Glycolytic Promotersfor Regulated Protein Expression: Protease Inhibitor

1. Field of the Invention

The ability to obtain expression of foreign, i.e., exogenous, DNA in unicellular microorganisms provided the opportunity to conveniently prepare long polypeptide chains of interest. Almost immediately, varied polypeptides, such as the small hormone somatostatin and more sophisticated polypeptides, such as insulin, interferons, thymosin and a variety of vaccines having capsid proteins, were prepared and reported in the literature. For the most part, the initial work was performed in the bacterium E. coli which had been the subject of intensive study because scientists were familiar with many aspects of its genetic structure and properties. Initial attention was therefore directed to producing foreign proteins in E. coli. Once the ability to employ E. coli as a host was established, the limitations and disadvantages of employing E. coli encouraged the use of other hosts.

One host which appeared to be particularly attractive because it lacked many of the shortcomings of E. coli was yeast. However, yeast is a eukaryote and, therefore, has a more sophisticated genetic system. Furthermore, less is known about the yeast genome than is known about E. coli. In order to use yeast as a host for the production of proteins foreign to yeast, a number of discoveries are required, and new materials must be made available.

Initially, a replication system was required which provided stability in yeast, either as an extrachromosomal element or by integration into the yeast chromosome. In addition, the regulatory functions concerned with transcription and expression had to be developed in order to allow for expression of the desired protein. There was also the uncertainty whether foreign DNA sequences would be transcribed and translated and, if expressed, whether the resulting polypeptides would survive in the yeast cell. Also remaining to be determined was the effect of the foreign proteins on the viability of the yeast cell, such as the effect of recombinant DNA (RDNA) on mitosis, sporulation and vegetative growth.

There have, therefore, been substantial efforts to develop novel RDNA systems in yeast, which will allow for regulated expression of a protein of interest, as well as highly efficient production of such proteins.

2. Description of the Prior Art

Hitzeman et al., J. Biol. Chem. (1980) 255:12073-12080 describe a plasmid having a yeast 3-phosphoglycerate kinase (PGK) gene and accompanying regulatory signals capable of expression in yeast. Other references of interest include Clifton, et al., Genetics (1978) 88:1-11; Clark and Carbon, Cell (1976) 9:91-99; Thomson, Gene (1977) 1:347-356; Holland and Holland, J. Biol. Chem. (1979) 254:5466-5474; Holland and Holland, ibid. (1979) 254:9830-9845; Nasmyth and Reed, Proc. Nat. Acad. Sci. (1980) 77:2119-2123; Broach, et al., Gene (1979) 8:121-133; and Williamson, et al., Nature (1980) 283:214-216.

Novel yeast promoters are provided which control the transcription of genes in the glycolytic pathway and which find use in the regulated production of proteins foreign to the yeast. Promoters of particular interest include the promoters for triose phosphate isomerase, pyruvate kinase, phosphoglucose isomerase, phosphoglycerate mutase, hexokinase 1, hexokinase 2, glucokinase, phosphofructokinase, and aldolase, as well as the glycolytic regulatory gene. The protease inhibitor, mammalian .alpha..sub.1 -antitrypsin, is expressed using the promoter for triose phosphate isomerase.

Methods and compositions are provided for regulated efficient expression of alien or foreign DNA in a yeast host. (Alien or foreign DNA is DNA not naturally occurring in the wild type particularly from a different species and which does not normally exchange genetic information with the host.) Novel promoters are employed which are involved in the glycolytic pathway and provide for high levels of protein production, so that a substantial proportion of the total protein produced by the yeast cells can be dedicated to the protein of interest. In addition, regulatory mechanisms associated with regulation of production of the glycolytic enzymes are achieved, so that production of the desired products may be modulated. Furthermore, viable cells can be maintained to enhance the efficiency and amount of expression.

The promoters of interest are particularly those promoters involved with expression of triose phosphate isomerase, pyruvate kinase, phosphoglucose isomerase, phosphoglycerate mutase, hexokinase 1, hexokinase 2, glucokinase, phosphofructokinase, and aldolase, which are controlled by the glycolytic regulation gene GCR1. The genes of the glycolytic pathway include hexokinase 1 and 2 (HXK1,2); phosphoglucose isomerase (PGI), triose phosphate isomerase (TPI); phosphoglycerate kinase (PGK), phosphoglycerate mutase (GPM), pyruvate kinase (PYK); phosphofructokinase (PFK), enolase (ENO); fructose 1,6-diphosphate aldolase (FDA); glyceraldehyde 3-phosphate dehydrogenase (PGK); and glycolysis regulation protein (GCR).

The promoters may be obtained by employing a gene bank having large fragments of yeast DNA. By introducing the fragments into appropriate vectors, particularly shuttle vectors having replicons for prokaryotes and yeast, one can readily amplify and clone the yeast DNA in a bacterium and then introduce the yeast DNA into mutant yeast cells for complementation. In this manner, yeast fragments can be identified which complement auxotrophic lesions or mutations in a yeast host.

Of particular interest, is where the host is auxotrophic in both the glycolytic pathway step of interest and a separate biochemical pathway, which is complemented by a marker in the vector. Once having established a DNA segment having the desired gene, one may reclone by various techniques to shorten the DNA segment and provide for a segment which is primarily the gene of interest in conjunction with its regulatory signals for transcription and expression.

In order to retain the promoter, it is essential that the initiator methionine be determined and this codon be used for developing the strategy for introducing the alien DNA downstream from the promoter. Various techniques can be employed for providing a site for introduction of the alien DNA so as to be under the regulatory control of the promoter in the glycolytic pathway.

Where a restriction site is conveniently adjacent to the initiator methionine codon, the glycolytic gene may be cleaved at that site and the DNA chewed back with Ba131 for varying periods of time, so as to chew into or past the initiator methionine codon or retain the initiator methionine codon.

Where there is no convenient restriction site, other splicing techniques such as primer repair may be employed. Also, by employing in vitro mutagenesis, one can introduce a restriction site adjacent the initiator methionine, which encodes for the initial amino acids of the desired protein. In each instance, a linearized DNA segment is obtained having the intact promoter for the glycolytic product and normally includes other DNA sequences, such as an intact replicon, one or more markers, and the like.

Exemplary of the above procedure is the development of a vector having the promoter for the TPI1 gene. An exemplary vector CV13 having the replicons or replication systems from pBR322 and 2.mu.-plasmid of yeast, as well as the LEU2 gene was employed for insertion of a yeast fragment which was shown to have the TPI1 gene. This was achieved by employing double selection with a mutant yeast which was leu.sup.-, tpi.sup.-. The TPI1 gene was found to have a unique KpnI site. The vector was cleaved at the KpnI site and then treated with the double stranded exonuclease Ba131 for varying times to chew back the DNA to about the f-met codon. Linkers were then inserted providing desired restriction sites. Alien DNA could then be inserted providing a sequence having a f-met codon in the appropriate position for initiation. Alternatively, the foreign DNA can be expressed using the f-met codon of the TPI1 gene.

Similar procedures can be performed with the other subject glycolytic genes in order to provide the promoters associated with those genes. The PYK sequence has a convenient XbaI site for restriction, where the few additional bases may be removed, if required, using Ba131 for a short period of time to chew to or through the methionine codon. Of particular interest is the use of the GCR promoter to control the expression of the other genes involved in the glycolytic pathway. By employing the GCR gene, in conjunction with other glycolytic promoters regulating expression of alien DNA, one can turn on and off the other promoters, so as to regulate the expression of the alien DNA. Thus, one can allow vegetative growth to proceed until a desired cell density is achieved, before permitting production of the desired polypeptide.

By employing appropriate auxotrophs, one can further regulate the expression of the polypeptides of interest in choosing the appropriate nutrient medium. Where the chosen promoter is repressed by the particular nutrient because of a metabolic block, a change in the nature of the nutrient can induce expression. Furthermore, the activity of a number of promoters in the glycolytic pathway can be affected by the repression or activation of expression by the GCR gene or other regulatory controls. Also, the GCR regulatory signals can be used to titrate the polypeptide functioning as the regulator for expression of GCR. By having vectors whose copy number can be controlled, one can vary the activity of the wild type GCR gene.

In order to obtain expression, an extrachromosomal element construct will be prepared having a number of sequences defining different functions. One function is the replication system, which forms part of a vector. Another function is a promoter by itself or in conjunction with the alien DNA. Other functions include initiators and terminators of expression. Also, there will be selectable markers.

In developing an appropriate vector, while not necessary, it will be common to have both a replication system for yeast and a replication system for a prokaryote (a shuttle vector). The replication system for yeast may be one which provides for stable maintenance of an extrachromosomal element or one which provides a sufficient lifetime for the DNA in the host, that there is an acceptable probability of integration of the DNA into the host. Integration can be greatly aided by providing for a sequence homologous to the host DNA, so as to provide for recombination. Generally, the homologous sequence will be at least about 800bp usually not more than about 2000bp. Therefore, either integration or an autonomous replication system, such as the use of the ARS1 gene, may be employed to provide for the maintenance of the alien DNA in the yeast host. The replication system which is chosen should provide for a reasonable copy number usually greater than 1, preferably greater than 5. A wide variety of replication systems are available on a wide variety of prokaryotic vectors, such as pBR322, pACYC184, pSC101, pMB9, etc. Alternatively, one or more copies of the DNA construct can be integrated into the host chromosome. The replication systems may also be conditionally regulated, usually being temperature sensitive so that replication can be turned on and off by varying the temperature.

In addition to the replication system, there will also be one or more selectable markers, there usually being at least one marker in addition to the alien DNA, which may serve as a marker. Conventional markers include biocidal markers providing antibiotic resistance and those providing resistance to toxins and heavy metal. Also useful is employing an auxotrophic host and providing prototrophy by complementation. In addition to the conventional selection systems just described, the glycolytic genes of the present invention are particularly desirable markers since they can provide for selection, using sugars as selective substrates, in appropriate mutant host strains.

Other genes may also be inserted into the extrachromosomal element for a variety of purposes. Where integration is desirable in the genome of the host, a homologous sequence for a particular region of the host genome may be included in the extrachromosomal element. Where amplification of one or more sequences is desired, genes known to provide such amplification, such as dihydrofolate reductase genes, which respond to methotrexate stress or metallothionein genes, which respond to heavy metal stress, may be included in the extrachromosomal element, flanked by the DNA regions to be reiterated. Other regulatory signals may also be included, such as centromeres, autonomously replicating segments, etc.

In order to isolate the promoters of interest, clones can be made of yeast chromosomal DNA by random digestion or mechanical shearing of the yeast genome. The presence of the desired gene is then determined by introducing a homogeneous clone of a yeast fragment into an auxotrophic host for complementation. Desirably, the cloning vehicle may have another gene which allows for an additional basis for selection, so that double selection techniques can be used. The mutants are substantially incapable of growing on limited nutrient medium, so that one can select for the presence of the desired glycolytic gene by the choice of medium. After isolating the yeast fragment having the desired gene, the fragment may be subcloned so as to remove superfluous DNA flanking regions and provide for a fragment which is more easily manipulated. The smaller fragment containing the desired gene, of a size less than about 500 base pairs may then be further cloned, restriction mapped and sequenced, so as to provide a useful source for the desired promoters and insertion of the alien DNA. Also, as indicated, the promoters in themselves may be useful, in acting as a titrater for repressor or activator, where it is desirable to modulate the production of a particular enzyme in the yeast host.

The alien DNA may be from any source, either naturally occurring or synthetic, either prokaryotic or eukaryotic. Of particular interest are mammalian genes which express a poly(amino acid), that is, polypeptide or protein which has physiological activity. To varying degrees, poly(amino acids) prepared in yeast may be modified by glycosylation, where the glycosylation may not occur or may occur at different sites from the naturally occurring mammalian polypeptide and/or in different degrees with different saccharides. It is therefore of great interest to be able to prepare polypeptides which are different from the naturally occurring polypeptide by the degree and manner of glycosylation and in many instances may differ in one or more ways as to the amino acid sequences, where there may be deletions of one or more amino acids or substitutions of one or more amino acids. Mammalian genes may come from a wide variety of mammalian sources, such as domestic animals (e.g. bovine, porcine, ovine and equine) and primates e.g. humans and monkeys.

As exemplary of the use of the subject promoters in preparing an active polypeptide composition, as well as being of particular interest for a variety of purposes, a protease inhibitor is described and made. The protease inhibitor has the same or substantially the same amino acid sequence of human .alpha..sub.1 -antitrypsin and is capable of inhibiting a number of proteolytic enzymes. The human .alpha..sub.1 -antitrypsin gene appears to reside within a 9.6 kb EcoRI DNA fragment in the human genome. The mature mRNA appears to have about 1400 nucleotides. One human .alpha..sub.1 -antitrypsin cDNA has the following sequence, although other naturally-occurring forms (polymorphisms) are known. ##STR1## ##STR2## ##STR3## ##STR4## ##STR5## ##STR6## ##STR7## ##STR8## ##STR9## ##STR10## ##STR11## ##STR12## ##STR13## ##STR14## ##STR15## ##STR16## ##STR17## ##STR18## ##STR19##

The human .alpha..sub.1 -AT has a BamHI restriction site which allows the cutting of the gene with the removal of information for a single glutamic acid from the mature protein. Various schemes can be employed for introducing the human .alpha..sub.1 -AT gene adjacent the glycolytic promoter to be under the regulation of the promoter. Where the promoter does not have a convenient restriction site near the f-met codon, the glycolytic gene may be cleaved and chewed back to the promoter with Ba131. A linker may then be introduced downstream from the promoter to provide a convenient cohesive end or flush end for joining to the human .alpha..sub.1 -AT gene. The linker can also provide one or more codons for amino acids at the N-terminus of the .alpha..sub.1 -AT gene, which may be the same or different from the naturally occurring amino acids.

The gene for human .alpha..sub.1 -AT may then be inserted into the extrachromosomal element downstream from the glycolytic promoter, where an f-met codon is provided for initiation of expression of the human .alpha..sub.1 -AT.

The resulting extrachromosomal element containing the human .alpha..sub.1 -AT gene may then be introduced into a yeast host, particularly an auxotrophic host and the yeast host grown for expression of a polypeptide having .alpha..sub.1 -antitrypsin activity. The resulting polypeptide differs from the naturally occurring human .alpha..sub.1 -AT in its degree of glycosylation.

The .alpha..sub.1 -antitrypsin can be used as an antigen for production of polyclonal and monoclonal antibodies to human .alpha..sub.1 -AT, for introduction into a host having a deficiency of .alpha..sub.1 -AT, or for modulating proteolytic activity in a mammalian host. In particular, the .alpha..sub.1 -antitrypsin can be administered to humans to replace .alpha..sub.1 -antitrypsin which has been inactivated (oxydized) by tobacco and other smoke.

The following examples are offered by way of illustration and not by way of limitation.

Strains.

Isogenic strains carrying mutations in PGI1, PGK1, GPM1, PYK1, and GCR1 where obtained by ethyl methane sulfonate (EMS) mutagenesis of S. cerevisiae (S. c.) X2180-1A (MATa SUC2 CUP1 ga12, from the Berkeley Yeast Stock Center). 35,000 independent colonies were grown on YEP-3% glycerol-2% ethanol and were screened by replica plating for the inability to grow on YEP-4% dextrose (Table 1).

Identification of specific lesions was made by complementation tests with known glycolysis mutants (Ciriacy and Breitenbach (1979) J.Bacteriol. 139:152-60), while at least 15 additional complementation groups were found by intercrossing mutant strains. Enzyme assays (Clifton et al. (1980) Genetics 88:1-11) confirmed the glycolytic defects in pgi1, pgk1, gpm1, pyk1, and gcr1 mutants.

A LEU2 mutant was also derived from S. cerevisiae X2180-1A by EMS treatment and was crossed to X2180-1B (an isogenic MAT.alpha. strain) to produce N501-1B (MAT.alpha. leu2 SUC2 CUP1 ga12). Cycloheximide (cyh2) and canavanine (can1) resistances were then selected as spontaneous mutations in N501-1B. The glycolysis mutants were crossed to N501-1B to produce a series of isogenic leu2 strains each defective in a single glycolytic function or in GCR1.

A tpil mutant, S. cerevisiae GLU77 was crossed to N551-1A (MATa leu2 SUC2 CUP1 ga12); strains derived from this mating were crossed twice to N501-1B to produce a tpil leu2 strain, N587-2D, which was similar in genetic background to the other glycolysis mutants.

Mutations in three glucose phosphorylating enzymes produce a strain which is unable to grow on dextrose as the sole carbon source and which is resistant to catabolite repression by 2-deoxyglucose and glucosamine. N517-6C (hxk1 hxk2 glk1 leu2 can1-100 cyh2 ade2-1) was derived from a hxk1 hxk2 glk1 strains, D308.3, by screening for glucosamine-resistant spore colonies. Defects in glucose kinasing activities were confirmed by assay.

The homothallic diploid strain, S. c. AB320 was the source of the yeast DNA pool (Nasmyth and Reed, Proc. Nat. Acad. Sci. (1980) 77:2119-2123 and was used as a control in some experiments.

The triose phosphate isomerase gene (including the upstream sequence having the regulatory signals) is as follows: ##STR20## ##STR21## ##STR22## ##STR23## ##STR24## ##STR25## ##STR26## ##STR27## ##STR28## ##STR29## ##STR30## ##STR31## ##STR32## ##STR33## ##STR34## ##STR35## ##STR36## ##STR37## ##STR38## ##STR39## ##STR40## ##STR41## ##STR42## ##STR43## ##STR44## ##STR45## ##STR46## ##STR47##

The pyruvate kinase gene upstream sequence having the regulatory signals is as follows:

Screening of clone bank.

The leu2 glycolysis mutants were transformed with a yeast DNA pool inserted into pYE13, a high copy plasmid carrying a selectable LEU2 wild-type gene (Broach et al., Gene (1979) 8:121-133). The glycolytic genes were obtained by complementation, involving the simultaneous selection for growth on glucose and leucine prototrophy. A synthetic medium containing yeast nitrogen base, 4% glucose, and the following supplements was used: per liter, 40 mg adenine, 20 mg arginine, 50 mg aspartate, 10 mg histidine, 60 mg isoleucine, 40 mg lysine, 10 mg methionine, 60 mg phenylalanine, 50 mg threonine, 40 mg tryptophan, 50 mg tyrosine, 20 mg uracil, and 60 mg valine.

The transformants were purified on leucineless media and were then grown on a non-selective medium (YEPGE) to allow mitotic segregation of the plasmids. Strains which cosegregated the leu2 and glycolysis mutant phenotypes, as determined by replica plating on selective media, were assayed for glycolytic enzyme activities. Yeast DNA preps were made, and the E. coli strain, RR1, was transformed, selecting for ampicillin resistance, to verify the presence of plasmid DNAs in these yeast glycolytic transformants.

Enzyme Assays.

The transformed yeast strains were selectively grown on minimal medium with 8% glucose (adenine was added to a final concentration of 50 mg/1). The wild-type control, N501-1B, was grown on the same medium plus leucine (100 mg/1). The glycolysis mutant strains were grown on YEP-5% glycerol-1% lactate. Overnight cultures were fed fresh media and were aerobically grown at 30.degree. for four hours before harvesting. The cells were washed two times with water and resuspended in 50mM K.sub.2 HPO.sub.4 2mM EDTA 3mM 2-mercaptoethanol (adjusted to pH 7.4 with HCl). Extracts were obtained by vortexing the cells with an equal volume of glass beads (0.45 mm diam.) at high speed for two minutes. The cell debris was removed by centrifugation in a microfuge for 15 min. at 4.degree.. Enzymes were assayed as described by Clifton and Breitenbach, supra. Protein concentrations were determined by the Biuret-TCA method.

In order to determine the activity of the various glycolytic genes in the transformants, the various enzymes were assayed and the results for the transformants were compared to mutant and wild-type strains. The gcr1 mutant had 5-10% of the wild-type levels of most glycolytic activities (exemplified by PGI, aldolase and enolase) and grows very poorly on glucose media. In contrast, the GCR1 transformants had nearly wild-type levels of enzymes and were virtually identical to wild-type for growth on glucose media. The other glycolysis mutants had less than 5% of the normal levels of their respective enzyme activities. However, when transformed with a complementing high copy plasmid, the specific enzyme activities were substantially elevated above wild-type levels (typically 5-10 fold higher). The following Table 2 indicates the results.

In order to demonstrate that the hyperproduction of glycolytic enzymes was specific to the mutational defect complemented by the particular plasmid, assays for ten different glycolytic proteins were conducted on the various transformants. The following Table 3 reports the results for one transformant for each of the six different glycolysis genes which were examined in detail.

The GCR-8 transformant gave nearly wild-type levels of all ten enzymes, while PGI-19, TPI-10, PGK-2, GPM-2 and PYK-1 transformants overproduced their respective glycolytic proteins, but not other enzymes.

It was noted that the plasmids readily segregated (typically 5-50% segregation in fully grown cultures even under selective pressure of leucine prototrophy, so the assayed cultures probably contain cells with a range of number of plasmids. By complementation in E. coli and/or sequencing, TPI1 and PYK1 have both been shown to be the structural gene.

Exploitation of the promoter for TPI1 for the production of human .alpha..sub.1 -antitrypsin was demonstrated as follows. The plasmid CV13 was employed. CV13 can be maintained by selection of yeast with an average of about ten copies per cell. CV13 is comprised of pBR322, the replicon for the 2.mu.-plasmid and the yeast LEU2 gene. TPI1 promoter fragment was obtained by cutting the TPI1 gene at the unique KpnI site (bases 511 to 518); and the resulting linearized DNA was then treated with Ba131 for four to five minutes in order to remove the TPI1 structural sequences. Linkers, either EcoRI, Hind III or BamHI, were then inserted. The linkers will then cleave with the appropriate restriction enzyme to provide cohesive ends for insertion of human .alpha..sub.1 -antitrypsin genes. The human .alpha..sub.1 -antitrypsin gene was digested with BamHI, which cleaves at the 5'-terminus of the coding strand to remove the information for a single glutamic acid codon from the mature protein. Four different constructions were prepared, as set forth in the following Table 4. From this table it is noted that the glutamic acid codon is substituted by the codons for alanine and proline in three of the constructions having the initiator methionine.

After ligation of the human .alpha..sub.1 -AT construction into the CV13 plasmid, the resulting plasmid was transformed into S. c. N501-1B. The resulting yeast cells were then grown on a minimal synthetic medium.

Yeast cells containing the human .alpha..sub.1 -AT genes were broken open by vortexing with glass beads (0.45mm) at high speed for 2-3 minutes. The extraction buffer contained 50mM K.sub.2 HPO.sub.4, 2mM EDTA, 2mM 2-mercaptoethanol and 1 mM PMSF (pH7.4) cell debris was removed by centrifugation and the extracts contain 3-4mg/ml protein as determined by Lowry assays.

The presence of human .alpha..sub.1 -antitrypsin was determined using a RIA, employing tritium-labeled human .alpha..sub.1 -AT and antibody directed against the protein. The following Table 5 indicates the results.

It is evident from the above results that an immunologically active product is obtained, which is capable of competing with naturally occurring human .alpha..sub.1 -AT for antibodies to the native protein. Furthermore, the expression of the .alpha..sub.1 -AT gene is regulated by the TPI promoter, for as is seen, where a portion of the TPI promoter is removed, no .alpha..sub.1 -AT is produced. In addition, the production of the mammalian protein human .alpha..sub.1 -AT has not been optimized in the above study, so that the results indicate a minimum production of product which can be further enhanced. Thus, the TPI promoter is found to be an effective promoter for efficiently producing high yields of expression products of alien DNA.

It is evident from the above results that yeast promoters can be efficiently used for the production of foreign proteins by regulating the expression of alien DNA in yeast. The promoters are found to be strong promoters, so as to provide for a high degree of expression. Furthermore, it would appear that the messengers are sufficiently stable as to allow for a significant degree of translation into the desired expression product. Furthermore, by employing the glycolytic promoters and appropriate nutrient media, the expression of the alien DNA can be modulated. In this way, production of the alien DNA can be turned on and off. Thus, the subject invention provides a method for using yeast as efficient host in the production of foreign proteins, where the production may be modulated. In addition, by using the glycolytic regulation gene, one can turn on and off a plurality of glycolytic promoters.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modification may be practiced within the scope of the appended claims.