and 148-bp downstream of the translation termination codon. This was ligated with SmaI linearised/calf intestinal alkaline phosphatase treated pDB2688, to create plasmid pDB2690 (FIG. 10), with the PDI1 gene transcribed in the same direction as REP2. A S. cerevisiae strain was transformed to leucine prototrophy with pDB2690.
An expression cassette for a human transferrin mutant (N413Q, N611Q) was subsequently cloned into the NotI-site of pDB2690 to create pDB2711 (FIG. 11). The expression cassette in pDB2711 contains the S. cerevisiae PRB1 promoter, an HSA/MFα fusion leader sequence (EP 387319; Sleep et al, 1990, Biotechnology (N.Y.), 8, 42) followed by a coding sequence for the human transferrin mutant (N413Q, N611Q) and the S. cerevisiae ADH1 terminator. Plasmid pDB2536 (FIG. 36) was constructed similarly by insertion of the same expression cassette into the NotI-site of pSAC35.
The advantage of inserting “genes of interest” into the US-region of 2 μm-vectors was demonstrated by the approximate 7-fold increase in recombinant transferrin N413Q, N611Q secretion during fermentation of yeast transformed with pDB2711, compared to the same yeast transformed with pDB2536. An approximate 15-fold increase in recombinant transferrin N413Q, N611Q secretion was observed in shake flask culture (data not shown).
The relative stabilities of plasmids pDB2688, pDB2690, pDB2711, pDB2536 and pSAC35 were determined in the same yeast strain grown in YEPS media, using the method described above (Table 2).
In this analysis, pDB2690 was 32% stable, compared to 100% stability for pDB2688 without the PDI1 insert. This decrease in plasmid stability was less than the decrease in plasmid stability observed with pDB2536, due to insertion of the rTF (N413Q, N611Q) expression cassette into the NotI-site within the large unique region of pSAC35 (Table 2).
Furthermore, selective growth in minimal media during high cell density fermentations could overcome the increased plasmid instability due to the PDI1 insertion observed in YEPS medium, as the rTF (N413Q, N611Q) yield from the same yeast transformed with pDB2711 did not decrease compared to that achieved from the same yeast transformed with pDB2536.







TABLE 2







Summary of plasmid stability data for PDI1 insertion into the


small unique region of pSAC35. Data from 3 days growth in


non-selective shake flask culture before plating on YEPS-agar.













Insertion

Relative



Plasmid
Site(s)
Additional Details
Stability







pSAC35
—
—
100% 



pDB2688
XcmI
Linker in Inverted
100% 





Repeat



pDB2690
XcmI
PDI1 in XcmI Linker
32%



pDB2711
XcmI, NotI
PDI1 in XcmI Linker,
10%





rTf Cassette at NotI



pDB2536
NotI
rTf Cassette at NotI
17%










Example 3
Insertion of DNA Linkers into the REP2 Gene and Downstream Sequences in the Inverted Repeat of pSAC35
To define the useful limits for insertion of additional DNA into the REP2 gene and sequences in the inverted repeat downstream of it, further linkers were inserted into pSAC35. FIG. 12 indicates the restriction sites used for these insertions and the effects on the Rep2 protein of translation termination at these sites.
The linker inserted at the XmnI-site in REP2 was a 44-bp sequence made from oligonucleotides CF108 and CF109.




To avoid insertion into other XmnI-sites in pSAC35, the 3,076-bp XbaI fragment from pSAC35 that contained the REP2 and FLP genes was first sub-cloned into the E. coli cloning vector pDB2685 (FIG. 13) to produce pDB2783 (FIG. 14).
Plasmid pDB2685 is a pUC18-like cloning vector derived from pCF17 containing apramycin resistance gene aac(3)IV from Klebsiella pneumoniae (Rao et al, 1983, Antimicrob. Agents Chemother., 24, 689) and multiple cloning site from pMCS5 (Hoheisel, 1994, Biotechniques, 17, 456). pCF17 was made from pIJ8600 (Sun et al., 1999, Microbiology, 145 (9), 2221-7) by digestion with EcoRI, NheI and the Klenow fragment of DNA polymerase I, and self-ligation, followed by isolation from the reaction products by transformation of competent E. coli DH5α cells and selection with apramycin sulphate. Plasmid pDB2685 was constructed by cloning a 439 bp SspI-SwaI fragment from pMCS5 into pCF17, which had been cut with MscI and treated with calf intestinal alkaline phosphatase. Blue/white selection is not dependant on IPTG induction.
Plasmid pDB2783 was linearised with XmnI and ligated with the CF108/CF109 XmnI-linker to produce pDB2799 (FIG. 15) and pDB2780 (not shown). Plasmid pDB2799 contained the CF108/CF109 XmnI linker in the correct orientation for translation termination at the insertion site to produce Rep2 (1-244), whereas pDB2780 contained the linker cloned in the opposite orientation. DNA sequencing with primers CF98 and CF99 confirmed the correct linker sequences.
The 3,120 bp XbaI fragment from pDB2799 was subsequently ligated with a 7,961-bp pSAC35 fragment which had been produced by partial XbaI digestion and treatment with calf intestinal alkaline phosphatase, to create plasmid pDB2817 (B-form) and pDB2818 (A-form) disintegration vectors (FIGS. 16 and 17 respectively).
Insertion of linkers at the ApaI-site in pSAC35 was performed with and without 3′-5′ exonuclease digestion by T4 DNA polymerase. This produced coding sequences for either Rep2 (1-271) or Rep2 (1-269) before translation termination. In the following figure, the sequence GGCC marked with diagonal lines was deleted from the 3′-overhang produced after ApaI digestion resulting in removal of nucleotides from the codons for Glycine-170 (GGC) and Proline-171.




The linker inserted at the ApaI-site without exonuclease digestion was a 50-bp 5′-phosphorylated linker made from oligonucleotides CF116 and CF117.




This was ligated with pSAC35, which had been linearised with ApaI and treated with calf intestinal alkaline phosphatase, to produce pDB2788 (FIG. 18) and pDB2789 (not shown). Within pDB2788, the linker was in the correct orientation for translation termination after proline-271, whereas in pDB2789 the linker was in the opposite orientation.
The linker inserted at the ApaI-site with exonuclease digestion by T4 DNA polymerase was a 43-bp 5′-phosphorylated linker made from oligonucleotides CF106 and CF107, which was called the core termination linker.




The core termination linker was ligated with pSAC35, which had been linearised with ApaI, digested with T4 DNA polymerase and treated with calf intestinal alkaline phosphatase. This ligation produced pDB2787 (FIG. 19) with the linker cloned in the correct orientation for translation termination after glutamate-269.
The correct DNA sequences were confirmed in all clones containing the ApaI-linkers, using oligonucleotide primers CF98 and CF99.
The core termination linker (CF106+CF107) was also used for insertion into the FspI-sites of pDB2783 (FIG. 14). The core termination linker (CF106+CF107) was ligated into pDB2783 linearised by partial FspI digestion, which had been treated with calf intestinal alkaline phosphatase. Plasmids isolated from apramycin resistant E. coli DH5α transformants were screened by digestion with FspI, and selected clones were sequenced with M13 forward and reverse primers.
Plasmid pDB2801 (not shown) was identified containing two copies of the linker cloned in the correct orientation (with the PacI-site nearest the REP2 gene). The extra copy of the linker was subsequently removed by first deleting a 116-bp NruI-HpaI fragment containing an FseI-site from the multiple cloning site region, followed by digestion with FseI and re-ligation to produce pDB2802 (FIG. 20). DNA sequencing using oligonucleotide CF126 confirmed the correct linker sequence.
The 3,119-bp pDB2802 XbaI fragment was subsequently ligated with a 7,961-bp pSAC35 fragment produced by partial XbaI digestion and treatment with calf intestinal alkaline phosphatase to create pDB2805 (B-form) and pDB2806 (A-form) disintegration vectors (FIGS. 21 and 22, respectively).
Example 4
Insertion of DNA Linkers into the FLP Gene and Downstream Sequences in the Inverted Repeat of pSAC35
DNA linkers were inserted into pSAC35 to define the useful limits for insertion of additional DNA into the FLP gene and sequences downstream in the inverted repeat. FIG. 3 indicates the restriction sites used for these insertions and the affects on the Flp protein of translation termination at these sites.
The linker inserted at the BclI-site was a 49-bp 5′-phosphorylated linker made from oligonucleotides CF18 and CF119.




Due to Dam-methylation of the BclI-site in pSAC35, the BclI-linker was cloned into non-methylated pSAC35 DNA, which had been isolated from the E. coli strain ET12567 pUZ8002 (MacNeil et al, 1992, Gene, 111, 61; Kieser et al, 2000, Practical Streptomyces Genetics, The John Innes Foundation, Norwich). Plasmid pSAC35 was linearised with BclI, treated with calf intestinal alkaline phosphatase, and ligated with the BclI-linker to create pDB2816 (FIG. 23). DNA sequencing with oligonucleotide primers CF91 and CF100 showed that three copies of the BclI-linker were present in pDB2816, which were all in the correct orientation for translational termination of Flp after histidine-353.
Digestion of pDB2816 with PacI followed by self-ligation, was performed to produce pDB2814 and pDB2815, containing one and two copies of the BclI-linker respectively (FIGS. 24 and 25). The DNA sequences of the linkers were confirmed using primers CF91 and CF100. In S. cerevisiae a truncated Flp (1-353) protein will be produced by yeast transformed with pDB2814, pDB2815 or pDB2816.
An additional plasmid pDB2846 (data not shown) was also produced by ligation of a single copy of the BclI-linker in the opposite orientation to pDB2814. This has the coding sequence for the first 352-residues from Flp followed by 14 different residues before translation termination.
The linker inserted at the HgaI-site was a 47-bp 5′-phosphorylated linker made from oligonucleotides CF114 and CF115.




The HgaI-linker was ligated with pDB2783, which had been linearised by partial HgaI digestion and treated with calf intestinal alkaline phosphatase to create pDB281 (FIG. 26). DNA sequencing with oligonucleotides CF90, CF91 and CF100 confirmed the correct linker insertion.
The 3,123-bp XbaI fragment from pDB2811 was subsequently ligated with the 7,961-bp pSAC35 fragment, produced by partial XbaI digestion and treatment with calf intestinal alkaline phosphatase to produce pDB2812 (B-form) and pDB2813 (A-form) disintegration vectors containing DNA inserted at the HgaI-site (FIGS. 27 and 28, respectively).
Plasmids pDB2803 and pDB2804 (FIGS. 29 and 30, respectively) with the core termination linker (CF106+CF107) inserted at the FspI after FLP, were isolated by the same method used to construct pDB2801. The correct linker insertions were confirmed by DNA sequencing. Plasmid pDB2804 contained the linker inserted in the correct orientation (with the PacI-site closest to the FLP gene), whereas pDB2803 contained the linker in the opposite orientation.
The pDB28043,119-bp XbaI fragment was ligated with the 7,961-bp pSAC35 fragment produced by partial XbaI digestion and treatment with calf intestinal alkaline phosphatase to create pDB2807 (B-form) and pDB2808 (A-form) disintegration vectors containing DNA inserted at the FspI-site after FLP (FIGS. 31 and 32 respectively).
Example 5
Relative Stabilities of the LEU2 Marker in Yeast Transformed with pSAC35-Like Plasmids Containing DNA Linkers Inserted into the Small Unique Region and Inverted Repeats
A S. cerevisiae strain was transformed with the pSAC35-like plasmids containing DNA linkers inserted into the US-region and inverted repeats. Cryopreserved trehalose stocks were prepared for testing plasmid stabilities (Table 3). Plasmid stabilities were analysed as described above for linkers inserted at the XcmI-sites in pSAC35. Duplicate flasks were set up for each insertion site analysed. In addition, to the analysis of colonies derived from cells after 3-days in shake flake culture, colonies were grown and analysed from cells with a further 4-days shake flask culture. For this, 100 μL samples were removed from each 3-day old flask and sub-cultured in 100 mL YEPS broth for a further period of approximately 96 hours (94-98 hrs) at 30.0° C. in an orbital shaker, after which single colonies were obtained and analysed for loss of the LEU2 marker. In this case analysis was restricted to a single flask from selected strains, for which 50 colonies were picked. The overall results are summarised in Table 4.







TABLE 4







Summary of plasmid stability data for DNA insertions into pSAC35


Set 1 represents data from 3 days in non-selective shake flask culture.


Set 2 represents data from 7 days in non-selective shake flask culture.













Relative



Insertion
Additional
Stability











Plasmid(s)
Site
Details
Set 1
Set 2










A) REP2 Insertion Sites











pSAC35
—
Control
99%
100%


pDB2817 & pDB2818
XmnI
REP2 (1-244)
39%
16%


pDB2787
ApaI/T4 pol.
REP2 (1-269)
45%
0%


pDB2788
ApaI
REP2 (1-271)
33%
0%


pDB2688
XcmI
Inverted Repeat
100%
100%


pDB2805 & pDB2806
FspI
Inverted Repeat
100%
100%







B) FLP Insertion Sites











pDB2814
BclI
FLP (1-353)
67%
64%


pDB2823
XcmI
FLP (1-382)
64%
53%


pDB2812 & pDB2813
HgaI
Inverted Repeat
100%
100%


pDB2808
FspI
Inverted Repeat
100%
100%









All of the modified pSAC35 plasmids were able to transform yeast to leucine prototrophy, indicating that despite the additional DNA inserted within the functionally crowded regions of 2 μm DNA, all could replicate and partition in S. cerevisiae. This applied to plasmids with 43-52 base-pair linkers inserted at all the sites in the 2 μm US-region, as well as the larger DNA insertion containing the PDI1 gene.
For the linker insertion sites, data was reproducible between both experiments and duplicates. All sites outside REP2 or FLP open reading frames, but within inverted repeats appeared to be 100% stable under the test conditions used. Plasmid instability (i.e. plasmid loss) was observed for linkers inserted into sites within the REP2 or FLP open reading frames. The observed plasmid instability of REP2 insertions was greater than for FLP insertions. For the REP2 insertions, loss of the LEU2 marker continued with the extended growth period in non-selective media, whereas there was little difference for the FLP insertions.
Insertions into the REP2 gene produced Rep2 polypeptides truncated within a region known to function in self-association and binding to the STB-locus of 2 μm (Sengupta et al, 2001, J. Bacteriol., 183, 2306).
Insertions into the FLP gene resulted in truncated Flp proteins. All the insertion sites were after tyrosine-343 in the C-terminal domain, which is essential for correct functioning of the Flp protein (Prasad et al, 1987, Proc. Natl. Acad. Sci. U.S.A., 84, 2189; Chen et al, 1992, Cell, 69, 647; Grainge et al, 2001, J. Mol. Biol., 314, 717).
None of the insertions into the inverted repeat regions resulted in plasmid instability being detected, except for the insertion into the FLP XcmI-site, which also truncated the Flp protein product. The insertions at the FspI-sites in the inverted repeat regions were the closest to the FRT (Flp recognition target) regions, important for plasmid replication.
pSAC35-like plasmids have been constructed with 43-52 base-pair DNA linkers inserted into the REP2 open reading frame, or the FLP open reading frame or the inverted repeat sequences. In addition, a 1.9-kb DNA fragment containing the PDI1 gene was inserted into a DNA linker at the XcmI-site after REP2.
All of the pSAC35-like vectors with additional DNA inserted were able to transform yeast to leucine prototrophy. Therefore, despite inserting DNA into functionally crowded regions of 2 μm plasmid DNA, the plasmid replication and partitioning mechanisms had not been abolished.
Determination of plasmid stability by measuring loss of the LEU2 selectable marker during growth in non-selective medium indicated that inserting DNA linkers into the inverted repeats had not destabilised the plasmid, whereas plasmid stability had been reduced by insertions into the REP2 and FLP open reading frames. However, despite a reduction in plasmid stability under non-selective media growth conditions when insertions were made into the REP2 and FLP open reading frames at some positions defined by the first and second aspects of the invention, the resulting plasmid nevertheless has a sufficiently high stability for use in yeast when grown on selective media.
Example 6
Insertion of DNA Sequences Immediately after the Rep2 Gene in the Small Unique Region of pSAC35
To further define the useful limits for insertion of additional DNA into the REP2 gene and sequences in the inverted repeat downstream of it, a synthetic DNA linker was inserted into pSAC35 immediately after the REP2 translation termination codon (TGA). As there were no naturally occurring restriction endonuclease sites conveniently located immediately after the REP2 coding sequence in 2 μm (or pSAC35), a SnaBI-site was introduced at this position by oligonucleotide directed mutagenesis. The pSAC35 derivative with a unique SnaBI-site immediately downstream of REP2 was named pDB2938 (FIG. 37). In pDB2938, the end of the inverted repeat was displaced from the rest of the inverted repeat by insertion of the SnaBI-site. pDB2954 (FIG. 38) was subsequently constructed with a 31-bp sequence identical to the SnaBI-linker made from oligonucleotides CF104 and CF105 (supra) inserted into the unique SnaBI site of pDB2938, such that the order of restriction endonuclease sites located immediately after the TGA translation termination codon of REP2 was SnaBI-PacI-FseI/SfiI-SmaI-SnaBI.
To construct pDB2938, the 1,085-bp NcoI-BamHI fragment from pDB2783 (FIG. 14) was first sub-cloned into pMCS5 (Hoheisel, 1994, Biotechniques, 17, 456), which had been digested with NcoI, BamHI and calf intestinal alkaline phosphatase. This produced pDB2809 (FIG. 39), which was subsequently mutated using oligonucleotides CF127 and CF128, to generate pDB2920 (FIG. 40).








The 51-bp mutagenic oligonucleotides CF127 and CF128



The SnaBI recognition sequence is underlined










CF127
5′-CGTAATACTTCTAGGGTATGATACGTATCCAATATCAAAGGAAATGATAGC-3′
(SEQ ID NO: 43)



 


CF128
5′-GCTATCATTTCCTTTGATATTGGATACGTATCATACCCTAGAAGTATTACG-3′
(SEQ ID NO: 44)







Oligonucleotide directed mutagenesis was performed according to the instruction manual of the Statagene's QuickChangeTM Site-Directed Mutagenesis Kit. SnaBI and HindIII restriction digestion of plasmid DNA was used to identify the ampicillin resistant E. coli transformants that contained pDB2920. The inserted 6-bp sequence of the SnaBI restriction site and the correct DNA sequence for the entire 1,091-bp NcoI-BamHI fragment was confirmed in pDB2920 by DNA sequencing using oligonucleotide primers CF98, CF99, CF129, CF130, CF131 and M13 forward and reverse primers (Table 1).
The 1,091-bp NcoI-BamHI fragment from pDB2920 was isolated by agarose gel purification and ligated with the approximately 4.7-kb NcoI-BamHI fragment from pDB2783 to produce pDB2936 (FIG. 41). The pDB2783 4.7-kb NcoI-BamHI fragment was isolated by complete BamHI digestion of pDB2783 DNA that had first been linearised by partial digestion with NcoI and purified by agarose gel electrophoresis. E. coli DH5α cells were transformed to apramycin resistance by the ligation products. pDB2936 was identified by SnaBI digestion of plasmid DNA isolated from the apramycin resistant clones.
The 3,082-bp XbaI fragment from pDB2936 was subsequently ligated with a 7,961-bp pSAC35 fragment, which had been produced by partial XbaI digestion and treatment with calf intestinal alkaline phosphatase, to create the disintegration vector pDB2938 (2 μm B-form, FIG. 37)
pDB2938 was digested with SnaBI and calf intestinal phosphatase and ligated with an approximately 2-kb SnaBI fragment from pDB2939 (FIG. 42). pDB2939 was produced by PCR amplifying the PDI1 gene from S. cerevisiae S288c genomic DNA with oligonucleotide primers DS248 and DS250 (FIG. 43), followed by digesting the PCR products with EcoRI and BamHI and cloning the approximately 1.98-kb fragment into YIplac211 (Gietz & Sugino, 1988, Gene, 74, 527-534), that had been cut with EcoRI and BamHI. DNA sequencing of pDB2939 identified a missing ‘G’ from within the DS248 sequence, which is marked in bold in FIG. 43. The approximately 2-kb SnaBI fragment from pDB2939 was subsequently cloned into the unique SnaBI-site of pDB2938 to produce plasmid pDB2950 (FIG. 44). The PDI1 gene in pDB2950 is transcribed in the same direction as the REP2 gene.
pDB2950 was subsequently digested with SmaI and the approximately 11.1-kb DNA fragment was circularised to delete the S288c PDI1 sequence. This produced plasmid pDB2954 (FIG. 38) with the SnaBI-PacI-FseI/SfiI-SmaI-SnaBI linker located immediately after the TGA translation termination codon of REP2.
In addition to cloning the S. cerevisiae S288c PDI1 gene into the unique SnaBI-site of pDB2938, the S. cerevisiae SKQ2n PDI1 gene was similarly inserted at this site. The S. cerevisiae SKQ2n PDI1 gene sequence was PCR amplified from plasmid DNA containing the PDI1 gene from pMA3a:C7 (U.S. Pat. No. 6,291,205), also known as Clone C7 (Crouzet & Tuite, 1987, supra; Farquhar et al, 1991, supra). The SKQ2n PDI1 gene was amplified using oligonucleotide primers DS248 and DS250 (FIG. 43). The approximately 2-kb PCR product was digested with EcoRI and BamHI and ligated into YIplac211 (Gietz & Sugino, 1988, Gene, 74, 527-534) that has been cut with EcoRI and BamHI, to produce plasmid pDB2943 (FIG. 45). The 5′ end of the SKQ2n PDI1 sequence is analogous to a blunt-ended SpeI-site extended to include the EcoRI, SacI, SnaBI, PacI, FseI, SfiI and SmaI sites, the 3′ end extends up to a site analogous to a blunt-ended Bsu36I site, extended to include a SmaI, SnaBI and BamHI sites. The PDI1 promoter length is approximately 210 bp. The entire DNA sequence was determined for the PDI1 fragment and shown to code for the PDI protein of S. cerevisiae strain SKQ2n sequence (NCBI accession number CAA38402), but with a serine residue at position 114 (not an arginine residue). Similarly to the S. cerevisiae S288c sequence in pDB2939, pDB2943 had a missing ‘G’ from within the DS248 sequence, which is marked in bold in FIG. 43. The approximately 1,989-bp SnaBI fragment from pDB2943 was subsequently cloned into the unique SnaBI-site in pDB2938. This produced plasmid pDB2952 (FIG. 46), in which the SKQ2n PDI1 gene is transcribed in the same direction as REP2.
Example 7
Relative Stabilities of the LEU2 Marker in Yeast Transformed with pSAC35-Like Plasmids Containing DNA Inserted Immediately after the Rep2 Gene
The impact on plasmid stability from insertion of the linker sequence at the SnaBI-site introduced after the REP2 gene in pSAC35 was assessed for pDB2954. This was determined in the same S. cerevisiae strain as used in the earlier examples by loss of the LEU2 marker during non-selective growth on YEPS. The stability of pDB2954 was compared to the stabilities of pSAC35 (control plasmid), pDB2688 (XcmI-linker) and pDB2817 (XmnI-linker) by the method described in Example 1.
The yeast strain was transformed to leucine prototrophy using a modified lithium acetate method (Sigma yeast transformation kit, YEAST-1, protocol 2; (Ito et al, 1983, J. Bacteriol., 153, 163; Elble, 1992, Biotechniques, 13, 18)). Transformants were selected on BMMD-agar plates, and were subsequently patched out on BMMD-agar plates. Cryopreserved trehalose stocks were prepared from 10 mL BMMD shake flask cultures (24 hrs, 30° C., 200 rpm) by mixing with an equal volume of sterile 40% (w/v) trehalose and freezing aliquots at −80° C. (i.e. minus 80° C.).
For the determination of plasmid stability, a 1 mL cryopreserved stock was thawed and inoculated into 100 mL YEPS (initial OD600≈0.04-0.09) in a 250 mL conical flask and grown for approximately 72 hours (typically 70-74 hrs) at 30° C. in an orbital shaker (200 rpm, Innova 4300 incubator shaker, New Brunswick Scientific). Each strain was analysed in duplicate.
Samples were removed from each flask, diluted in YEPS-broth (10−2 to 10−5 dilution), and 100 μL aliquots plated in duplicate onto YEPS-agar plates. Cells were grown at 30° C. for 3-4 days to allow single colonies to develop. For each yeast stock analysed, 100 random colonies were patched in replica onto BMMS-agar plates followed by YEPS-agar plates. After growth at 30° C. for 3-4 days the percentage of colonies growing on both BMMS-agar plates and YEPS-agar plates was determined as the measure of plasmid stability.
The results of the above analysis are shown below in Table 5A. These results indicate that pDB2954 is essentially as stable as the pSAC35 control and pDB2688. In this type of assay a low level of instability can occasionally be detected even with the pSAC35 control (see Table 4). Hence, the SnaBI-site artificially introduced into the inverted repeat sequence immediately after the translation termination codon of REP2 appeared to be equivalent to the XcmI-site in the inverted repeat for insertion of synthetic linker sequences. However, the XcmI-site appeared to be preferable to the SnaBI-site for insertion of the approximately 2-kb DNA fragment containing the PDI1 gene.







TABLE 5A







Relative stabilities of pSAC35-based vectors containing various DNA


insertions












Insertion

Gene(s) inserted




site in

at SnaBI/NotI-



US-
Gene inserted
site in UL-
Relative


Plasmid
Region
in US-Region
Region
Stability (%)














pSAC35
—
—
LEU2
100


pDB2688
XcmI
—
LEU2
99.5


pDB2954
SnaBI
—
LEU2
99


pDB2817
XmnI
—
LEU2
27


pDB2690
XcmI
PDI1 (SKQ2n)
LEU2
39.5


pDB2952
SnaBI
PDI1 (SKQ2n)
LEU2
0


pDB2950
SnaBI
PDI1 (S288c)
LEU2
0









A “zero percent stability” result of this assay for plasmids pDB2952 and pDB2950 was obtained in non-selective media, which gives an indication of the relative plasmid stabilities. This assay was optimised to compare the relative stabilities of the different linker inserts. In selective media, plasmids with PDI1 at the SnaBI-site (even when comprising an additional transferrin gene at the NotI site, which is known to further destabilise the plasmid (such as pDB2959 and pDB2960 as described below)) produced “precipitin halos” of secreted transferrin on both non-selective YEPD-agar and selective BMMD-agar plates containing anti-transferrin antibodies. Precipitin halos of secreted transferrin were not observed from pDB2961, without the PDI1 gene inserted at the SnaBI-site. These results demonstrate that the SnaBI-site is useful for the insertion of large genes such as PDI1, which can increase the secretion of heterologous proteins. These results were all generated in the control strain. An increase was also seen for Strain A containing pDB2959 and pDB2960, but in this case there was also a lower level of secretion observed with pDB2961 (because of the extra PDI1 gene in the genome of Strain A). Results from the control strain are summarised in Table 5B below. Antibody plates were used contained 100 μL of goat polyclonal anti-transferrin antiserum (Calbiochem) per 25 mL BMMD-agar or YEPD-agar. Strains were patched onto antibody plates and grown for 48-72 hours at 30° C., after which the precipitin “halos” were observed within the agar around colonies secreting high levels of recombinant transferrin. Very low levels of transferrin secretion are not observed in this assay.
Plasmids pDB2959, pDB2960 and pDB2961 were constructed from pDB2950 (FIG. 44), pDB2952 (FIG. 46) and pDB2954 (FIG. 38) respectively, by inserting the same 3.27-kb NotI cassette for rTf (N413Q, N611Q) as found in pDB2711 (FIG. 11), into the unique NotI-site, in the same orientation as pDB2711.







TABLE 5B







Increased transferrin secretion from the Control Strain transformed with pSAC35-


based vectors containing various PDI1 gene insertions immediately-site after REP2












Insertion

Gene(s) inserted
Transferrin secretion Detected



site in
Gene inserted
at SnaBI/NotI-site
on Anti-Transferrin Ab-plates












Plasmid
US-Region
in US-Region
in UL-Region
BMMD-Anti Tf
YEPD-Anti Tf





pDB2960
SnaBI
PDI1 (SKQ2n)
LEU2 + rTf
Yes
Yes


pDB2959
SnaBI
PDI1 (S288c)
LEU2 + rTf
Yes
Yes


pDB2961
SnaBI
—
LEU2 + rTf
No
No









Example 8
Stabilities of the LEU2 Marker in Yeast Transformed with pSAC35-Like Plasmids Determined Over Thirty Generations of Growth in Non-Selective Conditions
The stabilities of pSAC35-like plasmids with DNA inserted in the US-region were determined using a method analogous to that defined by Chinery & Hinchcliffe (1989, Curr. Genet., 16, 21-25) This was determined in the same S. cerevisiae strain as used in previous examples by loss of the LEU2 marker during logarithmic growth on non-selective YEPS medium over a defined number of generations. Thirty generations was suitable to show a difference between a control plasmid, pSAC35, or to shown comparable stability to the control plasmid. Plasmids selected for analysis by this assay were; pSAC35 (control), pDB2688 (XcmI-linker), pDB2812 (HgaI-linker), pDB2817 (XmnI-linker), pDB2960 (PDI1 gene inserted at XcmI site after REP2) and pDB2711 (PDI1 gene inserted at XcmI site after REP2 and a transferrin expression cassette inserted at the NotI-site in the UL-region).
Strains were grown to logarithmic phase in selective (BMMS) media at 30° C. and used to inoculate 100 mL non-selective (YEPS) media pre-warmed to 30° C. in 250 mL conical flasks, to give between 1.25×105 and 5×105 cells/ml. The number of cells inoculated into each flask was determined accurately by using a haemocytometer to count the number of cells in culture samples. Aliquots were also plated on non-selective (YEPS) agar and incubated at 30° C. for 3-4 days, after which for each stock analysed, 100 random colonies were replica plated on selective (BMMS) agar and non-selective (YEPS) agar to assess the proportion of cells retaining the plasmid. After growth at 30° C. for 3-4 days the percentage of colonies growing on both BMMS agar and YEPS agar plates was determined as a measure of plasmid stability.
Non-selective liquid cultures were incubated at 30° C. with shaking at 200 rpm for 24 hours to achieve approximately 1×107 cells/ml, as determined by haemocytometer counts. The culture was then re-inoculated into fresh pre-warmed non-selective media to give between 1.25×105 and 5×105 cells/ml. Aliquots were again plated on non-selective agar, and subsequently replicated plated on selective agar and non-selective agar to assess retention of the plasmid. Hence, it was possible to calculate the number of cell generations in non-selective liquid media. Exponential logarithmic growth was maintained for thirty generations in liquid culture, which was sufficient to show comparable stability to a control plasmid, such as pSAC35. Plasmid stability was defined as the percentage cells maintaining the selectable LEU2 marker.
Results of the above analysis to measure the retention of the plasmid-encoded phenotype through growth in non-selective media are shown in Table 6 and FIG. 47.







TABLE 6







The Relative Stabilities of Selected pSAC35-Like Plasmids


in a S. cerevisiae Strain grown for Thirty Generations in


Non-Selective Media













Gene
Gene(s)
Percentage




inserted
inserted
Stability



Linker
in
at SnaBI/NotI-
after



Insertion site in
US-
site in
30


Plasmid
US-region
region
UL-region
generations














pSAC35
—
—
LEU2
100


pDB2688
XcmI after REP2
—
LEU2
100


pDB2812
HgaI after FLP
—
LEU2
100


pDB2817
XmnI in REP2
—
LEU2
1


pDB2690
XcmI after REP2
PDI1
LEU2
33




(SKQ2n)


pDB2711
XcmI after REP2
PDI1
LEU2 + rTf
2




(SKQ2n)









FIG. 47 shows the loss of the LEU2 marker with increasing number generation in non-selective liquid culture for each strain analysed.
The control plasmid pSAC35 remained 100% stable over the entire 30-generations of this assay. Plasmids pBD2688 and pDB2812 both appeared to be as stable as pSAC35. Therefore, insertion of the linker into the XcmI-site after REP2 or the HgaI-site after FLP respectively had no apparent effect on plasmid stability. In contrast, insertion of the XmnI-linker within the REP2 gene appeared to have reduced plasmid stability.
Plasmid pDB2690, which contains a S. cerevisiae PDI1 gene in the XcmI-linker after REP2, was approximately 33% stable after thirty generations growth, indicating that insertion of this large DNA fragment into the US-region of the 2 μm-based vector caused a decrease in plasmid stability. However, this decrease in stability was less than that observed with pDB2711, where insertion of the recombinant transferrin (N413Q, N611Q) expression cassette into the NotI-site within the large unique region of pSAC35 acted to further destabilise the plasmid. These observations are consistent with the results of Example 2 (see Table 2).
The stability of plasmid pDB2711 was assessed by the above method in an alternative strain of S. cerevisiae, and similar results were obtained (data not shown). This indicates that the stability of the plasmid is not strain dependent.
Example 9
PDI1 Gene Disruption, Combined with a PDI1 Gene on the 2 μm-Based Plasmid Enhanced Plasmid Stability
Single stranded oligonucleotide DNA primers listed in Table 7 were designed to amplify a region upstream of the yeast PDI1 coding region and another a region downstream of the yeast PDI1 coding region.







TABLE 7







Oligonucleotide primers









Primer
Description
Sequence





DS299
5′ PDI1
5′-CGTAGCGGCCGCCTGAAAGGGGTTGACCG


(SEQ
primer,
TCCGTCGGC-3′


ID NO:
38 mer



45)




 


DS300
5′ PDI1
5′-CGTAAAGCTTCGCCGCCCGACAGGGTAAC


(SEQ
primer,
ATATTATCAC-3′


ID NO:
40 mer



46)




 


DS301
3′ PDI1
5′-CGTAAAGCTTGACCACGTAGTAATAATAA


(SEQ
primer,
GTGCATGGC-3′


ID NO:
38 mer



47)




 


DS302
3′ PDI1
5′-CGTACTGCAGATTGGATAGTGATTAGAGT


(SEQ
primer,
GTATAGTCCCGG-3′


ID NO:
41 mer



48)




 


DS303
18 mer
5′-GGAGCGACAAACCTTTCG-3′


(SEQ




ID NO:




49)




 


DS304
20 mer
5′-ACCGTAATAAAAGATGGCTG-3′


(SEQ




ID NO:




50)




 


DS305
24 mer
5′-CATCTTGTGTGTGAGTATGGTCGG-3′


(SEQ




ID NO:




51)




 


DS306
14 mer
5′-CCCAGGATAATTTTCAGG-3′


(SEQ




ID NO:




52)









Primers DS299 and DS300 amplified the 5′ region of PDI1 by PCR, while primers DS301 and DS302 amplified a region 3′ of PDI1, using genomic DNA derived S288c as a template. The PCR conditions were as follows: 1 μL S288c template DNA (at 0.01 ng/μL, 0.1 ng/μL, 1 ng/μL, 10 ng/μL and 100 ng/μL), 5 μL 10× Buffer (Fast Start Taq+Mg, (Roche)), 1 μL 10 mM dNTP's, 5 μL each primer (2 μM), 0.4 μL Fast Start Taq, made up to 50 μL with H2O. PCRs were performed using a Perkin-Elmer Thermal Cycler 9700. The conditions were: denature at 95° C. for 4 min [HOLD], then [CYCLE] denature at 95° C. for 30 seconds, anneal at 45° C. for 30 seconds, extend at 72° C. for 45 seconds for 20 cycles, then [HOLD] 72° C. for 10 min and then [HOLD] 4° C. The 0.22 kbp PDI1 5′ PCR product was cut with NotI and HindIII, while the 0.34 kbp PDI1 3′ PCR product was cut with HindIII and PstI.
Plasmid pMCS5 (Hoheisel, 1994, Biotechniques 17, 456-460) (FIG. 48) was digested to completion with HindIII, blunt ended with T4 DNA polymerase plus dNTPs and religated to create pDB2964 (FIG. 49).
Plasmid pDB2964 was HindIII digested, treated with calf intestinal phosphatase, and ligated with the 0.22 kbp PDI1 5′ PCR product digested with NotI and HindIII and the 0.34 kbp PDI1 3′ PCR product digested with HindIII and PstI to create pDB3069 (FIG. 50) which was sequenced with forward and reverse universal primers and the DNA sequencing primers DS303, DS304, DS305 and DS306 (Table 7).
Primers DS234 and DS235 (Table 8) were used to amplify the modified TRP1 marker gene from YIplac204 (Gietz & Sugino, 1988, Gene, 74, 527-534), incorporating HindIII restriction sites at either end of the PCR product. The PCR conditions were as follows: 1 μL template YIplac204 (at 0.01 ng/μL, 0.1 ng/μL, 1 ng/μL, 10 ng/μL and 100 ng/μL), 5 μL 10× Buffer (Fast Start Taq+Mg, (Roche)), 1 μL 10 mM dNTP's, 5 μL each primer (2 μM), 0.4 μL Fast Start Taq, made up to 50 μL with H2O. PCRs were performed using a Perkin-Elmer Thermal Cycler 9600. The conditions were: denature at 95° C. for 4 min [HOLD], then [CYCLE] denature at 95° C. for 30 seconds, anneal for 45 seconds at 45° C., extend at 72° C. for 90 sec for 20 cycles, then [HOLD] 72° C. for 10 min and then [HOLD] 4° C. The 0.86 kbp PCR product was digested with HindIII and cloned into the HindIII site of pMCS5 to create pDB2778 (FIG. 51). Restriction enzyme digestions and sequencing with universal forward and reverse primers as well as DS236, DS237, DS238 and DS239 (Table 8) confirmed that the sequence of the modified TRP1 gene was correct.







TABLE 8







Oligonucleotide primers









Primer
Description
Sequence





DS230
TRP1
5′-TAGCGAATTC AATCAGTAAAAATCAACG


(SEQ
5′ UTR
G-3′


ID NO:




53)




 


DS231
TRP1
5′-GTCAAAGCTTCAAAAAAAGA AAAGCTCC


(SEQ
5′ UTR
GG-3′


ID NO:




54)




 


DS232
TRP1
5′-TAGCGGATCCGAATTCGGCGGTTGTTTGC


(SEQ
3′ UTR
AAGACCGAG-3′


ID NO:




55)




 


DS233
TRP1
5′-GTCAAAGCTTTAAAGATAATGCTAAATCA


(SEQ
3′ UTR
TTTGG-3′


ID NO:




56)




 


DS234
TRP1
5′-TGACAAGCTTTCGGTCGAAAAAAGAAAAG


(SEQ

G AGAGG-3′


ID NO:




57)




 


DS235
TRP1
5′-TGACAAGCTTGATCTTTTATGCTTGCTTT


(SEQ

TC-3′


ID NO:




58)




 


DS236
TRP1
5′-AATAGTTCAGGCACTCCG-3′


(SEQ




ID NO:




59)




 


DS237
TRP1
5′-TGGAAGGCAAGAGAGCC-3′


(SEQ




ID NO:




60)




 


DS238
TRP1
5′-TAAAATGTAAGCTCTCGG-3′


(SEQ




ID NO:




61)




 


DS239
TRP1
5′-CCAACCAAGTATTTCGG-3′


(SEQ




ID NO:




62)




 


CED005
ΔTRP1
5′-GAGCTGACAGGGAAATGGTC-3′


(SEQ




ID NO:




63)




 


CED006
ΔTRP1
5′-TACGAGGATACGGAGAGAGG-3′


(SEQ




ID NO:




64)









The 0.86 kbp TRP1 gene was isolated from pDB2778 by digestion with HindIII and cloned into the HindIII site of pDB3069 to create pDB3078 (FIG. 52) and pDB3079 (FIG. 53). A 1.41 kb pdi1::TRP1 disrupting DNA fragment was isolated from pDB3078 or pDB3079 by digestion with NotI/PstI.
Yeast strains incorporating a TRP1 deletion (trp1Δ) were to be constructed in such a way that no homology to the TRP1 marker gene (pDB2778) should left in the genome once the trp1Δ had been created, so preventing homologous recombination between future TRP1 containing constructs and the TRP1 locus. In order to achieve the total removal of the native TRP1 sequence from the genome of the chosen host strains, oligonucleotides were designed to amplify areas of the 5′ UTR and 3′ UTR of the TRP1 gene outside of TRP1 marker gene present on integrating vector YIplac204 (Gietz & Sugino, 1988, Gene, 74, 527-534). The YIplac204 TRP1 marker gene differs from the native/chromosomal TRP1 gene in that internal HindIII, PstI and XbaI sites were removed by site directed mutagenesis (Gietz & Sugino, 1988, Gene, 74, 527-534). The YIplac204 modified TRP1 marker gene was constructed from a 1.453 kbp blunt-ended genomic fragment EcoRI fragment, which contained the TRP1 gene and only 102 bp of the TRP1 promoter (Gietz & Sugino, 1988, Gene, 74, 527-534). Although this was a relatively short promoter sequence it was clearly sufficient to complement trp1 auxotrophic mutations (Gietz & Sugino, 1988, Gene, 74, 527-534). Only DNA sequences upstream of the EcoRI site, positioned 102 bp 5′ to the start of the TRP1 ORF were used to create the 5′ TRP1 UTR. The selection of the 3′ UTR was less critical as long as it was outside the 3′ end of the functional modified TRP1 marker, which was chosen to be 85 bp downstream of the translation stop codon.
Single stranded oligonucleotide DNA primers were designed and constructed to amplify the 5′ UTR and 3′ UTR regions of the TRP1 gene so that during the PCR amplification restriction enzyme sites would be added to the ends of the PCR products to be used in later cloning steps. Primers DS230 and DS231 (Table 8) amplified the 5′ region of TRP1 by PCR, while primers DS232 and DS233 (Table 8) amplified a region 3′ of TRP1, using S288c genomic DNA as a template. The PCR conditions were as follows: 1 μL template S288c genomic DNA (at 0.01 ng/μL, 0.1 ng/μL, 1 ng/μL, 10 ng/μL and 100 ng/μL), 5 μL 10× Buffer (Fast Start Taq+Mg, (Roche)), 1 μL 10 mM dNTP's, 5 μL each primer (2 μM), 0.4 μL Fast Start Taq, made up to 50 μL with H2O. PCRs were performed using a Perkin-Elmer Thermal Cycler 9600. The conditions were: denature at 95° C. for 4 min [HOLD], then [CYCLE] denature at 95° C. for 30 seconds, anneal for 45 seconds at 45° C., extend at 72° C. for 90 sec for 20 cycles, then [HOLD] 72° C. for 10 min and then [HOLD] 4° C.
The 0.19 kbp TRP1 5′ UTR PCR product was cut with EcoRI and HindIII, while the 0.2 kbp TRP1 3′ UTR PCR product was cut with BamHI and HindIII and ligated into pAYE505 linearised with BamHI/EcoRI to create plasmid-pDB2777 (FIG. 54). The construction of pAYE505 is described in WO 95/33833. DNA sequencing using forward and reverse primers, designed to prime from the plasmid backbone and sequence the cloned inserts, confirmed that in both cases the cloned 5′ and 3′ UTR sequences of the TRP1 gene had the expected DNA sequence. Plasmid pDB2777 contained a TRP1 disrupting fragment that comprised a fusion of sequences derived from the 5′ and 3′ UTRs of TRP1. This 0.383 kbp TRP1 disrupting fragment was excised from pDB2777 by complete digestion with EcoRI.
Yeast strain DXY1 (Kerry-Williams et al., 1998, Yeast, 14, 161-169) was transformed to leucine prototrophy with the albumin expression plasmid pDB2244 using a modified lithium acetate method (Sigma yeast transformation kit, YEAST-1, protocol 2; (Ito et al, 1983, J. Bacteriol., 153, 163; Elble, 1992, Biotechniques, 13, 18)) to create yeast strain DXY1 [pDB2244]. The construction of the albumin expression plasmid pDB2244 is described in WO 00/44772. Transformants were selected on BMMD-agar plates, and were subsequently patched out on BMMD-agar plates. Cryopreserved trehalose stocks were prepared from 10 mL BMMD shake flask cultures (24 hrs, 30° C., 200 rpm).
DXY1 [pDB2244] was transformed to tryptophan autotrophy with the 0.383 kbp EcoRI TRP1 disrupting DNA fragment from pDB2777 using a nutrient agar incorporating the counter selective tryptophan analogue, 5-fluoroanthranilic acid (5-FAA), as described by Toyn et al., (2000 Yeast 16, 553-560). Colonies resistant to the toxic effects of 5-FAA were picked and streaked onto a second round of 5-FAA plates to confirm that they really were resistant to 5-FAA and to select away from any background growth. Those colonies which grew were then were re-patched onto BMMD and BMMD plus tryptophan to identify which were tryptophan auxotrophs.
Subsequently colonies that had been shown to be tryptophan auxotrophs were selected for further analysis by transformation with YCplac22 (Gietz & Sugino, 1988, Gene, 74, 527-534) to ascertain which isolates were trp1.
PCR amplification across the TRP1 locus was used to confirm that the trp− phenotype was due to a deletion in this region. Genomic DNA was prepared from isolates identified as resistant to 5-FAA and unable to grow on minimal media without the addition of tryptophan. PCR amplification of the genomic TRP1 locus with primers CED005 and CED006 (Table 8) was achieved as follows: 1 μL template genomic DNA, 5 μL 10× Buffer (Fast Start Taq+Mg, (Roche)), 1 μL 10 mM dNTP's, 5 μL each primer (2 μM), 0.4 μL Fast Start Taq, made up to 50 μL with H2O. PCRs were performed using a Perkin-Elmer Thermal Cycler 9600. The conditions were: denature at 94° C. for 10 min [HOLD], then [CYCLE] denature at 94-C for 30 seconds, anneal for 30 seconds at 55° C., extend at 72° C. for 120 sec for 40 cycles, then [HOLD] 72° C. for 10 min and then [HOLD] 4° C. PCR amplification of the wild type TRP1 locus resulted in a PCR product of 1.34 kbp in size, whereas amplification across the deleted TRP1 region resulted in a PCR product 0.84 kbp smaller at 0.50 kbp. PCR analysis identified a DXY1 derived trp− strain (DXY1 trp1Δ [pDB2244]) as having the expected deletion event.
The yeast strain DXY1 trp1Δ [pDB2244] was cured of the expression plasmid pDB2244 as described by Sleep et al., 1991, Bio/Technology, 9, 183-187. DXY1 trp1Δ cir0 was re-transformed the leucine prototrophy with either pDB2244, pDB2976, pDB2977, pDB2978, pDB2979, pDB2980 or pDB2981 (the production of pDB2976, pDB2977 and pDB2980 or pDB2981 is discussed further in Example 10) using a modified lithium acetate method (Sigma yeast transformation kit, YEAST-1, protocol 2; (Ito et al, 1983, J. Bacteriol., 153, 163; Elble, 1992, Biotechniques, 13, 18)). Transformants were selected on BMMD-agar plates supplemented with tryptophan, and were subsequently patched out on BMMD-agar plates supplemented with tryptophan. Cryopreserved trehalose stocks were prepared from 10 mL BMMD shake flask cultures supplemented with tryptophan (24 hrs, 30° C., 200 rpm).
The yeast strains DXY1 trp1Δ [pDB2976], DXY1 trp1Δ [pDB2977], DXY1 trp1Δ [pDB3078], DXY1 trp1Δ [pDB3079], DXY1 trp1Δ [pDB2980] or DXY1 trp1Δ [pDB2981] was transformed to tryptophan prototrophy using the modified lithium acetate method (Sigma yeast transformation kit, YEAST-1, protocol 2; (Ito et al, 1983, J. Bacteriol., 153, 163; Elble, 1992, Biotechniques, 13, 18)) with a 1.41 kb pdi1::TRP1 disrupting DNA fragment was isolated from pDB3078 by digestion with NotI/PstI. Transformants were selected on BMMD-agar plates and were subsequently patched out on BMMD-agar plates.
Six transformants of each strain were inoculated into 10 mL YEPD in 50 mL shake flasks and incubated in an orbital shaker at 30° C., 200 rpm for 4-days. Culture supernatants and cell biomass were harvested. Genomic DNA was prepared (Lee, 1992, Biotechniques, 12, 677) from the tryptophan prototrophs and DXY1 [pDB2244]. The genomic PDI1 locus amplified by PCR of with primers DS236 and DS303 (Table 7 and 8) was achieved as follows: 1 μL template genomic DNA, 5 μL 10× Buffer (Fast Start Taq+Mg, (Roche)), 1 μL 10 mM dNTP's, 5 μL each primer (2 μM), 0.4 μL Fast Start Taq, made up to 50 μL with H2O. PCRs were performed using a Perkin-Elmer Thermal Cycler 9700. The conditions were: denature at 94° C. for 4 min [HOLD], then [CYCLE] denature at 94° C. for 30 seconds, anneal for 30 seconds at 50° C., extend at 72° C. for 60 sec for 30 cycles, then [HOLD] 72° C. for 10 min and then [HOLD] 4° C. PCR amplification of the wild type PDI1 locus resulted in no PCR product, whereas amplification across the deleted PDI1 region resulted in a PCR product 0.65 kbp. PCR analysis identified that all 36 potential pdi1::TRP1 strains tested had the expected pdi1::TRP1 deletion.
The recombinant albumin titres were compared by rocket immunoelectrophoresis (FIG. 55). Within each group, all six pdi1::TRP1 disruptants of DXY1 trp1Δ [pDB2976], DXY1 trp1Δ [pDB2978], DXY1 trp1Δ [pDB2980], DXY1 trp1Δ [pDB2977] and DXY1 trp1Δ [pDB2979] had very similar rHA productivities. Only the six pdi1::TRP1 disruptants of DXY1 trp1Δ [pDB2981] showed variation in rHA expression titre. The six pdi1::TRP1 disruptants indicated in FIG. 55 were spread onto YEPD agar to isolate single colonies and then re-patched onto BMMD agar.
Three single celled isolates of DXY1 trp1Δ pdi1::TRP1 [pDB2976], DXY1 trp1Δ pdi1::TRP1 [pDB2978], DXY1 trp1Δ pdi1::TRP1 [pDB2980], DXY1 trp1Δ pdi1::TRP1 [pDB2977], DXY1 trp1Δ pdi1::TRP1 [pDB2979] and DXY1 trp1Δ pdi1::TRP1 [pDB2981] along with DXY1 [pDB2244], DXY1 [pDB2976], DXY1 [pDB2978], DXY1 [pDB2980], DXY1 [pDB2977], DXY1 [pDB2979] and DXY1 [pDB2981] were inoculated into 10 mL YEPD in 50 mL shale flasks and incubated in an orbital shaker at 30° C., 200 rpm for 4-days. Culture supernatants were harvested and the recombinant albumin titres were compared by rocket immunoelectrophoresis (FIG. 56). The thirteen wild type PDI1 and pdi1::TRP1 disruptants indicated in FIG. 56 were spread onto YEPD agar to isolate single colonies. One hundred single celled colonies from each strain were then re-patched onto BMMD agar or YEPD agar containing a goat anti-HSA antibody to detect expression of recombinant albumin (Sleep et al., 1991, Bio/Technology, 9, 183-187) and the Leu+/rHA+, Leu+/rHA−, Leu−/rHA+ or Leu−/rHA− phenotype of each colony scored (Table 9).










TABLE 9









PDI1
pdi1::TRP1
















Leu+
Leu−
Leu+
Leu−
Leu+
Leu−
Leu+
Leu−



rHA+
rHA+
rHA−
rHA−
rHA+
rHA+
rHA−
rHA−



















pDB2244
100
0
0
0






PDB2976
7
0
47
46
97
0
3
0


pDB2978
86
0
0
14
100
0
0
0


pDB2980
98
0
0
2
100
0
0
0


pDB2977
0
0
4
96
100
0
0
0


pDB2979
69
0
6
25
100
0
0
0


pDB2981
85
0
0
15
92
0
0
8









These data indicate plasmid retention is increased when the PDI1 gene is used as a selectable marker on a plasmid in a host strain having no chromosomally encoded PDI, even in non-selective media such as this rich medium. These show that an “essential” chaperone (e.g. PDI1 or PSE1), or any other any “essential” gene product (e.g. PTK1 or FBA1) which, when deleted or inactivated, does not result in an auxotrophic (biosynthetic) requirement, can be used as a selectable marker on a plasmid in a host cell that, in the absence of the plasmid, is unable to produce that gene product, to achieve increased plasmid stability without the disadvantage of requiring the cell to be cultured under specific selective conditions. By “auxotrophic (biosynthetic) requirement” we include a deficiency, which can be complemented by additions or modifications to the growth medium. Therefore, “essential marker genes” in the context of the present invention are those that, when deleted or inactivated in a host cell, result in a deficiency which can not be complemented by additions or modifications to the growth medium.
Example 10
The Construction of Expression Vectors Containing Various PDI1 Genes and the Expression Cassettes for Various Heterologous Proteins on the Same 2 μm-Like Plasmid
PCR Amplification and Cloning of PDI1 Genes into YIplac211
The PDI1 genes from S. cerevisiae S288c and S. cerevisiae SKQ2n were amplified by PCR to produce DNA fragments with different lengths of the 5′-untranslated region containing the promoter sequence. PCR primers were designed to permit cloning of the PCR products into the EcoRI and BamHI sites of YIplac211 (Gietz & Sugino, 1988, Gene, 74, 527-534). Additional restriction endonuclease sites were also incorporated into PCR primers to facilitate subsequent cloning. Table 10 describes the plasmids constructed and Table 11 gives the PCR primer sequences used to amplify the PDI1 genes. Differences in the PDI1 promoter length within these YIplac211-based plasmids are described in Table 10.
pDB2939 (FIG. 57) was produced by PCR amplification of the PDI1 gene from S. cerevisiae S288c genomic DNA with oligonucleotide primers DS248 and DS250 (Table 11), followed by digesting the PCR product with EcoRI and BamHI and cloning the approximately 1.98-kb fragment into YIplac211 (Gietz & Sugino, 1988, Gene, 74, 527-534), that had been cut with EcoRI and BamHI. DNA sequencing of pDB2939 identified a missing ‘G’ from within the DS248 sequence, which is marked in bold in Table 5. Oligonucleotide primers used for sequencing the PDI1 gene are listed in Table 6, and were designed from the published S288c PDI1 gene sequence (PDI1/YCL043C on chromosome III from coordinates 50221 to 48653 plus 1000 base pairs of upstream sequence and 1000 base pairs of downstream sequence. (http://www.yeastgenome.org/ Genebank Accession number NC001135).







TABLE 10







YIplac211-based Plasmids Containing PDI1 Genes











Plasmid
PDI1 Gene













Plasmid
Base
Source
Promoter
Terminator
PCR Primers





pDB2939
YIplac211
S288c
Long (~210-bp)
→ Bsu36I
DS248 + DS250


pDB2941
YIplac211
S288c
Medium (~140-bp)
→ Bsu36I
DS251 + DS250


pDB2942
YIplac211
S288c
Short (~80-bp)
→ Bsu36I
DS252 + DS250


pDB2943
YIplac211
SKQ2n
Long (~210-bp)
→ Bsu36I
DS248 + DS250


pDB2963
YIplac211
SKQ2n
Medium (~140-bp)
→ Bsu36I
DS267 + DS250


pDB2945
YIplac211
SKQ2n
Short (~80-bp)
→ Bsu36I
DS252 + DS250
















TABLE 11







Oligonucleotide Primers for PCR Amplification


of S. cerevisiae PDI1 Genes








Primer
Sequence





DS248
5′-GTCAGAATTCGAGCTCTACGTATTAATTAAGGCCGGCCAGG


(SEQ
CCCGGGCTAGTCTCTTTTTCCAATTTGCCACCGTGTAGCATTTT


ID NO:
GTTGT3′


65)



 


DS249
5′-GTCAGGATCCTACGTACCCGGGGATATCATTATCATCTTTG


(SEQ
TCGTGGTCATCTTGTGTG3′


ID NO:



66)



 


DS250
5′-GTCAGGATCCTACGTACCCGGGTAAGGCGTTCGTGCAGTGT


(SEQ
GACGAATATAGCG-3′


ID NO:



67)



 


DS251
5′-GTCAGAATTCGAGCTCTACGTATTAATTAAGGCCGGCCAGG


(SEQ
CCCGGGCCCGTATGGACATACATATATATATATATATATATATA


ID NO:
TATTTTGTTACGCG-3′


68)



 


DS252
5′-GTCAGAATTCGAGCTCTACGTATTAATTAAGGCCGGCCAGG


(SEQ
CCCGGGCTTGTTGCAAGCAGCATGTCTAATTGGTAATTTTAAAG


ID NO:
CTGCC-3′


69)



 


sDS267
5′-GTCAGAATTCGAGCTCTACGTATTAATTAAGGCCGGCCAGG


(SEQ
CCCGGGCCCGTATGGACATACATATATATATATATATATATATA


ID NO:
TATATATTTTGTTACGCG-3′


70)
















TABLE 12







Oligonucleotide Primers for DNA Sequencing


S. cerevisiae PDI1 Genes










Primer
Sequence







DS253
5′-CCTCCCTGCTCCTCGCC-3′



(SEQ ID NO: 71)




 



DS254
5′-CTGTAAGAACATGGCTCC-3′



(SEQ ID NO: 72)




 



DS255
5′-CTCGATCGATTACGAGGG-3′



(SEQ ID NO: 73)




 



DS256
5′-AAGAAAGCCGATATCGC-3′



(SEQ ID NO: 74)




 



DS257
5′CAACTCTCTGAAGAGGCG-3′



(SEQ ID NO: 75)




 



DS258
5′-CAACGCCACATCCGACG-3′



(SEQ ID NO: 76)




 



DS259
5′-GTAATTCTGATCACTTTGG-3′



(SEQ ID NO: 77)




 



DS260
5′-GCACTTATTATTACTACGTGG-3′



(SEQ ID NO: 78)




 



DS261
5′-GTTTTCCTTGATGAAGTCG-3′



(SEQ ID NO: 79)




 



DS262
5′-GTGACCACACCATGGGGC-3′



(SEQ ID NO: 80)




 



DS263
5′-GTTGCCGGCGTGTCTGCC-3′



(SEQ ID NO: 81)




 



DS264
5′-TTGAAATCATCGTCTGCG-3′



(SEQ ID NO: 82)




 



DS265
5′-CGGCAGTTCTAGGTCCC-3′



(SEQ ID NO: 83)




 



DS266
5′-CCACAGCCTCTTGTTGGG-3′



(SEQ ID NO: 84)




 



M13/pUC
5′-GTTTTCCCAGTCACGAC-3′



Primer




(−40)




(SEQ ID NO: 85)










Plasmids pDB2941 (FIG. 58) and pDB2942 (FIG. 59) were constructed similarly using the PCR primers described in Tables 10 and 11, and by cloning the approximately 1.90-kb and 1.85-kb EcoRI-BamHI fragments, respectively, into YIplac211. The correct DNA sequences were confirmed for the PDI1 genes in pDB2941 and pDB2942.
The S. cerevisiae SKQ2n PDI1 gene sequence was PCR amplified from plasmid DNA containing the PDI1 gene from pMA3a:C7 (U.S. Pat. No. 6,291,205), also known as Clone C7 (Crouzet & Tuite, 1987, supra; Farquhar et al., 1991, supra). The SKQ2n PDI1 gene was amplified using oligonucleotide primers DS248 and DS250 (Tables 10 and 11). The approximately 2.01-kb PCR product was digested with EcoRI and BamHI and ligated into YIplac211 (Gietz & Sugino, 1988, Gene, 74, 527-534) that has been cut with EcoRI and BamHI, to produce plasmid pDB2943 (FIG. 60). The 5′ end of the SKQ2n PDI1 sequence is analogous to a blunt-ended SpeI-site extended to include the EcoRI, SacI, SnaBI, PacI, FseI, SfiI and SmaI sites, the 3′ end extends up to a site analogous to a blunt-ended Bsu361 site, extended to include a SmaI, SnaBI and BamHI sites. The PDI1 promoter length is approximately 210 bp. The entire DNA sequence was determined for the PDI1 fragment using oligonucleotide primers given in Table 12. This confirmed the presence of a coding sequence for the PDI protein of S. cerevisiae strain SKQ2n (NCBI accession number CAA38402), but with a serine residue at position 114 (not an arginine residue as previously published). Similarly, in the same way as in the S. cerevisiae S288c sequence in pDB2939, pDB2943 also had a missing ‘G’ from within the DS248 sequence, which is marked in bold in Table 5.
Plasmids pDB2963 (FIG. 61) and pDB2945 (FIG. 62) were constructed similarly using the PCR primers described in Tables 10 and 11, and by cloning the approximately 1.94-kb and 1.87-kb EcoRI-BamHI fragments, respectively, into YIplac211. The expected DNA sequences were confirmed for the PDI1 genes in pDB2963 and pDB2945, with a serine codon at the position of amino acid 114.
The Construction of pSAC35-Based rHA Expression Plasmids with Different PDI1 Genes Inserted at the XcmI-Site After REP2:
pSAC35-based plasmids were constructed for the co-expression of rHA with different PDI1 genes (Table 13).







TABLE 13







pSAC35-based plasmids for co-expression of rHA with different PDI1 genes













Heterologous Protein



Plasmid
PDI1 Gene at XcmI-site after REP2
Expression Cassette













Plasmid
Base
Source
Promoter
Terminator
Orientation
(at NotI-site)





pDB2982
pSAC35
SKQ2n
Long
→ Bsu36I
A
rHA


pDB2983
pSAC35
SKQ2n
Long
→ Bsu36I
B
rHA


pDB2984
pSAC35
SKQ2n
Medium
→ Bsu36I
A
rHA


pDB2985
pSAC35
SKQ2n
Medium
→ Bsu36I
B
rHA


pDB2986
pSAC35
SKQ2n
Short
→ Bsu36I
A
rHA


pDB2987
pSAC35
SKQ2n
Short
→ Bsu36I
B
rHA


pDB2976
pSAC35
S288c
Long
→ Bsu36I
A
rHA


pDB2977
pSAC35
S288c
Long
→ Bsu36I
B
rHA


pDB2978
pSAC35
S288c
Medium
→ Bsu36I
A
rHA


pDB2979
pSAC35
S288c
Medium
→ Bsu36I
B
rHA


pDB2980
pSAC35
S288c
Short
→ Bsu36I
A
rHA


pDB2981
pSAC35
S288c
Short
→ Bsu36I
B
rHA









The rHA expression cassette from pDB2243 (FIG. 63, as described in WO 00/44772) was first isolated on a 2,992-bp NotI fragment, which subsequently was cloned into the NotI-site of pDB2688 (FIG. 4) to produce pDB2693 (FIG. 64). pDB2693 was digested with SnaBI, treated with calf intestinal alkaline phosphatase, and ligated with SnaBI fragments containing the PDI1 genes from pDB2943, pDB2963, pDB2945, pDB2939, pDB2941 and pDB2942. This produced plasmids pDB2976 to pDB2987 (FIGS. 65 to 76). PDI1 transcribed in the same orientation as REP2 was designated “orientation A”, whereas PDI transcribed in opposite orientation to REP2 was designated “orientation B” (Table 13).

## Claims

1. A 2 μm-family plasmid comprising a polynucleotide sequence insertion, deletion and/or substitution between a first base after a last functional codon of at least one of either an REP2 gene or an FLP gene and a last base before an FRT site in an inverted repeat adjacent to said gene.

2. The 2 μm-family plasmid of claim 1 wherein, other than the polynucleotide sequence insertion, deletion and/or substitution, the FLP gene and/or the REP2 gene has the sequence of an FLP gene and/or an REP2 gene from a naturally occurring 2 μm-family plasmid.

3. The 2 μm-family plasmid of claim 1, wherein the plasmid comprises pSR1, pSB3 or pSB4 from Zygosaccharomyces rouxii, pSB 1 from Zygosaccharomyces bailli, pSB2 from Zygosaccharomyces balli, pSM1 from Zygosaccharomyces fermentati, pKD1 from Kluyveromyces drosophilarum, pPM1 from Pichia membranaefaciens, or the 2 μm plasmid from Saccharomyces cerevisiae.

4. The 2 μm-family plasmid of claim 2 wherein the sequence of the inverted repeat adjacent to said FLP and/or REP2 gene is from the sequence of the corresponding inverted repeat in the same naturally occurring 2 μm-family plasmid as the sequence from which the gene is from.

5. The 2 μm-family plasmid of claim 2 wherein the naturally occurring 2 μm-family plasmid is the 2 μm plasmid as from Saccharomyces cerevisiae.

6. The 2 μm-family plasmid of claim 5 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at a position between a first base of codon 59 of the REP2 gene and the last base before the FRT site in the adjacent inverted repeat.

7. The 2 μm-family plasmid of claim 5 wherein, other than the polynucleotide sequence insertion, deletion and/or substitution, the sequence of the REP2 gene and the adjacent inverted repeat comprises the nucleotides of SEQ ID NO: 1, or a nucleotide sequence 95% identical to SEQ ID NO:1.

8. The 2 μm-family plasmid of claim 1 wherein polynucleotide sequence insertion, deletion and/or substitution occurs at a position between a first base of the inverted repeat and a last base before the FRT site.

9. The 2 μm-family plasmid of claim 1 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs between a first base after the end of the REP2 coding sequence and the last base before the FRT site.

10. The 2 μm-family plasmid of claim 1 wherein, other than the polynucleotide sequence insertion, deletion and/or substitution, the inverted repeat that follows the REP2 coding sequence has a sequence from a corresponding region of the 2 μm plasmid from Saccharomyces cerevisiae.

11. The 2 μm-family plasmid of claim 5 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at a position between a first base of codon 344 of the FLP gene and the last base before the FRT site in the adjacent inverted repeat.

12. The 2 μm-family plasmid of claim 5 wherein, other than the polynucleotide sequence insertion, deletion and/or substitution, the sequence of the FLP coding sequence and the adjacent inverted repeat comprises the nucleotides of SEQ ID NO: 2, or a nucleotide sequence 95% identical to SEQ ID NO:2.

13. The 2 μm-family plasmid of claim 11 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at a position between a first base of the inverted repeat and the last base before the FRT site.

14. The 2 μm-family plasmid of claim 13 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at a position between a first base after the end of the FLP coding sequence and the last base before the FRT site.

15. The 2 μm-family plasmid of claim 14 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at a first base after the end of the FLP coding sequence.

16. The 2 μm-family plasmid of claim 11 wherein, other than the polynucleotide sequence insertion, deletion and/or substitution, the inverted repeat that follows the FLP gene has a sequence from a corresponding region of the 2 μm plasmid from Saccharomyces cerevisiae.

17. The 2 μm-family plasmid of claim 1 comprising polynucleotide sequence insertions, deletions and/or substitutions between a first base after the last functional codons of both of the REP2 gene and the FLP gene and a last base before the FRT sites in the inverted repeats adjacent to each of said genes, which polynucleotide sequence insertions, deletions and/or substitutions can be the same or different.

18. The 2 μm-family plasmid of claim 1, comprising a polynucleotide sequence insertion, deletion and/or substitution which is not between the first base and the last base.

19. The 2 μm-family plasmid of claim 18 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs within an untranscribed region around an ARS sequence.

20. The 2 μm-family plasmid of claim 1 wherein the, or at least one, polynucleotide sequence insertion, deletion and/or substitution is a polynucleotide sequence insertion.

21. The 2 μm-family plasmid of claim 20 in which the polynucleotide sequence insertion encodes an open reading frame.

22. The 2 μm-family plasmid of claim 21 in which the open reading frame encodes a non-2 μm-family plasmid protein.

23. The 2 μm-family plasmid of claim 22 in which the non-2 μm-family plasmid protein comprises the sequence of a protein involved in protein folding, or which has chaperone activity or is involved in the unfolded protein response, albumin, a monoclonal antibody, an etoposide, a serum protein, antistasin, a tick anticoagulant peptide, transferrin, lactoferrin, endostatin, angiostatin, collagens, immunoglobulins or immunoglobulin-based molecules or fragments of either, a Kunitz domain protein, interferons, interleukins, IL 10, IL 11, IL2, interferon α species and sub-species, interferon β species and sub-species, interferon γ species and subspecies, leptin, CNTF, CNTFAx15, IL 1-receptor antagonist, erythropoietin (EPO) and EPO mimics, thrombopoietin (TPO) and TPO mimics, prosaptide, cyanovirin-N, 5-helix, T20 peptide, T1249 peptide, HIV gp4I, HIV gp120, urokinase, prourokinase, tPA, hirudin, platelet derived growth factor, parathyroid hormone, proinsulin, insulin, glucagon, glucagon-like peptides, insulin-like growth factor, calcitonin, growth hormone, transforming growth factor β, tumour necrosis factor, G-CSF, GM-CSF, M-CSF, FGF, coagulation factors in both pre and active forms, including but not limited to plasminogen, fibrinogen, thrombin, pre-thrombin, pro-thrombin, von Willebrand's factor, α1-antitrypsin, plasminogen activators, Factor VII, Factor VIII, Factor IX, Factor X and Factor XIII, nerve growth factor, LACI, platelet-derived endothelial cell growth factor (PD-ECGF), glucose oxidase, serum cholinesterase, aprotinin, amyloid precursor protein, inter-alpha trypsin inhibitor, antithrombin III, apo-lipoprotein species, Protein C, or Protein S.

24. The 2 μm-family plasmid of claim 23 in which the 2 μm-family plasmid protein comprises the sequence of albumin.

25. The 2 μm-family plasmid of claim 23 in which the non-2 μm-family plasmid protein comprises the sequence of transferrin.

26. The 2 μm-family plasmid of claim 23 in which the non-2 μm-family plasmid protein comprises the sequence of lactoferrin.

27. The 2 μm-family plasmid of claim 23 in which the non-2 μm-family plasmid protein comprises the sequence of Fc.

28. The 2 μm-family plasmid of claim 23 in which the non-2 μm-family plasmid protein comprises the sequence of a protein involved in protein folding, or which has chaperone activity or is involved in the unfolded protein response as encoded by anyone of AHA1, CCT2, CCT3, CCT4, CCT5, CCT6, CCT7, CCT8, CNS1, CPR3, CPR6, EPS1, ERO1, EUG1, FMO1, HCH1, HSP10, HSP12, HSP104, HSP26, HSP30, HSP42, HSP60, HSP78, HSP82, JEM1, MDJ1, MDJ2, MPD1, MPD2, PDI1, PFD1, ABC1, APJ1, ATP11, ATP12, BTT1, CDC37, CPR7, HSC82, KAR2, LHS1, MGE1, MRS11, NOB1, ECM10, SSA1, SSA2, SSA3, SSA4, SSC1, SSE2, SIL1, SLS1, UBI4, ORM1, ORM2, PER1, PTC2, PSE1 and HAC1 or a truncated intronless HAC1.

29. The 2 μm-family plasmid of claim 23 in which the chaperone is protein disulphide isomerase (PDI), or is a protein encoded by ORM2, SSA1 or PSE1.

30. The 2 μm-family plasmid of claim 22 in which the non-2 μm-family plasmid protein comprises a secretion leader sequence.

31. The 2 μm-family plasmid of claim 22 in which the non-2 μm-family plasmid protein comprises the sequence of a bacterial selectable marker and/or a yeast selectable marker.

32. The 2 μm-family plasmid of claim 31 in which the bacterial selectable marker is a β-lactamase gene and/or the yeast selectable marker is a LEU2 selectable marker.

33. The 2 μm-family plasmid according to claim 1, which plasmid comprises (i) a heterologous sequence encoding a non-2 μm-family plasmid protein; (ii) a heterologous sequence encoding a protein comprising the sequence of a protein involved in protein folding, a chaperone or a protein involved in the unfolded protein response; and (iii) a heterologous sequence encoding a protein comprising the sequence of a selectable marker; wherein at least one of the heterologous sequences occurs between the first base after the last functional codon of at least one of either the REP2 gene or the FLP gene and the last base before the FRT site in an inverted repeat adjacent to the gene.

34. A method of preparing a plasmid as defined by claim 1 comprising:
(a) providing a plasmid comprising the sequence of a REP2 gene and the inverted repeat that follows the REP2 gene, or a FLP gene and the inverted repeat that follows the FLP gene, in each case the inverted repeat comprising an FRT site;
(b) providing a polynucleotide sequence and inserting the polynucleotide sequence into the plasmid of claim 1 between the first base after the last functional codon of at least one of either the REP2 gene or the FLP gene and the last base before the FRT site in an inverted repeat adjacent to the gene; and/or
(c) deleting some or all of the nucleotide bases between the first base after the last functional codon of at least one of either the REP2 gene or the FLP gene and the last base before the FRT site in an inverted repeat adjacent to the gene of claim 1; and/or
(d) substituting some or all of the nucleotide bases between the first base after the last functional codon of at least one of either the REP2 gene or the FLP gene and the last base before the FRT site in an inverted repeat adjacent to the gene with alternative nucleotide bases.

35. A plasmid obtainable by the method of claim 34.

36. A host cell comprising a plasmid as defined by claim 1.

37. A host cell according to claim 36 which is a yeast cell.

38. A host cell according to claim 36 in which the plasmid is stable as a multicopy plasmid.

39. A host cell according to claim 38 in which the plasmid comprises a polynucleotide sequence insertion, deletion and/or substitution between a first base after a last functional codon of at least one of either an REP2 gene or an FLP gene and a last base before an FRT site in an inverted repeat adjacent to said gene.

40. A host cell according to claim 38 in which, if the plasmid contains, or is modified to contain, a selectable marker then stability, as measured by the loss of the marker, is at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9% or 100% after 5 generations.

41. A method of producing a protein comprising the steps of—
(a) providing a plasmid as defined by claim 1;
(b) providing a suitable host cell;
(c) transforming the host cell with the plasmid; and
(d) culturing the transformed host cell in a culture medium;
(e) thereby to produce the protein.

42. A method of producing a protein comprising the steps of providing a host cell as defined by claim 36 which host cell comprises a plasmid comprising a polynucleotide sequence insertion, deletion and/or substitution between the first base after the last functional codon of at least one of either a REP2 gene or an FLP gene and the last base before the FRT site in an inverted repeat adjacent to said gene as and culturing the host cell in a culture medium thereby to produce the protein.

43. A method according to claim 41 further comprising the step of isolating the thus produced protein from the cultured host cell or the culture medium.

44. A method according to claim 43 further comprising the step of purifying the thus isolated protein.

45. A method according to claim 44 further comprising the step of formulating the thus purified protein with a carrier or diluent, and optionally presenting the thus formulated protein in a unit form.

46. A method according to claim 44 further comprising the step of formulating the purified protein with a pharmaceutically acceptable carrier or diluent and optionally presenting the thus formulated protein in a unit dosage form.

47. The 2 μm-family plasmid of claim 11, wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at an HgaI site or an FspI site within the inverted repeat.

48. The 2 μm-family plasmid of claim 1, wherein the plasmid comprises a heterologous sequence encoding protein disulphide isomerase.

49. The 2 μm-family plasmid of claim 1, wherein the plasmid comprises a heterologous sequence encoding a protein of interest.

50. The 2 μm-family plasmid of claim 22 in which the non-2 μm-family plasmid protein comprises immunoglobulin-based molecules or fragments thereof selected from the group consisting of dAb, Fab′, F(ab′)2, scAb, scFv andor scFv.

51. A 2 μm-family plasmid comprising a polynucleotide sequence insertion between a first base after a last functional codon of at least one of either an REP2 gene or an FLP gene and a last base before an FRT site in an inverted repeat adjacent to said gene, wherein the polynucleotide sequence insertion encodes an open reading frame which encodes a non-2 μm-family plasmid protein comprising a secretion leader sequence.