GENES WHICH INFLUENCE PICHIA PROTEOLYTIC ACTIVITY, AND USES THEREFOR

Abstract: The isolation and characterization of genes involved in proteolytic processing in species of the genus Pichia is described. The availability of such genes has enabled the generation of strains of Pichia that are deficient in proteolytic activity and useful as hosts for the expression of proteolytically sensitive recombinant products. The isolation and characterization of additional genes from species of the genus Pichia is also described, as well as uses therefor.

Description: GENES WHICH INFLUENCE PICHIA PROTEOLYTIC ACTIVITY, AND USES THEREFOR This invention relates to recombinant DNA technology. In a particular aspect, the present invention relates to yeast strains produced employing recombinant techniques, and DNA encoding proteins involved in proteolytic processing, as well as auxotrophic marker proteins. In another aspect, the present invention relates to methods of producing recombinant products, especially recombinant products which are susceptible to proteolytic degradation. BACKGROUND OF THE INVENTION Strains of the genus Pichia have been developed as an efficient expression system for the production of recombinant products. Unfortunately, however, some protein products which are desirably produced by recombinant means (e.g., IGF-1, EGF, GRF, and the like) are susceptible to degradation by proteases produced by the host organism. In such cases, even if high levels of the desired product are expressed, reduced product recoveries are sometimes realized due to degradation of the product in the presence of certain of the host strain's proteolytic enzymes. Product recovery is further complicated by the presence of various proteolysis degradation products. It would be desirable, in view of the excellent performance of the Pichia-based expression system for the production of many recombinant products, to reduce or eliminate certain proteolytic activities of Pichia . This would reduce the likelihood of degradation of protease-sensitive products when produced in recombinant Pichia hosts. Reduced likelihood of degradation would result in an enhanced ability to express and recover such products in substantially intact form. Various techniques can be applied in an effort to reduce or eliminate the problem of proteolytic degradation of recombinantly produced products. For example, one could modify the conditions under which recombinant strains are grown so as to inhibit protease activity. This could be accomplished, for example, by adjusting the pH of the medium sufficiently to inhibit the action of various proteases. This approach, however, may affect the ability of the host organism to express certain recombinant products (as well as the stability of the resulting product, once expressed) . Moreover, this approach is limited only to its effect on extracellular proteolysis. Alternatively, one could attempt to modify or eliminate some or all of the host organism's processing enzymes which are responsible for the proteolytic activity which degrades recombinantly produced, proteolytically sensitive products. Proteolytic processes in eukaryotic organisms are, however, quite complicated and involved. Thus, it is not possible to predict if elimination and/or modification of one or more of the enzyme(s) that are involved in proteolytic processing pathways will have an impact on the viability of the host cells, and/or the stability of the recombinantly produced products. Some of the proteolytic activities of the yeast Saccharomyces cerevisiae have been characterized. Proteinase A, for example, is encoded by the S . cerevisiae PEP4 gene. Proteinase A is a vacuolar, aspartyl protease capable of self-activation, as well as subsequent activation of additional vacuolar proteases, such as carboxypeptidase Y, and proteinase B. Although carboxypeptidase Y appears to be completely inactive prior to proteinase A-mediated proteolytic processing of the enzyme, proteinase B (encoded by the PRB-1 gene of S . cerevisiae) reportedly is approximately 50% bioactive in its precursor form, the form that exists prior to proteinase A-mediated processing of the enzyme. S . cerevisiae and filamentous fungi deficient in proteolytic activity have been used for the recombinant expression of heterologous peptides. These organisms, however, differ substantially from the methylotrophic yeast, Pichia . There are numerous metabolic and physiological differences between Saccharomyces, Aspergillus, and Pichia , so that the proteolytic processing systems of these various organisms are not necessarily similar. Indeed, very little is presently known regarding the types of proteolytic activities present in Pichia . In addition, unlike Saccharomyces or Aspergillus, Pichia cells used for the recombinant expression of heterologous peptides are typically grown to high cell density, which has been made possible, at least in part, by selection of strains which minimize the occurrence of foaming during the fermentation process. Selection of such cells is accomplished by selecting for cells which produce large amounts of endo- and exo-proteases, which reduce foaming by reducing the size of proteins secreted into the medium. Furthermore, while growth at high cell density the production of heterologous peptides in high yields, growth at high cell density also provides for a relatively high level of vacuolar proteases in the fermentation medium. The high cell density is accompanied by the release of substantial quantities of cellular material into the media, including vacuolar proteases, since -1% of cells typically undergo lysis during yeast fermentation. Therefore, during the production of heterologous peptides in a high cell density process, some of the secreted, heterologous peptides produced by Pichia could be subjected to substantial proteolysis. Therefore, it is an object herein, to provide protease deficient strains of Pichia and to provide means for generating such strains. It is also an object to use the protease deficient strains for expression of heterologous proteins. SUMMARY OF THE INVENTION In accordance with the present invention, we have isolated and characterized genes involved in proteolytic processes of species of the genus Pichia . The availability of such genes provides a means to generate strains of Pichia which are deficient in proteolytic activity and which are useful as hosts for the expression of proteolytically sensitive products. The strains of Pichia which have been modified so as to be defective in proteolytic activity, compared to wild-type Pichia cells, are excellent hosts for the expression of recombinant constructs encoding proteolytically sensitive products. The advantage of high levels of recombinant product expression using the Pichia expression system, coupled with the low level of proteolytic activity in the protease-deficient host cells provided herein, provides a highly efficient expression system for the production of proteolytically sensitive products. In accordance with another embodiment, a gene that encodes the Pichia orotidine-5•-phosphate decarboxylase protein (the URA3 gene) is provided. The availability of this gene, in combination with strains of Pichia which are Ura " , provides a selection system for use in producing recombinant strains of Pichia which are deficient in proteolytic activity. Such Ura" strains are also useful as hosts for transformation with recombinant DNA constructs, which are then used for the recombinant expression of a variety of heterologous products. BRIEF DESCRIPTION OF THE FIGURES Figure 1 is a restriction map of a Pichia paεtoris gene which influences the carboxypeptidase Y activity of Pichia . Figure 2 is a restriction map of plasmid pEP202. Figure 3 is a restriction map of plasmid pEP205. Figure 4 is a restriction map of plasmid pEP301. Figure 5 is a restriction map of plasmid pDR401. Figure 6 is a restriction map of plasmid pPU201. Figure 7 is a restriction map of plasmid pPU202. Figure 8 is a restriction map of plasmid pPU203. Figure 9 is a restriction map of plasmid pPU205. Figure 10 is a restriction map of plasmid pPU206. Figure 11 is a restriction map of plasmid pDR421. Figure 12 is a restriction map of the Pichia pastor iε orotidine-5'-phosphate decarboxylase gene (i.e., the URA3 gene) . Figure 13 summarizes the steps employed in the construction of pDR601 and pDR602. Figure 14 is a restriction map of plasmid pDR601. Figure 15 is a restriction map of plasmid pDR602. Figure 16 is a restriction map of plasmid pDL521. Figure 17 is a restriction map of a portion of the Pichia pastoris proteinase B gene. Figure 18 is a restriction map of plasmid pDR911. DETAILED DESCRIPTION OF THE INVENTION In accordance with the present invention, there is provided an isolated DNA fragment obtained from a strain of the genus Pichia which comprises a gene encoding a protein which, directly or indirectly, influences the proteolytic activity of said strain. In accordance with another embodiment of the present invention, there is provided a method of producing modified strain(s) of the genus Pichia which are deficient in proteolytic activity, relative to host strain(s) of the same species which are not so modified, said method comprising: contacting said host strain(s) with a modified form of the above-described gene, wherein said modification renders the gene incapable of producing functional product, or alters the ability of the gene product to influence proteolytic activity, wherein said contacting is carried out under conditions suitable for the site- directed integration of said modified form of the above- described gene into the genome of said host strain(s) , wherein said site-directed integration occurs at the speci ic locus of said gene which encodes said protein which influences proteolytic activity. In accordance with yet another embodiment of the present invention, there are provided strains of the genus Pichia which are deficient in proteolytic activity. Such strains can be produced in a variety of ways, with the above-described method being the presently preferred way of producing such strains. In accordance with still another embodiment of the present invention, there is provided a method for the expression of proteolytically sensitive recombinant product(s), said method comprising expressing said proteolytically sensitive product(s) in the above- described Pichia cells which are deficient in proteolytic activity. In accordance with a further embodiment of the present invention, there is provided an isolated DNA fragment obtained from a species of the genus Pichia which comprises the orotidine-5'-phosphate decarboxylase gene. In accordance with a still further embodiment of the present invention, there is provided a yeast cell of the genus Pichia as a host capable of being transformed with recombinant DNA material, wherein said host is defective in the orotidine-5'-phosphate decarboxylase gene. As employed herein, the term "proteolytic activity" refers to any one or more of the enzyme activities displayed by enzymes involved in the proteolytic pathway. Proteolytic activities include proteinase A activity, proteinase B activity, carboxypeptidase Y activity, carboxypeptidase S activity, aminopeptidase C activity, dipeptidyl aminopeptidase activity, proteinase D activity, proteinase E activity, and the like. As used herein, a gene encoding a protein which, directly or indirectly, influences the proteolytic activity of a yeast strain, includes genes that encode proteinases or that encode proteins that act on proteinases. As used herein, a protein that acts on a protein refer to proteins that alter or modulate the activity of a proteinase. Thus, for example, a protein that directly influences proteolytic activity is a protein that encodes a proteinase, and a protein that indirectly influences proteolytic activity is a protein that activates or increases the activity of a protein by proteolytic processing. Saccharomyces cerevisiae proteinase is an example of a protein that directly and indirectly influences the proteolytic activity of Saccharomyces cerevisiae . In accordance with one embodiment of the present invention, the Pichia gene that encodes a protein which, directly or indirectly, influences at least the carboxypeptidase Y activity of strains of the genus Pichia has been identified and isolated from a species of the genus Pichia . This gene is referred to herein, for convenience, as the Pichia PEP4 gene, based on the existence of some similarity between this gene and the S. cerevisiae PEP4 gene. It should be recognized, however, that the nucleotide sequences of the Pichia gene and the Saccharomyces gene differ substantially. The Pichia PEP4 gene is characterized by the restriction map set forth in Figure 1 of the drawings. A fragment containing sequences encoding this gene can be readily obtained for easy handling from a variety of sources. One such source is the approximately 10.6 kbp EcoRI fragment of plasmid pEP202 (see Figure 2), or alternatively, the approximately 2.7 kbp EcoRI-SacI fragment of plasmid pEP301 (see Figure 4) . DNA encoding the proteinase A gene is also provided. The proteinase A gene of the present invention can be further characterized by reference to the amino acid sequence set forth in Sequence ID No. 2. DNA having any nucleic acid sequence which encodes substantially the same amino acid sequence as set forth in Sequence ID No. 2 or that has sufficient homology to be useful for disruption of homologous genes can be employed in the practice of the present invention. An exemplary nucleic acid sequence which encodes the above-described amino acid sequence is set forth in Sequence ID No. 1. The Pichia gene that encodes a protein which, directly or indirectly, influences the proteolytic activity of strains of the genus Pichia can be modified in a variety of ways, so as to render the gene incapable of producing functional product, or so as to alter the ability of the gene product to influence the proteolytic activity of said Pichia strain(s) . Those of skill in the art recognize that there are many methods for the modification of the above-described gene. For example, the coding sequence can be mutated to modify the amino acid sequence of the protein encoded by the -gene. Alternatively, various portions of the coding sequence can be deleted from the gene. The deletion need only be sufficient to render the expressed product (if it is still capable of being expressed) non-functional. Thus, a deletion of even one nucleotide, by throwing the remaining coding sequence out of reading frame, can render a product, if still capable of expression, non¬ functional. Of course, larger deletions can result in a complete lack of expression of product, or can cause a substantially modified product to be expressed, and such a product is likely to have very different proteolytic properties, if any, relative to product produced by intact gene. As yet another alternative, additional sequences can be inserted into the coding sequence to disrupt the reading frame of the gene of interest, which would cause a dramatically altered product to be expressed, or a complete lack of expression of the product. A particularly convenient method for the modification of the Pichia gene that encodes a protein which, directly or indirectly, influences the proteolytic activity of strains of the genus Pichia is to insert an auxotrophic marker gene into said Pichia gene, thereby disrupting the Pichia gene. Such auxotrophic marker genes can be selected from the Pichia or Saccharomyces HIS4 gene , the Pichia or Saccharomyces ARG4 genes, the Pichia or Saccharomyces URA3 genes, and the like. Strains of Pichia deficient in proteolytic activity can be prepared in a variety of ways. The presently preferred method involves modifying, in a suitable host, genes of the present invention (which genes, in their unmodified form, encode a product which, directly or indirectly, affects the proteolytic activity of strains of the genus Pichia) . Alternatively, host strains can be subjected to random (i.e., non-selective) mutagenesis. then screened to select for mutants which are deficient in proteolytic activity. When proteolytically deficient strains are produced by modifying the gene of the invention in a host, such modifying is carried out, for example, by introducing a modified gene under transformation conditions suitable for the site-directed integration of the modified gene into the genome of the host at the specific locus of such gene which encodes a protein which influences proteolytic activity (i.e., the target gene). Integration will replace or alter the host's endogenous gene. A convenient means to introduce the modified gene into the target locus of a yeast host is to include the modified gene in a linear DNA fragment having ends homologous to two separate portions of the intact gene within the host. This will direct, upon transformation, homologous recombination occur at the specific locus of the gene whose expression product influences proteolytic activity. When Pichia strains deficient in proteolytic activity are prepared by the preferred method described above (i.e., by introducing a modified gene of the invention into a suitable host by site-directed integration at the specific locus of the gene whose expression product influences proteolytic activity, thereby replacing all or a portion of the endogenous gene with all or a portion of the modified gene) , the endogenous gene is said to be disrupted. As used herein, the term gene "disruption" refers to any manipulation of the target locus that ultimately results in the presence of a gene that does not yield a functional product, or that yields a product with altered function. Disruption can, therefore, result from the presence of added sequence (e.g., by the introduction of auxotrophic marker, or by the introduction of any sequence which causes a shift in the reading frame) , the loss of nucleotides from the target gene (e.g., by deletion) , or other mutations of the target gene. For the preferred method of preparing Pichia strains deficient in proteolytic activity, gene disruption is achieved by gene addition, gene replacement, or a combination of addition and replacement referred to herein as "pop-in-pop-out". In gene replacement, the endogenous target gene is physically removed from the target locus, and replaced with the modified gene. This is accomplished by transforming the host with a linear fragment having ends which are homologous to the 5' and 3' ends of the target gene, respectively. Gene addition involves adding the transforming DNA to the endogenous target gene. Depending on the manner in which the modified gene of the transforming DNA was altered, gene addition can result in the presence of either two non¬ functional copies of the target gene, or one functional and one non-functional copy of the target gene. Each of the two copies consists of a portion of the endogenous gene, and a portion of the transforming DNA. If a functional copy of the target gene remains after gene addition, it can then be removed by homologous recombination between the two copies of the target gene. The combination process of gene addition followed by homologous recombination constitutes the pop-in-pop-out process. Methods of transforming yeast of the genus Pichia , as well as methods applicable for culturing such yeast cells, are known generally in the art. Constructs containing the above-described modified gene are transformed into Pichia cells either by the spheroplast technique, described by Cregg et al., in Mol. Cell. Biol. 5:3376 (1985) and U.S. 4,879,231, or by the whole-cell lithium chloride yeast transformation system [Ito et al., Aσric. Biol. Chem. 48_:341 (1984)], with modification necessary for adaptation to Pichia [See European Patent Application No. 312,934; also available as U.S. Pat. No. 4,929,535]. The whole-cell lithium chloride method is frequently more convenient in that it does not require the generation and maintenance of εpheroplasts. For the purpose of the present invention, the spheroplast method is preferred because the spheroplast method is generally a more efficient means of transformation. Those of skill in the art recognize that host Pichia strains for transformation with the above-described modified gene can be wild-type Pichia cells, which upon transformation with a defective gene from the proteolytic pathway, could be screened for reduced proteolytic activity. The host strains employed can have one or more defects therein, to assist in the identification and selection of desired transformants. Preferred hosts employed for transformation with a modified form of the gene which encodes a protein which, directly or indirectly, influences the proteolytic activity of strains of Pichia , is a strain which is defective in at least one auxotrophic marker gene. The use of such host organisms is preferred because simultaneous transformation of such a host with the modified form of the invention gene and an auxotrophic marker gene enables rapid selection of strains which have incorporated the transforming DNA, and thus, should have a disrupted form of the gene which encodes a protein which directly or indirectly influences the proteolytic activity of the host. Exemplary auxotrophic marker genes useful in the practice of the present invention (i.e., marker genes that are defective in the preferred host strains employed herein) include the histidinol dehydrogenase gene, the argininosuccinate lyase gene, or the orotidine-5•-phosphate decarboxylase gene, and the like. When employing such host strains in the transformation of Pichia , the above-described modified gene, included on a linear DNA fragment, is preferably associated with an intact form of the auxotrophic marker gene for which the host strain is defective, e.g., the auxotrophic marker gene either is contained within the modified gene, or is located 5' or 3' of the modified gene on the transforming linear DNA fragment. Exemplary host strains contemplated for use in the practice of the present invention include the HIS4-defective Pichia strain, GS115 (ATCC 20864), the ARG4-defective Pichia strain, GS190, the HIS4/URA3-defective Pichia strain, GS4-2, the HIS4/ARG4-defective Pichia strain PPFl (NRRL Y-18017; see U.S. 4,812,405), and the like. An exemplary fragment of DNA which contains the above-described modified gene having inserted therein a functional gene encoding histidinol dehydrogenase can be obtained from the approximately 5.3 kbp SacI-EcoRI fragment of plasmid pDR401. Another exemplary fragment of DNA which contains a modified form of the above-described gene (located 5 1 of a functional gene encoding orotidine-5•-phosphate decarboxylase) can be obtained from the approximately 5.0 kbp Bglll fragment of plasmid pDR421. A particularly advantageous application of the Pichia strains that are deficient in proteolytic activity is for the expression of proteolytically sensitive recombinant products, such as, for example, epidermal growth factor (EGF) , growth hormone releasing factor (GRF) , insulin-like growth factor-1 (IGF-1) , and the like. When expressed in recombinant Pichia strains, which are deficient in proteolytic activity, the resulting recombinant product is subjected to a reduced level of proteolytic activity, due to modifications in the proteolysis apparatus of the host organism. Proteolytically deficient Pichia expression systems for the production of proteolytically sensitive products can be generated in a variety of ways. For example, Pichia host strains can be rendered proteolytically deficient, as described hereinabove, and then further transformed with DNA encoding a heterologous protein of interest (especially a proteolytically sensitive protein) . Alternatively, a recombinant Pichia strain already bearing DNA encoding a heterologous protein of interest can thereafter be rendered proteolytically deficient, for example, as described hereinabove. As yet another alternative, a Pichia strain could be co-transformed with the above described modified gene and a DNA encoding a heterologous, proteolytically sensitive protein of interest. The use of strains of the genus Pichia as host strains in the recombinant expression of peptide products has previously been described in great detail. The presently preferred yeast species for use in the practice of the present invention is Pichia pastoris , a known industrial yeast strain that is capable of efficiently utilizing methanol as the sole carbon and energy source. There are a number of methanol-responsive genes in methylotrophic yeast, the expression of each being controlled by methanol-responsive regulatory regions (also referred to as promoters) . Any of such methanol- responsive promoters are suitable for use in the practice of the present invention. Examples of specific regulatory regions include the promoter for the primary alcohol oxidase gene from Pichia pastoris AOXl, the promoter for the secondary alcohol oxidase gene from P. pastoris AOX2 (P. pastoris is known to contain two functional alcohol oxidase genes: alcohol oxidase I (AOXl) and alcohol oxidase II (AOX2) ; the coding portions of the two AOX genes are closely homologous at both the DNA and the predicted amino acid sequence levels and share common restriction sites; the proteins expressed from the two genes have similar enzymatic properties but the promoter of the AOXl gene is more efficient and gene products are frequently more highly expressed therefrom) , the promoter for the dihydroxyacetone synthase gene from P. pastoris (DAS) , the promoter for the P40 gene from P. pastoris , the promoter for the catalase gene from P. pastoris , the promoter for the formaldehyde dehydrogenase gene from P. pastoris, the promoter for the formate dehydrogenase gene from P. pastoris , and the like. The presently preferred promoter region for regulating expression of a gene encoding a proteolytically sensitive product, in P. pastoris hosts, is the promoter of the methanol-regulated primary alcohol oxidase gene of P. pastoris . The AOXl gene, including its promoter, has been isolated and thoroughly characterized; see Ellis et al.. Mol. Cell. Biol. 5_: 1111 (1985) and U.S. Patent No. 4,855,231. The presently preferred expression cassette used in transforming Pichia cells for the generation of recombinant protein-expressing strains comprises, in the reading frame direction of transcription, the following DNA sequences: (i) a promoter region of a methanol-responsive gene of a methylotrophic yeast, (ii) a DNA sequence encoding a polypeptide consisting essentially of: (a) an optional secretion signal sequence, and (b) a heterologous protein of interest; and (iii) a transcription terminator functional in a methylotrophic yeast; wherein said DNA sequences are operationally associated with one another for transcription of the sequences encoding said polypeptide. DNA sequences encoding a secretion signal sequence which are optionally contained in expression vectors used in the practice of the present invention include the DNA encoding the native secretion signal sequence associated with the proteolytically sensitive product, the DNA encoding the S . cerevisiae α-mating factor (αMF) leader sequence, (including a DNA sequence encoding the processing site, lys-arg) , and signal sequences that function as such in methylotrophic yeast cells, such as the bovine lysozyme C signal sequence. The transcription.terminator functional in a methylotrophic yeast used in accordance with the present invention has either (a) a subsegment which provides a polyadenylation signal and polyadenylation site in the transcript, and/or (b) a subsegment which provides a transcription termination signal for transcription from the promoter used in the expression cassette. The term "expression cassette" as used herein, and throughout the specification and claims, refers to a DNA sequence which includes sequences functional for the expression process. The entire transcription terminator is taken from a protein-encoding gene, which may be the same or different from the gene which is the source of the promoter. In the DNA constructs of the present invention, used to transform hosts for recombinant expression of proteolytically sensitive products, the segments of the expression cassette(s) are said to be "operationally associated" with one another. The DNA sequence encoding proteolytically sensitive products is positioned and oriented functionally with respect to the promoter, the secretion signal sequence, if employed, and the transcription terminator. Thus, the polypeptide-encoding segment is transcribed, under regulation of the promoter region, into a transcript capable of providing, upon translation, the desired polypeptide. Appropriate reading frame positioning and orientation of the various segments of the expression cassette are within the knowledge of persons of ordinary skill in the art; further details are given in the Examples. For the practice of the present invention it is preferred that hosts for the recombinant expression of proteolytically sensitive products be transformed with multiple copies of the above-described expression cassettes contained on one DNA fragment, preferably in a head-to-tail orientation. In addition, when DNA constructs according to the invention are used to transform hosts for the recombinant expression of proteolytically sensitive products by site-directed integration, the expression cassette- containing construct is a linear DNA fragment that is directed to the desired locus of the host to effect integration of the DNA fragment therein. One-step gene integrations are usually successful if the DNA to be introduced has as little as 0.2 kb homology with the fragment locus of the target gene; it is however, preferable to maximize the degree of homology for efficiency. The DNA constructs used according to the invention to transform hosts for the recombinant expression of proteolytically sensitive products optionally further comprise a selectable marker gene, in addition to one or more expression cassettes. For this purpose, any selectable marker gene functional in methylotrophic yeast may be employed, i.e., any gene which confers a phenotype upon methylotrophic yeast cells, thereby allowing them to be identified and selectively grown from among a vast majority of untransformed cells. Suitable selectable marker genes include, for example, selectable marker systems composed of an auxotrophic mutant P. pastoris host strain and a wild-type biosynthetic gene which complements the host's defect. For transformation of HIS4' P. pastoris strains, for example, the S. cerevisiae or P. pastoris HIS4 gene may be employed, or for transformation of ARG4' mutant P. pastoris strains, the S. cerevisiae ARG4 gene or the P. pastoris ARG4 gene may be employed, or for transformation of URA3' mutant P. pastoris strains, the S . cerevisiae URA3 gene or the P. pastoris URA3 gene may be employed. In addition, DNA constructs used to transform hosts for the recombinant expression of proteolytically sensitive products according to this aspect of the invention optionally further comprise selectable marker genes which are functional in bacteria. Thus, any gene can be used which confers a phenotype on bacteria that allows transformed bacterial cells to be identified and selectively grown from among a vast majority of untransformed cells. This additional selectable marker enables DNA of the invention to be transformed into bacteria such as E. coli for amplification. Suitable selectable marker genes include the ampicillin resistance gene (Amp r ) , tetracycline resistance gene (Tc r ) , and the like. When it is contemplated to pass DNA of the invention though bacterial cells, it is desirable to include in the DNA construct a bacterial origin of replication, to ensure the maintenance of the invention DNA from generation to generation of the bacteria. Exemplary bacterial origins of replication include the fl-ori, colisin, col El, and the like. The term "expression vector", as employed herein, is intended to include vectors capable of expressing DNA sequences contained therein, where such sequences are in operational association with other sequences capable of effecting their expression, i.e., promoter sequences. In general, expression vectors usually used in recombinant DNA technology are often in the form of "plasmids", i.e., circular, double-stranded DNA loops, which in their vector form are not bound to the chromosome. In the present specification the terms "vector" and "plasmid" are used interchangeably. However, the invention is intended to include other forms of expression vectors as well, which function equivalently. Methods of transforming yeast of the genus Pichia , as well as methods applicable for culturing such yeast cells, are known generally in the art. According to the invention, constructs containing the above-described modified gene and/or expression cassettes encoding the production of heterologous, proteolytically sensitive products are transformed into Pichia cells either by the spheroplast technique, or by the whole-cell lithium chloride yeast transformation system, as described above. Transformed strains, which are of the desired phenotype and genotype, are grown in fermentors in either batch or continuous mode. For the large-scale production of recombinant DNA-based products in methylotrophic yeast, a three-stage, high cell-density fermentation system is the presently preferred fermentation protocol employed. In the first, or growth stage, expression hosts are cultured in defined minimal medium with an excess of a non-inducing carbon source (e.g., glycerol) . When grown on such carbon sources, heterologous gene expression is completely repressed, which allows the generation of cell mass in the absence of heterologous protein expression. It is presently preferred, during this growth stage, that the pH of the medium be maintained at about 5, because the P. paεtoris cells generally prefer a pH of about 5 for optimal growth. Next, a short period of non-inducing carbon source limitation growth is allowed to further increase cell mass and derepress the methanol-responsive promoter. The pH of the medium during this limitation growth period is maintained at an appropriate pH value (the actual pH employed is a function of the particular host strain used for expression and the specific product being expressed) . Subsequent to the period of growth under limiting conditions, methanol is added in the fermentor either on a continuous basis, with concurrent removal of product via the broth; or on a batch-wise basis wherein methanol is added at such a rate that the methanol content of the broth is maintained at a low level (referred to herein as "methanol excess fed-batch mode") . The addition of methanol induces the expression of the gene driven by a methanol-responsive promoter. This third stage is referred to as the production stage, because it is at this stage that the majority of the recombinant product is expressed. The pH of the medium during the production stage is maintained at an appropriate pH value (the actual pH employed is a function of the particular host strain used for expression and the specific product being expressed) . The term "culture" means a propagation of cells in a medium conducive to their growth, and all sub-cultures thereof. The term "subculture" refers to a culture of cells grown from cells of another culture (source culture) , or any subculture of the source culture, regardless of the number of subculturing steps that have been performed between the subculture of interest and the source culture. According to a preferred embodiment of the present invention, the heterologous protein expression system used for the production of proteolytically sensitive products utilizes the promoter derived from the methanol- regulated AOXl gene of P. paεtoriε, which is very efficient and tightly regulated. This gene can be the source of the transcription terminator as well. The presently preferred expression cassette comprises, operationally associated with one another, the P. paεtoriε AOXl promoter, optional DNA encoding a secretion signal sequence, a DNA sequence encoding a proteolytically sensitive product (e.g., mature IGF-1, EGF, GRF, and the like) , and a transcription terminator derived from the P. paεtoris AOXl gene. Preferably, two or more of such expression cassettes are contained on one DNA fragment, in head-to-tail orientation, to yield multiple expression cassettes on a single contiguous DNA fragment. The presently preferred host cells to be transformed with multiple expression cassettes are P. pastoris cells having at least one mutation that can be complemented with a marker gene present on a transforming DNA fragment. Preferably HIS4' (GS115) or ARG4 ' (GS190) single auxotrophic mutant P. paεtoriε strains are employed, or HIS4-/URA3- (GS4-2) or HIS4-/ARG4 ' (PPFl) double auxotrophic mutant P. paεtoris strains are employed. The fragment containing one or more expression cassette(s) is inserted into a plasmid containing a marker gene complementing a metabolic defect in the host, and optionally containing additional sequences such as bacterial marker genes, yeast DNA sequences which direct vector integration, and the like. In accordance with a specific embodiment of the present invention, there is provided an isolated DNA fragment obtained from a species of the genus Pichia which comprises the orotidine-5'-phosphate decarboxylase gene. The orotidine-5'-phosphate decarboxylase gene is frequently referred to as URA3 . It can be used, for example, to complement URA3-deficient strains. Another use for the novel gene is the ability to target DNA into a specific locus of the Pichia genome (i.e., into the URA3 locus) . This novel gene can be characterized by reference to the restriction map shown in Figure 12. Alternatively, this novel gene can be characterized as encoding a protein having substantially the same amino acid sequence as set forth in Sequence ID No. 4. While those of skill in the art recognize that the above- referenced amino acid sequence can be encoded by a variety of nucleotide sequences, a presently preferred nucleotide sequence encoding the above-referenced amino acid sequence is substantially the same as that set forth in Sequence ID No. 3. In accordance with another specific embodiment of the present invention, there are provided yeast cells of the genus Pichia as a host capable of being transformed with recombinant DNA material, wherein the host is defective in the orotidine-5'- phosphate decarboxylase gene. Host strains defective in the URA3 gene can be used for transformation with DNA containing an intact form of the L7. A3 gene, thereby enabling a ready determination of whether the desired transformation event has occurred (by return of successfully transformed cells to uracil prototrophy) . The combination of URA3 ~ Pichia strains and the Pichia orotidine-5•-phosphate decarboxylase marker gene provides a particularly useful selection system for use in producing recombinant strains of Pichia deficient in proteolytic activity. Such a selection system is referred to herein as a "bidirectional selection process". This selection system for the generation of Pichia strains which are deficient in proteolytic activity uses a "pop-in-pop-out" gene disruption technology in which a DNA fragment containing a defective gene is added to the genome of a host organism, with subsequent removal of portions of the DNA fragment and endogenous sequences from the host through homologous recombination between the endogenous target gene sequence and the integrated vector sequence. Initially, transformants are selected for incorporation of the disruption vector which contains a marker gene such as XJRA3 (i.e., the "pop-in" step). Next, the selected transformants must be screened to identify strains in which a recombination event between endogenous gene sequences and integrated vector sequences has occurred and has thereby excised portions of the vector, including the marker gene, and endogenous sequences of the host (i.e., the "pop-out" step). A double selection system based on the URA3 gene and URA3 ~ hosts provides for the sequential identification of the desired strains. This type of gene disruption is typically conducted in Ura " strains, which can be identified by resistance to 5-fluoro-orotic acid (5-FOA) . Disruption vectors contain a defective copy of the target gene to be disrupted and a functional URA3 gene. Integration of the disruption vector into the genome of the Ura" host cells generates Ura + transformants containing one functional target gene and one non-functional (i.e., defective) target gene. Ura + transformants are easily identified by their ability to grow in the absence of uracil. In order to isolate strains in which a recombination event has resulted in the elimination of the functional target gene, leaving only a defective gene, the Ura + transformants are screened for restoration of 5-FOA resistance resulting from the loss ("pop-out") of the URA3 gene which accompanies recombination. The regeneration of the URA3 genotype enables repetition of the "pop-in-pop-out" process for the subsequent disruption of other genes in the genome. To use this selection system for the generation of Pichia strains which are deficient in proteolytic activity, a URA3 ' host is transformed with a DNA construct containing a modified form of a gene encoding a protein involved in the Pichia proteolytic pathway, and the URA3 gene. Site-directed integration of the transforming DNA by gene addition (i.e., "pop-in") yields one functional and one non¬ functional gene at the locus of the gene which directly or indirectly influences proteolytic activity, as well as an intact URA3 gene. Strains which incorporate the URA3 gene are identified by positive selection (using techniques well known to those of skill in the art, e.g., by growing the strains on minimal media lacking uracil and selecting those strains capable of growth on such media) . The configuration of the functional, non- functional and URA3 genes at the locus of the gene which encodes a protein which influences proteolytic activity enables recombination to occur between the functional and non-functional genes, resulting in the loss of one of these genes and the URA3 gene (i.e., "pop-out"). Thereafter, it is possible to positively select for strains lacking a functional URA3 gene by plating cells on medium containing a non-toxic analog of a uracil pathway intermediate, 5-fluoro-orotic acid (5-FOA) , which, when metabolized by URA3 + strains, produces a compound toxic to the cells. Because URA3 ~ strains blocked at a specific point in the uracil pathway do not metabolize 5-FOA, they are not subjected to its toxic effects, and can thus be referred to as "5-FOA resistant". In contrast, URA3 + strains metabolize 5-FOA to produce a toxic compound which will prevent growth of the URA3 + cells. The resulting URA3' cells that also lack the functional target gene are deficient in proteolytic activity. Because the URA3 ~ phenotype is restored, the resulting cells can be transformed again using the URA3 gene as a selectable marker. The ability to positively select strains lacking a functional URA3 gene employing a toxic analog of a uracil pathway intermediate allows the use of this very convenient "pop-out" method for imparting multiple phenotypic changes in Pichia hosts. C7JRA3" Pichia strains which are also deficient in proteolytic activity, relative to the proteolytic activity present in wild-type strains of the same species, are particularly useful for transformation with expression vectors which contain an intact form of the URA3 gene, and a gene encoding a proteolytically sensitive product (either as part of the same vector, or as a second vector which is transformed into the host) . Those transformants which return to uracil prototrophy (which can be readily determined by simple screening procedures) should have incorporated therein the gene encoding a proteolytically sensitive product, and thus would be directly applicable to product expression. The invention will now be described in greater detail by reference to the following non-limiting examples. EXAMPLES EXAMPLE I: ISOLATION OF THE P. PASTORIS PEP4 GENE The P. pastoris PEP4 gene was identified in a bacteriophage lambda-based EMBL3 P. paεtoriε genomic DNA library by its ability to hybridize with a radiolabeled fragment of the homologous Saccharomyces cerevisiae PEP4 gene. The P. paεtoriε PEP4 gene was cloned by isolating positive plaques containing the hybridizing recombinant phage DNA. A. Construction of a P. pastoris EMBL3 Genomic DNA Library Bacteriophage λ was used as a vehicle for cloning the P. paεtoriε PEP4 gene. Fragments of a partial Sau3A digest of P. paεtoris genomic DNA were inserted into the bacteriophage λ vector EMBL3 [Frischauf, A.-M. et al. (1983). J. Mol. Biol. 170:827] . which contains elements of the bacteriophage λ genome essential for propagation of the recombinant DNA in bacterial hosts. The P. paεtoriε DNA-containing EMBL3 vectors were packaged in vitro into infectious virions to yield a bacteriophage λ P. paεtoriε genomic DNA library. Amplification of the library was achieved by propagation of the recombinant DNA in Escherichia coli host cells that had been infected with the recombinant virus. Pichia paεtoriε genomic DNA (from strain NRRL Y-11430, from the Northern Regional Research Center, Peoria, IL) isolated using a glass rod swirl technique [Cregg et al. Mol. Cell. Biol. 5.:3376-3385 (1985)] was digested with Sau3A at an effective concentration of 0.1 u/μg in 7, 14, 21 and 28 minute incubations conducted at 37°C. An aliquot from each incubation mixture was electrophoretically separated on a 1% agarose gel to determine the sizes of the digested DNA fragments. Digests incubated for 7 and 14 minutes appeared to consist primarily of 9-23 kb fragments. These digests were pooled and ligated to EMBL3 vector arms, prepared as described below. EMBL3 vector arms were prepared by double digestion of the vector (obtained from EMBL3 Cloning Kit, Stratagene Cloning Systems, San Diego, CA; catalog #241211) with BamHI and EcoRI. The small Ba HI/EcoRI linker that separates the arms from the stuffer fragment was removed from the digest by selective precipitation with ethanol. Ligation of the Sau3A-di ested Pichia genomic DNA (0.5 μg) to 1 μg of EMBL3 pre-digested arms was accomplished by incubation of the 5-μl reaction mixture at 4°C for two days. The recombinant bacteriophage λ DNA prepared by ligation of P. paεtoriε genomic DNA fragments and EMBL3 vector arms was packaged in vitro using commercial packaging extracts (Stratagene EMBL3 Cloning Kit) . The EMBL3-based P. pastoris genomic library was amplified by plating the recombinant phage along with the E. coli lysogenic host strain P2 392 (provided in Stratagene EMBL3 Cloning Kit) which contains prophage P2. Wild-type bacteriophage do not grow in E. coli strain P2 392. Recombinant EMBL3-based bacteriophage, which lack two of the wild-type genes that confer P2 sensitivity, are able to grow well in this P2-containing E. coli strain. The use of E. coli P2 392 as the host strain in the amplification ensured that only recombinant phage would be reproduced in the bacterial host. All of the plates encompassing the EMBL3-based P. pastoriε genomic DNA library were overlayed with SM buffer (5.8 g NaCl, 2g MgS0 4 H 2 0, 50 ml 1M TrisΗCl, pH 7.5, and 5 ml 2% gelatin per liter). After five hours, the supernatants were collected and pooled, and the titer and genome equivalents were calculated according to the manufacturer's instructions. The library contained approximately 10 genome equivalents, and its titer was 6 X 10" plaque-forming units/ml (pfu/ml) . B. Screening of the EMBL3 P. paεtoris Genomic DNA Library Using the S. cerevisiae PEP4 Gene as a Probe In order to adequately screen the Pichia genome for the PEP4 gene, 50,000 recombinant phage and the E. coli lysogenic host strain LE 392 (provided in Stratagene EMBL3 Cloning Kit) were plated onto four large 150-mm plates. After 6-7 hours of growth, the plates were chilled to 4°C. Each plate was marked and duplicate plaque lifts of each plate were prepared by placing nitrocellulose onto each plate. The filters were denatured, neutralized, baked and probed with the S . cerevisiae PEP4 gene [a gel-purified, 32 P-labeled 4.0 kb fragment of S . cerevisiae DNA containing the S. cerevisiae PEP4 gene obtained from the laboratory of Thomas Stevens, University of Oregon, Eugene, Oregon; see Rothman et al., Proc. Natl. Acad. Sci. USA .83.: 3248-3252 (1986)]. Hybridization was conducted at 37°C in a solution containing 30% formamide, 6 X SSC, 5 X Denhardt's solution, 20 mM TrisΗCl, pH 8.0, 1 mM EDTA, 0.1% SDS and 100 μg/ml salmon sperm DNA. After hybridization, the filters were washed three times at room temperature using 2 X SSC and 0.1% SDS. Following these initial washes, the filters were then washed twice at 55°C using 2 X SSC and 0.1% SDS. Fifteen positive plaques containing DNA that hybridized to the fragment of the S . cerevisiae PEP4 gene were identified in duplicate from autoradiograms of the filters. The area around each of the 15 positive plaques was isolated and placed in SM buffer. Six of the isolates were plated at dilutions of 10" 5 and 10" 7 with E. coli strain LE 392 onto smaller 100-mm plates. Single plaque lifts of each plate were probed with the S. cerevisiae PEP4 gene fragment under the same hybridization and wash conditions used in the first plaque screening. In this second round of screening, 12 positive plaques were detected on the autoradiogram. Nine of these single plagues were isolated and placed in SM buffer. Each of these nine plaques was plated at dilutions of 10 "5 and 10" 7 with E. coli strain LE 392 onto small 100-mm plates. Again, single plaque lifts of each plate were probed with the S . cerevisiae PEP4 gene fragment under the same hybridization and wash conditions used in the first two screenings. Each plate contained approximately 10-20 plaques distributed evenly across the plate. Autoradiograms of the filters revealed that every plaque on each plate hybridized to the PEP4 probe. Five separate plaques from different plates were isolated and placed in SM buffer. DNA from large-scale cultures of three of these isolates, designated 4721, 5111 and 5131, respectively, was prepared using the induction method of bacteriophage isolation [Maniatis, T. , Fritsch, E.F. and Sambrook, J. Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA (1982)] in order to identify, characterize and subclone the PEP4 gene contained in the recombinant phage. C. Characterization of the Insert in Isolates of the EMBL3 P. pastoris Genomic DNA Library that Hybridized to the S. cerevisiae PEP4 Gene Recombinant phage DNA prepared from the three isolates, referred to above, from the EMBL3 Pichia genomic DNA library (4721, 5111 and 5131), were digested with various restriction endonucleases, separated on a 0.8% agarose gel and visualized by ethidium bromide staining. In addition, 1 μl aliquots of these digests were separated on a second agarose gel which was blotted onto nitrocellulose and probed with the radiolabeled S . cerevisiae PEP4 gene fragment. Hybridization was conducted at 37°C in a solution containing 30% formamide, 6 X SSC, 5 X Denhardt's solution, 20 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.1% SDS and 100 μg/ml salmon sperm DNA. The filter was then washed in three 5-minute washes at room temperature with 2 X SSC and 0.1% SDS followed by two 5- inute washes at 55°C with 2 X SSC and 0.1% SDS. Identical digests of DNA from two of the clones, 5111 and 5131, yielded the same pattern of restriction enzyme fragments, as determined by ethidium bromide staining, whereas the same digest of DNA from the third clone, 4721, yielded a different fragment pattern. Analysis of the restriction enzyme fragments of DNA from each clone by Southern blot hybridization to the S. cerevisiae PEP4 gene fragment revealed that the two classes of clones both contained a series of hybridizing fragments of the same size indicating that the two classes of clones had a common overlapping DNA sequence that hybridized with the probe. D. Subcloning and Characterization of the Cloned P. pastoris PEP4 Gene As determined by Southern blot hybridization of EcoRI-digested P. pastoris genomic DNA using the homologous S. cerevisiae PEP4 gene as a probe, the P. pastoris PEP4 gene is contained within a 10.6 kb EcoRI fragment of the P. paεtoriε genome. Southern blot hybridization of EcoRI-digested DNA of clone 4721, as described in Example IC, revealed that it contained a 10.6 kb fragment that hybridized to the S . cerevisiae PEP4 gene. To facilitate manipulation of the cloned P. pastoris PEP4 gene, P. paεtoriε genomic DNA contained on an EcoRI fragment of DNA from isolate 4721 was subcloned into pUC19. Clone 4721 (25 μg) was digested with EcoRI (60 units) in a total volume of 300 μl. The digested DNA was separated on a 0.65% agarose gel, and the 10.6 kb EcoRI fragment was isolated with DE81 paper. The purified fragment was washed from the paper with 400 μl of 1 M NaCl and extracted with phenol/chloroform. The DNA was then precipitated with ethanol and resuspended in water to a total volume of 10 μl. Approximately 50 ng of the 10.6 kb fragment were ligated with an equal amount of pUC19 which had been cut with EcoRI and dephosphorylated. The ligation mixture was used to transform E. coli strain MC1061. Ampicillin-resistant colonies were selected and screened by analysis of restriction enzyme digests of colony DNA for the presence of the diagnostic 10.6 kb EcoRI fragment. A large-scale plasmid preparation was made from a colony containing the correct plasmid, which was named pEP202. Plasmid pEP202 contains the complete P. paεtoriε PEP4 gene (see Figure 2) . To facilitate sequence analysis of the cloned P. paεtoriε PEP4 gene, a portion of the P. paεtoriε PEP4 gene was subcloned into pUC19. Plasmid pEP202 was digested with BamHI and EcoRI. The reaction mixture was separated on a 0.7% agarose gel, and the 0.45 kb BamHI fragment of DNA (see Fig. 2) was isolated using DE81 paper. The purified fragment was ligated to pUC19 (-20 ng) that had been linearized by digestion with BamHI and dephosphorylated. The ligation mixture was used to transform E. coli strain MC1061. Transformants were selected for a picillin resistance and screened by analysis of restriction enzyme digests of colony DNA for the presence of a single BamHI fragment. A single colony arising from this transformation was found to contain the appropriate DNA construct, and was named pEP205 (see Figure 3) . Sequence analysis of plasmid pEP202 identified a DNA sequence with -70% homology to the PEP4 gene of S . cereviεiae . The amino acid sequence encoded by this DNA sequence of pEP202 is 69% homologous to that encoded by the S. cereviεiae PEP4 gene. EXAMPLE II: DEVELOPMENT OF A PEP4-DEFICIENT IPEP4 STRAIN OF P. PASTORIS A. Construction of the P. pastoris PEP4 Gene Disruption Vector PDR401 Vector pDR401 was constructed for use in developing a PEP4-deficient (PEP4') strain of P. pastoriε . This vector contains a defective P. paεtoriε PEP4 gene, which, when used to transform PEP4 strains of P. paεtoris , integrates into the host genome by replacement of the wild-type PEP4 gene. pDR401 was constructed in a two-step procedure as follows. In the first step, the base vector in the construction of pDR401, base vector pEP301, was constructed from pEP202. Vector pEP301 constains pUC19 sequences and the cloned P. paεtoriε PEP4 gene from pEP202. Plasmid pEP202 (15 μg) was digested with Sacl. A 5.5 kb Sacl fragment (the fragment extending from the Sacl linker clockwise to the Sacl site at -5:00, and containing all of the pUC19 sequence and the entire PEP4 gene; see Figure 2) was isolated from a 0.7% agarose gel using DE81 paper. The fragment was eluted from the paper with 400 μl of 1 M NaCl, extracted with 400 μl of phenol/chloroform and precipitated with ethanol. This DNA was then ligated with itself in a volume of 100 μl containing 1 μl of ligase and 1 μl (-10 ng) of DNA. The ligation mixture was incubated at room temperature for 1 hr and then used to transform E. coli strain MC1061. Ampicillin-resistant colonies were selected and screened by analysis of restriction enzyme digests of colony DNA for the presence of a single 5.5 kb Bglll fragment. Plasmid DNA was prepared from a transformed colony of MC1061 that contained the correct plasmid, which was named pEP301 (Figure 4) . In the second step of the construction of pDR401, the P. pastoris HIS4 gene was inserted into the PEP4- containing plasmid pEP301 to yield the final vector. The P. pastoris HIS4 gene was isolated on a 2.6 kb Bglll fragment derived from pYJ8ΔCla [Cregg, j. et al. Mol. Cell. Biol. 5_:3376-3385 (1985)]. Plasmid pYJδΔCla (15 μg) was digested with Bglll and the digested DNA was separated on a 0.7% agarose gel. The HIS4 gene- containing 2.6 kb fragment was isolated with DE81 paper, eluted with 400 μl of 1 M NaCl, extracted with 400 μl of phenol/chloroform, precipitated with ethanol and resuspended in 10 μl of water. Prior to inserting this 2.6 kb Bglll fragment into the unique Bglll site of pEP301, approximately 20 μg of pEP301 were digested with Bglll. dephosphorylated and extracted with phenol/ chloroform. The 2.6 kb HIS4-containing fragment was then inserted into pEP301 by ligation of approximately 50 ng of the fragment to approximately 50 ng of the BgJ.II- digested pEP301 in a total volume of 10 μl containing 1 μl of buffer, 1 μl of ligase and water. Ligation was conducted at room temperature for 3 hrs and the ligation ix was used to transform MC1061 cells. Plasmid DNA prepared from an ampicillin-resistant colony was digested with Bglll, Sail. Bglll/SalI, Pvul. Ncol and Kpnl to confirm the construction of pDR401. The restriction fragment pattern was consistent with that expected for the correct plasmid pDR401 (see Figure 5) . Plasmid pDR401 is pUC19 with the P. paεtoris HIS4 gene inserted at the unique Bglll site within the PEP4 structural gene, thus disrupting it. B. Transformation of HIS4 P. pastoriε Strain GS115 with a Fragment of PDR401 In order to create a PEP4 strain of P. pastoriε , the HIS4 PEP4 P . pastoriε strain GS115 (ATCC 20864) was transformed with 20 μg of the 5.3 kb EcoRI/Sacl fragment of pDR401 according to the spheroplast method (see US patent 4,879,231). This fragment of pDR401 consists of the HIS4 gene-containing defective PEP4 gene. Transformant strains resulting from this type of integration are prototrophic and can be distinguished from untransformed cells on this basis. The frequency of transformation was approximately 10 3 μg' 1 DNA. C. Characterization of Transformants 1. Analysis of transformant carboxypeptidase Y activities His + transformants were subsequently analyzed for carboxypeptidase Y activity using a colony overlay colorimetric screening procedure [see Jones, E. in Genetics 8_5: 23-33 (1977)]. In this assay, the His + transformant cells were released from the transformation agar plates and grown on YEPD (yeast extract, 1% peptone, 2% dextrose and 2% agar) plates at a density of "300 colonies per plate. The plates were overlayed with 0.6% agarose containing 40% dimethylformamide (DMF) to permeabilize the cells, and 1.2 mg/ml of the substrate APNE (N-acetyl DL phenylalanine |S-naphthyl ester) . Because the cells were permeabilized, some of the vacuolar content of the cell was accessible to the reagent APNE. After the agarose overlay had solidified, the plates were soaked in a solution of 5 mg/ml Fast garnet salt. APNE is cleaved by the esterolytic activity of carboxypeptidase Y. The products of this reaction bind the fast garnet salt to produce a red color in the colony. Colonies lacking carboxypeptidase Y activity do not bind the salt and therefore stain less intensely than do colonies that possess this activity. PEP4* colonies developed a red/pink center during the first 10-15 minutes after exposure to the garnet salt. In contrast, colonies defective at the PEP4 locus were slow to develop this color and were distinguished as pink relative to the red PEP4 + colonies. Colonies that appeared to have low carboxypeptidase Y activities based on the results of this assay (i.e.. colonies that failed to develop a strong red color indicative of PEP4 + colonies) were isolated, transferred to a master plate, subcultured along with control colonies and re-screened using the overlay assay. Twenty colonies which again failed to develop a strong red color were selected for analysis by Southern blot hybridization to determine if the PEP4 locus of these transformants had been disrupted by integration of the fragment of vector pDR401. 2- Southern blot hybridization analysis Genomic DNA was extracted from 20 transformant strains that exhibited low carboxypeptidase activity, designated pl-p20, and digested with Sacl and EcoRI. This procedure should liberate the HIS4-containing defective PEP4 gene as the 5.3 kb EcoRI/Sacl fragment that was used to transform the strains. Two Southern blot filters were prepared from these digested DNAs; one blot was probed with a radiolabeled 1.4 kb Xbal/EcoRV fragment from pEP301 (see Fig. 4) , which contained a portion of the cloned P. pastoris PEP4 gene and the other blot was probed with a radiolabeled 2.6 kb Bglll fragment of pDR401 containing the HIS4 gene. Control DNA from the transformation host strain GS115, which had been digested with Sacl and EcoRI, was included in this analysis for comparative purposes. Digestion of genomic DNA from GS115 with Sacl and EcoRI yielded a 2.9 kb fragment that hybridized to the portion of the PEP4 gene contained in the radiolabeled Xbal/EcoRV fragment of pEP301. In contrast, this probe hybridized to fragments of a different size in Sacl/EcoRI-digested DNA from 19 of the 20 transformants analyzed. Only DNA from strain pl7 yielded a hybridization pattern identical to that of DNA from the parental strain. The remaining 19 strains lacked a 2.9 kb hybridizing fragment characteristic of an undisrupted PEP4 locus and contained an approximately 5.3 kb fragment and/or larger fragments that hybridized to the PEP4 gene probe. The 5.3 kb fragment was the same size as the transforming DNA released from vector pDR401 upon digestion with Sacl and EcoRI. The results of Southern blot hybridization of DNA from strains pl-pl6 and pl8-p20 revealed that these strains contained a defective PEP4 gene with an intact HIS4 gene therein, and that the PEP4 locus of the strains had been disrupted. Strain pl3 was grown in a one-liter fermentation, as described in Example III, in order to analyze the proteolytic activity of the broth of a larger culture of a PEP4 strain of P. paεtoriε . 3. Analysis of the transformant proteinase A activities a. Protocol The proteinase A activities of eight transformant strains were evaluated using an enzyme assay based on the method of Jones et al. [Genetics 102:655 (1982)]. Several control strains were also evaluated in this assay: PEP4 and PEP4 strains of S . cereviεiae (strains DBY747 and 20B12, respectively, from the Yeast Genetic Stock Center, University of California, Berkeley, CA) and a PEP4 wild-type strain of P. pastoris (strain NRRL Y-11430 from the Northern Regional Research Center, Peoria, IL) . Proteinase A is a vacuolar enzyme responsible for the aspartyl protease activity encoded by the PEP4 gene in S. cerevisiae . The procedure used to evaluate the proteinase activities of transformant cell extracts is based on the measurement of proteinase A-mediated release of amino acids from acid-denatured hemoglobin. Transformant cell extracts were incubated with acid-denatured hemoglobin, and the proteinase A activity present in the extract was determined by estimating the difference in the amount of amino acid released at time zero and after 90 minutes of incubation. Cultures of the S . cerevisiae control strains DBY747 (PEP4 ) and 2OB12 (PEP4 ) , the PEP4 P. pastoriε strain NRRL Y-11430 and the experimental PEP4 strains of P. pastoris were grown to stationary phase in YEPD medium. Cultured cells (20 OD^ units) were washed in 10 mM sodium azide and then lysed in 400 μl of 100 mM Tris, pH 7.5, by vortexing the cells with acid-washed glass beads for one minute. The lysed cells were centrifuged in Eppendorf tubes for 10 minutes to remove cell debris. The supernatant obtained after centrifugation (crude extract) was then examined for proteinase A activity as follows. Acid-denatured 1% hemoglobin (400 μl) was added to 50 μl of crude extract and incubated for 90 minutes at 37°C. Reactions were stopped by the addition of 0.2 ml of 1 N perchloric acid. Insoluble material was removed by centrifugation, and 200 μl of 0.31 M NaCl was added to 200 μl of supernatant. A 40 μl aliquot of this solution was then assayed using the Pierce BCA protein assay kit (see, for example, US Patent No. 4,839,295) for free amino acids. The amount of free amino acids present in the sample that had been incubated for 90 minutes was compared to the amount present in a blank which consisted of a sample of a reaction mixture that was stopped at zero minutes. The relative difference in free amino acids between these two samples is a measure of proteinase A activity. b. Results The results of proteinase A assays of control and transformant strains (see Table I; ΔOD is a measure of the concentration of free amino acids in the sample) indicate that the proteinase A activity of the PEP4 strain of S . cereviεiae represents only 10% of that of the PEP4 strain of S . cereviεiae . Similarly, the proteinase A activities of the PEP4 transformant strains (strains pi, p2, p5, p8, pl3, pl6 and p20) also are only approximately one-tenth of that of the PEP4 strain of S. cereviεiae . The PEP4 wild-type strain of P. paεtoris displayed approximately half of the proteinase A activity of the PEP4 strain of S. cereviεiae . TABLE I PROTEINASE A ASSAY RESULTS The data obtained in proteinase A assays of PEP4 P. paεtoris strains generated by transformation of a PEP4 strain with a defective PEP4 gene are consistent with the results of Southern blot analyses of DNA from these transformants which indicate that the PEP4 locus of the transformants was disrupted upon transformation. EXAMPLE Ills FERMENTATION OF A PEP4 STRAIN OF P. PASTORIS A. Procedure A PEP4 strain of P. pastoriε , pl3, generated by transformation of strain GS115 with a defective PEP4 gene-containing Sacl/EcoRI fragment of vector pDR401, was grown in a one-liter fermentation according to a three- phase protocol consisting of a glycerol batch growth phase, a limited glycerol fed-batch phase and a methanol fed-batch phase as follows. A two-liter fermentor was autoclaved with 1000 ml of minimal salts medium (21 ml 85% phosphoric acid, 0.9 g calcium sulfate2H 2 0, 14.3 g potassium sulfate, 11.7 g magnesium sulfate and 3.2 g potassium hydroxide) and 2% glycerol. After sterilization, 4 ml PTM, trace salts solution (6 g/1 cupric sulfate5H 2 0, 0.8 g/1 sodium iodide, 3 g/1 manganese sulfateH 2 0, 0.2 g/1 sodium molybdate2H 2 0, 0.02 g/1 boric acid, 0.5 g/1 cobalt chloride, 20 g/1 zinc chloride, 65 g/1 ferrous sulfateH 2 0, 0.2 g/1 biotin and 5 ml sulfuric acid) were added to the fermentor and the pH was adjusted to 5 with concentrated NH 4 0H. The pH of the medium was maintained at 5 by addition of 50% NH 4 OH containing 0.1% Struktol J673 antifoam. Inocula were prepared from buffered yeast nitrogen base (YNB) glycerol plates (phosphate-buffered YNB, 2% glycerol, 2% agar) and grown overnight at 30°C in phosphate-buffered YNB (11.5 g/L KH 2 P0 4 , 2.66 g/L K 2 HP0 4 , 0.67% yeast nitrogen base, pH 5) containing 2% glycerol. The fermentor was inoculated with 10-50 ml of the cultured cells which had grown to an OD^ of 1-8, and the batch growth regimen was continued for approximately one day until glycerol was exhausted. At the point of glycerol exhaustion, as indicated by increased dissolved oxygen, a glycerol feed (50% glycerol plus 12 ml/L of PTM,) was initiated at 10 ml/h and continued until 40 ml of glycerol feed had been added. After termination of the glycerol feed, a methanol feed (100% methanol plus 12 ml/L PTM j ) was started at an initial rate of approximately 2 ml/h. After 3 hours, the methanol feed rate was increased to 6 ml/h. The methanol feed rate was maintained at 6 ml/h for 12-18 hours and was then increased to 10 ml/h and maintained at 10 ml/h for the duration of the fermentation. The vessel was harvested after 400 ml of methanol had been added to the fermentor. B. Sample Preparation Samples (15 ml aliquots) of the fermentor culture were removed from the fermentor at various time intervals throughout the course of the fermentation. Aliquots of each sample were centrifuged at 6500 x g for 5 minutes to separate broth and cells. The levels of the NH 4 OH, antifoam, glycerol, and methanol reservoirs were recorded at these time points. Methanol and ethanol concentrations in the supernatant were determined by gas chromatography using a PorapakQ column (Alltech) . In addition, the wet weight of the culture was determined as an indicator of cell growth in the fermentor. For this purpose, a one ml aliquot of the fermentor culture was centrifuged for four minutes in a microfuge, the supernatant was decanted, and the wet pellet was weighed. C. Results Growth of the PEP4 strain of P. paεtoriε pl3 in a one-liter fermentation was monitored by determining the wet cell weight of the fermentor culture (in g/1) at various times during the fermentation. A time course of the growth of strain pl3 during the methanol fed-batch phase of the fermentation, when compared with the time course of the growth of the HIS4 PEP4 strain G+PAO804H2 (generated by transformation of the HIS4 PEP4 P. paεtoriε strain GS115 with an expression vector containing the wild-type HIS4 gene) during a similar one liter fermentation, demonstrates that the growth capabilities of the PEP4 strain of P. paεtoriε are comparable to those of a PEP4 strain. EXAMPLE IV: ANALYSIS OF THE PROTEOLYTIC ACTIVITY OF THE BROTH OF A PEP4 STRAIN OF P. PASTORIS GROWN IN A ONE-LITER FERMENTATION To determine if disruption of the P. paεtoriε PEP4 gene was associated with a change in the proteolytic activity of the broth of P. paεtoriε, the proteolytic activities of the broths from one-liter fermentations of a PEP4 strain, strain pl3, and a PEP4 strain were compared. In this study, two different peptides, epidermal growth factor (EGF; a recombinantly synthesized molecule consisting of the first 52 amino acids of the authentic 53 amino acid EGF molecule, as described in US patent application Serial No. 323,964) and growth hormone releasing factor (GRF; recombinantly synthesized as described in EP 206783) were separately incubated at room temperature in cell-free broth from the one-liter fermentation of the PEP4 P. paεtoriε strain pl3, and in the cell-free broth from a similar one-liter fermentation of the HIS4 PEP4 P. paεtoriε strain G+PAO804H2. After incubation for a specified period, aliquots of each incubation mixture were examined by reverse phase high performance liquid chro atography (HPLC) , described below, to determine the amount of intact peptide remaining in each sample and thereby determine the extent of proteolytic degradation of the peptide. A. Reverse-Phase High-Pβrfoπnance Liquid Chro atographv (HPLC) The reverse-phase HPLC system used in the analysis of EGF and GRF peptides in buffer and broth from fermentations of P. paεtoriε strains included a Waters 600 (Bedford, MA) solvent delivery system. Waters Model 481 Lambda Max variable wavelength detector. Wisp 710B autoinjector and a Shimadzu Chrom-Pac integrator (Cole Scientific, Moorepark, CA) . Samples of broth from the fermentations of the PEP4 P. paεtoriε strain pl3 and the HIS4 PEP4 P. paεtoriε strain G+PAO804H2 were diluted 1:10 in 0.1 M sodium phosphate, pH 5.0. Fifteen microliters of concentrated GRF stock was added to 285 μl of diluted broth and incubated for four hours. A similar dilution of GRF stock in the phosphate buffer was also incubated for four hours as a control. Sixty microliters of EGF stock were added to 240 μl of diluted broth or buffer and incubated for eight hours. Samples of each incubation mixture were separately injected into a Waters μ Bondapak C18 reverse phase column. The peptides were eluted from the column in a 20-minute linear gradient of 20-60% mobile phase B (95% acetonitrile, 5% water, 0.1% trifluoroacetic acid). Mobile phase A (0.1% trifluoroacetic acid) was used to dilute mobile phase B in preparing the elution gradient. B. Results The amount of intact peptide (of the EGF or GRF molecules that were incubated in the fermentation broth of the PEP4 P. pastoris strain pi3 and the broth of the PEP4 P. pastoris strain G+PAO804H2) was evaluated by comparing chromatograms obtained in HPLC analyses of intact EGF or GRF contained in 0.1 M sodium phosphate buffer, pH 5.0, and of EGF or GRF contained in broth. Chromatograms from HPLC analyses of the standard intact peptides consist of a major peak reflecting the amount of the standard peptide present in the sample and the retention time characteristic of the peptide. In contrast, proteolytic fragments of either peptide are retained on the HPLC column for varying lengths of time that differ from the retention time associated with the intact peptide. Therefore, chromatograms from HPLC analysis of proteolytic fragments of either peptide (EGF or GRF) differ from chromatograms generated in HPLC analyses of intact peptides in terms of the number and sizes of the peaks and the retention times associated with the fragmented species. Based on these differences, it was possible to estimate the amount of intact EGF or GRF peptide in the broth incubation samples. Based on HPLC analyses of GRF and EGF samples incubated in PEP4 P. pastoris control broth, it has been determined that less than 10% of each of the two peptides remains intact after incubation in broth from the fermentation of the PEP4 strain G+PAO804H2. In contrast, the level of proteolytic degradation of these peptides in the broth of the PEP4 P. pastoris strain is significantly less than that in the broth of the PEP4 strain (GRF remained >60% intact, even after 4 hr incubation; EGF remained >90% intact, even after 8 hr incubation) . These data demonstrate that disruption of the PEP4 gene of P. pastoriε results in a substantial reduction of the proteolytic activity in the broth of the strain. EXAMPLE V: ISOLATION OF THE P. PASTORIS URA3 GENE The P. paεtoriε URA3 gene was identified in a plasmid (YEpl3)-based Pichia genomic library by its ability to complement the pyrF mutation (corresponding to a defect in the orotidine monophosphate decarboxylase activity) in E. coli strain CSH-28. The P. paεtoriε URA3 gene was cloned by isolating colonies of E. coli strain CSH-28 that had been transformed with library DNA and were capable of growth on media lacking uracil. A. P. pastoris YEpl3 Genomic DNA Library Plasmid YEpl3 [Broach et al. , Gene 8_: 121-133 (1979) ] is a convenient shuttle vector that contains an origin of replication for both S . cerevisiae (2μ replicon) and E. coli (pBR ori) . In addition, YEpl3 contains the Amp R (ampicillin resistance) gene for use as a selectable marker for transformation of E. coli and the LEU2 gene (a leucine biosynthetic pathway gene) for use as a selectable marker in S . cerevisiae . A P. paεtoriε (strain NRRL Y-11430) genomic DNA library has been prepared using plasmid YEpl3, as described by Cregg et al. [Mol. Cell. Biol. 5: 3376-3385 (1985)]. B. Screening of the P. pastoris YE l3 Genomic DNA Library for the URA3 Gene The pyrF E. coli strain CSH-28 [see Miller, J. H. , in Experiments in Molecular Genetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1972) ] is defective for orotidine-5'-phosphate decarboxylase activity and requires uracil when grown on defined medium. It has been demonstrated that the S. cervisiae URA3 gene can complement the pyrF mutation in E. coli [Rose, M. , Grisafi, P. and Botstein, D. Gene 29:113-124 (1984)]. Therefore, E. coli strain CSH-28 was transformed with DNA from the P. paεtoriε YEpl3 genomic DNA library in order to screen the library for the P. paεtoriε URA3 gene capable of complementing the pyrF mutation of the strain. Transformed CSH-28 cells were plated onto a semi- defined medium which did not contain uracil. Untransformed cells would not grow on this medium. CSH-28 transformants (transformed with P. paεtoriε genomic library DNA) capable of growing on plates lacking uracil arose at a frequency of -10/μg of transforming DNA. Plasmid DNA was isolated from ten of the transformants that did not require uracil for growth. These plasmids were used to transform E. coli strain CSH-28, and ten of ten plasmids complemented the uracil auxotrophy of this strain at high frequency. One of the selected transformants generated by transformation of CSH-28 with P. paεtoriε genomic library DNA harbored a 9.0 kb insert that contained a 6.6 kb SphI fragment. The 6.6 kb SphI fragment was subcloned into the SphI site of pUC19 for further analysis. Plasmid DNA from this transformant was digested with SphI and subjected to electrophoresis on a 0.6% agarose gel. The 6.6 kb fragment was isolated using DE81 paper and was eluted from the paper with 400 μl of 1 M NaCl. DNA was extracted with 400 μl of phenol/chloroform and precipitated with ethanol. The 6.6 kb fragment was then ligated with 10 ng of alkaline phosphatase-treated, Sphl-digested pUC19. The ligation mixture was used to transform E. coli MC1061 cells. Ampicillin-resistant transformants were screened by analysis of restriction enzyme-digested colony DNA for the presence of a 6.6 kb SphI fragment. The correct plasmid was called pPU201. Plasmid pPU201 was used to transform CSH-28 and was able to complement the uracil auxotrophy of this strain. C. Characterization of the Insert in Plasmid PPU201 A map of the restriction enzyme recognition sites of the 6.6 kb insert of P. paεtoriε DNA in plasmid pPU201 (Figure 6) was prepared by digesting pPU201 with a variety of enzymes and analyzing the resulting fragments using a DNA length computer program (MapSort; University of Wisconsin Genetics, Madison, WI) to determine the approximate sizes of the fragments. In order to delineate the URA3 gene contained in the 6.6 kb insert of pPU201, a 5 ng aliquot of each restriction enzyme digest of pPU201 was separated by electrophoresis on a 1% agarose gel, transferred to nitrocellulose, and probed with a radiolabeled 1.3 kb Bglll fragment of the C. tropicaliε URA3A. gene (see PCT Publication No. WO 90/09449) . The filters were hybridized to the probe at 27°C using a solution containing 25% formamide, 6x SSC, 5x Denhardt's solution, 20 mM TrisΗCl, pH 8.0, 1 mM EDTA, 0.1% sodium dodecyl sulfate (SDS) and 100 μg/ml salmon sperm DNA. After hybridization, the filters were washed three times at room temperature using lx SSC and 1% SDS for 5-10 minutes per wash, and then washed twice with 0.5x SSC and 0.5% SDS at 45°C for 10 minutes per wash. These low stringency conditions permitted hybridization between divergent URA3 gene sequences. Additional samples of each digest of pPU201 were separated on an identical 1% agarose gel and stained with ethidium bromide for comparison of hybridizing and non- hybridizing fragments. Comparison of the hybridizing fragments and the restriction map of pPU201 made it possible to localize the URA3 gene in pPU201 to the approximately 1.3 kb Ncol-Sall fragment as shown in Figure 6. With this knowledge, it was then possible to construct subclones suitable for sequencing and further characterization of the P. paεtoris URA3 gene. Plasmid pPU202 (Figure 7) was constructed by digesting pPU201 with EcoRV and Pstl. isolating the approximately 4.0 kb fragment containing the URA3 gene, and ligating it into pUC19 at the Smal and Pstl sites. Plasmids pPU203, pPU205 and pPU206 (Figures 8-10) were constructed by digesting pPU202 with Sacl. Kpnl and EcoRI. respectively, and then religating in a large volume (200 μl) . Because there is a recognition site for each of these enzymes in the cloned P. pastoriε genomic insert DNA fragment as well as the pUC19 polylinker of pPU202, this strategy allowed for the convenient removal of DNA between these sites in pPU202. The resulting plasmids were then used to transform E. coli strain CSH- 28 to determine whether or not each deletion construct could complement the pyrF mutation. The results indicated that pPU203 and pPU205, but not pPU206, contained a functional URA3 gene allowing growth of the pyrF strain on defined medium lacking uracil. These findings are consistent with the mapped position of the P. paεtoris URA3 gene in pPU201. The subclones of the P. pastoris genomic DNA fragment carrying the putative URA3 gene were sequenced using the Sanger dideoxy method [see Sanger et al., Proc. Natl. Acad. Sci. USA 74.: 5463-5467 (1977)]. The sequence for the structural gene and approximately 100 bp of flanking sequence was determined in both directions and is presented in Sequence ID No. 3. The amino acid sequence deduced from the cloned P. pastoriε URA3 gene (see Sequence ID No. 4) has 73% homology with the amino acid sequence deduced from the S. cereviεiae URA3 gene, 71% homology with the amino acid sequence deduced from the URA3A and URA3B genes of C. tropicaliε and 72% homology with the amino acid sequence deduced from the URA3 gene of Kleuveromyceε lactiε . EXAMPLE VI: DEVELOPMENT OF IGF-1-EXPRESSING PEP4- DEFICIENT (PEP4 \ STRAINS OF PICHIA A. Generation of GF-l-Expressing PJ5.P4' Strains by Gene Addition 1- Construction of the P. pastoris PEP4 gene disruption vector pDR421 Plasmid pDR421 was constructed for use in the development of PEP4-deficient (PJ5P4") strains of Pichia pastoriε by disruption of a host PEP4 gene through addition of an incomplete PEP4 gene to the endogenous PEP4 locus. This vector contains an internal portion of the PEP4 gene, which, when used to transform PEP4 strains of P. paεtoriε, integrates into the host genome at the PEP4 locus to generate two incomplete and nonfunctional copies of the PEP4 gene. In order to generate the disruption vector pDR421, the URA3 gene of Pichia was cloned into vector pEP205 (consisting of pUC19 sequences and the portion of the PEP4 gene contained in the -450 bp BamHI fragment derived from pEP202) . This was achieved by subcloning the URA3 gene from pPU205 (see Figure 9) as a 2 kb Spel-SphI DNA fragment into the Xbal-SphI sites of pEP205 (see Fig. 3) . Plasmid pPU205 was digested with Spel and SphI and the reaction mixture was separated on a 0.8% agarose gel. The 2 kb DNA fragment containing the URA3 gene was isolated from the gel using DE81 paper, eluted and purified. Plasmid pEP205 was digested with Xbal and SphI. The 2 kb URA3 gene-containing Spel-SphI fragment isolated from pPU205 was ligated to Xbal/Sphl-digested pEP205 and the mixture was used to transform E. coli strain MC1061 to ampicillin resistance. Ampicillin- resistant colonies were screened by analysis of BamHI/SphI restriction enzyme-digested colony DNA for the presence of 2.7 kb, 0.4 kb and 1.9 kb diagnostic fragments. A transformant was found to harbor a plasmid with the correct DNA construct called pDR421 (Figure 11) . 2. Transformation of an IGF-1-eχpressing DRA3 P. pastoris strain (IGF-U) with pDR421 The URA3 IGF-1-expressing strain of P. pastoriε , IGF-U, was transformed with pDR421 to generate PEP4 ~ , IGF-1-expressing strains of P. paεtoriε . a. Generation of IGF-U 5-Fluoro-orotic acid (5-FOA) is an analog of a uracil biosynthetic pathway intermediate that, when metabolized by Ura + strains, yields a toxic compound. Because the uracil biosynthetic pathway of Ura' strains is blocked at certain steps, these strains do not metabolize 5-FOA (to produce a compound toxic to the cells) and are therefore 5-FOA resistant. In contrast, Ura + strains metabolize 5-FOA and cannot survive on 5-FOA-containing medium. Therefore, plating cells on 5-FOA-containing medium can be used as a method to generate Ura " strains by spontaneous mutation [see, for example, Boeke et al., Mol. Gen. Genet. 197: 345-346 (1984)]. A URA3' derivative of the IGF-1-producing strain G+IMB206S1 [for a description of this strain, see commonly assigned U.S. Patent Application Serial No. 07/578,728, filed September 4, 1990,which is hereby incorporated by reference herein in its entirety] was generated by direct plating of -5 x 10 7 cells this strain into 5-FOA-containing medium supplemented with uracil (0.67% yeast nitrogen base, 2% agar, 2% glucose, 750 mg/1 of 5-FOA and 48 mg/1 of uracil) . After one week of incubation at 30°C, a colony, designated IGF-U, growing on the plate was isolated. This colony, which required uracil in order to grow, was unable to complement a DRA3 strain of Pichia paεtoris. b. Transformation of GF-ϋ Approximately 20 μg of pDR421 was digested with Bglll was used to transform IGF-U using the standard spheroplast transformation procedure. Transformants were selected by their ability to grow in the absence of uracil over a 6 day period. 3. Characterization of transformants a. Analysis of transformant carboxypeptidase Y activities Ura + transformants were subsequently analyzed for carboxypeptidase Y activity using a colony overlay colorimetric screening procedure, as described in Example II. Colonies of Ura + transformants that appeared to have low carboxypeptidase Y activities based on the results of this assay (i.e., colonies that failed to develop a strong red color indicative of PEP4 + colonies) were isolated, transferred to a master place, subcultured along with control colonies and rescreened using the overlay assay. One colony which again failed to develop a strong red color was called M+IMB206S1. b. Analysis of intact IGF-1 expression levels of an IGF-1-βxpressing PEP4 strain of P. pastoris grown in one- and ten-liter fermentations i. Fermentation of an lGF-l-expressing PEP4 strain of P. pastoris An IGF-1-expressing PEP4 strain of P. paεtoriε , M+IMB206S1, generated as described in Example VI.A.2.b., was grown in one- and ten-liter fermentations according to a three-phase protocol consisting of a glycerol batch growth phase, a limited glycerol fed-batch phase and a methanol fed-batch phase. In order to compare the intact IGF-1 expression levels of PJ5P4 and PEP4 IGF-1-expressing strains of P. paεtoriε , two PEP4 strains of P. paεtoriε , G+IMB204S14 and G+IMB206S1, containing four and six copies of an IGF-1 gene expression cassette, respectively (see, U.S. application Serial No. 07/578,728), were also grown in comparable fermentations as follows. One-liter fermentation protocol A two-liter fermentor (Biolafitte, Princeton, NJ) was autoclaved with 900 ml of minimal salts medium (21 ml 85% phosphoric acid, 0.9 g calcium sulfate2H 2 0, 14.3 g potassium sulfate, 11.7 g magnesium sulfate, and 3.2 g potassium hydroxide) and 30 g of glycerol. After sterilization, 4 ml PTMj trace salts solution (6 g/1 cupric sulfate-5H 2 0, 0.08 g/1 sodium iodide, 3 g/1 manganese sulfateΗ 2 0, 0.2 g/1 sodium molybdate2H 2 0, 0.02 g/1 boric acid, 0.5 g/1 cobalt chloride, 20 g/1 zinc chloride, 65 g/1 ferrous sulfateH 2 0, 0.2 g/1 biotin and 5 ml sulfuric acid) were added to the fermentor and the pH was adjusted to 5 with concentrated NH 4 OH. The pH was controlled by addition of 50% NH 4 OH containing 0.1% Struktol J673 antifoam (added to control foaming) . The temperature was maintained at 30°C, and dissolved oxygen was maintained above 20% of saturation by increasing agitation, aeration, or the supplementation of the air feed with oxygen. Inocula were prepared from cells grown overnight at 30°C in buffered YNB containing 2% glycerol. The fermentor was inoculated with 40-70 ml of the cultured cells which had grown to an OD^x, of 2-8, and the batch growth regimen was continued for 18-24 hours until glycerol was exhausted. At the point of glycerol exhaustion, indicated by an increase in dissolved oxygen concentration, a glycerol feed (50% w/v glycerol plus 12 ml/L PTMi) was initiated at 10 ml/hr. In pH 5.0 fermentations, the pH of the culture was maintained at 5 throughout the fermentation. In low pH fermentations (i.e., pH 2.8 or pH 3.5), the set point of the pH controller was adjusted to the desired pH after initiation of the glycerol feed. After four hours, the pH of the culture decreased to the set point value as a result of cellular metabolism. This lower pH was then maintained throughout the remainder of the fermentation. The glycerol feed was then terminated and a methanol feed (100% methanol plus 12 ml/L PTM j ) was initiated at a rate of 2 ml/hr. After three hours of methanol feeding, the feed rate was increased to 6 ml/hr and maintained at this rate for the remainder of the fermentation. The vessel was harvested 72 hours after initiation of the methanol feed. The fermentation was monitored in terms of NH 4 0H, antifoam, glycerol, methanol, ethanol, and wet cell weight levels as described in Example III. Broth and cell samples were collected throughout the fermentation as also described in Example III. Ten-liter fermentation protocol A 15-liter fermentor containing 3.5 liters of 10X basal salts (42 ml 85% phosphoric acid/1, 1.8 g calcium sulfate2H 2 0/l, 28.6 g potassium sulfate/1, 23.4 g magnesium sulfate/1, 6.5 g potassium hydroxide/1) and 220 g glycerol in a total volume of 5.5 liters was sterilized. After the fermentor had cooled, 24 ml PTM, trace salts were added and the pH was adjusted to 5.0 with the addition of 28% ammonium hydroxide. The pH was controlled by the addition of the same solution. Foaming was controlled with the addition of a 5% solution of Struktol J673. Temperature was maintained at 30°C, and dissolved oxygen was maintained above 20% of saturation by increasing agitation, aeration, reactor pressure or by supplementation of the air feed with oxygen. Inocula were prepared from P. pastoriε cells grown overnight in buffered yeast nitrogen base (YNB; 11.5 g/L KH 2 P04, 2.66 g/L K 2 HP0 4 , 6.7 g/L yeast nitrogen base, pH 6) containing 2% glycerol. The fermentor was inoculated with 500-700 ml of the cultured cells which had grown to an ODeoo of 2-8, and the batch growth regime was continued for 18-24 hours. At the point of glycerol exhaustion, indicated by an increase in dissolved oxygen concentration, a glycerol feed (50% w/v glycerol plus 12 ml/L PTM j ) was initiated at 100 ml/hour and continued for 4 hours. The glycerol feed was then terminated and a methanol feed (100% methanol plus 12 ml/L PTM,) was initiated at 20 ml/hr. With the initiation of the methanol feed, the set point of the pH controller was adjusted to 2.8. The pH then gradually decreased to the set point value as a result of cellular metabolism. After 4 hours of methanol feeding, the methanol feed rate was increased to 60 ml/hour and maintained at this rate for a total of approximately 72 hours, at which point the vessel was harvested. ii. IGF-1 expression levels of PE 4 and PEP4 IGF-l-expressing strains One of the several forms of IGF-1 produced in fermentations of recombinant IGF-1-secreting strains of P. pastoris is a nicked species consisting of two or more fragments of the IGF-1 molecule held together by disulfide bonds. The fragments are generated by proteolytic cleavage of one or more peptide bonds of the amino acid backbone of the IGF-1 molecule. Although nicked and intact IGF-1 molecules are indistinguishable on the basis of apparent molecular weight [under non- reducing conditions, as determined by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) ] , these species can be resolved by reverse phase HPLC under non-reducing conditions and by SDS-PAGE under reducing conditions (i.e., in the presence of a reducing agent such as dithiothreitol) . Reduction of the disulfide bonds holding the fragments of nicked IGF-1 together results in liberation of the individual proteolytically generated IGF-1 fragments which have smaller molecular weights than the intact molecule. Ouantitation of IGF-1 expression levels The yields of nicked and authentic (intact, correctly folded, monomeric) IGF-1 in the cell-free broth were determined by quantitative reverse phase HPLC. The HPLC system that was used was the same as that described in Example IV, except a Vydac C4 column (0.46 x 5 cm) was employed instead of a C18 column. A 1%/minute gradient of 25-42% mobile phase B was passed through the column during a period of 17 minutes at a flow rate of 1 ml/minute to elute samples from the column. The detector was set at 0.05 absorbance units full scale (AUFS), and a wavelength of 215 nm was used for maximum sensitivity. To distinguish the authentic and nicked IGF-1 species in P. paεtoriε broth by HPLC, it was necessary to clean-up the broth by removing some endogenous P. paεtoriε contaminants from the broth prior to loading broth samples onto the HPLC column. This was accomplished by passing the broth through a sulphopropyl- based cation exchange resin contained in a 0.25 ml column. The resin was first washed with 2 ml of 0.2 M acetic acid, then equilibrated with 2 ml of 0.02 M acetic acid. A volume of crude cell-free broth (1 ml) was loaded onto the column which was then washed with l ml of 0.02 M acetic acid. The IGF-1 was eluted with 2 ml of 0.02 M sodium acetate, pH 5.5, plus 1 M NaCl. The first 1 ml of eluate contained 75-80% of the total IGF-1 and was usually the only elution volume collected. The column was then regenerated by washing with 2 ml of 100% methanol and thereby available for re-use. In order to quantitate the levels of Pichia-produced IGF-1, known amounts of standard IGF-1 (Amgen, Thousand Oaks, CA) were injected into the HPLC column and the area under the corresponding peaks in the chromatograms was measured. A standard curve was generated by plotting area versus μg of IGF-1 loaded onto the HPLC column. A correlation coefficient for use in converting the area under HPLC chromatogram peaks to IGF-1 concentration was calculated from the standard curve. When the detector was set at 0.05 AUFS and a wavelength of 215 nm, the correlation coefficient was 350 units/μg of IGF-1 injected onto the column. Using this information, it was possible to determine the concentration of correctly folded, intact monomeric IGF-1 present in a cleaned-up broth sample by measuring the area under the corresponding peak on the chromatogram from HPLC analysis of the sample. This correlation coefficient was also used to estimate the approximate concentration of the nicked IGF-1 species as well. However, the absolute concentrations of the nicked species may vary depending on differences in the specific correlation coefficients of intact and nicked IGF-1. Results of one-liter fermentations One-liter low pH (pH 2.8) fermentations of the PEP4 IGF-1-expressing strain consistently yielded greater amounts of total monomeric (authentic plus nicked) IGF-1 (-200-250 mg/1) than one-liter low pH fermentations of the PEP4 IGF-1-expressing strains (-160-190 mg/L) . Furthermore, the percentage of authentic IGF-1 in the broth of the PEP4 strain was somewhat higher (77%) than that in the broth of the PEP4 strains (65%) . However, a much more dramatic difference in the monomeric IGF-1 production levels of the PEP4 and PEP4 strains was detected in pH 5.0 fermentations of these strains. Essentially no IGF-1 was detected in one-liter pH 5.0 fermentations of the PEP4 IGF-1-expressing strains G+IMB204S14 and G+IMB206S1. This result indicates that the authentic IGF-1 produced in fermentations of PEP4 strains is subjected to extensive proteolysis at pH 5.0, but to only limited proteolysis at lower pH. In contrast, one-liter pH 5.0 fermentations of the PEP4 IGF- 1-expressing strain M+IMB206S1 yielded at least 200 mg of monomeric IGF-1/1, approximately 80% of which was authentic IGF-1. The PEP4 IGF-1-expressing strain thus appears to be significantly improved relative to the PEP4 IGF-1-expressing strains for production of authentic IGF- 1 at pH 5.0 and somewhat improved for production of authentic IGF-1 at pH 2.8. Results of ten-liter fermentations Ten-liter fermentations of the PEP4 IGF-1-expressing strain of P. paεtoriε yielded greater amounts of total monomeric IGF-1 (-200 mg/1) than did ten-liter fermentations of the PEP4 IGF-1-expressing strains (-170 mg/1) . The compositions of the total monomeric IGF-1 produced in 10-liter fermentations of the PEP4 and PEP4 strains also differed. Greater than 75% (164 mg/1) of the total monomeric IGF-1 in the 10-liter fermentation of the PEP4 strain M+IMB206S1 was authentic IGF-1, whereas only about 50% (88 mg/1) of the total monomeric IGF-1 in the 10-liter fermentation of the PEP4 strain G+IMB204S14 was authentic IGF-1. Furthermore, because the cell yield in the fermentation of the PEP4 strain was -30% less than the cell yield in the fermentation of the PEP4 strain, the per cell yield of authentic IGF-1 was greatly enhanced in the fermentation of the PEP4 strain. As a consequence of lower cell yield in the fermentation of the PEP4 strain, a greater volume of cell-free broth was recovered from the fermentation of the PEP4 strain (relative to the volume of cell-free broth recovered from the fermentation of the PEP4 strain) . This results in the recovery of higher levels of secreted IGF-1 from the fermentation of the PEP4 strains (relative to the amount of secreted IGF-1 recovered from the fermentation of the PEP4 strain) . The results presented above demonstrate that the PEP4 IGF-1-expressing strain is improved, relative to the PEP4 IGF-1-expressing strain, for production of authentic IGF-1 on a large scale. B. Generation of an IGF-1-Eχpressing PEP4' Strain by Gene Replacement 1. Construction of the P. pastoris gene disruption vectors PDR601 and PDR602 Vectors pDR601 and pDR602 were used in the development of PEP4-deficient (PEP4 ) strains of P. pastoriε by disruption of a host PEP4 gene through replacement of the endogenous PEP4 gene with a defective PEP4 gene. This vector was constructed in several steps as follows (see also diagram in Figure 13) . Plasmid pEP301 (see Figure 4) , consisting of pUC19 sequences and the cloned P. paεtoriε PEP4 gene from pEP202, was cleaved with Ncol, and the DNA was then precipitated with ethanol, harvested, resuspended and ligated in ligation reaction mixture. This digestion and ligation effectively removed an internal portion of the PEP4 gene contained in an -0.5 kb Ncol fragment. After ligation, the DNA was digested with Bglll to linearize any remaining parental plasmid, and the DNA was used to transform E. coli strain MC1061. Ampicillin-resistant colonies were selected and screened by analysis of restriction enzyme digests of colony DNA for the presence of a 0.5 kb Ncol fragment. The correct plasmid, containing the defective PEP4 gene lacking an -0.5 kb Ncol fragment, was named pDL321. A second plasmid, pUC19XX, was generated by cleaving pUC19 with Smal and Hindi and religating, effectively removing a portion of the polylinker containing the BamHI and Xbal sites. Plasmid pUC19XX was then cut with Sacl and EcoRI and -10 ng was ligated with -50 ng of the Sacl/EcoRI 2.2 kb fragment of pDL321, which had been gel-purified and isolated with DE81 paper. The ligation mix was used to transform MC1061 cells, and ampicillin-resistant colonies were screened by analysis of BstEII/Xbal-digested colony DNA. Plasmid showing the correct digest pattern was designated pDL322. pDL322 was then cut with Xbal and 10 ng were ligated with 10 ng of an oligonucleotide linker of the sequence 5'-CTAGCGGCCG-3' , which destroyed the Xbal site and generated a unique NotI site when ligated into the Xbal site. The ligation mix was used to transform MC1061 cells. Ampicillin-resistant colonies were screened by analysis of Notl-digested colony DNA. The correct plasmid was called pDL323. To generate vectors pDR601 and pDR602, the Pichia URA3 gene was inserted into pDL323 as follows. Plasmid pPU205 (see Figure 9) was digested with PvuII and AatI to liberate the URA3 gene on an approximately 2.5 kb PvuII fragment. The digest was separated on a 0.8% agarose gel. The -2.5 kb fragment was isolated from the gel using DE81 paper, eluted and purified. Plasmid pDL323 was linearized by cutting it with EcoRV. This linearized plasmid (-10 ng) was ligated with the URA3-bearing PvuII fragment of pPU205 to generate pDR601 and pDR602 (see Figures 14 and 15, respectively) , depending upon the orientation of the inserted DRA3 gene. 2. Transformation of IGF-U with pDRβQl and PDR602 The URA3 IGF-1-expressing P. paεtoris strain IGF-U (see Example VI.A.2.a.) was transformed with linear fragments of DNA derived from pDR601 and pDR602. The linear fragments contained the URA3 gene flanked on each side with DNA coding for a portion of the PEP4 gene. Homology between the ends of the fragments and the PEP4 gene stimulated integration of the fragments at the PEP4 locus resulting in a gene replacement event. Stable integration of either fragment into the host genome yielded prototrophic transformants due to the stable presence of the URA3 gene contained in the fragments. The transformation was conducted as follows: Linear DNA fragments (-4.0 kb in length), consisting of the URA3 gene flanked on each side with DNA coding for a portion of the PEP4 gene, were obtained by digesting both pDR601 and pDR602 with NotI and BstEII. The digested DNA (20 μg) was used to transform strain IGF-U using the standard spheroplast procedure. Ura "1" colonies isolated from transformants growing on regeneration medium and subcultured onto YEPD medium were screened for carboxypeptidase Y activity using the overlay procedure described in Example II. Colonies that did not develop a red color relative to control colonies were selected for analysis by Southern blot hybridization. 3. Southern blot hybridization of DNA from transformants Genomic DNA was isolated from the selected transformants using the method of Hoffman and Winston [Gene 57: 267-272 (1987)]. Genomic DNA from each strain was digested with BstEII. This procedure liberates a portion of the P2?P4 locus containing the region of integration of fragments of pDR60l or pDR602. Therefore, the size of this region is diagnostic for correct integration of the transforming DNA into the genome of IGF-U. The digested DNA was subjected to electrophoresis on a 0.8% agarose gel and blotted to a nitrocellulose filter. The filter was hybridized with a radiolabeled 1.4 kb Xbal/EcoRV fragment of pEP301 which contains part of the P. pastoriε PEP4 gene using standard procedures [Maniatis, T., Fritsch, E.F. and Sambrook, J. Molecular Cloning. A Laboratory Manual, pp 385-388, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA. (1982)]. Hybridization was conducted at 37°C in a solution containing 50% formamide, 6 X SSC, 5X Denhardt's solution, 20 mM Tris HC1, pH 8.0, 1 mM EDTA, 0.1% SDS and 100 μg/ml salmon sperm DNA. The filter was then washed three times in 1 x SSC, 0.1% SDS (10 min per wash) and then in 0.5 x SSC, 0.1% SDS at 65°C for 1 hr. As a comparative control, genomic DNA from P. paεtoriε strain GS115, a PEP4 strain, was included in this analysis. Digestion of genomic DNA from GS115 with BstEII yielded a 4.4 kb fragment that hybridized to the portion of the PEP4 gene contained in the probe. In contrast, this probe hybridized to a 6.9 kb fragment in DNA from at least two of the transformants, IGFU2601-5 and IGFU2602- 5. The larger size of the transformant PEP4 locus as compared to the control PEP4 locus (6.9 vs. 4.4 kb) is consistent with replacement of the host PEP4 gene with a nonfunctional PEP4 gene carrying the URA3 gene within its structural region. From these results, it was concluded that strains IGFU2601-5 and IGFU2602-5 were examples of the several PEP4 strains generated by disruption of the PEP4 gene of host strain IGF-U through gene replacement. EXAMPLE VII: GENERATION OF A PEP4' PICHIA STRAIN USING "POPOUT" VECTORS 1. Construction of P. pastoris gene disruption vector PDL521 Vector pDL521 was used in the development of PEP4- deficient (PEP4 ) strains of P. pastoris by disruption of a host PEP4 gene through "pop-in/pop-out" methods. In this method, a defective PEP4 gene containing a small deletion is added to a host PEP4 locus, and a functional PEP4 gene is removed from the PEP4 locus (i.e., pop- in/pop-out) . pDL521 was constructed in two steps. First, an intermediate plasmid, pDL501, was constructed by ligation of the 2.2 kb EcoRI/Sad fragment of pDL323, the 2.2 kb Sad/Pstl fragment of pPU205 and the 2.7 kb EcoRI/Pstl fragment of pUC19 in a three-way ligation. These three fragments were obtained as follows. pPU205, which contains the P. pastoriε URA3 gene (Figure 9) , was digested with Pstl and Sad. A 2.2 kb Pstl-SacI fragment containing the URA3 gene was gel isolated and purified using DE81 paper. Plasmid pDL323, harboring a defective PEP4 gene which lacks a 0.5 kb Ncol fragment present in an intact PEP4 gene (see Fig. 13) , was digested with EcoRI and Sad. A 2.2 kb fragment containing the defective PEP4 gene was gel isolated and purified using DE81 paper. pUC19 was digested with EcoRI and Pstl. The three fragments (0.02 μg of the EcoRI/Pstl-digested pUC19, 0.02 μg of the 2.2 kb Pstl/Sad fragment of pPU205 and 0.02 μg of the 2.2 kb EcoRI/Sad fragment of pDL323) were ligated in a three-way ligation. The ligation mix was used to transform E. coli strain MC1061. Ampicillin- resistant colonies were screened by analysis of Ncol- digested colony DNA. Plasmid containing the correctly ligated fragments was called pDL501. pDL501 was then cut with Sad, treated with calf alkaline phosphatase and 0.02 μg were ligated with 0.02 μg of a 1.9 kb Sad fragment isolated from Sacl-digested pEP202 and purified using DE81 paper. This added more PEP4 flanking sequence to the 3' end of the defective PEP4 gene in pDL501 and ensured a greater amount of homologous sequence for recombination with the endogenous PEP4 gene during transformation of P. paεtoris host IGF-U. The ligation mix was used to transform E. coli strain MC1061. DNA from ampicillin-resistant colonies was digested with Bglll and Spel and screened for the presence of the diagnostic 0.8 kb fragment indicative of the presence of the added Sad fragment from pEP202. Correct plasmid was called pDL521 (see Figure 16) . 2. Transformation of GS4-2 with pDL521 »• Generation of GS4-2 A URA3 strain of P. pastoriε was required as a host in the generation of a PEP4 strain by the pop-out process. A E7.RA3 strain was developed by direct plating of 10 6 cells of the general HIS4 P. paεtoris host strain GS115 in 5-fluoroorotic acid medium supplemented with uracil (0.67% yeast nitrogen base, 2% agar, 2% glucose, 750 ng 5-F0A/1 and 48 mg uracil/1) . After one week of incubation at 30°C, a colony growing on the plate was isolated. This HisTJra" strain was named GS4-2. b. Transformation of GS4-2 and generation of a PgP4" strain Plasmid pDL521 was linearized by digestion with Notl. The NotI site is located immediately 5' of the site at which sequence had been deleted from the PEP4 gene to make it defective. The ends of the Notl fragment are homologous to sequences in the endogenous PEP4 gene of GS4-2, which promotes integration of the fragment by homologous recombination at the PEP4 locus. The His" Ura " strain GS4-2 was transformed according to the spheroplast method with 20 μg of pDL521 which had been linearized by digestion with Notl. Transformants were selected by their ability to grow on media lacking uracil. Twelve of these transformants were picked, genomic DNA isolated from these transformants (as described in Example VLB.3.), cut with Sail and subjected to electrophoresis on a 0.8% agarose gel. The DNA was transferred to a nitrocellulose filter and probed with a radiolabeled 1.2 kb EcoRV/Xbal fragment of the PEP4 gene. Two strains, GS4-2521-3 and GS4-2521-4, which appeared to have integrated pDL521 into the PEP4 locus, based on the Southern blot hybridization pattern of genomic DNA, were chosen for further selection. These strains contained the URA3 marker gene with an intact complete PEP4 gene on one side and a defective PEP4 gene (lacking "0.5 kb of sequence) on the other side of the marker gene. This configuration of the PEP4 locus permits recombination between the two copies of the PEP4 gene that would result in elimination of one of the PEP4 genes and the URA3 gene (i.e., pop-out). Either one of the two PEP4 genes could be evicted in this recombination event. To identify if, and when, recombination between the two PEP4 genes occurred, strains GS4-2521-3 and GS4-2521-4 were plated onto YPD medium containing 5-FOA in a serial 10-fold dilution manner. Only Ura" strains grow in the presence of 5-FOA, and thus growth in such medium indicates the occurrence of the desired recombination event. Strains able to grow on 5-FOA- containing medium were uracil auxotrophs generated by recombination between the two copies of the PEP4 gene. Ura " colonies appeared on the 5-FOA-containing plate after 1 week of culture at 30"C: 10 of these colonies were derived from GS4-2521-3, and 14 of these colonies were derived from GS4-2521-4. 3. Characterization of transformants Fourteen of the Ura " transformant colonies were purified, genomic DNA was prepared from each, digested with EcoRI and EcoRV, subjected to electrophoresis on a 0.8% agarose gel, blotted to nitrocellulose and hybridized with a radiolabeled 1.2 kb Xbal/EcoRV fragment of the P. pastoriε PEP4 gene. DNA from 7 of the 14 isolates analyzed in this way had a hybridization profile consistent with a PEP4 locus consisting of only a defective PEP4 gene lacking -0.5 kb of sequence present in an intact PEP4 gene. Two of these strains are GS4- 2521-3/7 and GS4-2521-4/1. EXAMPLE VIII: CLONING OF A PORTION OF THE PRB-1 GENE OF P. PASTORIS The proteinase B gene, PRB-1 , encodes a vacuolar serine endoprotease in S . cereviεiae [Moehle et al., Mol. Cell Bio. 2: 4390-4399 (1987)]. A portion of the equivalent gene was cloned from P. paεtoriε using polymerase chain reaction (PCR) gene amplification techniques [see, for example, Gould et al., in Proc. Natl. Acad. Sci. USA Bβ : 1934-1938 (1989)]. Degenerate oligonucleotides, which had homology to sequences of the PRB-1 gene that encode regions of the proteinase B protein which are conserved across species (Moehle et al. supra.) ) were synthesized for use as primers in the PCR amplification of P. paεtoriε PRB-1 DNA. The oligonucleotides had the following sequences: Oligonucleotide 1: A A A G 5'- GATAGAATTCTGCAG GGT AAT GGT CAT GGT ACT CAT TGT GC-3 » C C C C C C C C A Oligonucleotide 2: GA A A A 5'- GATCGCATGC AAT CCT GCA ACA TGT GGA GAT GCC AT-3' G G G G G G CTG To facilitate subcloning of the amplified DNA fragments into shuttle plasmids, each oligonucleotide also contained one or more restriction endonuclease recognition sites on its 5' end: a SphI site on oligonucleotide 2 and both Pstl and EcoRI sites on oligonucleotide 1. The PCR reaction medium consisted of 100 ng of P. pastoris (Strain NRRL Y-11430) genomic DNA in 2 μl of T.E. (10 mM Tris-HCl, 1 mM EDTA) , 10 μl of oligonucleotide 1 and 10 μl of oligonucleotide 2, 16 μl of a 1.25 mM solution of dGTP, dCTP, dATP, and dTTP, 10 μl of lOx buffer (500 mM KCl, 100 mM Tris-HCl, pH 8.3, 15 mM MgCl 2 ) , 0.1% gelatin, 70 μl of water and 0.5 μl of 5 units/μl Tag DNA polymerase. The solution was heated at 94°C for 2 minutes. The PCR cycling reaction, which was repeated 31 times, included denaturating for 2 minutes at 96°C, annealing for 1 minute at 50°C and polymerizing for 3.5 minutes at 72°C. The product of this PCR was subjected to electrophoresis on an agarose gel, and a fragment of the size predicted (-500 bp) for the product of amplification of the PRB-1 gene between positions corresponding to oligonucleotides l and 2 was isolated on DE81 paper, and digested with EcoRI and SphI. subjected to electrophoresis on an agarose gel. The 500 bp fragment was isolated using DE81 paper and was ligated into 10 ng of pUC19, which had been linearized by cutting with EcoRI and SphI in the polylinker. The ligation mix was used to transform E. coli MC1061 cells. Restriction enzyme- digested plasmid DNA from ampicillin-resistant transformants was analyzed for the presence of the correct 500 bp EcoRI-SphI fragment. One colony contained the correct plasmid, designated pPRBPP. A restriction map of the Pichia portion of this plasmid is set forth in Figure 17. The sequence of the cloned portion of the P. pastoris PRB-1 gene contained in pPRBPP was generated using the Sanger dideoxy method (see Sanger et al., supra) and is shown in Sequence ID No. 5. This sequence of the P. paεtoriε PRB-1 gene has approximately 74% homology to the sequence of the S . cereviεiae PRB-1 gene. EXAMPLE IX: DEVELOPMENT OF A PRB-1 STRAIN OF P. PASTORIS Plasmid pDR911 was constructed for use in developing PiRB-1 strains of P. pastoris . This vector contains an internal portion of the P. pastoriε PRB-1 gene, which, when used to transform PRB-2 strains of P. pastoriε, integrates into the host genome at the PRB-1 locus to generate two incomplete and non-functional copies of the P B-1 gene. Vector pDR911 also contains a complete functional P. paεtoriε URA3 gene for use as a selectable marker in URA3 host strains of P. paεtoriε . A. Construction of pDR911 The PRB-1 gene fragment of P. paεtoris in pPRBPP was isolated by restriction digestion of pPRBPP with Pstl and SphI. The reaction mixture was loaded onto a 0.8% agarose gel and the 0.5 kb fragment was purified with DE81 paper. This 0.5 kb fragment was ligated into a linear form of plasmid pPU203, a P. pastoriε URA3-containing pUC- based plasmid (see Figure 8) . Plasmid pPU203 was linearized by cleavage with SphI and Pstl. and -10 ng was ligated with -100 ng of the Pichia DNA fragment. The ligation mixture was used to transform E. coli strain MC1061 to ampicillin resistance. Ampicillin-resistant colonies were screened by analysis of Pstl/SphI-digested colony DNA for the diagnostic fragment. Correct plasmid was named pDR911 (see Figure 18) . B. Transformation of GS4-2 with pDR911 To generate PRB-1 strains of P. paεtoris , one could transform GS4-2 by standard spheroplast transformation with pDR911 that had been linearized by digestion with Bglll. Southern blot hybridization of DNA from Ura + transformants would enable confirmation of PRB-1 strains created by disruption of the PRB-1 locus. Proteinase B activity assays [see, for example, Jones et al., in Genetics 102: 665-677 (1982) ] of transformants would further confirm the proteinase B deficiency of the strains. C. Development of a prb-i, pep4 strain of P. pastoris The PRB-1 gene of the pep4, ura3, his4 strain of P. pastoris GS4-2521-4-5, which is an isolate of GS4-2521-4 (see Example VII) , was disrupted by transformation with the vector pDR911, which had been linearized by cleavage with Bglll. Transformants exhibiting the Ura +3 phenotype were selected and analyzed by Southern blot hybridization. A selected transformant exhibiting the expected hybridization band pattern was designated MG18. This strain was used as a host for expression of IGF-1. The IGF-1 expressing strain was designated C+IGF816S1. While the invention has been described in detail with reference to certain preferred embodiments thereof, it will be understood that modifications and variations are within the spirit and scope of that which is described and claimed. SEQUENCE LISTING (1) GENERAL INFORMATION: (i) APPLICANT: Gleeson, Martin A Howard, Bradley D (ii) TITLE OF INVENTION: GENES WHICH INFLUENCE PICHIA PROTEOLYTIC ACTIVITY, AND USES THEREFOR (iii) NUMBER OF SEQUENCES: 6 (iv) CORRESPONDENCE ADDRESS: (A) ADDRESSEE: Fitch, Even, Ta in £ Flannery (B) STREET: 135 South LaSalle Street, Suite 900 (C) CITY: Chicago (D) STATE: Illinois (E) COUNTRY: U.S.A. (F) ZIP: 60603 (v) COMPUTER READABLE FORM: (A) MEDIUM TYPE: Floppy disk (B) COMPUTER: IBM PC compatible (C) OPERATING SYSTEM: PC-DOS/MS-DOS (D) SOFTWARE: PatentIn Release #1.0, Version #1.25 (vi) CURRENT APPLICATION DATA: (A) APPLICATION NUMBER: (B) FILING DATE: 01-APT-1992 (C) CLASSIFICATION: (vii) PRIOR APPLICATION DATA; (A) APPLICATION NUMBER: 07/678,916 (B) FILING DATE: 01-APR-1991 (viii) ATTORNEY/AGENT INFORMATION: (A) NAME: Seidman, Stephanie (B) REGISTRATION NUMBER: 33,779 (C) REFERENCE/DOCKET NUMBER: 50848PCT (ix) TELECOMMUNICATION INFORMATION: (A) TELEPHONE: (619)552-1311 (B) TELEFAX: (619)552-0095 (C) TELEX: 20 6566 PATLAW CGO (2) INFORMATION FOR SEQ ID NO:l: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 2032 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: unknown (D) TOPOLOGY: unknown (ii) MOLECULE TYPE: CDNA (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: 239..1468 (ix) FEATURE: (A) NAME/KEY: mat_peptide (B) LOCATION: 239..1468 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:l: GAATTCATAA TGGTGAGATT AGGTAATCGT CCGGAATAGG AATAGTGGTT TGGGGCGATT 60 AATCGCACCT GCCTTATATG GTAAGTACCT TGACCGATAA GGTGGCAACT ATTTAGAACA 120 AAGCAAGCCA CCTTTCTTTA TCTGTAACTC TGTCGAAGCA AGCATCTTTA CTAGAGAACA 180 TCTAAACCAT TTTACATTCT AGAGTTCCAT TTCTCAATTA CTGATAATCA ATTTAAAG 238 ATG ATA TTT GAC GGT ACT ACG ATG TCA ATT GCC ATT GGT TTG CTC TCT 286 Met lie Phe Asp Gly Thr Thr Met Ser lie Ala lie Gly Leu Leu Ser 1 5 10 15 ACT CTA GGT ATT GGT GCT GAA GCC AAA GTT CAT TCT GCT AAG ATA CAC 334 Thr Leu Gly lie Gly Ala Glu Ala Lys Val His Ser Ala Lys lie His 20 25 30 AAG CAT CCA GTC TCA GAA ACT TTA AAA GAG GCC AAT TTT GGG CAG TAT 382 Lys His Pro Val Ser Glu Thr Leu Lys Glu Ala Asn Phe Gly Gin Tyr 35 40 45 GTC TCT GCT CTG GAA CAT AAA TAT GTT TCT CTG TTC AAC GAA CAA AAT 430 Val Ser Ala Leu Glu His Lys Tyr Val Ser Leu Phe Asn Glu Gin Asn 50 55 60 GCT TTG TCC AAG TCG AAT TTT ATG TCT CAG CAA GAT GGT TTT GCC GTT 478 Ala Leu Ser Lys Ser Asn Phe Met Ser Gin Gin Asp Gly Phe Ala Val 65 70 75 80 GAA GCT TCG CAT GAT GCT CCA CTT ACA AAC TAT CTT AAC GCT CAG TAT 526 Glu Ala Ser His Asp Ala Pro Leu Thr Asn Tyr Leu Asn Ala Gin Tyr 85 90 95 TTT ACT GAG GTA TCA TTA GGT ACC CCT CCA CAA TCG TTC AAG GTG ATT 574 Phe Thr Glu Val Ser Leu Gly Thr Pro Pro Gin Ser Phe Lys Val lie 100 105 110 CTT GAC ACA GGA TCC TCC AAT TTA TGG GTT CCT AGC AAA GAT TGT GGA 622 Leu Asp Thr Gly Ser Ser Asn Leu Trp Val Pro Ser Lys Asp Cys Gly 115 120 125 TCA TTA GCT TGC TTC TTG CAT GCT AAG TAT GAC CAT GAT GAG TCT TCT 670 Ser Leu Ala Cys Phe Leu His Ala Lys Tyr Asp His Asp Glu Ser Ser 130 135 140 ACT TAT AAG AAG AAT GGT AGT AGC TTT GAA ATT AGG TAT GGA TCC GGT 718 Thr Tyr Lys Lys Asn Gly Ser Ser Phe Glu lie Arg Tyr Gly Ser Gly 145 150 155 160 TCC ATG GAA GGG TAT GTT TCT CAG GAT GTG TTG CAA ATT GGG GAT TTG 766 Ser Met Glu Gly Tyr Val Ser Gin Asp Val Leu Gin lie Gly Asp Leu 165 170 175 ACC ATT CCC AAA GTT GAT TTT GCT GAG GCC ACA TCG GAG CCG GGG TTG 814 Thr lie Pro Lys Val Asp Phe Ala Glu Ala Thr Ser Glu Pro Gly Leu 180 185 190 GCC TTC GCT TTT GGC AAA TTT GAC GGA ATT TTG GGG CTT GCT TAT GAT 862 Ala Phe Ala Phe Gly Lys Phe Asp Gly lie Leu Gly Leu Ala Tyr Asp 195 200 205 TCA ATA TCA GTA AAT AAG ATT GTT CCT CCA ATT TAC AAG GCT TTG GAA 910 Ser lie Ser Val Asn Lys lie Val Pro Pro lie Tyr Lys Ala Leu Glu 210 215 220 TTA GAT CTC CTT GAC GAA CCA AAA TTT GCC TTC TAC TTG GGG GAT ACG 958 Leu Asp Leu Leu Asp Glu Pro Lys Phe Ala Phe Tyr Leu Gly Asp Thr 225 230 235 240 GAC AAA GAT GAA TCC GAT GGC GGT TTG GCC ACA TTT GGT GGT GTG GAC 1006 Asp Lys Asp Glu Ser Asp Gly Gly Leu Ala Thr Phe Gly Gly Val Asp 245 250 255 AAA TCT AAG TAT GAA GGA AAG ATC ACC TGG TTG CCT GTC AGA AGA AAG 1054 Lys Ser Lys Tyr Glu Gly Lys lie Thr Trp Leu Pro Val Arg Arg Lys 260 265 270 GCT TAC TGG GAG GTC TCT TTT GAT GGT GTA GGT TTG GGA TCC GAA TAT 1102 Ala Tyr Trp Glu Val Ser Phe Asp Gly Val Gly Leu Gly Ser Glu Tyr 275 280 285 GCT GAA TTG CAA AAA ACT GGT GCA GCC ATC GAC ACT GGA ACC TCA TTG 1150 Ala Glu Leu Gin Lys Thr Gly Ala Ala lie Asp Thr Gly Thr Ser Leu 290 295 300 ATT GCT TTG CCC AGT GGC CTA GCT GAA ATT CTC AAT GCA GAA ATT GGT 1198 lie Ala Leu Pro Ser Gly Leu Ala Glu lie Leu Asn Ala Glu lie Gly 305 310 315 320 GCT ACC AAG GGT TGG TCT GGT CAA TAC GCT GTG GAC TGT GAC ACT AGA 1246 Ala Thr Lye Gly Trp Ser Gly Gin Tyr Ala Val Asp Cys Asp Thr Arg 325 330 335 GAC TCT TTG CCA GAC TTA ACT TTA ACC TTC GCC GGT TAC AAC TTT ACC 1294 Asp Ser Leu Pro Asp Leu Thr Leu Thr Phe Ala Gly Tyr Asn Phe Thr 340 345 350 ATT ACT CCA TAT GAC TAT ACT TTG GAG GTT TCT GGG TCA TGT ATT AGT 1342 lie Thr Pro Tyr Asp Tyr Thr Leu Glu Val Ser Gly Ser Cys lie Ser 355 360 365 GCT TTC ACC CCC ATG GAC TTT CCT GAA CCA ATA GGT CCT TTG GCA ATC 1390 Ala Phe Thr Pro Met Asp Phe Pro Glu Pro lie Gly Pro Leu Ala lie 370 375 380 ATT GGT GAC TCG TTC TTG AGA AAA TAT TAC TCA GTT TAT GAC CTA GGC 1438 lie Gly Asp Ser Phe Leu Arg Lys Tyr Tyr Ser Val Tyr Asp Leu Gly 385 390 395 400 AAA GAT GCA GTA GGT TTA GCC AAG TCT ATT TAGGCAAGAA TAAAAGTTGC 1488 Lys Asp Ala Val Gly Leu Ala Lys Ser lie 405 410 TCAGCTGAAC TTATTTGGTT ACTTATCAGG TAGTGAAGAT GTAGAGAATA TATGTTTAGG 1548 TATTTTTTTT TAGTTTTTCT CCTATAACTC ATCTTCAGTA CGTGATTGCT TGTCAGCTAC 1608 CTTGACAGGG GCGCATAAGT GATATCGTGT ACTGCTCAAT CAAGATTTGC CTGCTCCATT 1668 GATAAGGGTA TAAGAGACCC ACCTGCTCCT CTTTAAAATT CTCTCTTAAC TGTTGTGAAA 1728 ATCATCTTCG AAGCAAATTC GAGTTTAAAT CTATGCGGTT GGTAACTAAA GGTATGTCAT 1788 GGTGGTATAT AGTTTTTCAT TTTACCTTTT ACTAATCAGT TTTACAGAAG AGGAACGTCT 1848 TTCTCAAGAT CGAAATAGGA CTAAATACTG GAGACGATGG GGTCCTTATT TGGGTGAAAG 1908 GCAGTGGGCT ACAGTAAGGG AAGACTATTC CGATGATGGA GATGCTTGGT CTGCTTTTCC 1968 TTTTGAGCAA TCTCATTTGA GAACTTATCG CTGGGGAGAG GATGGACTAG CTGGAGTCTC 2028 AGAC 2032 (2) INFORMATION FOR SEQ ID NO:2: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 410 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: Met lie Phe Asp Gly Thr Thr Met Ser lie Ala lie Gly Leu Leu Ser 1 5 10 15 Thr Leu Gly lie Gly Ala Glu Ala Lys Val His Ser Ala Lys lie His 20 25 30 Lys His Pro Val Ser Glu Thr Leu Lys Glu Ala Asn Phe Gly Gin Tyr 35 40 45 Val Ser Ala Leu Glu His Lys Tyr Val Ser Leu Phe Asn Glu Gin Asn 50 55 60 Ala Leu Ser Lys Ser Asn Phe Met Ser Gin Gin Asp Gly Phe Ala Val 65 70 75 80 Glu Ala Ser His Asp Ala Pro Leu Thr Asn Tyr Leu Asn Ala Gin Tyr 85 90 95 Phe Thr Glu Val Ser Leu Gly Thr Pro Pro Gin Ser Phe Lys Val lie 100 105 110 Leu Asp Thr Gly Ser Ser Asn Leu Trp Val Pro Ser Lys Asp Cys Gly 115 120 125 Ser Leu Ala Cys Phe Leu His Ala Lys Tyr Asp His Asp Glu Ser Ser 130 135 140 Thr Tyr Lys Lys Asn Gly Ser Ser Phe Glu lie Arg Tyr Gly Ser Gly 145 150 155 160 Ser Met Glu Gly Tyr Val Ser Gin Asp Val Leu Gin lie Gly Asp Leu 165 170 175 Thr lie Pro Lys Val Asp Phe Ala Glu Ala Thr Ser Glu Pro Gly Leu 180 185 190 Ala Phe Ala Phe Gly Lys Phe Asp Gly lie Leu Gly Leu Ala Tyr Asp 195 200 205 Ser lie Ser Val Asn Lys lie Val Pro Pro lie Tyr Lys Ala Leu Glu 210 215 220 Leu Asp Leu Leu Asp Glu Pro Lys Phe Ala Phe Tyr Leu Gly Asp Thr 225 230 235 240 Asp Lys Asp Glu Ser Asp Gly Gly Leu Ala Thr Phe Gly Gly Val Asp 245 250 255 Lys Ser Lys Tyr Glu Gly Lys lie Thr Trp Leu Pro Val Arg Arg Lys 260 265 270 Ala Tyr Trp Glu Val Ser Phe Asp Gly Val Gly Leu Gly Ser Glu Tyr 275 280 285 Ala Glu Leu Gin Lys Thr Gly Ala Ala lie Asp Thr Gly Thr Ser Leu 290 295 300 lie Ala Leu Pro Ser Gly Leu Ala Glu lie Leu Asn Ala Glu lie Gly 305 310 315 320 Ala Thr Lys Gly Trp Ser Gly Gin Tyr Ala Val Asp Cys Asp Thr Arg 325 330 335 Asp Ser Leu Pro Asp Leu Thr Leu Thr Phe Ala Gly Tyr Asn Phe Thr 340 345 350 lie Thr Pro Tyr Asp Tyr Thr Leu Glu Val Ser Gly Ser Cys lie Ser 355 360 365 Ala Phe Thr Pro Met Asp Phe Pro Glu Pro lie Gly Pro Leu Ala lie 370 375 380 lie Gly Asp Ser Phe Leu Arg Lys Tyr Tyr Ser Val Tyr Asp Leu Gly 385 390 395 400 Lys Asp Ala Val Gly Leu Ala Lys Ser lie 405 410 (2) INFORMATION FOR SEQ ID NO:3: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 2688 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: unknown (D) TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA ( i ) FEATURE : (A) NAME/KEY: CDS (B) LOCATION: 643..1431 (ix) FEATURE: (A) NAME/KEY: mat_peptide (B) LOCATION: 643..1431 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3: CTGCAGAAAT GGGGAGATAA CCACCTTTGA CGAATTGACT AAAGTTCTAC AGATCATGTT 60 TACAAATGCC ATCATCTATA ACGATGAAGA CAGTGATGTT TCGAAGCTAA CGATTGAAAT 120 GATGGAAGAA ACTACTAAGA TTATAGAGCT GTTCAGAGAA AGTCTGGATT AGTCCTGGAC 180 AATGAACTTT ATGTACAAAA ATATGGGGTT AACGTCTTAG CTGTTGCATC ATAAGTTGGT 240 TTTGTTCTTG GAAACGTTGA CCAACTCTCT CACTGTGCTT GAGGAACTTT TCTGCACACT 300 TGTTGATGCA GCCTTCCTCC TTAGAAGTCA ACTTGTTAGA TGTAAAATCA TTGACACAGT 360 CTGTAAAACA TTTGCTAACC AAATCGGAGT AAAGACGCAT GAAGTCTTTC ATTTGTTTTT 420 GTTCAACGAG TTTCTGGAAC TCTTGTTGTT CTTTAGCGTT CAATGCGTCC ATTTTGTGAT 480 GTACTTGGTT GGGGTAGAGT TAGCACTTGC TCTCTCTGTT ACCAGTTTTT GTCAAGATTG 540 AAGAAAAAAG TTTTTTGGAC GGTACACGTC GCACCTATCC TTCGCATTGA TCCACTCTAA 600 TGAGTTAACA TCAACCTGAT CAAAGGGATA GATACCTAGA CA ATG GCT CGC AGT 654 Met Ala Arg Ser 1 TAT GCC GAG AGA GCA AAT ACT CAT CAA TCA CCT GTG GCA CGA CGA CTG 702 Tyr Ala Glu Arg Ala Asn Thr His Gin Ser Pro Val Ala Arg Arg Leu 5 10 15 20 TTT GCG CTT ATG GAA CAG AAA CAG AGT AAC CTA TGC GCA TCA GTC GAC 750 Phe Ala Leu Met Glu Gin Lys Gin Ser Asn Leu Cys Ala Ser Val Asp 25 30 35 GTG AGA ACA ACT AAA GAA TTA TTG GAG CTT CTA GAT AAA TTG GGC CCA 798 Val Arg Thr Thr Lys Glu Leu Leu Glu Leu Leu Asp Lys Leu Gly Pro 40 45 50 TTT ATC TGT TTG GCC AAG ACT CAT ATC GAC ATA ATT GAT GAC TTC ACG 846 Phe lie Cys Leu Ala Lys Thr His He Aβp He He Asp Asp Phe Thr 55 60 65 TAT GAT GGA ACT ATT CTG CCT TTA TTG GAA CTA TCA AAG AAA CAC AAG 894 Tyr Asp Gly Thr He Leu Pro Leu Leu Glu Leu Ser Lys Lys His Lys 70 75 80 TTT TTA ATT TTT GAG GAC AGA AAG TTT GCT GAT ATA GGC AAC ACT GTC 942 Phe Leu He Phe Glu Asp Arg Lys Phe Ala Asp He Gly Asn Thr Val 85 90 95 100 AAG CAT CAA TAT CAA GGA GGT GTC TAC AAG ATT GCA CAA TGG GCA GAT 990 Lys His Gin Tyr Gin Gly Gly Val Tyr Lys He Ala Gin Trp Ala Asp 105 110 115 ATT ACA AAT GCT CAT GGT GTC ATT GGT AGT GGA ATT GTA AAG GGT CTA 1038 He Thr Asn Ala His Gly Val He Gly Ser Gly He Val Lys Gly Leu 120 125 130 AAG GAG GCA GCC ACT GAG ACA ACA GAT CAA CCA AGG GGA CTA TTG ATG 1086 Lys Glu Ala Ala Thr Glu Thr Thr Asp Gin Pro Arg Gly Leu Leu Met 135 140 145 TTG GCT GAA CTG TCG TCA AAG GGA TCA ATT GCC CAT GGT AAG TAC ACC 1134 Leu Ala Glu Leu Ser Ser Lys Gly Ser He Ala His Gly Lys Tyr Thr 150 155 160 GAA GAA ACT GTA GAA ATT GCA AAA TCA GAC AAG GAA TTC GTC ATT GGG 1182 Glu Glu Thr Val Glu He Ala Lys Ser Asp Lys Glu Phe Val He Gly 165 170 175 180 TTT ATT GCT CAA AAT TCT ATG GGA GGA CAA GAT GAA GGG TTC GAT TGG 1230 Phe He Ala Gin Asn Ser Met Gly Gly Gin Asp Glu Gly Phe Asp Trp 185 190 195 ATT ATT ATG ACA CCA GGT GTT GGT TTG GAT GAC ACT GGT GAT GCT CTA 1278 He He Met Thr Pro Gly Val Gly Leu Asp Asp Thr Gly Asp Ala Leu 200 205 210 GGC CAA CAA TAT CGA ACA GTG AGT CAA GTA TTT TCC ACT GGC ACT GAC 1326 Gly Gin Gin Tyr Arg Thr Val Ser Gin Val Phe Ser Thr Gly Thr Asp 215 220 225 ATC ATA ATC GTA GGT CGT GGT TTG TTT GGC AAG GGC AGA GAT CCC TTA 1374 He He He Val Gly Arg Gly Leu Phe Gly Lys Gly Arg Asp Pro Leu 230 235 240 AAA GAA GGT GAA CGG TAT AGA AAA GCT GGG TGG GAA GCT TAC CAA AAT 1422 Lys Glu Gly Glu Arg Tyr Arg Lys Ala Gly Trp Glu Ala Tyr Gin Asn 245 250 255 260 ATT CTG AGG TAAATTACAA GTATGTACAG GGGATCAATT GTTTCGGGCG 1471 He Leu Arg ATTCAACTGA ATCGATCTTC AATTTCATCG CTCAATTTTT GACGCAGTAT TTCAAACACC 1531 AGAAGCCCCA CGGATGTTGC TGGAATGGTA GTTAACGCAT TCCTAACGAA CCCTTTATAA 1591 AACCAGCGGG TCCAAGATAG TTTAGACTTC TCATGTAAGC TCACCAACTG GTGGAATGTA 1651 TCTAAGTATG ATCGGTAATA TAGACGGAAT TTACTTTTCT TATCCCAGGA GTTCTCGTTG 1711 AAAATATCCA ACGCTTCCAA CCTTGCTAAA TGTATTGACT GAACTTTAGA AAATGGGTAT 1771 TGAACGGCTA GTAACGAACA TGCAGCGCTA GCACCAGCCA AAAGAATAAA AGTCGTCCTC 1831 AGGATATTTT CACTTTTCGT TTTCACTGTG TCACCTTGGG GCCTTCCAAG AAGACTATTT 1891 TTCATCCTAT CAATTCTCTC CATAGTGTTC TCGGTTATCC TGTAACCTCT ATTCTTAATG 1951 GCTTCGAATG TTGTGAAATA TATAGCAAAG GATGTGCTTT CTTTGACCAG ACTCAAGGAG 2011 TAGCCAGCAA ATACCCCCAG AAAACCACTA GTTTTTAGTT TATGAAGACC GTAAATCCAT 2071 AAGTTGTCAT TCTTGCCCCC AATAATCTCG 6AGGCATTAG ATCGGGCATA TATTGCATCA 2131 ATTGGGGCAG CTACCAATGA CTGCGCAGCT CCAGCTAGAA ACCCAGCTCG AAATACATCC 2191 ACTAGTCTTG GATTTGCTAT CGATCTGCCC TCTTGACCGT CAGTATATGA CTGCAAACAT 2251 GATAAATACG TTGTGTAAAG TACAATTCCC ATCACAGAAT TGGCTACCAA TGGTGGCAGG 2311 ACCTTGTTTG GTATCAACTC CCAACCATGG GTTTTGACGG CTCGTAACAA TAGAGCTGGA 2371 TTTGAGTGGA AAATGGGCTG TAAGGTTTAC CTTTCAAATG AGCTCCAAAG AAGATGCGTA 2431 TTGGTGCCAT GTAGTCAAAA CGAGTGGGAC GAAACAGTTT GGCTGGTGTC CTCAGGTACA 2491 GTGAACTAAA TTGGACTAGA ACAGCTCTGA TCCCAGCTGT CGAAGCAGAC ACCACTTGAG 2551 TGTTTTTGTT GCTAAGAGTA GCCTTTTTAG AATCATCGTT GTCTTCCATA GGTTTCTGGA 2611 ACACAATGCC AGAGTTCATA GAGGATCAGA GGGGAATTGA GGTGTGTGTA TATGTATTTA 2671 TAGGGGTACC GAGCTCG 2688 (2) INFORMATION FOR SEQ ID NO: : (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 263 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO: : Met Ala Arg Ser Tyr Ala Glu Arg Ala Asn Thr His Gin Ser Pro Val 1 5 10 15 Ala Arg Arg Leu Phe Ala Leu Met Glu Gin Lys Gin Ser Asn Leu Cys 20 25 30 Ala Ser Val Asp Val Arg Thr Thr Lys Glu Leu Leu Glu Leu Leu Asp 35 40 45 Lys Leu Gly Pro Phe He Cys Leu Ala Lys Thr His He Asp He He 50 55 60 Asp Asp Phe Thr Tyr Asp Gly Thr He Leu Pro Leu Leu Glu Leu Ser 65 70 75 80 Lys Lys His Lys Phe Leu He Phe Glu Asp Arg Lys Phe Ala Asp He 85 90 95 Gly Asn Thr Val Lys His Gin Tyr Gin Gly Gly Val Tyr Lys He Ala 100 105 110 Gin Trp Ala Asp He Thr Asn Ala His Gly Val He Gly Ser Gly He 115 120 125 Val Lys Gly Leu Lys Glu Ala Ala Thr Glu Thr Thr Asp Gin Pro Arg 130 135 140 Gly Leu Leu Met Leu Ala Glu Leu Ser Ser Lys Gly Ser He Ala His 145 150 155 160 Gly Lys Tyr Thr Glu Glu Thr Val Glu He Ala Lys Ser Asp Lys Glu 165 170 175 Phe Val He Gly Phe He Ala Gin Asn Ser Met Gly Gly Gin Asp Glu 180 185 190 Gly Phe Asp Trp He He Met Thr Pro Gly Val Gly Leu Asp Asp Thr 195 200 205 Gly Asp Ala Leu Gly Gin Gin Tyr Arg Thr Val Ser Gin Val Phe Ser 210 215 220 Thr Gly Thr Asp He He He Val Gly Arg Gly Leu Phe Gly Lys Gly 225 230 235 240 Arg Asp Pro Leu Lys Glu Gly Glu Arg Tyr Arg Lys Ala Gly Trp Glu 245 250 255 Ala Tyr Gin Asn He Leu Arg 260 (2) INFORMATION FOR SEQ ID NO:5: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 555 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: unknown (D) TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: 3..554 (ix) FEATURE: (A) NAME/KEY: mat_peptide (B) LOCATION: 3..554 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5: GA ATT CTG CAG GGA AAC GGC CAC GGT ACA CAT TGT GCT GGT ACC ATT 47 He Leu Gin Gly Asn Gly His Gly Thr His Cys Ala Gly Thr He 1 5 10 15 GCT TCT GAA AGC TAC GGT GTT GCC AAG AAG GCT AAT GTT GTT GCC ATC 95 Ala Ser Glu Ser Tyr Gly Val Ala Lys Lys Ala Asn Val Val Ala He 20 25 30 AAG GTC TTG AGA TCT AAT GGT TCT GGT TCG ATG TCA GAT GTT CTG AAG 143 Lys Val Leu Arg Ser Asn Gly Ser Gly Ser Met Ser Asp Val Leu Lys 35 40 45 GGT GTT GAG TAT GCC ACC CAA TCC CAC TTG GAT GCT GTT AAA AAG GGC 191 Gly Val Glu Tyr Ala Thr Gin Ser His Leu Asp Ala Val Lys Lys Gly 50 55 60 AAC AAG AAA TTT AAG GGC TCT ACC GCT AAC ATG TCA CTG GGT GGT GGT 239 Asn Lys Lys Phe Lys Gly Ser Thr Ala Asn Met Ser Leu Gly Gly Gly 65 70 75 AAA TCT CCT GCT TTG GAC CTT GCA GTC AAT GCT GCT GTT AAG AAT GGT 287 Lys Ser Pro Ala Leu Asp Leu Ala Val Asn Ala Ala Val Lys Asn Gly 80 85 90 95 ATT CAC TTT GCC GTT GCA GCA GGT AAC GAA AAC CAA GAT GCT TGT AAC 335 He His Phe Ala Val Ala Ala Gly Asn Glu Asn Gin Asp Ala Cys Asn 100 105 110 ACC TCG CCA GCA GCT GCT GAG AAT GCC ATC ACC GTC GGT GCA TCA ACC 383 Thr Ser Pro Ala Ala Ala Glu Asn Ala He Thr Val Gly Ala Ser Thr 115 120 125 TTA TCA GAC GCT AGA GCT TAC TTT TCT AAC TAC GGT AAA TGT GTT GAC 431 Leu Ser Asp Ala Arg Ala Tyr Phe Ser Asn Tyr Gly Lys Cys Val Asp 130 135 140 ATT TTC GCT CCA GGT TTA AAC ATT CTT TCT ACC TAC ACT GGT TCG GAT 479 He Phe Ala Pro Gly Leu Asn He Leu Ser Thr Tyr Thr Gly Ser Asp 145 150 155 GAC GCA ACT GCT ACC TTG TCT GGT ACT TCA ATG GCC AGC CCT CAT GTT 527 Asp Ala Thr Ala Thr Leu Ser Gly Thr Ser Met Ala Ser Pro His Val 160 165 170 175 GCA GGC TTG CAT GCA AGC TTG GCA CTG G 555 Ala Gly Leu His Ala Ser Leu Ala Leu 180 (2) INFORMATION FOR SEQ ID NO:6: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 184 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6: He Leu Gin Gly Asn Gly His Gly Thr His Cys Ala Gly Thr He Ala 1 5 10 15 Ser Glu Ser Tyr Gly Val Ala Lys Lys Ala Asn Val Val Ala He Lys 20 25 30 Val Leu Arg Ser Asn Gly Ser Gly Ser Met Ser Asp Val Leu Lys Gly 35 40 45 Val Glu Tyr Ala Thr Gin Ser His Leu Asp Ala Val Lye Lys Gly Asn 50 55 60 Lys Lys Phe Lys Gly Ser Thr Ala Asn Met Ser Leu Gly Gly Gly Lys 65 70 75 80 Ser Pro Ala Leu Asp Leu Ala Val Asn Ala Ala Val Lye Asn Gly He 85 90 95 His Phe Ala Val Ala Ala Gly Asn Glu Asn Gin Asp Ala Cys Asn Thr 100 105 110 Ser Pro Ala Ala Ala Glu Asn Ala He Thr Val Gly Ala Ser Thr Leu 115 120 125 Ser Asp Ala Arg Ala Tyr Phe Ser Asn Tyr Gly Lys Cys Val Asp He 130 135 140 Phe Ala Pro Gly Leu Asn He Leu Ser Thr Tyr Thr Gly Ser Asp Asp 145 150 155 160 Ala Thr Ala Thr Leu Ser Gly Thr Ser Met Ala Ser Pro His Val Ala 165 170 175 Gly Leu His Ala Ser Leu Ala Leu 180

Claims: THAT WHICH IS CLAIMED IS: 1. An isolated DNA fragment obtained from a strain of the genus Pichia , comprising a gene encoding a protein which, directly or indirectly, influences the proteolytic activity of said strain. 2. The DNA fragment of Claim 1, wherein said protein influences the carboxypeptidase Y activity of said strain. 3. The DNA fragment of Claim 2, wherein said gene has the restriction map in FIG. 1 of the drawings. 4. The DNA fragment of Claim 2, wherein said fragment is the approximately 10.6 kbp EcoRI fragment of plasmid pEP202. 5. The DNA fragment of Claim 2, wherein said fragment is the approximately 2.7 kbp EcoRI-SacI fragment of plasmid pEP301, or portions thereof that encode a protein which influences the carboxypeptidase Y activity of said strain. 6. The DNA fragment of Claim 2, wherein said the nucleic acid sequence of said gene encodes an amino acid sequence which is substantially the same as the amino acid sequence set forth in Sequence ID No. 2. 7. The DNA fragment of Claim 2, wherein the nucleic acid sequence of said gene is substantially the same as the nucleic acid sequence set forth in Sequence ID No. 1. 8. An isolated DNA fragment containing a modified form of the gene of Claim 1, wherein said modification renders the gene incapable of producing functional product, or alters the ability of the gene product to influence the proteolytic activity of said strain. 9. The DNA fragment of Claim 8, wherein the modified form of said gene is suitable for introduction into a yeast host of the genus Pichia by homologous recombination, wherein homologous recombination occurs at the specific locus of said gene whose expression product influences proteolytic activity. 10. The DNA fragment of Claim 8, wherein the modified gene, in its unmodified form, encodes a protein that influences the carboxypeptidase Y activity of said strain. 11. The DNA fragment of Claim 9, wherein said gene is modified by the insertion of an auxotrophic marker gene therein. 12. A DNA fragment of Claim 11, wherein said auxotrophic marker gene is selected from the Pichia or Saccharomyces HIS4 gene, the Pichia or Saccharomyces ARG4 gene, or the Pichia or Saccharomyces URA3 gene. 13. The DNA fragment of Claim 12, wherein said fragment is included in plasmid pDR401. 14. The DNA fragment of Claim 9, wherein said gene is modified by making deletions therefrom. 15. The DNA fragment of Claim 14, wherein said fragment is included in plasmid pDR421. 16. A method of producing strain(s) of the genus Pichia which are deficient in proteolytic activity, compared to host strain(s) of the same species, comprising: contacting said host strain(s) with the DNA fragment of Claim 8 under conditions suitable for the site- directed integration of said DNA fragment into the genome of said host strain(s) , wherein said site-directed integration occurs at the specific locus of said gene which encodes a protein which influences proteolytic activity. 17. The method of Claim 16, further comprising: screening the strains obtained as a result of said contacting for the presence of strains which have reduced proteolytic activity, relative to said host strain(s) , and selecting those strains which have reduced proteolytic activity, relative to said host strain(s) . 18. The method of Claim 16, wherein integration of said DNA fragment influences the proteinase A and carboxypeptidase Y activities of said host organism. 19. A strain of Pichia deficient in proteolytic activity produced by the method of Claim 16. 20. The strain of Claim 19, which is deficient in proteinase A and carboxypeptidase Y activities. 21. The strain of Claim 20 selected from P. pastoris strain pi, p2, p5, p8, pl3, pl6, or p20. 22. The method of Claim 16, wherein said host strain is defective in at least one auxotrophic marker gene selected from the histidinol dehydrogenase gene, the argininosuccinate lyase gene, or the orotidine-5'- phosphate decarboxylase gene, and wherein the modified gene of said fragment is modified by the insertion therein of an intact form of the auxotrophic marker gene in which the host strain is defective. 23. A strain of Pichia deficient in proteolytic activity produced by the method of Claim 22. 24. A strain of Claim 23, wherein said strain is deficient in proteinase A and carboxypeptidase Y activity. 25. A strain of Claim 24 selected from P. pastoriε strain pi, p2, p5, p8, pl3, pl6, or p20. 26. The method of Claim 16, wherein the gene said fragment is modified by making deletions therefrom. 27. The method of Claim 22, wherein said host strain is GS115 and said DNA fragment is the approximately 5.3 kbp SacI-EcoRI fragment of plasmid pDR401. 28. A yeast cell of the genus Pichia which is deficient in proteolytic activity, compared to wild-type strains of the same species. 29. The yeast cell of Claim 28, wherein said cell deficient in proteinase A and carboxypeptidase Y activities. 30. A method for the expression of proteolytically sensitive recombinant product(s), comprising: transforming the cell of Claim 28 with DNA encoding said product and culturing said cell under conditions whereby said proteolytically sensitive product(s) is expressed. 31. The method of claim 30, wherein the cell is rendered deficient in proteolytic activity by replacement of a gene of the cell that encodes a protein which, upon expression, directly or indirectly, influences the carboxypeptidase Y activity of said host organism with a defective form of said gene modified by the insertion therein of a marker gene which complements an auxotrophic phenotype of said host strain; and wherein the marker gene is selected from the histidinol dehydrogenase gene, the argininosuccinate lyase gene, or the orotidine-5'-phosphate decarboxylase gene. 32. A method for the expression of proteolytically sensitive recombinant product(s), comprising rendering a host strain deficient in proteolytic activity using the method of Claim 16, wherein said host strain is defective in at least one auxotrophic marker gene; and said host strain has been transformed with at least one DNA fragment comprising an expression cassette comprising, in the reading frame direction of transcription, the following sequences of nucleotides: (i) a promoter region of a methanol-responsive gene of a methylotrophic yeast, (ii) a sequence encoding a polypeptide consisting essentially of: (a) an optional secretion signal sequence, and (b) a proteolytically sensitive protein; and (iii) a transcription terminator functional in a methylotrophic yeast; wherein said sequences are operationally associated with one another for transcription of the sequences encoding said polypeptide. 33. The method of Claim 32, wherein said host strain is defective in at least two auxotrophic marker genes. .34. A method of Claim 33, wherein said auxotrophic marker genes are the HIS 4 gene, and the URA3 gene. 35. A method of Claim 34, wherein the proteolytically sensitive product is IGF-1 and the marker gene employed for transforming said host with DNA encoding IGF-1 is the HIS4 gene. 36. A method of Claim 35, wherein the modified gene employed to render the host deficient in proteolytic activity, in its unmodified form, encodes a protein that influences the carboxypeptidase activity of the host. 37. A method of Claim 36, wherein the modified gene is produced by deletion of a portion of the coding sequence therefrom. 38. A method of Claim 37, wherein the recombinant strain from which said recombinant product(s) is expressed is strain M+IMB206S1. 39. An isolated DNA fragment, comprising the orotidine-5'-phosphate decarboxylase gene from species of the genus Pichia . 40. The DNA fragment of Claim 39, wherein said gene has substantially the same restriction map as shown in FIG. 12. 41. The DNA fragment of Claim 39, wherein said gene encodes substantially the same amino acid sequence as set forth in Sequence ID No. 4. 42. A DNA fragment of Claim 39, wherein said gene has substantially the same nucleic acid sequence as set forth in Sequence ID No. 3. 43. A yeast cell of the genus Pichia , which is defective in the orotidine-5'-phosphate decarboxylase gene. 44. The yeast cell of Claim 43, wherein said yeast cell is a strain of Pichia paεtoriε . 45. The yeast cell of Claim 44, wherein said yeast cell is the strain Pichia paεtoris GS4-2. 46. The yeast cell of Claim 43, further containing a deficiency in proteolytic activity. 47. A yeast cell of Claim 46, wherein said yeast cell is deficient in proteinase A and carboxypeptidase Y activities. 48. The yeast cell of Claim 47, wherein said yeast cell is selected from the Pichia pastoriε strains GS4-2521-3/7 or GS4-2521-4/1.

Inventors: GLEESON MARTIN ANTHONY, HOWARD BRADLEY DRAKE, GLEESON, MARTIN, ANTHONY, HOWARD, BRADLEY, DRAKE
Applicants: SALK INST BIOTECH IND, THE SALK INSTITUTE BIOTECHNOLOGY/INDUSTRIAL ASSOCI
Application year: 1992
Main classification: C12N1
IPC codes: C07K14, C09K13, C12N1, C12N9, C12N15, C12R1