Title of Invention

"A 2µM-FAMILY PLASMID AND ITS METHOD OF PREPARATION"

Abstract A 2µm-family plasmid characterized in that it comprise 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.
Full Text The present invention relates to a 2µm family plasmid and its method of preparation. FIELD OF THE INVENTION
The present application relates to modified plasmids and uses thereof.
BACKGROUND OP 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 2µm-family plasmids, include pSR1, pSB3 and pSB4 from Zygosaccharomyces ronxii (formerly classified as Zygosaccharomyces bisporus), plasmids pSBl and pSB2 from Zygosaccharomyces bailii, plasmid pSMl from Zygosaccharomyces fermentati, plasmid pKD1 from. Khyveromyces drosphilarum, an un-narned plasmid from Pichia membranaefaciens (hereinafter referred to as "pPM1") 'and the 2µm plasmid and variants (such as Scp1, Scp2 and Scp3) from Saccharomyces cerevisiae (Volkert, et ah, 1989, Microbiological RevieM's, 53, 299; Painting, et al., 1984, J. Applied Bacteriology, 5b, 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 autonornously 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 frarnes have demonstrated a common link between the family members.
The 2 µm plasmid (Figure 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-fonn and B-form of the
plasmid 277 vivo (Volkert & Broach, 1986, Cell, 46, 541). The two forms of 2um differ
only in the relative orientation of their unique regions.
While DNA sequencing of a cloned 2um plasmid (also known as Scpl) from
Saccharomyces cerevisiae gave a size of 6,318-bp (Hartley and Donelson, 19805 Nature,
286, 860), other slightly smaller variants of 2uni, 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 2pm (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 urn plasmids found in S.
cerevisiae and S. carlsbergensis, with the NCBI sequence (accession number
NC_001398) being one example.
The 2p.m. 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 2pm. 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. Bacterial, 157, 283; Bachmair & Ruis, 1984,
Monatshefte fiir Chemie, 115, 1229). A yeast strain, which contains a 2 urn plasmid is
known as [cir*], while a yeast strain which does not contain a 2um plasmid is known as
The US-region contains the REP2 and FLP genes, and the UL-region contains the KEPI
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. Bipl, 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
j*and control ofplasniid copy number m vivo (Senecoffef al. 19S5, Proc. Natl Acad. &ci.
U.S.A: 82, 7270: Jayaram, 1985. Proc. Natl Acad. Sci. U.S.A., 82, 5875). The copy
number of 2um-family plasmids can be significantly affected by changes in Flp
recombmase activity (Sleep e1 al, 2001, Yeast, 18, 403; Rose & Broach, 1990, Methods
Enzymol, 185. 234). The Repl and Rep2 proteins mediate plasmid segregation, although
then mode of action is unclear (Sengupta et al. 2001, J. Bacterial, 1&3, 23 06). They also
repress transcription of the FLP gene (Reynolds et al, 1987, Mol. Cell JBioL, 7, 3566).
The FLP and REP2 genes are transcribed from divergent promoters, with apparently no
rntenrening 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
17S-bp respectively after their translation tennrnation codons (Sutton & Broach. 1985,
Mol. Cell. Bid., 5, 2770).
In the case of FLP, the C-terrninal coding sequence also lies within the inverted repeat
sequence. Furthermore, fhe 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 sitespecific
recombination in -vitro (Senecoff et al, 1985, Proc. Natl. Acad. Sci. U.S.A., 82,
7270; Jayaram, 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 argiiri.ne-308 and tyrosine-343 (which is essential) with strand-cutting
facilitated by histidine-309 and Mstidine 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 Repl-binding
domain, and residues 59-296 contain a self-association and STB-binding region
(Sengupta et al, 2001, J. Bacteriol, 183, 2306).
Clumeric or large deletion mutant derivatives of 2um which lack many of the essential
functional regions of the 2 urn plasmid but retain functional the cis element ARS and STB,
cannot effectively partition between mother and daughter cells at cell division. Such
plasrnids can do so if these functions are supplied in trans, by for instance the provision
of a functional 2 urn plasmid within the host, a so called [cir+] host.
Genes of interest have previously been inserted into the UL-region of the 2um plasrnid.
For example, see plasmid pSACSUl 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(jm
plasmid without generating excessive asymmetry between the US and UL-regions.
Therefore, the US-region of the 2pm 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 Figure 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 Figure 2 includes a (3-lactamase
gene (for ampicillin resistance), a LEU2 selectable marker and an oligonucleotide linker,
the latter two of which are inserted into a unique SndBI-site within the UL-region of the
2(.tm-family disintegration vector, pSACS (see EP 0 286 424). The E. coli DNA between
the Xbal-sites that contains the ampicillin resistance gene is lost from the plasmid shown
in Figure 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 Figure 2, it is not readily
apparent where further polynucleotide insertions can be made. A JVM-site within the
linker has been used for the insertion of additional DNA fragments, but tin's 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 2um
plasrnid and maintain its high inherent plasmid stability. In the 2um-family
disintegration plasrnid pS ACS 00, a 1.1-Kb DNA fragment containing the URA3 gene was
inserted into JSagl-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 -:24']. When S150-2B [cirL'J was transformed to uracil protorrophy by pSAC300. it
was shown to be considerably less stable (50% plasrnid loss in under 30 generations) than
comparable vectors with URA3 inserted into the UL-region of 2um (0-.10% plasmid loss
m under 30 generations) (Chinery £ Hinchliffe, 1989, Ctirr. Genet, 16, 21; EP 0 286
424). Thus, insertion at the Eagl 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., 1993, Yeast,. 1, 347.
It is desirable to insert further potynucleotide sequences into 2p.ni-family plasniids. For
example, the insertion of polynucleotide sequences that encode host derived proteins.
recombinant proteins, or non-coding antisense or UNA interference (RNAi) transcripts
may be desirable. Moreover, it is desirable to introduce multiple farther polynucleotide
sequences into 2ajn-family plasmids, thereby to provide a plasrnid which encodes, for
example, multiple separate!}' 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 6,31£-bp 2um plasmid, and other 2 jam-family plasmids, are crowded with
functional genetic elements (Sutton & Broach, 1985, Mol. Cell. Biol, 5, 2770; Broach ei
al, 1979. Cell, 16, 827), with no obvious positions existing for the insertion of additional
DNA sequences without a concomitant loss in plasrnid stability. In fact, except for the
region between the origin of replication and the D gene locus, the entire 2pm 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 777 vivo.
Indeed, persons skilled in the art have given np on inserting heterologous porynucleotide
sequences into 2urn-family plasmids.
Robinson et al, 1994, Sio/TechnoJog)', 12, 3S1-384 reported that a recombinant
additional PDI gene cop}' in Saccharomyces cerevisiae could be used to increase the
recombinant expression of human platelet derived growth factor (PDGF) B homodinier
by ten-fold and Schizosacharomyces pombe acid phosphatase by four-fold. Robiiison
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 2um 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 5 integration
vector was superior to the use of a 2um-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 5 integration vector rather than a
2 urn-based, expression plasmid. The 2{.im-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 mat the KIPDI1 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, hi the light of the earlier findings in Bao et al, 2000,
Bao & Fukuliara, 2001, Gene, 272, 103-110, chose to introduce a single duplication of
KJ.PDI1 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 recornbinantry modified versions of 2pm~faniiry
plasmids.
A 2pjn-iamily plasmid is a circular, double stranded DMA plasmid. It is Typically small,
sucl) as between 3,000 to ] 0.000 bp, preferabty between 4,500 to 7000 bp, excluding
reconibinantly inserted sequences. Preferred 2 urn-family plasmids for use in the present
invention comprise sequences derived from one or more of plasmids pSE.1, pSB3, or
pSB4 as obtained from Zygosaccharomyces rouxii, pSBl or pSB2 both as obtained from
Zygosaccharomyces bailli, pSMl as obtained from Zygosaccharomyces fennemati,
pKDl as obtained from Khryveromyces1 drosophilarum, pPMl as obtained from Pichia
nembranaefadens and the 2f.Lm plasmid and variants (such as Scpl. Scp2 and Scp3) as
obtained from Saccharoinyces cerevisiae. for example as described hi Vollcert e1 al, 1989,
Microbiological Reviews, 53(3), 299-317, Murray et al 1988, Afo/. BioL, 200, 601-607
and Painting, et al., 1984, J. Applied Bacteriology, 56. 331.
A 2|im.-family plasmid is capable of stable multicopy maintenance within a yeast
population, although not necessaiity all 2um-faniiry plasmids will be capable of stable,
multicopy maintenance within all types of yeast population. For example, the 2inn
plasmid is capable of stable multicopy maintenance, inter alia, within Saccharomvcescerevisiae
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 jim-family plasmid is designated [cir4],
whereas a yeast cell that does not comprise 2pjn-family plasmid is designated [cir°J. A
[cir+] j^east cell typically comprises 10-100 copies of 2um-famil3' 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 2u.m-like
plasmid to above 100 per haploid genome (Gerbaud and Ohierineau, 1980, Citrr.
Genetics, 1, 219, Holm, 19S2, Cell, 29, 585, Sleep et al., 20013 Yeast, 18, 403 and
W099/00504). Multicopy stability is defined below.
A 2um~fainily plasmid typically comprises at least three open reading frames ("OJRPs")
that each encode a protein that functions in the stable maintenance of the 2u,m-family
plasmid as a: multicopy plasmid. The proteins encoded by the three ORFs can be
designated FLP, RJ3P1 and REP2. Where a 2jim-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. Hie 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 pSRl, pSBl, pSB2, pSB3, pSB4, pSMl,
pKDl, pPMl and the 2um plasmid, for example as described in Volkert et al, op. cit,
Murra}' 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 pSRl, pSBl, pSB2, pSB3, pSMl, pKDl and the 2um
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 2um 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|-im 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 urnfamily
plasmids., whereas no sequence alignment is currently possible between REP2
proteins derived from different 2 urn-family plasmids. Preferred REP1 and REP2
proteins comprise the sequence of the REP1 and REP2 proteins encoded by one of
plasmids pSRl, pSBl, pSB2, pSB3, pSB4, pSMl, pKDl, pPMl and the 2j.im plasmid,
for example as described in Vollcert et al, op. cit, Murray et al, op. cit. and Painting et al,
%JP. cii. Variants and fragments of these RE?] and R_h;.P2 proteins are. also included in the
present invention. "Fragments" and '"valiants" of REP 1 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 KEPI and REP2 wall usually have at least 5%, 10%r 20%, 30%, 40%., 50%, 60%, 70%,
80%, 90%, 95%, 98%, 99%, or more, honiology with a REP1 and REP2 protein,
respectively, as encoded by one of plasrnids pSRl, pSBl, pSB2; pSB3, pSB4, pSMl.
pICDl, pPMl and the 2 urn 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.
ORF's are specificall}' disrupted. If the disruption of an ORF impairs the stable multicop}^
maintenance of the plasmid then the ORF' can be concluded to contribute towards the
stable multicopy maintenance of the plasmid in the non-mntated version. It is preferred
that the REP1 and REP2 proteins have the sequences of REP1 and PJBP2 proteins
encoded by the same naturally occurring 2urn-family plasmid. such as pSRl, pSBl,
pSB2, pSB3, pSB4, pSMl, pKDl; pPMl and the 2um plasmid, or variant or fragments
thereof.
A 2urn-family plasmid comprises two inverted repeat sequences. The inverted repeats
ma}1 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. Prefen-ed 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 pSRl (959 bp), pSBl (675 bp), pSB2 (477 bp),pSB3 (391 bp), pSMl (352 bp),
pKDl (346 bp), the 2 urn plasmid (599 bp), pSB4 and pPMl.
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 2um-family plasmid as the ORF encoding the FLP
protein, such as pSRl, pSBl, pSB2, pSB3, pSB4, pSMl, pKDl, pPMl or the 2um
plasniid.
The inverted repeats are typically positioned within the 2p,m-family plasmid such that the
two regions defined between the inverted repeats (e.g. such as defined as UL and US in
the 2um plasmid) are of approximately similar size, excluding exogenously introduced
sequences such as transgenes. For example, one of the two regions ma}' have a length
equivalent to at least 40%, 50%, 60°/o, 70%, 80%, 90%, 95% or more, up to 100%, of the
length of the other region.
A 2urn-family plasniid comprises the ORF that encodes FLP and one inverted repeat
(arbitrarily termed "TR1" to distinguish it from the other inverted repeat mentioned in the
next paragraph) juxtaposed in such a manner that TR1 occurs at the distal end of the FLP
ORP, without any intervening coding sequence, for example as seen in the 2 pro 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 IPU.
A 2 urn-family plasmid comprises the ORF that encodes REP2 and the oilier inverted
repeat (arbitrarily termed "IEJ2" to distinguish it from IR.1 mentioned in the previous
paragraph) juxtaposed in sncfi a manner that IR2 occurs at the distal end of the REP2
ORF, without an}' intervening coding sequence, for example as seen in the 2f.im 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 OEFs encoding REP2 and FLP ma}' he present on the same
region of the two regions defined between the inverted repeats of the 2j.Lm-farnily
plasmid, which region ma}' be the bigger or smaller of the regions (if there is any
inequality in size between the two regions).
In one embodiment, the ORJFs 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 2um plasmid) of a 2um-family plasmid ma}' comprise not more than two
endogenous genes that encode a protein that functions in the stable maintenance of the
2urn-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 REPl; or REPl and REP2, as endogenous
coding sequence,
A 2um-family plasmid comprises an origin of replication (also laiown 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 ei ol, 1982, Cold Spr
•ing
Harbor Symp. Quant. Biol, 41, 1165-1174; Williamson, Yeast, 1985,1, 1-14). Preferred
ARSs include those isolated from pSRl, pSBl, pSB2, pSB3, pSB4, pSMl, pKDl, pPMl
and the 2um plasmid.
Thus, a 2(.Lm-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 REPl, although it may be supplied in trans, as discussed above. Preferably the
FRT sites are derived from the same 2um-famiry plasmid as the sequence of the encoded
FLP protein. Preferably the sequences of the encoded REPl and REP2 proteins are
derived from the same 2pm-family plasmid as each other. More preferably, the FRT sites
are derived from the same 2am-fainily plasmid as the sequence of the encoded FLP,
REPl and REP2 proteins. Even more preferably, the sequences of the ORFs encoding
FLP, REPl and REP2, and the sequence of the inverted repeats (including the FRT sites)
are derived from the same 2j.iin-family plasmid. Yet more preferably, the ARS site is
obtained from the same 2urn-family plasmid as one or more of the ORFs of FLP, REPl
and REP2, and the sequence of the inverted repeats (including the FRT sites). Preferred
plasmids include plasroids pSRl, pSB3 and pSB4 as obtained from Zygosaccharomyces
rouxii, pSBl or pSB2 both as obtained from Zygosaccharomyces bailli, pSMl as
obtained from Zygosaccharomyces fermentati, pKDl as obtained from Kluyveromyces
drosophilarum, pPMl as obtained from Pichia membranaefaciens, and the 2um plasmid
as obtained from Saccharomyces cerevisiae, for example as described in Volkert et al,
1989, op. tit, Murray et al, op. tit. and Painting et al, op. tit.
Optionally, a 2um-farnily plasmid may comprise a region equivalent to the STB region
(also known as REPS) of the 2um plasmid., as defined in Volkert et al, op. tit. The STB
region in a 2jim-family plasmid of the invention may comprise two or more tandern
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(.im 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
12
%& select an STB region from the- same plasmid as either or both of the REP1 and Klil-'2
OPLFs. The STB region is thought to be a czj-acting element and preferably is not
transcribed.
Optional!)-, a 2f.im-family plasmid ma}' comprise an additional ORP that encodes a
protein that functions in the stable maintenance of the 2uni-farnily plasmid as a
multicopy plasmid. The additional protein can be designated RAP or D, ORFs encoding
the RAP or D gene can be seen on, for example, the 2f.Lm plasmid and pSMl. Thus a
RAP or D ORP can comprise a sequence suitable to encode the protein product of the
RAP or D gene ORFs encoded by the 2urn plasmid or pSMl, or variants and fragments
thereof. Thus variants and fragments of the protein products of the RAF or D genes of the
2um plasmid or pSMl are also included in the present invention. "Fragments" and
'Variants" of the protein products of the RAF or D genes of the 2um plasmid or pSMl are
those which., when encoded by the 2uxn plasmid or pSMl in place of the native ORP, 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%, 95%, 98%, 99%, or more, homology with the protein
product of the RAF or D gene ORFs encoded by the 2urn plasmid or pSMl.
The present invention provides a 2pm-fainily 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 an}' additional polynucleotide sequence inserted
into the plasniid. 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, SO, 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, SO,
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 RJEP2 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 Ginnery &
Hinchliffe (1989, Ciirr. 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. cere-visiae 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 2j.im-like plasmid, and/or other differences in the 2|ini-like plasmid, such as the
size and nature of the inserted sequences within the 2j.im-like plasmid and/or insertions
elsewhere in the 2um-Iike plasmid. For yeast that do not grow in the non-selective
medium (YPD, also designated YEPD) defined in Chinery & Hinchliffe (1989, Cvrr.
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 p SACS 5 or pSACS 10, 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%, 50°/o, 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
(iO'J'(i when grown on non-selective media, that plasmid can siil] be of use \vhen cultured
in selective media. For example plasmid pDE2711 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
codoD in either gene, by insertion of a po^imcleotide sequence insertion, deletion or
substitution wili not lead to an unacceptable loss of multicopy' stability of the plasmid.
We have surprisingly found that the REP2 gene of the 2pm plasmid can be disrupted
after codon 59 and that the FLP gene of the 2um 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 hi other 2um-farnily plasmids can be
determined routinely by modifying the relevant genes and detenniuing stability as •
described above. Typicalty, 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 REP 2 and FLP genes hi a 2um 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 airy
inteiTening coding sequence, for example as seen hi the 2um 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.
hi 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 tennination 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 REP 2 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 seqxience insertion, deletion and/or
substitution may occur between the last base after the end of FLP and the .Fjpl-site in the
inverted repeat, but optionally not within the Fspl-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 2um-famiry 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 2um plasmid may have a modified promoter or other regulatory
sequence compared to that of the naturally occurring gene. Alternatrvefy, an FLP gene
having a sequence derived from the FLP gene of the 2um plasmid may have a modified
nucleotide sequence in the open reading frame which may encode the same protein as the
* natural] y occurring eerie, or may encode a modified FLP protein. The same
considerations apply to 1~IEP2 genes having a sequence derived from a particular source.
A natural]}' occurring 2u,m-family plasmid is any plasniid having the features defined
above as being essential features for a 2 jam-family plasniid. which plasmid is found to
naturally exist in yeast, i.e. has not been recombiaantly modified to include heterologous
sequence. Preferably the naturally occurring 2uxn--fami]y plasmid is selected from pSRl
(Accession No. X02398), pSB3 (Accession No. X02608) or pSB4 as obtained from
Zygosaccharomyces ronxii, pSBl or pSB2 (Accession No. NC_002055 or Ml 8274) both
as obtained from Zygosaccharomyces bailli, pSMl (Accession No. NC_002054) as
obtained from Zygosaccharomyces fermentati, pKDl (Accession No. X03961) as
obtained from. Khryveromyoes drosophilarum, pPMl as obtained from Pichia
membranaefaciens, or, most preferably, the 2p.ni plasmid (Accession No.. NC_OQ13 98 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 KEP2 gene is derived
from the sequence of the corresponding inverted repeat in the same naturally occurring
2um-family plasmid as the sequence from which the gene is derived. Thus, for example,
if the FLP gene is derived from the 2 urn 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 urn plasniid as obtained from
S cerevisiae. If the REP2 gene is derived from the 2um 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 2j.im
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 2jam 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 2um 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 N0:l or variant thereof. In SEQ ID N0:l, 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, pp7-10, 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 conesp ending regions of the
2jjm plasmid as obtained from S. cerevisiae and, in the absence of the interruption the
polynucleotide sequence insertion, deletion and/or substitution, comprise an Xcml site or
an Fspl site within the inverted repeat and the polynucleotide sequence insertion, deletion
and/or substitution occurs at Has Xcml site, or at the Fspl site. In SEQ ID N0:l, Has Xcml
site is represented by base numbers 935-949 and the Fspl site is represented by base
numbers 1172-1177.
;re. 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 2am
plasmid as obtained from S. cerevisiae., then it is preferred that the potyimcleotide
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 FP,T 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 Fspl 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 2um 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 denned by SEQ TD NO:2 or variant thereof. In SEQ ID NO:25 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 pofynucleotide sequence insertion, deletion and/or substitution, the FLP
gene and the adjacent inverted repeat sequence have sequences derived from the
corresponding regions of the 2um plasmid as obtained from S. cerevisiae and, in the
absence of the potynucleotide sequence insertion, deletion and/or substitution, comprise
an Hgal site or an Fspl sits "within the inverted repeat and the polynucleotide. sequence
insertion, deletion and/or substitution occurs at the cut formed by the action of Hgal on
the Hgal site (Hgal cuts outside the 5bp sequence that it recognises), or at the Fspl. In
SEQ ID NO:2, the Hgal site is represented by base numbers 1262-1266 and the Fspl site
is represented by base numbers 1375-1380.
The skilled person will appreciate that the features of the plasinid 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 N0:l 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 2umfamily
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 2um plasmids are known in the art, but do not provide the
advantages of using the insertion sites defined by the present invention. Nevertheless,
plasrnids 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 -urn-family plasmids o~ther
than as defined by the first and second aspects of the invention.
Typical modified 2,um plasmids laiown in the art include those described in Rose &
Broach (1990, Methods En=ymol, 185, 234-279), such as plasmids pCV19, pCV20,
CVneo, which utilise aa insertion at EcoRl in FLP, plasmids pCV21. pGT41 and pYE
which utilise EcoPJ in D as the insertion site, plasniid pHKB52 which utilises Pstl in D
as the insertion site, plasmid pJDB248 which utilises an insertion al Pstl in D and JEc-oFJ
in D. plasmid pJDB219 in which Pstl in D and EcoPJ in FLP are used as insertion sites,
plasmid Gl 8. plasmid pABIS which utilises an insertion at Clal in FLP, plasmids pGT39
and pA3, plasmids pYTl 1, pYT14 and pYTl 1-LEU which use Pstl in D as the insertion
site, and plasniid PTY39 which uses Eco'KL in FLP as the insertion site. Other 2.pm
plasmids include pSAC3, pSACSUl, pSAC3U2, pSACSOO, pSAC310, pSACBCl,
pSACSPLl, pSAC3SL4, and pSACSSCl are described in EP 0 286 424 and Chrnery &
HincHiffe (1989, Cvrr. Genet., 16, 21-25) which also described Pstl, EagI or Sna&I as...
appropriate 2um insertion sites. Further 2p:m plasmids include pAYE255. pAYE316,
pAYE443, pA^T522 (Kerry-Williams et al, 1998, Yeast, 14, 161-169), pDB2244 (TWO
00/44772) and pAYE329 (Sleep et al, 2001, Yeast, IS, 403-421).
In one preferred embodiment, a 2fim-lrke plasmid as defined by the first, second and
third preferred aspects of the present invention additionally comprises a po^TtucIeotide
sequence insertion, deletion and/or substitution which occurs within an untranscribed
region around the ARS sequence. For example, in the 2um plasmid obtained from S.
cerevisiae, the untranscribed region around the ARS sequence, extends from end of th_e D
gene to the beginning of ARS sequence. Insertion into SnaBl (near the origin of
replication sequence ARS) is described in Chinery & Hincliliffe, 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 imtranscribed region at
neighbouring positions to the SnaBl site described by Chinery & Hhchliffe.
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, Khnweromyces, Zygosaccharomyces, or Pichia genus, such
Saccharomyces cerevisiae, Saccharomyces carlsbergensis,, Kluyveromyces lactis, Pichia
pastoris and Pichia membranaefaciens, Zygosaccharomyces roiixii, Zygosaccharomyces
bailii, Zygosaccharomyces fermentati, or Kluyveromyces drosphilarum. S. cerevisiae and
5*. carlsbergensis are thought to provide a suitable host cell for the autonomous
replication of all known 2u-m plasmids.
In a preferred embodiment, the, or at least one, polynucleotide sequence insertion,
deletion and/or substitution included in a 2um-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%, 4-0%
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 }^east 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 hi length.
Usually, the polynucleotide sequence insertion will be up to 1kb, 2kb, 3kb, 4kb, 5kb, 6kb,
7kb: 8kb. 9kb, 10kb or more in length. The sldlled person will appreciate that the 2 urn
plasmid of the present invention may comprise multiple polynuclecnide sequence
insertions at different sites "within the plasmid. Typically, the total length of
pohoiucleoticle sequence insertions is no more than 5kb, 10kb. 15kb. 20kb, 25kb or 30kb
although .greater total length insertion ma)' 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 Fspl
site after the FLP gene, such as to introduce a further restriction site (e.g. BamKI).
The polynucleotide sequence insertion may contain a transcribed region or ma)' 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 pobynierase,
typically yeast RNA porymerase. A transcribed region can encode a functional RNA
molecule, such as ribosomal or transfer RNA or an RNA molecule that can function as an
aniisense or RNA interference ("RNAi") molecule. Alternatively a transcribed region
can encode a messenger RNA molecule (rnRNA), which inRNA can contain an open
reading frame (ORF) which can be translated 271 vivo to produce a protein. The term
"protein" as used herein includes all natural and non-natural proteins, porypeptides and
peptides. Preferably, the ORF encodes a heterologous protein. B)' "heterologous
protein" we mean a protein that is not naturally encoded by a 2|jm-family plasmid (i.e. a
c:non- 2j.m>famiry plasmid protein"). For convenience the terms "heterologous protein"
and "non- 2um-fainily plasmid protein" are used synonymous!}7 throughout this
application. Preferably, therefore, the heterologous protein is not a FLP, REP15 REP2, or
a RAFfD protein as encoded by any one of pSRl, pSB3 or pSB4 as obtained from Z.
roiKii, pSBl or pSB2 both as obtained from Z. bailli, pSMl as obtained from Z
fermentati, pKDl as obtained from X. drosophilarum, pPMl as obtained from P.
membranaefaciens and the 2um 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, PklAl, CYC1, PHO5, TRP1, ADH2, ADH2, the genes
for glyceraldehyde-3-phosphate dehydrogenase, hexolcinase, pyruvate decarboxylase,
phosphofructokinase, triose phosphate isomerase, phosphoglucose isomerase,
glucokinase, oc-mating factor pherornone, 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
be host is a yeast, preferably S. fji-cvisiac, then the termination signal of the 5.
ewisi-acADHJ.ADH2, CYCJ, or PGICJ 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 PDIL to be flanked by transcription temiination
sequences so that the transcription termination sequences are located both upstream and
downstream of the promoter and open reading frame, hi order to prevent transcriptional
read-through into neighbouring genes, such as 2 urn genes, and vice versa.
hi one embodiment, the favoured regulator)' sequences hi 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, hi order to
minimise traaslational read-through and thus avoid the production of elongated, nonaatural
fusion proteins. The translation stop codon UAA is preferred. Preferably, at least
two translation stop codons are incorporated.
The term "operabty 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 regulator)' sequence.
Where the potynucleotide 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 ma}' 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, Kinder omyces lactis and Pichia pastoris,
laiown 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 (Hspl50p) (see WO 95/33833).
Additionally, leader sequences from the S. cerevisiae mating factor alpha-1 protein
(MFoc-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 MFa-1 and HSA leader
sequences, which advantageously reduces the production of a contarninating fragment of
human albumin relative to the use of the MFcc-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.
hi 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, hi 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 tke same host from which the
2um-lilce plasmid is derived.
hi 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 hi the unfolded protein response (Stanford
Genome Database (SGD), htrp:://db.yeastgenome.org). Preferred proteins may be
"selected from protein encoded by ANAL CCT2, CCT3, CCT4, CCT5, CCT6.. CCT7,
CCTS, CtfSJ, CPR3, CPR6: EROJ, EUG1, FMO.L HCHL HSPKL HSPJ2.. KSPJ04,
HSP26, HSP30: HSP42: ESP60, PISP7S, HSP82, JEM1, MDJ1, MDJ2, MPDL MPD2,
PDnj'PD],ABCl,APJLATPn,ATP12,.BTTl, CDC57, CNSJ: CPR6; CPR7,HSC82,
KAX2, LP1S1, MGEL MRS11, NOBJ, ECM10, SSAJ, SSA2, SSA3, SSA4, SSCJ, SSE2>
SILL. SLSJ, OJtMJ, UBJ4, ORM2, PEfJ, PTC2, PSE1 and EAC1 or a truncated
introoless HA CJ (Valkonen el al. 2003, Applied Environ. Micro. 69, 2065).
A preferred protein involved in protein foldings or protein with chaperone activit3r 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, SSS1 and SSB2), a protein that is a member of tie
HSP90-famiry, or a protein that is a member of the HSP40-family or proteins
involved in their modulation (e.g. SiJlp), including DNA-J and DNA-J-like
proteins (e.g. Jemlp, Mdj2p):
• a protein that is a member of the IcaiyopherhVimportin famify of proteins, such as
the alpha or beta families of Icaiyopherin/importin proteins, for example the
Icaryopherin beta protein encoded byPSEJ;
• a protein that is a member of the ORMDL farnity described by Hjelmqvist ef al,
2002, Genome Biology. 3(6), research0027.1-0027.16, such as Orm2p.
a protein that is naturally located in the endoplasmic reticulum or elsewhere in the
secretory patlrwa}', such as the golgi. For example, a protein that naturalty acts in
the lumen of the endoplasmic reticulum (ER), particularly in secretory cells, such
asPDJ
• a protein that is a transmembraiie protein anchored in the ER, such as a member
of the ORMDL family described by Hjelmqvist et al, 2002, supra, (for example,
Onn2p);
• a protein that acts in the cytosol, such as the hsp70 proteins, including SSA and
SSB proteins, for example proteins encoded by SSA2, SSA2, SSA3, SSA4, SSB1
andSSB2;
• a protein that acts in the nucleus, the nuclear envelope and/or the cytoplasm, such
' as Pselp;
• a protein that is essential to the viability of the cell, such as PDI or an essential
karyopherin protein, such as Pselp;
• a protein that is involved in sulphydryl oxidation or disulphide bond formation,
breakage or isomerization, or a protein that catalyses thiolidisulphide interchange
reactions in proteins, particularly during the biosynthesis of secretory and cell
surface proteins, such as protein disulphide isomerases (e.g. Pdilp, Mpdlp),
homologues (e.g. Euglp) and/or related proteins (e.g. Mpd2p, Fmolp, Erolp);
• a protein that is involved in protein synthesis, assembly or folding, such as PDI
and Ssalp;
• 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 andSSB2;
• a protein that prevents aggregation of precursor proteins in the cytosoi, such as the
hsp70 proteins, including SSA and SSB proteins, for example proteins encoded
by SSA2, SSA2, SSA3, SSA4, SSB1 and SSB2;
• a protein that binds to and stabilises damaged proteins, for example Ssalp;
•d protein that is involved in the unfolded protein response or provides for
increased resistance to agents (such as tunicanrycin and dittoothreitol) that induce
the unfolded protein response., such as a member of the ORMDL family described
by Pljehnqvist el 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. hsp!04p, Mdjlp);
a protein that is involved in the nucleocytoplasmic transport of macroinolecules.
suchasPselp;
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 Pselp;
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 Ercymol, 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 Nterminal
ATP-binding domain and a C-terminal peptide-binding domain, such as
Ssalp.
a protein that is a peptidyl-prolyl cis-trans isomerases (e.g. CprSp, Cpr6p):
a protein that is a liomologues of known chaperones (e.g. HsplOp);
a protein that is a mitochondria! chapeione (e.g CprSp);
• a protein that is a cytoplasrnic or nuclear chaperone (e.g Cnslp);
• a protein that is a membrane-bound chaperone (e.g, Orm2p, Fmolp);
• a protein that has chaperone activator activity or chaperone regulatory activity
(e.g. Alialp, Haclp, Hchlp);
• 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. Lhslp) or their site of
action within the cell (e.g. Pselp);
• a protein mat is a involved in protein complex assembly and/or ribosome
assembly (e.g. Atpl Ip, Pselp, Noblp);
• a protein of the chaperonin T-complex (e.g. Cct2p); or
• a protein of the prefoldin complex (e.g. Pfdlp).
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 thiolrdisulphide
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. Set., 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 disulphkl? fonnation I'Bulleid and i-'reedman, I98S, A'ahire. 335,
649-51) implies that the enzyme functions as a catal.vsi of native disulpliide bond
formation duiiiig the biosynthesis of secretory and cell surface proteins. Tins role is
consistent with what is known of the enzyme's catalytic properties 177 vitro: it catatyz.es
tliiol: disulphide interchange reactions leadhig 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
(Treedman et al., 19S9, Biochem. Soc. Symp., 55. 167-192). PDI also functions as a
diaperone since mutant PDI lacking isomerase activity accelerates protein folding
fHayano et al, 1995, FEBS Letters, 377, 505-511). Recently, sulphyoryl oxidation, not
disulphide isornerisation 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 arnino acid sequence of the enzyme is known for several species (Scherens
et al, 1991, Yeast, 1, 185-193; Farquhar et al 1991, Gene, 108, 81-89; EP074661;
EP0293793; EP0509S41) and there is increasing information on the mechanism of action
of the enzyme purified to homogeneity from mammalian liver (Creighlon et al, 1980., J.
Mol. Biol, 142, 43-62: Fieedman 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
trans-location in the cell (Rothrnan, 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
homodirner (2x57 kD) with characteristically acidic pi (4.0-4.5) (Hillson et al. 1984,
Methods ErirymoL, 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, 19S7, Biochem.
Biophys. Res. Comm., 146, 1485-1492), human (Piluajaniemi et al, 1987, EhfBO J., 6,
643-9), yeast (Scherens et al, supra; Farquhar ef al, supra] and chick (Parldconen 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:
1 mkfsagavls wsslllassv faqqeavape dsawklatd sfneyiqshd Ivlaeffapw
61 cghcknmape yvkaaetlve knitlagidc tenqdlcmeh nipgfpslki fknsdvnnsi
121 dyegprtaea ivqfmikqsq pavawadlp aylanetfvt pvivqsgkid adfnatfysm
181 ankhfndydf vsaenadddf klsiylpsam depwyngkk adiadadvfe kwlgvealpy
241 fgeidgsvfa qyvesglplg ylfyndeeel eeykplftel akknrglmnf vsidarkfgr
301 hagnlnmkeq fplfaihdmt edlkyglpql seeafdelsd kivleskaie slvkdflkgd
361 aspivksqei fenqdssvfq Ivgknhdeiv ndpkkdvlvl yyapwcghck rlaptyqela
421 dtyanatsdv liakldhten dvrgvviegy ptivlypggk ksesvvyqgs rsldslfdfi
481 kenghfdvdg kalyeeaqek aaeeadadae ladeedaihd el
An alternative PDI sequence can be found as Genbanlc accession no. CAA38402. It has
the following sequence of 530 amino acids
1 mkfsagavls wsslllassv faqqeavape dsawklatd sfneyi'qshd Ivlaeffapw
61 cghcknmape yvkaaetlve knitlaqidc tenqdlcmeh nipgfpslki fknrdvnnsi
121 dyegprtaea ivqfmikqsq pavawadlp aylanetfvt pvivqsgkid adfnatfysm
161 ankhfndydf vsaenadddf klsiylpsam depvvyngkk adiadadvfe kwlqvealpy
241 fgeidgsvfa qyvesglplg ylfyndeeel eeykplftel akknrglmnf vsidarkfgr
301 hagnlnmkeq fplfaihdmt edlkyglpql seeafdelsd kivleskaie slvkdflkgd
361 aspivksqei fenqdssvfq Ivgknhdeiv 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
"*tliai such changes resuli in a protein whose basic properties, ior example enzymatic aciivity
(type of and specific activity;, thennostability, activity in a certain pH-range (pH-stability')
have, not significant!}7 been changed. "Significant]}'" in tliis contort' 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 Hie ones of the original protein.
By "conservative substitutions" is intended combinations such as Val. Be, Leu. Ala, Met;
Asp, Glu; Asn, Gin: Ser, Tbr. Gly, Ala; Lys, Arg, His; and Phe, Tyr, Tip. Preferred
conservative substitutions include Glys Ala; Val, He, Leu; Asp, Glu: Asn, Gin: Ser, Thr;
Lys, Arg: and Phe. Tyr.
A "variaat" 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 preferably7 at least 95%. yet moie
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 ait.
A "fragment", in the context of PDI, refers to a protern 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 preferabhy
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 recombinantty 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 natural!}' occmrizig
homolog of PDI, such as a hornolog encoded by another organism, sucli 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:
MSKAVGIDLGTTYSCVAHFANDRVDIIANDQGNRTTPSFVAFTDTERLIGDAAKNQAAMN
PSNTVFDAKRLIGRNFNDPEVQADMKHFPFKLIDVDGKPQIQVEFKGETKNFTPEQISSM
VLGKMKETAESYLGAKVNDAWTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAMIA
YGLDPCKGKEEHVLIFDLGGGTFDVSLLFIEDGIFEVKATAGDTHLGGEDFDNRLVNHFIQ
EFKRKNKKDLSTNQRALRRLRTACERAKRTLSSSAQTSVEIDSLFEGIDFYTSITRRRFE
ELCADLFRSTLDPVEKVLRDAKLDKSQVDEIVLVGGSTRIPKVQKLVTDYFNGKEPNRSI
MPDEAVAYGAAVQAAILTGDESSKTQDLLLLDVAPLSLGIETAGGVMTKLIPRNSTISTK
KFEIFSTYADNQPGVLIQVFEGERAKTKDNNLLGKFELSGIPPAPRGVPQIEVTFDVDSN
GILNVSAVEKGTGKSNKITITNDKGRLSKEDIEKMVAEAEKFKEEDEKESQRIASKNQLE
SIAYSLKNTISEAGDKLEQADKDTVTKKAEETISWLDSNTTASKEEFDDKLKELQDIANP
IMSKLYQAGGAPGGAAGGAPGGFPGGAPPAPEAEGPTVEEVD
A published coding sequence for SSA1 is as 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:
ATGTCAAAAGCTGTCGGTATTGATTTAGGTACAACATACTCGTGTGTTGCTCACTTTGCT
AATGATCGTGTGGACATTATTGCCAACGATCAAGGTAACAGAACCACTCCATCTTTTGTC
GCTTTCACTGACACTGAAAGATTGATTGGTGATGCTGCTAAGAATCAAGCTGCTATGAAT
CCTTCGAATACCGTTTTCGACGCTAAGCGTTTGATCGGTAGAAACTTCAACGACCCAGAA
GTGCAGGCrGACATGAAGCACTTCCCATTCAAGTTGATCGATGTTGACGGTAAGCCTCAA
ATTCAAGTTGAATTTAAGGGTGAAACCAAGAACTTTACCCCAGAACAAATCTCCTCCATG
GTCTTGGGTAAGATGAAGGAAACTGCCGAATCTTACTTGGGAGCCAAGGTCAATGACGCT
GTCGTCACTGTCCCAGCTTACTTCAACGATTCTCAAAGACAAGCTACCAAGGATGCTGGT
ACCATTGCTGGTTTGAATGTCTTGCGTATTATTAACGAACCTACCGCCGCTGCCATTGCT
TACGGTTTGGACAAGAAGGGTAAGGAAGAACACGTCTTGATTTTCGACTTGGGTGGTGGT
ACTTTCGATGTCTCTTTGTTGTTCATTGAAGACGGTATCTTTGAAGTTAAGGCCACCGCT
GGTGACACCCATTTGGGTGGTGAAGATTTTGACAACAGATTGGTCAACCACTTCATCCAA
TCT\ACCAiC^
ATT'GACTCTTTGTTCGMGGTATCGATTTCTACACTTCCATCACCAGAGCCAGATT'CGAA
GAATTGTGTGCTGACTTGTTCAGATCTACTTTGGACCCAGTTGAAAAGGTCTTGAGAGAT
GCTAAATTGGACAAATCTCAAGTCGATGAAATTGTCTTGGTCGGTGGTTCTACCAGAATT
CCAAAGGTCCAAAAATTGGTCACTGACTACTTCAACGGTAA.GGAACCAAACAGATCTATC
AACCCAGATGAAGCTGTTGCTTACGGTGCTGCTGTTCAAGCTGCTATTrTGACTGGTGAC
GAATCTTCCAAGACTCAAGATCTATTGTTGTTGGATGTCGCTCCATTArCCTTGGGTA.TT
GA>ACrGCTGGTGGTGTCATGACCAAGTTGA-TTCCAAGAAACTCTACCATrTCAACAAAG
AA.GTTCGAGATCTTTTCCACTTATGCTGATAACCAACCAGGTGTCTTGATTCAAGTCTTT
GAAGGrGAAAGAGCCAAGACTAAGGACAACAACTTGT7GGG?AAGTTCGAATTGAGTGGT
ATTCCACCAGCTCCAAGAGGTGTCCCACAAATTGAAGTCACTTTCGATGTCGACTCTAAC
GGrATTTTGAArGTTTCCGCCGTCGAAAAGGGTACTGGTAAGTCTAACAAGATCACTATT
ACCAACGACAAGGGTAGATTGrCCAAGGAAGATATCGAAAAGATGGTTGCTGAAGCCGAA
AAATTCAAGGAAGAAGATGAZaAGGAATCTCAAAGAATTSCTTCCAAGAACCAATTGGAA
TCCATTGCTTACTCTTTGAAGAACACCATTTCTGAAGCTGGTGACAAATTGGAACAAGCT
GACAAGGACACCGTCACCAAGAAGGCTGAAGAGACTATTTCTTGGTTAGACAGCAACACC
ACTGCCAGCAAGGAAGAATTCSATGACAAGTTGAAGGAGTTGCAAGACATTGCCAACCCA
ATCATGTCTAAGTTGTACCAZkGCTGGTGGTGCrCCAGGTGGCGCTGCAGGTGGTGCTCCA
GGCGGTTTCCCAGGTGGTGCTCCTCCAGCTCCAGAGGCTGAAGGTCCAACCGTTGAAGAA
GTTGATTAA
Tlie protein Ssalp 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
sj'nthesis., assembly and folding: mediating translocation of polypeptides to various
intracellulai' locations, and resolution of protein aggregates (Becker & Craig, 1994, Ew.
J. Biochem. 219, 11-23). Hsp70 genes are highly conserved, possessing an N-terrninal
ATP -binding domain and a C-tenninal 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 C3^tosolic 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,
suprci). 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 orgauelles (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 eta!., 1998, Proc. Natl. Acad. Sci. USA. 95,12860-12865; Ngosuwan
et aL, 2003, J. Biol Chem. 278 (9), 7034-7042). Ssalp lias 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 hi 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 hi 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, lie, Leu, Ala, Met;
Asp, Glu; Asn, Gin; Ser, Thr, Gly, Ala; Lys, Arg, His; and Phe, Tyr, Tip. Preferred
conservative substitutions include Gly, Ala; Val, He, Leu; Asp, Glu; Asn, Gin; 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 identify between TWO poK'pepiides may be: determined using
suitable computer programs, as discussed below. Such variaits may be natural or made
using th.e methods of protein engineering and site-directed mutagenesis as are well l;nown in
the art.
A "fragment", hi the context of SSAl . refers to a protein having the sequence of native
SSAl oilier 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 SSAl protein. Particularly preferred fragments of SSAl protein comprise- one or
more whole domains of the desired protein.
A fragment or variant of SSAl may be a protein that, when expressed recombinantly in a
host cell, such as S. cerevisiae, can complement the deletion of the endogenous^
encoded SSAl gene in the host cell and may, for example, be a naturally occurring
homolog of SSAl. such as a hornolog encoded by another organism, such as another
yeast or other fungi, 01 another eukaryote such as a human or other vertebrate, or animal
or by a plant.
Another preferred chapsrone is PSE1 or a fragment or variant thereof having equivalent
chapero tie-like activity.
PSEJ, also known as /C4.?-?2J, is an essential gene, located on chromosome XItL
A published protein sequence for the protein pselp is as follows:
MSALPE EVWRTLLQIVQAFAS PDNQIRSVAEKS.LSEEWI rENNIEYLLTFLAEQAAFS QD
TTVAALSAVIIFRKLJl!iLKfl.PPSSKLMIMSKl>riTBIPJCEVLAQIRSSLLKGFISEEADSIRH
KLSDArAECVQDDLPAWPELLQALIESLKSGNPWFRESSFRILTTVPYLITAVDINSILP
IFQSGFTDASD1WKIAAVTAFVGYFKQLPKSEWSKLGILLPSLLNSLPRFLDDGKDDALA
SVFESL, IELVELAPKLFKDMFDQI IQFTDMVI IWKDLEPPARTTALELLTVFSEWAPQMC
KSHQNYGQTLVlWTLIMMTEVSIDDDDAaEWISSDDTDDEEEVTYDHARQALDRVALKLG
HPRVQYGCCNVLGQISTDFSPFIQRTAHDRILPALISKLTSECTSRVQTHAAAALVNFSE
FASKDILEPYLDSLLTNLLVLLQSNKLYVQEQALTTIAFIAEAAKNKFIKYYDTLMPLLL
NVLKVWNKDNSVLKGKCMECATLIGFAVGKEKFHEHSQELISILVALQNSDIDEDDALRS
YLEQSWSRICRILGDDFVPLLPIVIPPLLITAKATQDVGLIEEEEMNFQQYPDWDVVQV
QGKHIAIHTSVLDDKVSAMELLQSYATLLRGQFAVYVKEVMEEIALPSLDFYLHDGVRAA
GATLIPILLSCLLAATGTQNEELVLLWHKASSKLIGGLMSEPMPEITQVYHNSLVNGIKV
MG DNCLSEDQLAAFTKGVSANLT DT YERMQDRHGDG DEYNENIDEEEDFTDEDLLDE INK
SIAAVLKTTNGHYLKNLENIWPMINTFLLDNEPILVIFALVVIGDLIQYGGEQTASMKNA
FIPKVTECLISPDARIRQAASYIIGVCAQYAPSTYADVCIPTLDT1VQIVDFPGSKLEEN
RSSTENASAAIAKILYAYNSNIPNVDTYTANWFKTLPTITDKEAASFNYQFLSQLIENNS
PIVCAQSNISAVVDSVIQALNERSLTEREGQTVISSVKKLLGFLPSSDAMAIFNRYPADI
MEKVHKWFA*
A published nucleotide coding sequence of PSE1 is as 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:
ATGTCTGCTTTACCGGAAGAAGTTAATAGAACATTACTTCAGArTGTCCAGGCGTTTGCT
TCCCCTGACAATCAAATACGTTCTGTAGCTGAGAAGGCTCTTAGTGAAGAATGGATTACC
GAAAACAATATTGAGTATCTTTTAACTTTTTTGGC'TGAACAAGCCGCTTTCTCCCAAGAT
ACAACAGTTGCAGCATTArCTGCTGTTCTGTTTAGAAAATTAGCATTAAAAGCTCCCCCr
TCTTCGAAGCTTATGATrATGTCCAAAAATATCACACATATTAGGAAAGAAGTTCTTGCA
CAAATTCGTTCTTCATTGTTAAAAGGGTTTTTGTCGGAAAGAGCTGATTCAATTAGGCAC
AAACTATCTGATGCTATTGCTGAGTGTGTTCAAGACGACTTACCAGCATGGCCAGAATTA
CTACAAGCTTTAATAGAGTCTTTAAAAAGCGGTAACCCAAATTTTAGAGAATCCAGTTTT
AGAATTTTGACGACTGTACCTTATTTAATTACCGCTGTTGACATCAACAGTATCTTACCA
ATTTTTCAATCAGGCTTTACTGATGCAAGTGATAATGTCAAAATTGCTGCAGTTACGGCT
TTCGTGGGTTATTTTAAGCAACTACCAAAATCTGAGTGGTCCAAGTTAGGTATTTTATTA
CCAAGTCTTTTGAATAGTTTACCAAGATTTTTAGATGATGGTAAGGACGATGCCCTTGCA
TCAGTTTTTGAATCGTTAATTGAGTTGGTGGAATTGGCACCAAAACTATTCAAGGATATG
TTTGACCAAATAATACAATTCACTGATATGGTTATAAAAAATAAGGATTTAGAACCTCCA
GCAAGAACCACAGCACTCGAACTGCTAACCGTTTTCAGCGAGAACGCTCCCCAAATGTGT
AAATCGAACCAGAATTACGGGCAAACTTTAGTGATGGTTACTTTAATCATGATGACGGAG
GTATCCATAGATGATGATGATGCAGCAGAATGGATAGAATCTGACGATACCGATGATGAA
GAGGAAGTTACATATGACCACGCTCGTCAAGCTCTTGATCGTGTTGCTTTAAAGCTGGGT
GGTGAATATTTGGCTGCACCATTGTTCCAATATTTACAGCAAATGATCACATCAACCGAA
TGGAGAGAAAGATTCGCGGCCATGATGGCACTTTCCTCTGCAGCTGAGGGTTGTGCTGAT
GTTCTGATCGGCGAGATCCCAAAAATCCTGGATATGGTAATTCCCCTCATCAACGATCCT
CATCCAAGAGTACAGTATGGATGTTGTAATGTTTTGGGTCAAATATCTACTGATTTTTCA
TCAG^JiTGCACGTCAAGAGrTCAT-ACGCACGCCGCAGCGGCTCTGGTTAACTTT'TCTGAA
TTCGCTTCGAAGGA^TATTCrTGAGCCTTACTTGGArAGTCTATTGACAAATTTATTAGTT
TTATTACAAAGCA?i.CAAACTTTACGTACAGGAACAGGCCCTAACAACCATTGCATTTATT
GCTGAAGCTGCARAGAATAAS.™TT?.TCAAGTATTACGATACTCTAATGCCATTATTATTA
AATGTTTTGAAGGTTAACAATAAAGAT>JlTAGTGTTTTGAAAGGTAAATGTATGGAATGT
GC>ACTCTGATTGGTTTTGCCGTTGGTAAGGAAA?L»TTTCATGAGCACTCTCAAGAGCTG
ATTTCTATATTGGTCGCTTTACAAAACTCAGATATCGATGAAGATGATGCGCTCAGATCA
TACrTAGAACAAASTTGGAGCAGGATTTGCCGAATTCTGGGTGATGATTTTGTTCCGTTG
TTACCGATTGTTArACCACCCCTGCTAATTACTGCCAAAGCAACGCAAGACGrCGGTTTA
ATTGAAGAAGAAGAAGCAGCAAATTTCCAACAATATCCAGATTGGGATGTTGTTCAAGTr
CAGGGAAAACACATTGCTATTCACACATCCGTCCTTGACGATAAAGTATCAGCAATGGAG
CrArTACAAAGCTATGCGACACTTTTAAGAGGCCAATTTGCTGTATATGTTAAAGAAGTA
ArGGAAGAAATAGCTCTACCATCGCTTGACTTTTACCTACArGACGGTGTTCGrGCTGCA
SGAGCAACTTTAArTCCTATTCTATTATCTTGTTTACTTGCAGCCACCGGTACTC.AAAAC
GAGGAATTGGTATrGTTGTGGCATAAAGCTTCGTCTAAACTAATCGGAGGCTrAATGTCA
GAACCAATGCCAGAAATCACGCAAGTTTATCACAACTCGTTAGTGAATGGTATTAAAGTC
ATGGGTGACAATTGCTTAAGCGAAGACCAATTAGCGGCATTTACTAAGGGTGTCTCCGCC
A» CTTAAC TGACAC T TACGAAAG GATGCAGGAT C G C CATGG TGAT GGT GAT GAATATAAT
GAAAATATTGATGAAGAGGAAGACTTTACTGACGAAGATCrTCTCGATGAAATCAACAAG
TCTATCGCGGCCGTTTTGAA-RACCACAAATGGTCATrATCTAAAGAATTTGGAGAATATA
TGGCCTATGATAAACACArrCCrTTTAGATAATG-AACCAATTTTAGTCATTTrTGCATTA
GTAGTGATTGGTGACTTGATrCAATATGGTGGCGAACAAACTGCTASCATGAAGAACGCA
TTTATTCCAAAGGTTACCGAGTGCTTGATTTCTCCrGACGCTCGTATrCGCCAAGCTGCT
TCrTATAT.AATCGGTGTTTGTGCCCAATACGCTCCATCTACATArGCTGACGTTTGCATA
CCGACTTTAGATACACTTGTTCAGATTGTCGATrTTCCAGGCTCCAaACTGGAAGAAAAT
CGTTCTTCAACAGAGAATGCCAGTGCAGCCATCGCCAAAATTCTTTATGCATACAATTCC
AACATTCCTAACGTAGACACGTACACGGCTAATTGGTTCAAAACGTTACCAACAATAACT
GACAAAGAAGCTGCCTCATTCAACTATCAATTTTTGAGTCAATrGATTGAAAATAATTCG
CCAATTGTGTGTGCTCAATCTAATATCTCCGCTGTAGTTGATTCAGTCATACAAGCCTTG
AATGAGAGAAGTTTGACCGAaAGGGAAGGCCAAACGGTGATAAGTTCAGTTAAAAAGTTG
TTGGGATTTTTGCCTTCTAGTGATGCTATGGCAATTTTCAATAGATATCCAGCTGATATT
ATGGAGAAAGTACATAAATGGTTTGCATAA
The PSEl gene is 3.25-kbp in size. Pselp is involved in the nucjeocj'toplasinic transport
ofmacroinolecules (Seedorf & Silver, 1997, Proc. Nail Acad. Sci USA. 94, 8590-8595).
This process occurs via the nuclear pore complex (NPC) embedded in the nuclear
envelope and made up of nucleoporiiis (Ryan & Wente., 2000, Ciirr. 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, Ciar. Opin. Cell Biol 10, 392-399). Pselp is a
karyopherin/importin, a group of proteins, which have been divided up into a and (3
families. Karyopherins are soluble transport factors that mediate the transport of
rnacromolecules 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). Pselp has been identified as a karyopherin p. 14 karyopherin (3 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). Pselp 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). Pselp 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), Mstones
(Mosammaparast et al., 2002, J. Biol. Chem. Ill (1), 862-86S), 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 pselp are novel candidate targets
for growth control (Seedorf & Silver, 1997, supra}Overexpression of Pselp (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 I'Sj^l are also included in the present invention. A "variant", in
the context of PSE1. refers to & protein having the sequence of native PSE1 other than for at
one or more positions where there have been aniino acid insertions, deletions, or
substitutions, either consen'ative or-non-conservative, provided that such changes result in a
protein whose basic properties, for example enzymatic activity (type of and specific
activity), thennoslabiiity. 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 tmobvious over the ones
of the original protern.
63' "conservative substitutions" is intended combinations such as Val. lie. Leu, Ala. Met;
Asp, Glu; Asn: Gin; Ser, Thr, Gly, Ala; Lys, Arg, His; and Phe, Tyr, Trp. Preferred
conservative substitutions include Gly, Ala; Val. lie. Leu; Asp, Glu; Asn, Gin; Ser. Thr;
Lys, Arg; and Phe, Tyr.
A "variant" of PSE1 typicalty 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%,
3ret 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 rrmtagenesis 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 hornolog 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 S28729 to
829379) of the S. cerevisiae genome and encodes an evolutionarily conserved protein
with similarity to the yeast protein Ormlp. Hjelrnqvist et al, 2002, Genome Biology,
3(6), research0027.1-0027.16 reports that ORM2 belongs to gene family comprising three
human genes (ORMDL1, ORMDL2 and ORMDL3) as well as homologs in
microsporidia, plants, Drosophila, tirochordates and vertebrates. The ORMDL genes are
reported to encode transmembrane proteins anchored hi the proteins endoplasmic
reticurum (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 runicamycin and ditMothreitol.
One published sequence of Orm2p is as follows:
MIDRTKKIESPAFEESPLTPMVSNLKPFPSQSNKISTPVTDHRRRRSSSVISHVEQETFED
ENDQQMLPNMNATWVDQRGAWLIHIWIVLLRLFYSLFGSTPKWTWTLTNMTYIIGFYIM
FHLVKGTPFDFNGGAYDNLTMWEQINDETLYTPTRKFLLIVPIVLFLISNQYYRNDMTLF
LSNLAVTVLIGWPKLGITHRLRISIPGITGRAQIS*
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 nucltolide sequences which encode
an identical protein product:
ATGATTGACCGCACTAAAAACGAATCTCCAGCTTTTGAaGAGTCTCCGCTTACCCCCA?iT
GTGrCTAACCTGAAACCATTCCCTTCTCAAA.GCAACAAAATATCCACTCCAGTGACCGAC
CATAGGAGAAGACGGTCATCCAGCGTAATATCACATGTGGAACAGGAAACCTTCGAAGAC
GMAATGACCAGCAGATGCTTCCCAACATGA.ACGCTACGTGGGTCGACCAGCGAGGCGCG
TGGTTGATTCATATCGTCGTAATAGTACTCTTGAGGCTCTTCTACTCCTTGTTCGGGTCG
ACGCCCAAATGGACGTGGACTTTAACAAACATGACCTACATCATCGGATTCTAT-ATCATG
TTCCACCTTGTCAAAGGTACGCCCTTCGACTTTAACGGTGGTGCGTACGACAACCTGACC
ATGTGGGAGCAGATTAACGATGAGACTTTGTACACACCCACTAGAAAATTTCTGCTGATT
GTACCCATTGTGTTGTTCCTGATTAGCAACCAGTACTACCGCAA.CGACATGACACTATTC
CTCTCCAACCTCGCCGTGACGGTGCTTATTGGTGTCGTTCCTAAGCTGGGAATTACGCAT
AGACTAAGAATATCCATCCCTGGTATTACGGGCCGTGCTCAAATTAGTTAG
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 arnhio 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 Avould not be unobvious over the ones •
of the original protein.
By "conservative substitutions" is intended combinations such as Val, He, Leu, Ala, Met;
Asp, Giu; Asn, Gin; Ser, Thr, Gly, Ala; Lys, Arg, His; and Phe, T)?, Trp. Preferred
conservative substitutions include G]y, Ala; Val, lie. Leu; Asp, Glu; Asn, Gin; Ser, Tlir;
Lys, Arg; and Phe, T}?.
A "vaiiant" of ORM2 topically has at least 25%, at least 50%, at least 60% or at least 70%,
preferabl)7 at least §0%, 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 MI
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 ma}' be a protein that, when expressed recom.bman.tly 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 valiants thereof. Preferably the albumin has the amino acid
sequence disclosed in "WO 90/13633 or a variant thereof. The HSA coding sequence is
obtainable by Icnown 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 arnino 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 albumin1' also includes the meaning of fragments of full-length bovine
serum albumin or variants thereof, as defined below.
In another preferred embodiment the albmrun is an albumin derived from (i.e. lias 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
073860), 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 ovalburnin) (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 Sigrna 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 nranber 089020), pigeon (e.g. as defined by Khan el al, 2002. Ini. J.
Biol. MacromoL, 30(3-4),!71-8), 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.
Man)' 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, California., p.170-1 SI). A variant as defined above
be one of these naturally occurring mutants.
A "variant albumin" refers to an albumin protein wherein at one or more positions there
have been amiuo acid insertions, deletions, or substitutions, either conservative or nonconservative,
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
bilinibin), osmolarity (oncotic pressure, colloid osmotic pressure), behaviour in a certain
pH-raiige (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, lie, Leu;
Asp, Glu; Asn, Gin; 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 US
Patent No 4,302,386 issued 24 November 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 albirmin. 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 aiot significantly been changed.
"Significant!}'" in this context means- that one skilled in the ait would say thai 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 ma}'
comprise at least one whole sub-domain of albumin. Domains of HSA have been
expressed as recombinant proteins (Dockal, M. ef a?., 1999., J. Eiol. Chem., 274, 29303-
29310), where domain I was defined as consisting of amino acids 1-197, domain II was
defined as consisting of arnino acids 189-385 and domain HI was defined as consisting of
amino acids 381-5S5. Partial overlap of the domains occurs because of the extended ahelix
structure (hlO-hl) which exists between domains I and n, and between domains II
and III (Peters, 1996, op. cit, Table 2-4). HSA also comprises six sub-domains (subdomains
LA, IB, HA, HJ3, IDA and IHB). Sub-domain LA. comprises amino acids 6-105,
sub-domain IB comprises amino acids 120-177, sub-doinaia HA comprises aminn acids
200-291, sub-domain HB comprises amino acids 316-369, sub-domain IHA comprises
amino acids 392-491 and sub-domain IHB 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 pohynucleotide 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 msy include within its genome a potynueleotide sequence
encoding a protein comprising the sequence of transferrin or a variant or fragment
thereof, either as an endogenous or heterologous sequence.
Tie term "rransferrin" as used herein includes all members of the traiisferrin family
(Testa, Proteins of iron metabolism, CRC Press. 2002; Harris & Aiseii, 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 a!, 1998, Biochem. J., 330(1), 35), truncated transfemns, 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, polypepticles or proteins (Shin et al, 1995, Proc.
Natl. Acad. Sci. USA, 92, 2820; Ali et al, 1999, J. Biol Ckem., 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 transfenin 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 hi the invention. Such mutants may have altered
irrrmunogenicity. 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 ammo acid glycosylation consensus sequences such as NX-
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 transferring 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 470nm:280nm
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, lOmM EDTA pH4.5. Protein
should be at approximately 20mg/mL in lOOmM HEPES, lOrnM NaHC03 pHS.O.
Measure the 470nm:280nm absorbance ratio of apo-transferrin (Calbiochem, CN
Biosciences, Nottingham, UK) diluted in water so that, absorbance at 280nm can be
accurately determined spectrophotometrically (0% iron binding). Prepare 20mM iron-
nitrilotri acetate (FeNTA) solution by dissolving I9hng nitroiriaceiic acid in 2mL ]M
NaOH, then add 2mL 0.5M fenic chloride. Dilute to 50mL with deionised watex. Full}'
load apo-transfenin with iron (100% iron binding) by adding a sufficient excess of
freshly prepared 20rnM FeNTA. then dialyse tlie halo-transferriii preparation completely'
against lOQmM HEPES, lOmM NaHC03 pHS.O to remove remaining FeNTA before
measuring the. absorbance ratio at 47Gnrn:280nm. Repeat the procedure using lest
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, transfenin or hnmunoglobins. or a
variant or fragment of any of these may be used. Such fusions include albumin Nterminal
fusions, albumin C-terrninal fusions and co-N-temiinal and C-terminal albumin
fusions as exemplified by WO 01/79271, and transfenin N-terminal fusions, transferrin
C-terminal fusions, and co-N-terminal and C-terminal transfenin fusions.
The skilled person will also appreciate that the open reading frame of airy other gene or
variant, or part or either, can be utilised to form a whole or part of an open reading frame
in fanning a pohoiucleotide sequence insertion for use with the present invention. For
example, the open reading frame may encode a protein comprising an}'- sequence, be it a
natural protein (including a zymogen), or a variant, or a fragment (winch may. for
example, be a domain) of a natural protein: or a totally s}'nthetic protein; or a single or
multiple fusion of different proteins (natural or synthetic). Such proteins can be talc en,
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 b}' 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 ma}' be presented alone or as fusion partners
for albumin, the Fc region of urummoglobului, transfenin., lactofenin or an}' other protein
or fragment or variant of any of the above, including fusion proteins comprising any of
the above, as a desired pohypeptide. Further examples of transfenin 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, angio statin, collagens, immuiio globulins or
immunoglobulin-based molecules or fragment of either (e.g. a Small Modular
ImmmioPhaiinaceutical™ ("SMTP") or dAb, Fab' fragments, F(ab')2, scAb, scFv or scFv
fragment), a Kmiitz domain protein (such as those described hi WO 03/066824-, with or
without albumin fusions) interferons, interleuldns, IL10, IL11, IL2, interferon a species
and sub-species, interferon P species and sub-species, interferou y species and subspecies,
leptin, CNTF, CNTFAxis, IL1-receptor antagonist, erythropoetin (EPO) and EPO
mimics, thrombopoetin (TPO) and TPO mimics., prosaptide, cyanovirin-N, 5-helix, T20
peptide, T1249 peptide, HTV gp41, HTV gp!20, uroldnase, prourolcinase, tPA (tissue
plasminogen activator), hirudin, platelet derived growth, factor, parathyroid hormone,
pro insulin, insulin, glucagon, glucagon-lilce peptides, insulin-like growth factor,
calcitonin, growth honnone, transforming growth factor (3, tumour necrosis factor, GCSF,
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, ai-antitrypsin, plasminogen activators, Factor VIE, Factor VIII,
Factor IX, Factor X and Factor XTfl, 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 Mrudin.
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 vmobvious over the ones of
the original protein.
By "conservative substitutions" is intended combinations such as Val. He. Leu. Ala, Met;
Asp. Glu; Asa, Gin; Ser, Thr, Gly, Ala; Lys, Arg. His: and Phe, 131', Trp. Preferred
conservative substitutions include Gly. Ala.; Val, lie. Leu; Asp, Glu: Asn, Gin: 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
st al, (1994) Nucleic Acids Res., 22(22), 4673-80). The parameters used imy be as
follows:
• Fast pairwise alignment parameters: K-tuplefword) 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 engmeering and sitedirected
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 ma}' comprise at most 5,103
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 plasrnid 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, hi 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 ma}' 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: 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 2jim-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 pofynucleotide sequence
into the plasmid at a position according to the first, second or third prefen-ed
aspects of the invention; and/or
(c) additionally or as an alternative to step (b). deleuug some or all of the riucleotide
bases at the positions according to the first, second or third preferred aspects of
the invention: and/or
(d) additionall}' or as an alternative to either of steps (b) and (c). substituting some or
all of the nucleoti.de 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 niutagenesis and the lice, such as are described in b}'
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 engines. These ends
will rapidly anneal through complementary base pairing and remaining nicies 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 ~bj bacteriophage T4 DNA porymerase or E. call
DNA polyrnerase I which remove protruding 3' termini and £11 in recessed 3s ends.
Synthetic linkers and pieces of blunt-ended double-stranded DNA, which contain
recognition sequences for defined restliction 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
tenrrini. Adaptors are also chemically synthesised DNA fragments which contain one blunt
end used for hgation 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 S}'nthetic 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 Sigrna-Genosys Ltd, London Road,
Pampisfordj Cambridge, United Kingdom.
According]y, 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 ceils 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
(Me et al, 1991, Gene, 108(1), 139-144; Me et al, 1991, Mol Gen. Genet, 225(2), 257-
265). For example, pSRl from Zygosaccharomyces rouxii can be maintained in
Saccharomyces cerevisiae. Where the plasmid is based on pSRl, pSB3 or pSB4 the host
cell may be Zygosaccharomyces rouxii, where the plasmid is based on pSBl or pSB2 the
host cell may be Zygosaccharomyces bailli, where the plasmid is based on pPMl the host
cell may be Pichia membranaefaciens, where the plasmid is based on pSMl the host cell
may be Zygosaccharomyces• fermentati, where the plasmid is based on pKDl the host cell
may be Kluyveromyces drosophilarum and where the plasmid is based on the 2|im
plasmid the host cell may be Saccharomyces cerevisiae or Saccharomyces
carlsbergensis. A 2um-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,
REPJ and RJEP2 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 eta! (1972)
Proc, Natl. Acad. Sci. USA 69, 2110 and Sarnbrook et al (2001) Molecular Cloning, A
Laboratory Manual, 3rd Ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
Transformation of yeast cells is described in Sherman et al (1986) Methods In Yeast
Genetics, A Laboratory Manual, Cold Spring Harbor, NY. 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 arid WO 90/01063, all of which are
incorporated herein by reference. With regard to vertebrate cells, reagents useful in
transfecting such cells, fox example calcium phosphate and DEAE-dextran or liposome
formulations, are available from Stratageue Cloning Systems, or Life Technologies Inc.,
Gaithersburg, I\dD 20877, USA.
Electroporation is also useful for transfonning cells and is well known, in the art for
transfonning yeast cell, bacterial cells and vertebrate, cells. Methods for transformation of
yeast by electroporation axe disclosed in Becker & Guarente (1990) Methods En^nnol 194,
182.
Generally, the plasmid will transform not all of "die 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 ms.y 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 j^east selectable marker. A typical bacterial
selectable marker is the p-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 p-lactamase malate dehydrogenase), TRP1, HISS, H1S4, URA3,
URA5, SFA1, ADE2, METIS, L7S5, 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 an)' 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 apgkl yeast strain (Piper
and Curran, 1990, Curr. Genet. 17, 119). Suitable essential genes can be found within
the Stanford Genome Database (SGD). http:://db.yeastgenorne,org).
Additionally, a plasmid according to any one of the first, second or third aspects of the
present invention ma]' 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, Avith 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 tetrac3'clin, kanamycin or ampicillin (i.e. (3-
lactamase) resistance genes for culttuing in Kcoli 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 recornbinant 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 recornbinant 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 ait
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 recornbinant DNA, successful
transformation can be confirmed by well known irnmunological methods when the
recornbinant 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.
L
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 iised 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,
5 sucli as fragrances, flavours and phamiaceuticals.
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 an}' ORF(s) in the one or more polynucleotide sequence
10 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
15 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
subnlis], yeasts, filamentous fungi (for example Aspergilhis], plant cells, whole plants,
20 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, J&vyvercmiyces lactis, Pichia pastoris, Zygosaccharomyces rouxii,
25 Zygosaccharojnyces bailli, Zygos-accharomyces ferm.enta.ti, 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,
30 as measured by the loss of the marker, is at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%,
25%, 30%, 40%5 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, SO, 90, 100 or more
PCT/GB 2004 / 0 0 5 4 3 5
WO 2005/061719 PCT/CB2004/005435
^ generations. Loss of a marker can be assessed as described above, with reference to
Chinery & Hinchliffe (1989, Cior. Genet, 16, 21-25).
It is particularly advantageous to use a yeast deficient in one or more protein rnannosyl
5 transferases involved in 0-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
10 does not contain any sites for N-linked glycosylation and has not been reported to be
modified., in nature, by 0-linked glycosylation. However, it has been found that
recombinant human albumin ("rHA") produced in a number of yeast species can be
modified by 0-linked glycosylation, generally involving mannose. The mannosylated
albumin is able to bind to the lectin Concanavalin A. The amount of mannosylated
15 albumin produced by the yeast can be reduced by using a yeast strain deficient in one or
more of the PMT genes (WO 94/04687). 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
Pint 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
20 regulating the expression of one of the PMT genes) such that little or no Pint protein is
produced. Alternatively, the yeast could be transformed to produce an anti-Pmt agent,
such as an anti-Pmt antibody.
If a 3'east other man S. cerevisiae is used, disruption of one or more of the genes
25 equivalent to the PMT genes of S. cerevisiae is also beneficial, e.g. in Pichia pastoris or
Khiyveromyces lactis. The sequence of PMTl (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 PMTl homologue of
Kluyveromyces lactis is described in WO 94/04687.
The yeast will advantageously have a deletion of the HSP150 and/or YAPS genes as
taught respectively hi WO 95/33833 and WO 95/23857.
58
The preseirl application also provides a method of producing, a protein comprising the
steps of providing a host ceil as defined above,, which host cell comprises a plasniid 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 periplasrnic 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 lipophihc phase; and WO '96/37515, US 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
chrornatography, hydrophobia interaction chromatography, affinity chromatograplxy,
hydroxylapatite chromatography., lectin chromatograprry, concentration, dilution, pH
adjustment, diafiltration, ultrafiltration, high performance liquid chromatography ("HPLC"),
reverse phase HPLC, conductivity adjustment and the like.
hi 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'J, 0.02 g.L"1, 0.03 g.L'3, 0.04 g.L"1, 0.05 g.L~].,0,06 g.L"
],0.07 gU\ O.OS gr1, 0.09 g.U\ 0.1 g.1/1, 0.2 gL~\ 0.3 gU1, 0.4 g.L'1, 0.5 g.L"3, 0.6 g.L'1,
59
0.7 g.1/1, 0.8 g.L-', 0.9 g.1/1, 1 gX-', 2 g.1/1, 3 g.L'1, 4 g.1/1, 5 gi;1, 6 gl"1, 7 g.I/1, S g.U9 gX-1, 10 gX-1, 15 gX-1, 20 g.1/1, 25 gX'1, 30 gX'1, 40 g-I/'pO gX'1, 60 gL'1, 70 g.L'1, 70
g.1/1, 90 g.L/1, 100 g.1/1, 150 gX-1, 200 g.L/1 ,250 g.L'1, 300 g.L/1, 350 g.1/1, 400 g.1/1, 500
gX"1, 600 g.L/1, 700 g.1/1, 800 g.1/1, 900 g.L/1, 1000 gX'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 bums, shock aad 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 canier(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 rilasTrn'd-bnme gene
sequence of an "essential" protein can be used to stably maintain the plasrnid 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 Tecombinant gene within the host cell. This system is advantageous because it allows
the use]- to minimise the number of recornbrnant genes that need to he carried by a
plasniid. For example, typical prior art plasmids carry marker genes (such as those as
described above) thai enable the plasniid to he stably maintained during bost cell
culturing process. Such marker genes need to be retained on the plasmid in addition to
any further gexies 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 ctilturing 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 grcnvth or
protein production, or may require inefficient or unduly expensive growth systems to be
used.
Thus, it is possible to use a gene that recombin.an.tly encodes a protein comprising the.,
sequence of an "essential protein" as a plasmid-bome 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
(bios3rnthetic) requirement. By "auxotrophic (bios37nthetic) requirement" we include a
deficiency that can be complemented by additions or modifications to tbe 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 S3rstem 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-
61
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 plasrnid 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 s)rsteni also has
the advantage that it minimises the number of recombinant genes that need to be
earned by the plasrnid 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 hi the host cell developing an auxotrophic
(biosynthetic) requirement.
Accordingly, in a fourth aspect, the present invention also provides a host cell comprising
a plasrnid (such as a plasrnid according to any of the first, second or third aspects of the
invention), the plasrnid 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 plasrnid 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 ma)-' be a 2urn-famihr
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
lieterologous 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, lyopMlising the thus purified protein.
The method ma}' further comprise the step of formulating the purified heterologous
protein with a carrier or diluent and optional!}7 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
Figure 1 shows a plasmid map of the 2 urn plasmid.
Figure 2 shows a plasmid map of pSAC35.
Figure 3 shows some exemplified FLP insertion sites.
Figures 4 to 8,10,11,13 to 32, 36 to 42, 44 to 46, 4S to 54 and 57 to 76 show maps of
various plasmids.
Figure 9 shows the DNA fragment from pDB2429 containing the PD11 gene.
Figure 12 shows some exemplified REP2 insertion sites,
Figure 33 shows table 3 as referred to in the Examples.
Figure 34 shows the sequence of SEQ ID NO: 1.
Figure 35 shows the sequence of SEQ ID NO: 2.
Figure 43 shows the sequence of PCR primers DS248 andDS250.
Figure 47 shows plasmid stabilities with increasing number of generation growth in nonselective
liquid culture for S. cerevisiae containing various pSAC35-derived plasmids.
Figure 55 shows the results of RIB. lOmL YEPD shake flasks were inoculated with
DXY1 trplA [pDB2976], DXY1 trplA [pDB2977], DXY1 tiplA [pDB2978], DXY1
trplA £pDB2979], DXY1 ti-plA [pDB2980] or DXY1 trplA [pDB2981] transformed to
tryptophan prototrophy with a 1.41kb Notl/Pstl pdil::TKPl disrupting DNA fragment
was isolated from pDB3078. Transformants were grown for 4-days at 30°C, 200rpm.
4jiL 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 p.g/mL. 700uL
Precipin was stained with Uoomassie blue. isolates seiecieu iur mruicr auaiysiis are
indicated (*)•
Figure 56 shows the results of RJE. lOmL YEPD shake flasks were inoculated with
DXY1 [pDB2244], DXY1 [pDB2976], DXY1 trplA pdil;:TRPl [pDB2976], DXY1
[pDB2978], DXY1 trplA pdil::TRPl [pDB2978], DXY1 [pDB2980]5 DXY1 trplA
pdil::TRPl [pDB2980], DXY1 [r,DB2977], DXY1 ti-plA pdil::TRPl \pDB2971],
DXY1 [pDB2979] DXY1 trplApdil::TKPl [pDB2979], DXY1 [pDB2981] and DXY1
trplApdil::TRPl [pDB2981]3 and were grown for 4-da}'s at 30°C, 200ipm. 4(j,L culture
supernatant loaded per well of a rocket ummmoelectrophoresis gel. rHA standards
concentrations are in ug/mL. SOOuL goai anti-HA (Sigma product A-l 151 resuspended
in 5mL water) /50mL agarose. Precipm was stained with Coomassie blue. Isolates
selected for furthei 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 2jj.rnfamily
plasmid, of the type shown hi Figure 2 and generally designated pSAC355 which
includes a |3-lactarnase gene (for ampicillin resistance, which is lost from the plasmid
following transformation into 3?east), a LEU2 selectable marker and an oligonucleotide
linlcer, the latter two of which are inserted into a unique SnaBI-site within the UL-region
of the 2}4.m-farrhly disintegration vector, pSACS (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 nonselective
media. Preferred sites for DNA insertions were identified. Insertion of larger
DNA fragments containing "a gene of interest" was demonstrated b}^ inserting a DNA
fragment containing the PDJ1 gene into the Ac/nl-site after REP2.
EXA1S1PLE 1
Insertion of Synthetic DNA Linker into Xcml-Sites in the Small Unique Region of
pSACSS
Sites assessed initially for insertion of additional DNA into the US-region of pSAC35.
were the JLcml-sites in the 599-bp inverted repeats. One JTcml-site cuts 51-bp after the
REP2 translation termination codon, whereas the other Xcml-site cuts 127-bp before the
end of the FLP coding sequence, due to overlap with the inverted repeat (see Figure 3).
The sequence inserted was a 52-bp linker made by annealing oligonucleotides CF86 and CF87. This DNA linker contained a core region "SndBIPacI-
Fsel/Sfil-Smal-SnaBl", which encoded restriction sites absent from pSAC35.
Xcml Linker rCF86+CF87)
Sfil
Pad SnaBI
SnaBI Fsal Smal
CF86 GGAGTGGTA CGTATTAATT AAGGCCGGCC AGGCCCGGGT ACGTACCAAT TGA
CF87 TCCTCACCAT GCATAATTAA TTCCGGCCGG TCCGGGCCCA TGCATGGTTA AC
Plasmid pSAC35 was partially digested with Xcml, the linear 11-lcb fragment was
isolated from a 0.7%(w/v) agarose gel, ligated with the CFS6/CFS7Xcml linker (neat, 10"
1 and 10"2 dilutions) and transformed into E. coll DH5a. Ampicillin resistant
transformants were selected and screened for the presence of plasmids that could be
linearised by Smal digestion.v Restriction enzyme analysis identified pDB2688 (Figure 4)
with the linker cloned into the Jfowl-site after REP2. DNA sequencing using
oligonucleotides primers CF88, CF98 and CF99 (Table 1) confirmed the insertion
contained the correct linker sequence.
Table 1: Oligonucleotide sequencing primers:
(Table Removed)
Restriction enzyme anafysis also identified pDB2689 (Figure 5), with the linker cloned
into the Xcml-silz in the PLP gene. However, the. linlcer in pDB2689 was sho^vn by DNA
sequencing using primers CF90 and CF91 to have a missing G:C hase-pair within, the
FseUSfil site (marked above in bold in the CFS6-J-CFS7 linker). This generated a coding
sequence for a mutant Pip-protein, with 39 C-terminal amino acid residues replaced loy 56
different amino acids before the translation termination codon.
The missing base-pair in the pDB2689 linker sequence was corrected to produce
pDB27S6 (Figure 6). To achieve this, a 31-bp 5'-phosphoiylated Sjia'BI-lmk&i was made
67
from oligonucleotides CF104 and CF105. This was ligated into the SnaBl site of
pDB2689, which had previously been treated with calf intestinal alkaline phosphatase.
DMA sequencing with primers CF90, CF91, CF100 and CF101 confirmed the correct
DNA linker sequence in pDB2786. This generated a coding sequence for a mutant Flpprotein,
with 39 C-temoinal residues replaced by 14 different residues before translation
termination.
SndBI Linker rCF104+CF105)
Sfil
Fsel
Pad Smal
CF104 P1-GTA.TTAATTA AGGCC6GCCA GGCCCGGGTA C
CF105 CATAATTAAT TCCGGCCGGT CCGGGCCCAT G-Pi
An. additional plasmid, pDB2798 (Figure 7), was also produced by ligation of the
linker in the opposite direction to pDB2786. The linker sequence in pDB2798 was
coiafirmed by 33NA 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 JTcml-site in the FLP gene to truncate the Flp protein at
the site of insertion. The linker used was a 45 -bp 5'-phosphorylated JTeml-linker made
from oligonucleotides CF120 and CF121.
Xcml Linker rCF120+CF121)
Sfil
Pad SnaBI
SnaBI Fsel Smal
CF120 Pi-GTAATAATA CGTATTAATT AAGGCCGGCC AGGCCCGGGT ACGTAA
CF121 TCATTATTAT GCATAATTAA TTCCGGCCGG TCCGGGCCCA TGCAT-Pi
This CF120/CF121 Xcml linker was ligated with 11-kb pSAC35 fragments produced by
partial digestion with Xcml, followed by treatment with calf intestinal alkaline
phosphatase. Analysis of ampicilHn resistant K coli DH5a transformants identified
:lons£ containing pDB2823 (Figure 8). DMA sequencing with primers CF90. CFP1.
CF100 and CF]f)3 confirmed the linker sequence in pDB2823. Translaiion temiination
witlini the linlcer inserted would result in the production of Flp (1-382), which lacked 41
C-tenninal residues.
The impact on plasmid stability from insertion of linlcer sequences into the J£c7j?I-sites
within the US-region of pSAC35 was assessed for pDB2688 and pDB26S9. Plasmid
stability' was determined in a S. cerevisiae strain by loss of the LEU2 marker during nonselective
grown, on YEPS. The same yeast strain, transformed with pSAC35, which is
structuraUy similar to pSAC3, but contains additional DNA inserted at the SndQl site that
contained &LEU2 selectable marker (Chinery & Hinchliffe, 1989, Cwr. 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.
BacferioL, 153, 163; Bible, 1992. Bioteclmiques, 13, IS)). Transformants were selected
on BMMD-agar plates, and were subsequent!}' patched out on BMMD-agar plates.
Cryopreserved trehalose stocks were prepared from lOmL BMMD shake flask cultures
(24hrs530°C,20Qipm).
The composition of YEPD and BMMD is described by Sleep et a!., 2002, Yeast IB, 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 ImL Cryopreserved stock was thawed and
inoculated into lOOinL YEPS (initial OD6oo ~ 0.04-0.09) in a 250mL conical flask and
grow for approximately 72 hours (70-74 hrs) at 30DC 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 ID"3 dilution), and
lOOuL 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. BMMSagar
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 pDB26S9 was 72% stable.
Hence, insertion of the linker into the Xcml-site after £EP2 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 Xcml-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 ofthePDIl Gene, into the XanILinker ofpDB2688
The insertion of a large DNA fragment into the US-region of 2(.un-lilce vectors was
demonstrated by cloning the S. cerevisiae PDI1 gene into the A'cml-linker of pDB2688.
The PDI1 gene (Figure 9) was cloned on a 1.9-kb SacI-Spel 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 US 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 Sad restriction site inserted at a unique Bsit3 61-
site in the 3' untranslated region of the PDI1 gene. The 1.9-kb Sacl-Spel fragment was
treated with T4 DNA polymerase to fill the Spel 5'-overhang and remove the iSizcI 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 Smal linearised/calf intestinal alkaline phosphatase treated
pDB2688, to create plasmid pDB2690 (Figure 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. N6I1Q) was
subsequently cloned into the jVo/I-site of pDB2690 to create pDB27J I (Figure 1 ]). The
expression cassette in pDB2711 contains the S. cerevisiae PRB] promoter, an HSA/MFa
fusion leader sequence (EP 387319; Sleep el al 1990, Bio1eclmolog)> (N.Y.), 8, 42)
followed by a coding sequence for the human transferrin mutant (N413Q, N611Q) and
the S. cerevisiae ADHJ terminator. Plasmid pDB253b (Figure 36) was constructed
similarly by insertion of the same expression cassette into the Nofl-site of pSAC35.
The advantage of inserting "genes of interest" into the US-region of 2jam-vectors was
demonstrated by the approximate 7-fold increase in recombinant transferrin N413Q,
N611Q secretion during fermentation of )feast transformed with pDB2711, compared to
the same yeast transformed with pDB2536. An approximate 15-fold increase in
recombinant transfenin N413Q, N611Q secretion was observed in shake flask culture
(data not shown).
The relative stabilities of plasmids pDB2688, pDB2690a 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 PD11 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 JVorl-site within the large unique region of pSAC35 (Table 2).
Furthermore, selective growth in minimal media during high cell density fennentations
could overcome the increased plasmid instability due to the PDI1 insertion observed in
YEPS medium, as the rTF (N413Q, N611Q) 37ield from the same yeast transformed with
pDB2711 did not decrease compared to that achieved from the same yeast transformed
with pDB2536.
Table 2: region of pS ACS 5. Data from 3 days growth in non-selective shake flask culture before
plating on YEPS-agar.
(Table Removed)
EXAMPLES
Insertion of DNA Linkers into the JREP2 Gene and Downstream Sequences in the
Inverted Repeat ofpSA C35
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. Figure 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 Xmnl-site in REP2 was a 44-bp sequence made from
oligonucleotides CF108 and CF109.
.Ymrcl Linlcer fCFl 08+CF1 09)
Pad
SnaEI Fsel Swal
CF10E: ATAATAATAC GTATTAATTA AGGCCGGCCA GGCCCGGGTA CGTA
CF109 TATTATTATG CATAATTAAT TCCGGCCGGT CCGGGCCCAT GCAT
To avoid insertion into other Amjd-sites in pSAC35. the 3,076-bp Xbal fragment from
pSAC35 that contained the REP2 and FLP genes was first sub-cloned into the E. call
clearing -vector pDB2685 (Figure. 13) to produce pDB2783 (Figure 14).
Plasmid pDB2685 is a pU CIS-like cloning vector derived from pCF17 containing
apramycin resistance gene aac(3)IV from Klebsiella pneumonias (Rao el al, 1983.,
Antimicrob. Agents Chemother., 24, 689) and multiple cloning site from pMCSS
(Hoheisel, 1994, Biotechmques, 17, 456). pCF17 was made from pIJ8600 (Sun et al,
1999, Microbiology, 145(9), 2221-7) by digestion with EcoRl, Nliel and the Klenow..
fragment of DNA polymerase I. and self-ligation, followed by isolation from the reaction
products by transformation of competent E. col: DH5a cells and selection with
apramycin sulphate. Plasmid pDB2685 was constructed by cloning a 439bp Sspl-Swal
fragment from pMCSS into pCF17, wliich had been cut with Msd and treated with calf
intestinal alkaline phosphatase. Blue/white selection is not dependant on IPTG induction.
Plasmid pDB2783 was linearised with AM and ligated with the CF108/CF109 Xmnllinker
to produce pDB2799 (Figure 15) and pDB2780 (not shown). Plasmid pDB2799
contained the CF108/CF109 Xmnl linlcer in me correct orientation for translation
tennination at the insertion site to produce Rep2 (1-244), whereas pDB27SO contained
the linlcer cloned in the opposite orientation. DNA sequencing with primers CF98 and
CF99 confirmed the correct linlcer sequences.
The 3,120bp Xbal fragment from pDB2799 was subsequently ligated with a 7,961-bp
pSAC35 fragment which had been produced by partial Xbal digestion and treatment with
calf intestinal alkaline phosphatase, to create plasmid pDB2817 (B-foim) and pDB2818
(A-form) disintegration vectors ("Figures 16 and 17 respecth^ely).
Insertion of linkers at the Apal-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 Apal digestion resulting in removal of nucleotides from the codons for
Glycine-170 (GGC) andProline-171.
Thr He Thr GIu
ACCATCACT
TGGTAGTGA
Apal
The linker inserted at the Apal-site without exonuclease digestion was a 50-bp
5'-phosphorylated linker made from oligonucleotides CF116 and CF117.
^pal-Linker fCF116+CFl 17)
Sfil
Pad SnaBI
SnaEI Fsel Smal
CF116 Pi-CTTAAT AATACGTATT AATTAAGGCC GGCCAGGCCC GGGTACGTAG GGCC
CF117 CCGGGAATTA TTATGCATAA TTAATTCCGG CCGGTCCGGG CCCATGCATC-Pi
This was ligated with pSACSS, which, had been linearised with Apal and treated with calf
intestinal alkaline phosphatase, to produce pDB2788 (Figure 18) and pDB2789 (not
shown). Within pDB278S, the linker was in the correct orientation for translation
termination after proline-271, whereas hi pDB2789 the linker was in the opposite
orientation.
The linker inserted at the Apal-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.
Core. Termination-Linker CCF106+CF107')
Sill
Ps cl S.naB:
SnaEI Fsei Smal
CF106 Pi-TAATAATACG TATTAATTAA GGCCGGCCAG GCCCGGGTAC GTA
CF107 ATTATTATGC ATAATTAATT CCGGCCGGTC CGGGCCCATG CAT-Pi
The core termination linker was ligaied with pSAC.35, which had been linearised with
Apal, digested with T4 DNA polymerase and treated with calf intestinal alkaline
phosphatase. This ligation produced pDB2787 (Figure 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 Apdl-\ink.Krs,
using oligonucleotide primers CF98 and CF99.
The core termination linker (CF106-+CF107) was also used for insertion into the pisites
of pDB2783 (Figure 14), The core terrnination linker (CF106-I-CF107) was ligated
into pDB2783 linearised by partial Fspl digestion, which had been treated with calf
intestinal alkaline phosphatase. Plasmids isolated from apramycin resistant E. coll DH5a
transformants were screened by digestion with Fspl, and selected clones were sequenced
with Ml3 forward and reverse primers.
Plasrnid pDB2801 (not shown) was identified containing two copies of the linker cloned
in the ccorect orientation (with the Pad-site nearest the REP 2 gene). The extra cop}' of
the linker was subsequent!}7 removed b}; first deleting a 116-bp Nrnl-Hpal fragment
containing an T^el-site from the multiple cloning site region, followed by digestion with
Fsel and re-ligation to produce pDB2802 (Figure 20). DNA sequencing using
oligonucleotide CF126 confirmed the correct linker sequence.
The 3,119-bp pDB2802 Xbal fragment was subsequently ligated with a 7,961-bp
pSAC35 fragment produced by partial Xbal digestion and treatment with calf intestinal
alkaline phosphatase to create pDB2805 (B-fonn) and pDB2806 (A-form) disintegration
vectors (Figures 21 and 22, respectively)-
EXAMPLE 4
Insertion of DNA Linkers into the FLP Gene and Downstream Sequences in the
Inverted Repeat ofpSAC35
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.
Figure 3 indicates the restriction sites used for these insertions and the affects on the Flp
protein of translation teamination at these sites.
The linker inserted at the JBc/I-site was a 49-bp 5'-phosphorylated linker made from
oligonucleotides CF118 and CF119.
ffcfl Linker (CF118+CF119)
Sfil
Pad SnaBI
S.naBI Fsel Smal
CF118 Pi-GATCACTAATAATACGTATTAATTAAGGCCGGCCAGGCCCGGGTACGTA
CF119 TGATTATTATGCATAATTAATTCCGGCCGGTCCGGGCCCATGCATCTAG-Pi
Due to Dam-methylation of the .BcZI-site rn pSAC35, the 5c/I-linker was cloned into nonmethylated
pSAC35 DNA, which had been isolated from the K coli straia 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
Bell, treated with calf intestinal alkaline phosphatase, and ligated with the 5c/l-linker to
create pDB2816 (Figure 23). DNA sequencing with oligonucleotide primers CF91 and
CF100 showed that three copies of the .Sc/I-lmker were present in pDB2816, which were
all in the correct orientation for translational termination of Flp after histidine-353.
Digestion of pDB2816 with Pad followed by self-ligation, was performed to produce
pDB2814 and pDB2815, containing one and two copies of the .Bc/I-linker respectively
(Figures 24 and 25). The DNA sequences of the linkers were confirmed using primers
CF.9] and CF100. In S. cercvisiae a truncated Fip (1-353) protein will be produced by
yeast transformed with pDB2814, pDB2815 or pDB2Sl 6.
An additional plasmid pDB2846 (data not shown) was also produced by ligation of a
single copy of the JJc/l-linker hi 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 Hgal-site, was a 47-bp 5 '-phosphorylated linker made from
oligonucleotides CF114 and CF115.
JfegJ Linker CCF114+CF115)
Sfil
Pad SnaBI
5naBI Fsel Smal
CF114 Pi-AGTACTATAAIACGTATTAATTAAGGCCGGCCAGGCCCGGGTACGTA
CF115 ATATTATGCATAATTAATTCCGGCCGGTCCGGGCCCATGCATTCATG-Pi
The Hgal-linker was ligated with pDB27S3, which had been linearised b}' partial Hgal
digestion and treated with calf intestinal allcalrne phosphatase. to create pDB2811 (Figure
26). DNA sequencing with oh'gonucleotides CF90, CF91 and CF100 confirmed the
correct hnker insertion.
The 3,123-bp Xbal fi-agment from pDB2Sl 3 was subsequently ligated with the 7,961-bp
pSAC35 fragment, produced by partial Xbal digestion and treatment with calf intestinal
alkaline phosphatase to produce pDB2S12 (B-form) and pDB2S13 (A-form)
disintegration vectors containing DNA inserted at the Hgal-site (Figures 27 and 28
respectively).
Plasmids pDB2S03 and pDB2S04 (Figures 29 and 30, respectively) with the core
termination linker (CF106+CF107) inserted at the Fspl after FLP, were isolated by the
same method used to construct pDB2801. The correct liiiker insertions were confirmed
by DNA sequencing, Plasmid pDB2S04 contained the linker inserted in the correct
orientation (with the Pad-site closest to the FLP gene), whereas pDB2803 contained the
linker in the opposite orientation.
The pDB2804 3,119-bp Xbal fragment was ligated with the 7,961-bp pSAC35 fragment
produced by partial Xbal digestion and treatment with calf intestinal alkaline phosphatase
to create pDB2807 (B-form) and pDB2808 (A-fornf) disintegration vectors containing
DNA inserted at the Fspl-site after FLP (Figures 31 and 32 respectively).
EXAMPLE 5
Relative Stabilities of the LEU2 Marker in Yeast Transformed with pSACS 5-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 Xcml-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, lOOuL samples were
removed from each 3-day old flask and sub-cultured in lOOmL 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 resticted to a single flask from selected strains, for which 50 colonies were
picked. The overall results are summarised in Table 4.
Table 4: Summary ofplasmid stability7 daia for DNA insertions into pSAC35
Set 1 represents data from 3 days in non-selective shake flask culture,
Set 2 represents data from 1 days in non-selective shake flask culture.
A) REP2 Insertion Sites
(Table Removed)
All of the modified pSAC35 plasmids were able to transform }'east to leucine
prototrophy, indicating that despite the additional DNA inserted within the functionally
crowded regions of 2u.m 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 2u,m USregion,
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 use;d. 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 2jim (Sengupta et
al, 2001, J. Bacterial., 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. Nati Acad. Set. U.S.A., 84,2189;
Chen etal, 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 Xcml-site, which also truncated the
Flp protein product. The insertions at the Fspl-sites in the inverted repeat regions were
pSAC35-lilce 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, hi-addition, a 1.9-kb DNA fragment containing the PJDI2 gene was inserted
into a DNA linker at the Jfcml-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|im plasmid DNA, the plasmid replication and partitioning mechanisms had
not been abolished.
Detennination of plasmid stability7 by measuring loss of the LEU2 selectable marker
during growth in non-selective medium indicated mat 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 REP 2- 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 lugh 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 ofpSAC35
To further define the useful limits for insertion of additional DNA into the REP2 gene
and sequences hi 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 2urn (or pSAC35), a SwaBl-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 (Figure 37). In pDB2938, the end of the inverted repeat was displaced from
the rest of the inverted repeat by insertion of the iSnoBI-site. pDB2954 (Figure 38) was
subsequently constructed with a 31-bp sequence identical to the Sno5I-linker made from
oligonucleotides CF104 and CF105 (supra] inserted into the unique SnaBI site of
pDB293S. such mat the order of restriction endonuclease sites located immediate]}'- after
the TGA translation termination codon ofREP2 was SndBl-Pacl-FsellSfil-Smdl.-SnaB'l.
To construct pDB2938, the 1,085-bp Ncol-BanKL fragment from. pDB27S3 (Figure 14)
was first sub-cloned into pMCSS (Hoheisel, 1994, Biolechniques, 17, 456), which had
81
been digested with Ncol, BamHI and calf intestinal alkaline phosphatase. This produced
pDB2809 (Figure 39), which was subsequent!}' mutated using oligonucleotides CF127
and CF128, to generate pDB2920 (Figure. 40).
The 51-bp mutagenic oligonucleotides CF127 and CF128
The SndBl recognition sequence is underlined
CF127 5 ' -CGTAATACTTCTAGGGTATGATACGTATCCAATATCAAAGGAAATGATAGC-3 '
CF12B 5 ' -GCTATCATTTCCTTTGATATTGGATACGTATCATACCCTAGAAGTATTACG-3 '
Oligonucleotide directed mutagenesis was performed according to the instruction manual
of the Statagene's QuiclcChange™ Site-Directed Mutagenesis Kit. SndBl and Hindis.
restriction digestion of plasmid DNA was used to identify the arnpicillin resistant E. coli
transformants that contained pDB2920. The inserted 6-bp sequence of the SndBl
restriction site and the correct DNA sequence for the entire 1,091-bp Ncol-BamHL
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 Ncol-BamHl fragment from pDB2920 was isolated by agarose gel
purification and ligated with the approximately 4.7-kb Ncol-BamHl fragment from
pDB2783 to produce pDB2936 (Figure 41). The pDB2783 4.7-kb Ncol-BamHL fragment
was isolated by complete BamHL digestion of pDB2783 DNA that had first been
linearised by partial digestion with Ncol and purified by agarose gel electrophoresis. E.
coli DHScc cells were transformed to apramycin resistance by the ligation products.
pDB2936 was identified by SndBl digestion of plasmid DNA isolated from the
apramycin resistant clones.
The 3,082-bp Xbal fragment from pDB2936 was subsequently ligated with a 7,961-bp
pSAC35 fragment, which had been produced by partial .So! digestion and treatment with
calf intestinal alkaline phosphatase, to create the disintegration vector pDB2938 (2pm Bform,
Figure 37)
pDB2938 was digested with SndBl and calf intestinal phosphatase and ligated with an
approximately 2-lcb SndBl fragment from pDB2939 (Figure 42). pDB2939 was produced
by PCR amplifying the PD11 gene from S. ccrcvi.si.ac S2SSc genomic DNA v^ith,
olieoiiucleotide pruners DS24S and DS250 (Figure 43). followed by digesting the PCR
products with EcoRl and i'^mHI and cloning the approximately 1.98-l:b fragment into
YIplac211 (Gietz & Sugino, 1988, Gene, 14, 527-534), that had been cut with EcoRl and
Bamlll. DNA sequencing of pDB2939 identified a missing "G' from within the DS24S
sequence, winch is marked in bold in Figure 43. The approximately 2-kb SnaBl fragment
from pDB2939 was subsequently cloned into the mn'que SnaBl-site of pDB2938 to
produce plasmid pDB2950 (Figure 44'). The PDI1 gene in pDB2950 is transcribed in -the
same direction as the REP2 gene.
pDB2950 was subsequently digested with Smal and the approximately 11.1-lcb DNTA
fragment was circularised to delete the S28Sc PDIJ sequence, This produced plasmid
pDB2954 (Figure 38) with the SnaBI-Pacl-FseUSfil-Smd[-SnaBI linker located
immediately after the TGA translation termination codon of KEP2.
hi addition to cloning the S. cerevlsiae S288c PDI1 gene into the unique SnaBl-site. of
pDB293S5 the S. cerevisiae SICQ2n PDI1 gene was similarly inserted at this site. The &
cerevisiae SKQ2n PDI1 gene sequence was PCR amplified from plasmid DNTA
containing the PDI1 gene from pMA3a:C7 (US 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 (Figure 43). The
approximately 2-kb PCR product was digested with EcoEI and BaniHI and ligated into
Ylplac211 (Gietz & Sugino, 1988, Gene, 74, 527-534) that has been cut with£coRI aoad
BamHI, to produce plasmid pDB2943 (Figure 45). The 5' end of the SKQ2n POI1
sequence is analogous to a blunt-ended Spel-site extended to include the EcoKL, Sael,
SnaBl, Pad, Fsel, Sfil and Smal sites, the 3' end extends up to a site analogous to a
blunt-ended Bsu36l site, extended to include a Smal, SnaBl and BaniHI sites. The PD>I1
promoter length is approximately 2lObp. The entire DNA sequence, was determined for
the PDI1 fragment and shown to code for the PDI protein ofS. cerevisiae strain SKQ2n
sequence (NCBI accession number CAA38402), but with a serine residue at position 1 14
(not an arginine residue). Similarly to the S. cerevisiae S28Sc sequence in pDB2939,
pDB2943 had a missing 'G' from within the DS248 sequence, which is marked in bold in
Figure 43. The approximately 1,989-bp SnaBl fragment from pDB2943 was
S3
subsequently cloned into the unique SnaBl-sitQ in pDJS2938. This produced plasmid
pDB2952 (Figure 46), in which the SKQ2n PDI1 gene is transcribed in the same
direction as REP 2.
EXAMPLE 7
Relative Stabilities of the LEU2 Marker in Yeast Transformed with pSAC35-Like
Plasmids Containing DNA Inserted Immediately after the KEP2 gene
The impact on plasmid stability from insertion of the linker sequence at the SnaBl-site
introduced after the KEP2 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 (A'c/nl-linker) and
pDB2817 (Imrcl-linker) by the method described in Example 1.
The 3'east strain was transformed to leuciie prototrophy using a modified lithium acetate
method (Sigma yeast transformation kit, YEAST-1, protocol 2; (Ito et at, 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 lOmL BMMD shake flask cultures
(24 hrs, 30°C, 200rpm) by mixing with an equal volume of sterile 40% (w/v) trehalose
o o and freezing aliquots at-80 C (i.e. minus 80 C).
For the determination of plasmid stability, a ImL cryopreserved stock was thawed and
inoculated into lOOmL YEPS (initial ODeoo « 0.04-0.09) in a 250mL 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
1 OOf.iL aliquots plated in duplicate onto YEPS-agar plates. Cells were grown at 30°C for
4 days to allow single colonies to develop. Fox each yeast stocl: analysed. 100 random
colonies were patched in replica onto BMMS-agar piaies followed by YEPS-agar plates.
After growth at 30°C for 3-4 days the percentage of colonies growing on both BlvlMSagar
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
thai pDE2954 is essential!)' as stable as the pSAC35 control and pDB26SS. In this type
of assay a low level of instability can occasionally be detected even with the pSAC35
control (see Table 4). Hence, the iSnoBI-site artificially introduced into the inverted
repeat sequence immediately after the translation termination codon of JfLE'P2 appeared to
be equivalent to the Xcml-stie. in the inverted repeat for insertion of sj^ntaetic linker
sequences. However, the JicwI-site appeared to be preferable to the iSnaBI-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
(Table Removed)
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 PDIl at the SnaBI-site (even when
comprising an additional transferrin gene at the Not/ 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 PDIl gene inserted at the
SwoBI-site. These results demonstrate that the iSfooBI-site is useful for the insertion of
large genes such as PDIl, 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 PDIl gene in the genome of
Strain A). Results from the control strain are summarised in Table SB below. Antibody
plates were used contained lOOuL of goat polyclonal anti-transferrin autiserum
(Calbiochem) per 25mL 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 (Figure
44), pDB2952 (Figure 46) and pDB2954 (Figure 38) respectively, by inserting the same
3.27-kb Not/ cassette for rTf (N413Q, N611Q) as found in pDB2711 (Figure 11), into the
unique Notl-site, in the same orientation as pDB2711.
Table 5E: Increased transfenin secretion from the Control Strain transformed with pSAC3>
bassd A'ectors containing various PDl] gene insertions inxcnediately-site after REP 2
(Table Removed)
EXAJSCPLE 8
Stabilities of the LEU2 Marker in Yeast Transformed with pSACBS-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 nonselective
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 (A'crol-linker), pDB2812 (Hgal-lmk&i), pDB2S17
(Jlffjnl-linker), pDB2960 (PDIl gene inserted at Xcml site after REP 2} and pDB2711
(PDIl gene inserted &\XcmI site after REP 2 and a transferrin expression cassette inserted
at the Nofl-site in the UL-region).
Strains were grown to logarithmic phase in selective (BMMS) media at 30°C and used to
inoculate lOOmL non-selective (YEPS) media pre-warmed to 30°C in 250mL conical
flasks, to give between 1.25x105 and 5x10D 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 winch 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 200rprn for 24
hours to achieve approximately 1x107 cells/nil, as determined by haemocytometer counts.
The culture was then re-inoculated into fresh pre-warmed non-selective media to give
between 1.25xl05 and 5x10D 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 Figure 47.
Table- 6: The Relative Stabilities of Selected pSAC35-Like Plasmids in a 5. ccrevisiae
Strain grown for Thirty Generaiionr, in Non-Selective Media
(Table Removed)
Figure 47 shows the loss of the LEU2 marker with increasing number generation in nonselective
liquid culture for each strain analysed.
The control plasmidpS ACS 5 remained 100% stable over the entire 30-generations of this
assay. Plasmids pBD268S and pDB2812 both appeared to be as stable as pSAC35.
Therefore, insertion of the linlcer into the Xcml-site after KEP2 or the Hgal-site. after FLP
respectively had no apparent effect on plasrnid stability. In contrast., insertion of the
Xmnl-linker within the REP 2 gene appeared to have reduced plasrnid stability.
Plasrnid pDB2690, which contains a S. cerevisiae PDIl gene in the _l'c777l-linker after
KEPI, was approximately 33% stable after thirty generations growth, indicating that
insertion of this large DNA fragment into the US-region of the 2um-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 Notl-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 2pn-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
(Table Removed)
Primers DS2P9 and DS300 amplified the 5' region of PDI1 by PCR, while primers
DS301 and DS302 amplified a region 3' of AD/7, using gsnomic DNA derived S288c as
a template. The PCR conditions were as follows: 1 uL S2S8c template DNA (at
0.01ng/uL; 0.1ng/j.LL, Ing/^L. lOng/uL and lOOng/pL), 5|iL lOXBuffer (Fast Start
Taq+Mg, (Roche))., luL lOmlvf dNTP's, 5uL each primer DfiMl G.4jiL Fast Stait Taq,
made up to 50uL with FbO. PCRs were performed using a Perkin-Ehner Thermal Cycler
9700. The conditions were: denature at 95°C for 4min [HOLD], then [CYCLE] denature
at 95°C for 30 seconds, anneal at 45DC for 30 seconds, extend at 72°Cfor 45 seconds for
20 cycles., then [HOLD] 72°C for lOmin and then [HOLD] 4°C. The 0.221cbp PDI1 5'
PCR product was cut with Noil and HindlR, while the 0.34kbp PDI1 3' PCR product was
cut with Hindlll and PstL
Plasmid pMCSS (Hoheisel, 1994, Biotechniques 17, 456-460) (Figure 48) was digested to
completion with HindUl, blunt ended with T4 DNA polymerase plus dNTPs and
religated to create pDB2964 (Figure 49).
Plasmid pDB2964 was HindlR digested, treated with caLf intestinal phosphatase, and
ligated with the 0.221chp PDI1 5' PCR product digested with Notl and HinSSl and the
0.34kbp PDI1 3' PCR product digested with HinSHl and Pstl to create pDB3069 (Figure
50) which, was sequenced with forward and reverse universal primers and the DNA
sequencing primers DS303, DS304; DS305 andDS306 (Tahle 7).
Primers DS234 and DS235 (Table 8) were used to amplify the modified TRP1 marker
gene from YIplac204 (Gietz & Sugrno, 1988, Gene, 74, 527-534), incorporating HindUl
restriction sites at either end of the PCR product. The PCR conditions were as follows:
IjiL template YIplac204 (at 0.01ng/uL3 O.lng/uL, Ing/uL, lOng/uL and lOOng/jaL), 5uL
lOXBuffer (Fast Start Taq+Mg, (Roche)), IjiL IQmM dNTP's, 5j.tL each primer (2uM),
0.4p.L Fast Stait Taq, made up to 50uL with H?0. PCRs were performed using a Perlcin-
Elmer Thermal Cycler 9600. The conditions were: denature at 95°C for 4min [HOLD],
then [CYCLE] denature at 95°C for 30 seconds, anneal for 45 seconds at 45°C; extend at
72°C for 90sec for 20 cycles, then [HOLD] 72°C for lOmin and then [HOLD] 4°C. The
O.S6kbp PCR product was digested with Hindlll and cloned into the HindHI site of
pMCSS to create pDB2778 (Figure 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: Oligonucleotideprimers
(Table Removed)
The 0.86kbp TRP1 gene was isolated from pDB2778 by digestion with HindTH. and
cloned into the HmSEL site of pDB3069 to create pDB3078 (Figure 52) andpDB3079
(Figure 53). A 1.41kb pdil::TRPl disrupting DNA fragment was isolated from
pDB307S or pDB3079 by digestion with Notl/Pstl.
Yeast strains incorporating a TRP1 deletion (trplA) were to be constructed in such a way
that no homology to the TRP1 marker gene (pDB2778) should left in the genome once
the trplA 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 TKP1 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
TIJ'J marker gene present on integrating vector YIplac204 f Gietz & Sugmo, 1988. to,*,
74. 527-534J. The YIplac204 TRP1 marker gene differs from the native/chromosomal
IKW sene in that internal P/mdllL Pstl and -M sites were removed by site directed
inutaaenesis (Gietz & Sugmo, 1988, Gem, 74, 527-534). The YIPla,204 modified TRP1
marker gene was constructed from a 1.453kbp blunt-ended genomic fragment EcoXl
fragment which contained the TKPJ gene and only 102bp of the TKP1 promoter f Gietz
& Sugmo, 1988, Gene, 74, 527-534). Although tins was a relatively short promoter
sequence it was clearly sufficient to complement tyl auxotrophic mutations (Gietz &
Sugmo, 1988, Gene, 74, 527-534). Only DNA sequences upstream of the EcoPJ site,
positioned 102bp 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
iunctional modified TSP1 marker, which was chosen to be 85bp 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 TSP1 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 Wl
by PCR, while primers DS232 andDS233 (Table 8) amplified a region 3' of TRP1, using
S2S8c genomic DNA as a template. The PCR conditions were as follows: 1 uL template
S288c genomic DNA (at O.Olng/uL, O.lng/pX, Ing/pL, 10ng/uL and lOOng/pX), 5uL
lOXBuffer (Fast Start Taq+Mg, (Roche)), luL lOmM dNTP's, 5|aL each primer (2^M),
0.4aL Fast Start Taq, made up to 50uL with H20. PCRs were performed using a Perldn-
Elmer Thennal Cycler 9600. The conditions were: denature at 95"C for 4mm [HOLD],
then [CYCLE] denature at 95°C for 30 seconds, anneal for 45 seconds at 45°C, extend at
72°C for 90sec for 20 cycles, fhen [HOLD] 72°C for lOmin and then [HOLD] 4°C.
The 0.19kbp TRP1 5' UTR PCR product was cut with EcoKL and HindEl, while the
0 2kbp TRP1 3' UTR PCR product was cut with BamSL 'and Hindlll and ligated into
pAYE505 linearised with BwWEcoXl to create plaSmid-pDB2777 (Figure 54). The
constmction of pAYESOS is described in WO 95/33833. DNA sequencing using forward
and reverse primers, designed to prune from the plasmid backbone and sequence the
cloned inserts, confirmed that in both cases the cloned 5' and 3' UTR sequences of the
TRP2 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 ofTRPl. This 0.383kbp TRP1 disrupting fragment was excised from pDB2777 by
complete digestion with Eco~Rl.
Yeast strain DXY1 (Kerry-Williams et al, 1998, Yeast, 14, 161-169) was transformed to
leucine prototrophy with the albiunin expression plasmid pDB2244 using a modified
lithium acetate method (Sigma yeast transformation kit, YEAST-1, protocol 2; (Ito et al,
1983, J. Bacterial, 153, 163; Elble, 1992, Biotechnigues, 13, 18)) to create yeast strain
DXY1 [pDB2244J. 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 1 OmL BMMD shake flask cultures (24 hrs, 30°C, 200rpm).
DXY1 [pDB2244] was transformed to tryptophan autotrophy with the 0.383kbp 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 trpl.
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 S) was achieved as follows: luL template genomic DNA, 5uL
lOXBuffer (Fast Start Taq+Mg, (Roche)), IjiL lOmM dNTP's, 5uL each primer (2uM),
0.4|.iJL Fast Start Taq, made up to 50uL with EkO. PCRs were performed using a Perlcin-
Elmer Thermal Cycler %00. The conditions were: denature al 94°C for 1 Omm [HOLD],
then [CYCLE] denature at 94 °C for 30 seconds, anneal for 30 seconds at 55°Cr extend at
72°C for 120sec for 40 cycles, then [HOLD] 72*C for lOmni and then [HOLD] 4°C.
PCR amplification of the wild type TRJP1 locus resulted in a PCR product of 1.34kbp in
size, whereas amplification across the deleted TEfl region resulted in a PCR product
0.84kbp smaller at O.SOkbp. PCR analysis identified a DXY1 derived tip- strain (DXY1
trplA [pDB2244]) as having the expected deletion event.
The yeast strain DXY1 trplA [pDB2244] was cured of the expression plasmid pDB2244
as described by Sleep el al, 1991, Bio/Technology, 9,183-187. DXY1 trplA cir° was retransformed
the leucme prototrophy with either PDB2244, pDB2976, PDB2977,
pDB297S, 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 lat, YEAST-1, protocol 2; ato et al, 1983, J.
BacterioL 153, 163; Elble, 1992, Biotechnigues, 13, 18)). Transformants were selected
on BMMD-agar plates supplemented with tryptophan, and were subsequently patched out
on BMMD-agar plates supplemented with tr3'PtoPhan. Cryopreserved trehalose stocks
were prepared from IGmL BMMD shake flask cultures supplemented with tryptophan
(24hrs,30°C,200rpm).
The yeast strains DXY1 *plA [pDB2976], DXY1 trplA [pDB2977], DXY1 trplA
[PDB3078], DXY1 *plA [pDB3079]9 DXY1 n-plA [pDB29BO] or DXY1 trplA
[PDB^981] was transformed to tryptophan prototrophy using the modified lithium acetate
xnetiod (Sigma yeast transformation lot YEAST-1, protocol 2; (Ito ,/ al, 1983, J.
Bacterial, 153, 163; Elble, 1992, Biotechnig^s, 13, 18)) with a 1.41kb Pdil::TRPl
disrupting DNA fragment was isolated from pDB3078 by digestion with NofUPstl.
Transformants were selected on BMMD-agar plates and were subsequently patched out
on BMMD-agar plates.
Six transformants of each strain were inoculated into 10mL YEPD in 50mL shake flasks
and incubated in an orbital shaker at 30°C, 200rpm for 4-days. Cultoe supernatant* and
cell biomass were harvested Genomic DNA was prepared (Lee, 1992, Biotechnigues,
V 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: luL template genomic DNA, 5uL lOXBuffer (Fast Start Taq+Mg, (Roche)),
luL lOmM dNTP's, 5uL each primer (2uM), 0.4uL Fast Start Taq, made up to 50fj.L
with HjO. PCRs were performed using a Perkin-Elmer Thermal Cycler 9700. The
conditions were: denature at 94°C for 4min [HOLD], then [CYCLE] denature at 94°C for
30 seconds, anneal for 30 seconds at 50°C, extend at 72°C for 60sec for 30 cycles, then
[HOLD] 72°C for lOmin 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 0.65kbp. PCR analysis identified that all 36 potential
pdil::TRPl strains tested had the expectedpdil::TRPl deletion.
The recombinant albumin titres were compared by rocket imniunoelectrophoresis (Figure
55). Within each group, all six pdil::TRPl disruptants of DXY1 trplA [pDB2976],
DXY1 trplA |pDB2978], DXY1 trplA [pDB2980], DXY1 trplA [pDB2977] and DXY1
trplA [pDB2979] had very similar rHA productivities. Only the six pdil::TRPl
disruptants of DXY1 trplA [pDB2981] showed variation in rHA expression titre. The
saipdil::TRPl disruptants indicated in Figure 55 were spread onto YEPD agar to isolate
single colonies and then re-patched onto BMMD agar.
Three single celled isolates of DXY1 trplA pdil::TEPl [pDB2976], DXY1 trplA
pdil::TRJPl [pDB2978], DXY1 trplApdil::TRPl [pDB2980], DXY1 trplApdil::TRPl
[pDB2977], DXY1 trplA pdil::TKPl [pDB2979] and DXY1 trplA pdil::TRPl
[pDB2981] along with DXY1 [pDB2244], DXY1 [pDB2976], DXY1 [pDB2978], DXY1
[pDB2980], DXY1 (j>DB2977], DXY1 [pDB2979] and DXY1 [pDB2981] were
inoculated into 1 OmL YEPD in 50mL shake flasks and incubated in an orbital shaker at
30°C, 200rpm for 4-days. Culture supernatants were harvested and the recombinant
albumin titres were compared by rocket imniunoelectrophoresis (Figure 56). The thirteen
wild type PDI1 and pdil::TRPl disruptants indicated in Figure 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 a/., 1991,
Bk<: and the leu- leu or ler-> of each colony scored (Table 9).
Table 9:
(Table Removed)
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 chromosomalty encoded PDl,
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. PGKl Or
FBA1) which, when deleted or inactivated, does not result hi an auxotroplijc
(biosjaithetic) 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 (biosjTithetic) requirement" -Ve
include a deficiency, which can be complemented by additions or modifications to the
growth medium. Therefore, "essential marker genes" hi 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 0/ expression vectors containing various PDIl genes and the
expression cassettes for various heterologous proteins on the same 2 fun-like plasmid
PCR amplification and cloning of PDIl genes into YIplac211
The PDIl 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 BamHL 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 PDIl
genes. Differences in the PDIl promoter length within these YIplac211-based plasmids
are described in Table 10.
pDB2939 (Figure 57) was produced by PCR amplification of the PDIl gene from S.
cerevisiae S288c genomic DNA with oligonucleotide primers DS248 and DS250 (Table
11), followed by digesting the PCR product with JEcoRI and BamHI and cloning the
approximately 1.98-kb fragment into YIplac211 (Gietz & Sugino, 1988, Gene, 74, 527-
534), that had been cut with EcoEl and BamHL DNA sequencing of pDB2939 identified
a missing CG' from within the DS248 sequence, which is marked in bold in Table 5.
Oligonucleotide primers used for sequencing the PDIl gene are listed in Table 6, and
were designed from the published S288c PDIl gene sequence (PDI1/YCL043C on
chromosome III from coordinates 50221 to 48653 plus 1000 basepairs of upstream
sequence and 1000 basepairs of downstream sequence, (http://www.veastgenome.org/
Genebank Accession number NC001135).
3(1: Ylplac211-based Plasmids Containing PD11 Genes
(Table Removed)
Table 11: Oligonucleotide Primers for PCR Amplification of S. cerevisiae PDI2 Genes
(Table Removed)
Table 12: Oligonucleotide Primers for DNA Sequencing S. cerevisiae PDIl Genes
(Table Removed)
Plasmids pDB2941 (Figure 58) and pDB2942 (Figure 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-lcb EcoEl-JBamHL fragments, respectively, into YIplac211. The con-ect
DNA sequences were confirmed for the PDIl genes in pDB2941 and pDB2942.
The S. cerevisiae SKQ2n PDIl gene sequence was PCR amplified from plasmid DNA
containing the PDIl gene from pMA3a:C7 (US 6,291,205), also Icnown as Clone C7
(Crouzet & Tuite, 1987, supra', Farquhar et al, 1991, supra}. The SKQ2n PDIl gene
100
was amplified using oligonucleotide primers US24B and DS250 (Tables 10 and 11). The
approximately 2.0]-l;b PCR product was digested with £coJ"J and BanJHi and ligated
into YIplac211 (Gietz & Sugiiio, 1988, Gene, 14, 527-534'] that has been cut with EcoRl
and Bamlil, to produce plasmid pDB2943 (Figure 60). The 5' end of the SKQ2n PDI1
sequence is analogous to a blunt-ended Spel-sile. extended to include the .EcoRl, SacL
iSrcoBl, Pad, Fsel, Sfil and Smal sites, the 3' end extends up to a site analogous to a
blunt-ended Bsu36I site, extended to include, a Smal, SnaBl and BamHl sites. The PDI1
promoter length is approximately 210bp. The entire DNA sequence was determined for
ih& PDIJ fragment using oligonucleotide primers given in Table 12. This confirmed the
presence of a coding sequence, for the PDI protein of S. cerevisiae strain SICQ2n (NCBI
accession number CAA3S402). but with a serine residue at position 114 (not an arginirte
residue as previously published). Similar!}7, in the same wa}' as in the S. cerevisiae S2SSc
sequence in pDB2939, pDB2943 also had a missing !G' from v\dthin the DS248
sequence, which is marked in bold in Table 5.
Plasmids pDB2963 (Figure 61) and pDB2945 (Figure 62) were constructed similarly
using the PCR primers described in Tables 10 and 11, and by cloning the approximately
1.94-lcb and 1.87-kb Eco'Rl-BamHI fragments, respectively, into "\lplac211. The
expected DNA sequences were confirmed for the PDI] genes in pDB2963 and pDB29455
with a serine codon at the position of ammo acid 114.
The constructioD of pSAC35-based rHA expression plasmids with different PDI1
genes inserted at the Xcml-site^ after KEP2:
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
(Table Removed)
.The rHA expression cassette from pDB2243 (Figure 63, as described in WO 00/44772)
was first isolated on a 2,992-bp Notl fragment, which subsequently was cloned into the
Noti-site of pDB2688 (Figure 4) to produce pDB2693 (Figure 64). pDB2693 was
digested with SndBls 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
(Figures 65 to 70. PDI1 transcribed in the same orientation as REP2 was designated
"orientation A", whereas PDI1 transcribed in opposite orientation to REP2 was
designated "orientation B" (Table 13).





We Claim:
1. A 2µm-family plasmid characterized in that it comprise 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.
2. The 2µm-family plasmid as claimed in 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 a FLP gene and/or a REP2 gene, respectively, derived from a naturally occurring 2µm-family plasmid.
3. The 2µm-family plasmid as claimed in claim 1 wherein the naturally occurring 2µm-family plasmid is selected from 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 2µm plasmid as obtained from Saccharomyces cerevisiae.
4. The 2µm-family plasmid as claimed in claim 2 or 3 wherein 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 2µm-family plasmid as the sequence from which the gene is derived.
5. The 2µm-family plasmid as claimed in any one of claims 2 to 4 wherein the naturally occurring 2µm-family plasmid is the 2µm plasmid as obtained from Saccharomyces cerevisiae.
6. The 2µm-family plasmid as claimed in claim 5 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at a position between the first base of codon 59 of the REP2 gene and the last base before the FRT site in the adjacent inverted repeat.
7. The 2µm-family plasmid as claimed in claim 5 or 6 wherein, 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 N0:1 or variant thereof of the kind such as herein described.
8. The 2µm-family plasmid as claimed in any one of claims 1 to 7 wherein polynucleotide sequence insertion, deletion and/or substitution occurs at a position between the first base of the inverted repeat and the last base before the FRT site.
9. The 2µm-family plasmid as claimed in any one of claims 1 to 7 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs between the first base after the end of the REP2 coding sequence and the last base before the FRT site, such as at the first base after the end of the REP 2 coding sequence.
10. The 2µm-family plasmid as claimed in any one of claims 1 to 7 wherein, other than the polynucleotide sequence insertion, deletion and/or substitution, the inverted repeat that follows the REP2 coding sequence has a sequence derived from the corresponding region of the 2µm plasmid as obtained from Saccharomyces cerevisiae.
11. The 2µm-family plasmid as claimed in a claim 10 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at an XcmI site or an FspI site within the inverted repeat
12. The 2µm-family plasmid as claimed in claim 5 wherein 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 FRT site in the adjacent inverted repeat.
13. The 2µm-family plasmid as claimed in claim 5, 11 or 12 wherein, other than the polynucleotide sequence insertion, deletion and/or substitution, the sequence of the FLP coding sequence and the adjacent inverted repeat is as defined by SEQ ID NO:2 or variant thereof of the kind such as herein described.
14. The 2µm-family plasmid as claimed in claim 11, 12 or 13 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at a position between the first base of the inverted repeat and the last base before the FRT site.

15. The 2µm-family plasmid as claimed in claim 14 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at a position between the first base after the end of the FLP coding sequence and the last base before the FRT site.
16. The 2µm-family plasmid as claimed in claim 15 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at the first base after the end of the FLP coding sequence.
17. The 2µm-family plasmid as claimed in any one of claims 11 to 16 wherein, other than the polynucleotide sequence insertion, deletion and/or substitution, the inverted repeat that follows the FLP gene has a sequence derived from the corresponding region of the 2µm plasmid as obtained from Saccharomyces cerevisiae.
18. The 2µm-family plasmid as claimed in claims 17 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs at an HgaI site or an FspI site within the inverted repeat
19. The 2µm-family plasmid as claimed in any one of the preceding claims comprising 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.
20. The 2µm-family plasmid as claimed in any preceding claim optionally comprising a polynucleotide sequence insertion, deletion and/or substitution which is not at a position as defined in any one of the preceding claims.
21. The 2µm-family plasmid as claimed in claim 20 wherein the polynucleotide sequence insertion, deletion and/or substitution occurs within an untranscribed region around an ARS sequence.
22. The 2µm-family plasmid as claimed in any one of the preceding claims wherein the, or at least one, polynucleotide sequence insertion, deletion and/or substitution is a polynucleotide sequence insertion.

23. The 2µm-family plasmid as claimed in claim 22 in which the polynucleotide sequence insertion encodes an open reading frame.
24. The 2µm-family plasmid as claimed in claim 23 in which the open reading frame encodes a non- 2µm-family plasmid protein.
25. The 2µm-family plasmid as claimed in claim 24 in which the non- 2µm-family plasmid protein comprises the sequence of a known 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 (such as a blood clotting factor), antistasin, a tick anticoagulant peptide, transferrin, lactoferrin, endostatin, angiostatin, collagens, immunoglobulins or immunoglobulin-based molecules or fragments of either (e.g. a dAb, Fab' fragments, F(ab')2, scAb, scFv or scFv fragment), a Kunitz domain protein, interferons, interleukins, IL10, IL11, IL2, interferon a species and sub-species, interferon ß species and sub-species, interferon y species and sub-species, leptin, CNTF, CNTFAX15, IL1-receptor antagonist, erythropoietin (EPO) and EPO mimics, thrombopoietin (TPO) and TPO mimics, prosaptide, cyanovirin-N, 5-helix, T20 peptide, T1249 peptide, HIV gp41, HIV gpl20, 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 ß, 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, Protein S, or a variant or fragment of any of the above of the kind such as herein described.
26. The 2µm-family plasmid as claimed in claim 25 in which the non- 2µm-family plasmid protein comprises the sequence of albumin, a variant or fragment thereof of the kind such as herein described, or a fusion protein comprising the sequence of any of these.

27. The 2µm-family plasmid as claimed in claim 25 in which the non- 2µm-family plasmid protein comprises the sequence of transferrin, a variant or fragment thereof of the kind such as herein described, or a fusion protein comprising the sequence of any of these.
28. The 2µm-family plasmid as claimed in claim 25 in which the non- 2µm-family plasmid protein comprises the sequence of lactoferrin, a variant or fragment thereof of the kind such as herein described, or a fusion protein comprising the sequence of any of these.
29. The 2µm-family plasmid as claimed in claim 25 in which the non- 2µm-family plasmid protein comprises the sequence of Fc, a variant or fragment thereof of the kind such as herein described, or a fusion protein comprising the sequence of any of these.
30. The 2µm-family plasmid as claimed in claim 25 in which the non- 2µm-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 any one 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, PDJ1, 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.
31. The 2µm-family plasmid as claimed in claim 25 or 30 in which the chaperone is protein disulphide isomerase (PDI), or is a protein encoded by ORM2, SSA1 or PSE1.
32. The 2µm-family plasmid as claimed in any one of claims 24 to 31 in which the non- 2µm-
family plasmid protein comprises a secretion leader sequence.
33. The 2µm-family plasmid as claimed in claim 24 in which the non- 2µm-family plasmid
protein comprises the sequence of a bacterial selectable marker and/or a yeast selectable
marker.
34. The 2µm-family plasmid as claimed in claim 33 in which the bacterial selectable marker is
a ß-lactamase gene and/or the yeast selectable marker is a LEU2 selectable marker.

35. The 2µm-family plasmid as claimed in any one of the preceding claims which plasmid
comprises (i) a heterologous sequence encoding a non- 2µm-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,
preferably protein disulphide isomerase; and (iii) a heterologous sequence encoding a
protein comprising the sequence of a selectable marker; wherein at least one of the
heterologous sequences occurs at a position as defined by any one of Claims 1 to 16.
36. A method of preparing a plasmid as claimed in any one of the preceding claims
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 at a position as defined in any one of Claims 1 to 18; and/or
(c) deleting some or all of the nucleotide bases at the positions defined in any one of Claims 1 to 18; and/or
(d) substituting some or all of the nucleotide bases at the positions defined in any one of Claims 1 to 18 with alternative nucleotide bases.
37. A plasmid obtainable by the method as claimed in claim 36.
38. A host cell comprising a plasmid as claimed in any one of claims 1 to 35 and 37.
39. A host cell as claimed in claim 38 which is a yeast cell.
40. A host cell as claimed in claim 38 or 39 in which the plasmid is stable as a multicopy plasmid.
41. A host cell as claimed in claim 40 in which the plasmid is based on pSR1, pSB3 or pSB4 and the yeast cell is Zygosaccharomyces rouxii, the plasmid is based on pSBl or pSB2 and

the yeast cell is Zygosaccharomyces bailli, the plasmid is based on pSM1 and the yeast cell is Zygosaccharomyces fermentati, the plasmid is based on pKDl and the yeast cell is Kluyveromyces drosophilarum, the plasmid is based on pPMl and the yeast cell is Pichia membranaefaciens or the plasmid is based on the 2jxm plasmid and the yeast cell is Saccharomyces cerevisiae or Saccharomyces carlsbergensis.
42. A host cell as claimed in claim 40 or 41 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.
43. A method as claimed in producing a protein comprising the steps of-

(a) providing a plasmid as claimed in any one of claims 1 to 35 or 37
(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.

44. A method as claimed in producing a protein comprising the steps of providing a host cell as defined by any one of Claims 38 to 42 which host cell comprises a plasmid as defined by any one of Claims 1 to 35 or 37 and culturing the host cell in a culture medium thereby to produce the protein.
45. A method as claimed in claim 43 or 44 further comprising the step of isolating the thus produced protein from the cultured host cell or the culture medium.
46. A method as claimed in claim 45 further comprising the step of purifying the thus isolated
protein to a commercially acceptable level of purity.

47. A method as claimed in claim 45 further comprising the step of purifying the thus isolated protein to a pharmaceutically acceptable level of purity.

Documents:

3664-DELNP-2006-Abstract-(15-06-2011).pdf

3664-DELNP-2006-Abstract-(16-07-2012).pdf

3664-delnp-2006-abstract.pdf

3664-DELNP-2006-Assignment (15-10-2009).pdf

3664-DELNP-2006-Claims-(15-06-2011).pdf

3664-DELNP-2006-Claims-(16-07-2012).pdf

3664-delnp-2006-claims.pdf

3664-DELNP-2006-Correspondence Others-(15-06-2011).pdf

3664-DELNP-2006-Correspondence Others-(16-07-2012).pdf

3664-DELNP-2006-Correspondence-Others (15-10-2009).pdf

3664-DELNP-2006-Correspondence-Others-(16-12-2011).pdf

3664-delnp-2006-correspondence-others-1.pdf

3664-delnp-2006-correspondence-others.pdf

3664-DELNP-2006-Description (Complete)-(15-06-2011).pdf

3664-DELNP-2006-Description (Complete)-(16-07-2012).pdf

3664-delnp-2006-description (complete).pdf

3664-DELNP-2006-Drawings-(15-06-2011).pdf

3664-delnp-2006-drawings.pdf

3664-DELNP-2006-Form-1-(15-06-2011).pdf

3664-DELNP-2006-Form-1-(16-07-2012).pdf

3664-delnp-2006-form-1.pdf

3664-delnp-2006-form-18.pdf

3664-DELNP-2006-Form-2-(15-06-2011).pdf

3664-DELNP-2006-Form-2-(16-07-2012).pdf

3664-delnp-2006-form-2.pdf

3664-DELNP-2006-Form-3-(15-06-2011).pdf

3664-DELNP-2006-Form-3-(16-12-2011).pdf

3664-delnp-2006-form-3.pdf

3664-delnp-2006-form-5.pdf

3664-DELNP-2006-GPA (15-10-2009).pdf

3664-DELNP-2006-GPA-(15-06-2011).pdf

3664-delnp-2006-gpa.pdf

3664-delnp-2006-pct-101.pdf

3664-delnp-2006-pct-210.pdf

3664-delnp-2006-pct-220.pdf

3664-delnp-2006-pct-237.pdf

3664-delnp-2006-pct-304.pdf

3664-delnp-2006-pct-409.pdf

3664-delnp-2006-pct-416.pdf

3664-DELNP-2006-Petition-137-(15-06-2011).pdf

3664-DELNP-2009-Correspondence-Others (20-10-2009).pdf

3664-DELNP-2009-GPA (20-10-2009).pdf

abstract.jpg


Patent Number 253998
Indian Patent Application Number 3664/DELNP/2006
PG Journal Number 37/2012
Publication Date 14-Sep-2012
Grant Date 12-Sep-2012
Date of Filing 26-Jun-2006
Name of Patentee NOVOZYMES BIOPHARMA DK A/S
Applicant Address KROGSHOEJVEJ 36, DK-2880 BAGSVAERD, DENMARK
Inventors:
# Inventor's Name Inventor's Address
1 DARRELL SLEEP 66 LADYBAG ROAD, WEST BRIDGFORD, NOTTINGHAM NG2 5DS, ENGLAND
2 CHRISTOPHER JOHN ARTHUR FINNIS 74 HARLAXTON DRIVE, LENTON, NOTTINGHAM NG7 1JB, ENGLAND
PCT International Classification Number C12N 15/81
PCT International Application Number PCT/GB2004/005435
PCT International Filing date 2004-12-23
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 0329722.3 2003-12-23 U.K.