EP1080210A2

EP1080210A2 - Methods for producing a polypeptide by modifying the copy number of a gene

Info

Publication number: EP1080210A2
Application number: EP99925956A
Authority: EP
Inventors: Debbie S. Yaver
Original assignee: Novo Nordisk Biotech Inc
Current assignee: Novozymes Inc
Priority date: 1998-05-27
Filing date: 1999-05-27
Publication date: 2001-03-07
Also published as: JP2002516116A; CN1307642A; WO1999061651A2; AU4213999A; WO1999061651A3

Abstract

The present invention relates to methods for producing a polypeptide, comprising: (a) cultivating a mutant cell under conditions conducive for production of the polypeptide, wherein (i) the mutant cell is related to a parent cell, which parent cell comprises at least two tandem copies of a nucleic acid sequence encoding the polypeptide or a nucleic acid sequence encoding the polypeptide, which nucleic acid sequence comprises repeat sequences at the 5' and 3' ends of the nucleic acid sequence, by the introduction of a nucleic acid construct into the genome of the parent cell at a locus which is within or not within the nucleic acid sequence(s), wherein the introduction of the nucleic acid construct into the locus modifies the copy number of the nucleic acid sequence(s) and the modification of the copy number is not a result of selective pressure; and (ii) the mutant cell produces more or less of the polypeptide than the parent cell when both cells are cultivated under the same conditions; and (b) recovering the poylpeptide from the cultivation medium. The present invention also relates to methods for obtaining a mutant cell and mutant cells.

Description

METHODS FORPRODUCING A POLYPEPTIDE BY MODIFYING THE COPY NUMBER OF A GENE

Background of the Invention

Field of the Invention The present invention relates to methods for producing a polypeptide by modifying the copy number of a gene. The present invention also relates to mutant cells and methods for obtaining the mutant cells.

Description of the Related Art The continual development of new genetic engineering techniques has enabled the manipulation of the expression of genes encoding proteins. However, the manipulation of the coding region or the transcriptional control regions of a gene has frequently involved the isolation of the gene, manipulation of the nucleic acids contained in the gene in order to increase or decrease expression of the gene, and introduction of the manipulated gene into a suitable expression host.

A widely used method for increasing production of a polypeptide is to obtain a strain with multiple copies of the gene encoding the polypeptide through a process called amplification.

U.S. Patent No. 5,578.461 discloses the inclusion via homologous recombination of an amplifiable selectable marker gene in tandem with a gene where cells containing amplified copies of the selectable marker in tandem with multiple copies of the gene can be selected for by culturing the cells in the presence of increasing amounts of the appropriate selectable agent.

Decreasing production of a particular polypeptide may be accomplished by disrupting, inactivating, or forcing loss by recombination of the gene encoding the polypeptide.

It is an object of the present invention to provide new methods for producing a polypeptide.

Brief Summary of the Invention

The present invention relates to methods for producing a polypeptide. comprising: (a) cultivating a mutant cell under conditions conducive for production of a polypeptide. wherein (i) the mutant cell is related to a parent cell, which parent cell comprises at least two tandem copies of a nucleic acid sequence encoding the polypeptide, by the introduction of a nucleic acid construct into the genome of the parent cell at a locus not within the copies of the nucleic acid sequence to produce the mutant cell, wherein the introduction of the nucleic acid construct into the locus modifies the copy number of the nucleic acid sequence and the modification of the copy number is not a result of selective pressure; and

(ii) the mutant cell produces more or less of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide; and

(b) recovering the polypeptide from the cultivation medium. The present invention also relates to methods for producing a polypeptide, comprising:

(a) cultivating a mutant cell under conditions conducive for production of a polypeptide, wherein

(i) the mutant cell is related to a parent cell, which parent cell comprises at least two tandem copies of a nucleic acid sequence encoding the polypeptide, by the introduction of a nucleic acid construct into the genome of the parent cell at a locus within one of the copies of the nucleic acid sequence to produce the mutant cell, wherein the introduction of the nucleic acid construct into the locus modifies the copy number of the nucleic acid sequence and the modification of the copy number is not a result of selective pressure; and

(b) recovering the polypeptide from the cultivation medium.

The present invention also relates to methods for producing a polypeptide, comprising:

(i) the mutant cell is related to a parent cell, which parent cell comprises a nucleic acid sequence encoding the polypeptide, which nucleic acid sequence comprises repeat sequences at the 5' and 3' ends of the nucleic acid sequence, by the introduction of a nucleic acid construct into the genome of the parent cell at a locus not within the nucleic acid sequence to produce the mutant cell, wherein the introduction of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence and the modification of the copy number is not a result of selective pressure; and (ii) the mutant cell produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide; and

(b) recovering the polypeptide from the cultivation medium. The present invention also relates to mutant cells and methods for obtaining the mutants cells.

Brief Description of the Figures

Figure 1 is a restriction map of pJaL292.

Figure 2 is a restriction map of pKS6.

Figure 3 is a restriction map of pBANel3.

Figure 4 is a restriction map of pBANeό.

Figure 5 is a restriction map of pMHan37. Figure 6 is a restriction map of pBANeδ.

Figure 7 is a restriction map of pSO2.

Figure 8 is a restriction map of pSO122 and shows the construction of pDSYδl and pDSY82 from pSO 122.

Figure 9 is a restriction map of pJaL400. Figure 10 shows the construction of pMT1935.

Figure 1 1 is a restriction map of pJaL394.

Figure 12 is a restriction map of pMT1931.

Figure 13 is a restriction map of pMT1936.

Figure 14 is a restriction map of pGAG3. Figure 15 is a restriction map of pJaL389.

Figure 16 is a restriction map of pJaL335.

Figure 17 is a restriction map of pJaL399.

Figure 18 is a restriction map of pDM176.

Figure 19 is a restriction map of pHB218. Figure 20 is a restriction map of pSE39.

Figure 21 is a restriction map of pDSY153.

Detailed Description of the Invention

In a first embodiment, the present invention relates to methods for producing a polypeptide. comprising:

(a) cultivating a mutant cell under conditions conducive for production of the polypeptide. wherein (i) the mutant cell is related to a parent cell, which parent cell comprises at least two tandem copies of a nucleic acid sequence encoding the polypeptide. by the introduction of a nucleic acid construct into the genome of the parent cell at a locus not within the copies of the nucleic acid sequence to produce the mutant cell, wherein the introduction of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence and the increase in the copy number is not a result of selective pressure; and

(ii) the mutant cell produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide; and

(b) recovering the polypeptide from the cultivation medium. The term "genome" is defined herein as the complete set of DNA of a cell including chromosomal, artificial chromosomal DNA. and extrachromosomal DNA. i.e., self- replicative genetic elements. The term "copy number^" is defined herein as the number of molecules, per genome, of a gene which is contained in a cell.

The term "selective pressure" is defined herein as culturing a cell, containing an expression cassette containing an amplifiable selectable marker gene linked in tandem with a nucleic acid sequence encoding a polypeptide of interest, in the presence of increasing amounts of an appropriate selectable agent which results in the amplification of the copy number of the selectable marker gene and the nucleic acid sequence in tandem.

A mutant cell that "produces more of the polypeptide" is defined herein as a cell from which more of the polypeptide is recovered relative to the parent cell.

In a second embodiment, the present invention relates to methods for producing a polypeptide, comprising:

(a) cultivating a mutant cell under conditions conducive for production of the polypeptide, wherein

(i) the mutant cell is related to a parent cell, which comprises at least two tandem copies of a nucleic acid sequence encoding the polypeptide, by the introduction of a nucleic acid construct into the genome of the parent cell at a locus not within the copies of the nucleic acid sequence to produce the mutant cell, wherein the introduction of the nucleic acid construct into the locus decreases the copy number of the nucleic acid sequence and the decrease in the copy number is not a result of selective pressure; and (ii) the mutant cell produces less of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide; and

(b) recovering the polypeptide from the cultivation medium. A mutant cell that "produces less of the polypeptide^" is defined herein as a cell from which less of the polypeptide is recovered relative to the parent cell.

In a third embodiment, the present invention relates to methods for producing a polypeptide, comprising: (a) cultivating a mutant cell under conditions conducive for production of the polypeptide, wherein

(i) the mutant cell is related to a parent cell, which parent cell comprises at least two tandem copies of a nucleic acid sequence encoding the polypeptide, by the introduction of a nucleic acid construct into the genome of the parent cell at a locus within one of the copies of the nucleic acid sequence to produce the mutant cell, wherein the introduction of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence and the increase in the copy number is not a result of selective pressure; and

(ii) the mutant cell produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide: and

(b) recovering the polypeptide from the cultivation medium. In a fourth embodiment, the present invention relates to methods for producing a polypeptide, comprising: (a) cultivating a mutant cell under conditions conducive for production of the polypeptide, wherein

(i) the mutant cell is related to a parent cell, which comprises at least two tandem copies of a nucleic acid sequence encoding the polypeptide, by the introduction of a nucleic acid construct into the genome of the parent cell at a locus within one of the copies of the nucleic acid sequence to produce the mutant cell, wherein the introduction of the nucleic acid construct into the locus decreases the copy number of the nucleic acid sequence and the decrease in the copy number is not a result of selective pressure; and

(ii) the mutant cell produces less of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide: and

(b) recovering the polypeptide from the cultivation medium. In a fifth embodiment, the present invention relates to methods for producing a polypeptide. comprising: (a) cultivating a mutant cell under conditions conducive for production of the polypeptide. wherein

(i) the mutant cell is related to a parent cell, which parent cell comprises a nucleic acid sequence encoding the polypeptide, which nucleic acid sequence comprises repeat sequences at the 5' and 3' ends of the nucleic acid sequence, by the introduction of a nucleic acid construct into the genome of the parent cell at a locus not within the nucleic acid sequence, wherein the introduction of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence and the modification of the copy number is not a result of selective pressure; and

(b) recovering the polypeptide from the cultivation medium. The term "at least two tandem copies of the nucleic acid sequence^" is defined herein as two or more copies of a nucleic acid sequence encoding a polypeptide of interest where the copies of the nucleic acid sequence are arranged one after another in the genome of a cell with or without intervening sequences. Where intervening sequences are present, the intervening sequences should be less than 10,000 bp, preferably less than 5,000 bp, more preferably less than 2.000 bp, even more preferably less than 1.000 bp. and most preferably less than 100 bp in length. However, the intervening sequences may be of any length as long as the length does not prevent an increase or decrease in the copy number. In a preferred embodiment, there are no intervening sequences present between the tandem copies of the nucleic acid sequence. The term "repeat sequences at the 5' and 3' ends of the nucleic acid sequence" is defined herein as a nucleotide sequence which is present at both the 5^" end and the 3' end of the nucleic acid sequence encoding a polypeptide of interest. The repeat sequences may be in the same (direct repeats) or in the opposite (inverted repeats) orientation to one another. The repeat sequences may be of any suitable length, but preferably are about 100 to about 1000 bp, more preferably about 100 to about 500 bp, and most preferably about 100 to about 300 bp.

Polypeptides

The term "polypeptide" encompasses peptides, oligopeptides. and proteins and. therefore, is not limited to a specific length of the encoded product. The polypeptide may be native to the cell or may be a heterologous polypeptide. Preferably, it is a heterologous polypeptide. The term "heterologous polypeptide" is defined as a polypeptide not native to a cell. The polypeptide may be a wild-type polypeptide or a variant thereof. The polypeptide may also be a recombinant polypeptide which is a polypeptide native to a cell, which is encoded by a nucleic acid sequence which comprises one or more control sequences, foreign to the nucleic acid sequence, which are involved in the production of the polypeptide. The nucleic acid sequence encoding the polypeptide may have been manipulated in some manner as described infra. The present invention also encompasses, within the scope of the term "heterologous polypeptide". such recombinant production of endogenous polypeptides native to the filamentous fungal cell, to the extent that such expression involves the use of a genetic element(s) not native to the cell, or use of a native element(s) which has been manipulated to function in a manner that does not normally occur in the host cell. The polypeptide may also be a hybrid polypeptide which contains a combination of partial or complete polypeptide sequences obtained from at least two different polypeptides where one or more of the polypeptides may be heterologous to the cell. Polypeptides further include naturally occurring allelic and engineered variations of the above mentioned polypeptides.

In a preferred embodiment, the polypeptide is an antibody or portions thereof, antigen, clotting factor, enzyme, a hormone or variant thereof, receptor or portions thereof, regulatory protein, structural protein, reporter, or transport protein.

In a more preferred embodiment, the enzyme is an oxidoreductase. transferase. hydrolase. lyase. isomerase. or ligase.

In an even more preferred embodiment, the enzyme is an aminopeptidase. amylase, carbohydrase. carboxypeptidase. catalase, cellulase, chitinase. cutinase. deoxyribonuclease. dextranase, esterase, alpha-galactosidase, beta-galactosidase. glucoamylase. alpha- glucosidase, beta-glucosidase, haloperoxidase, invertase, laccase. lipase. mannosidase. mutanase. oxidase, pectinolytic enzyme, peroxidase, phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease, transglutaminase, or xylanase. In another even more preferred embodiment, the polypeptide is human insulin or an analog thereof, human growth hormone, human factor VII, erythropoietin, or insulinotropin.

Nucleic Acid Sequences Encoding Heterologous and Recombinant Polypeptides

The nucleic acid sequence encoding a heterologous polypeptide may be obtained from any prokaryotic. eukaryotic, or other source, e.g., archaebacteria. For purposes of the present invention, the term "obtained from" as used herein in connection with a given source shall mean that the polypeptide is produced by the source or by a cell in which a gene from the source has been inserted.

In the methods of the present invention, the cells may also be used for the recombinant production of polypeptides which are native to the cell. The native polypeptides may be recombinantly produced, e.g., to enhance expression of the polypeptide by placing a gene encoding the polypeptide under the control of a different promoter, to expedite export of a native polypeptide of interest outside the cell by use of a signal sequence, and to increase the copy number of a gene encoding the polypeptide normally produced by the cell. The present invention also encompasses such recombinant production of native polypeptides.

The techniques used to isolate or clone a nucleic acid sequence encoding a polypeptide are known in the art and include isolation from genomic DNA, preparation from cDNA. or a combination thereof. The cloning of the nucleic acid sequence from such genomic DNA can be effected, e.g., by using the well known polymerase chain reaction (PCR) or antibody screening of expression libraries to detect cloned DNA fragments with shared structural features. See. e.g., Innis et al, 1990. PCR. A Guide to Methods and Application, Academic Press. New York. Other nucleic acid amplification procedures such 5 as ligase chain reaction (LCR), ligated activated transcription (LAT) and nucleic acid sequence-based amplification (NASBA) may be used. The cloning procedures may involve excision and isolation of a desired nucleic acid fragment comprising the nucleic acid sequence encoding the polypeptide, insertion of the fragment into a vector molecule, and incorporation of the recombinant vector into a cell. The nucleic acid sequence may be of 0 genomic, cDNA, RNA, semisynthetic, synthetic origin, or any combinations thereof.

The term "isolated nucleic acid sequence" as used herein refers to a nucleic acid sequence which is essentially free of other nucleic acid sequences, e.g., at least about 20% pure, preferably at least about 40% pure, more preferably at least about 60% pure, even more preferably at least about 80% pure, and most preferably at least about 90% pure as 5 determined by agarose electrophoresis.

An isolated nucleic acid sequence encoding a heterologous polypeptide may be manipulated in a variety of ways to provide for expression of the polypeptide. Manipulation of the nucleic acid sequence prior to its insertion into a vector may be desirable or necessary depending on the expression vector. The techniques for modifying nucleic acid sequences o utilizing cloning methods are well known in the art.

Modification of a nucleic acid sequence encoding a polypeptide may be necessary for the synthesis of polypeptides substantially similar to the polypeptide. The term "substantially similar^" to the polypeptide refers to non-naturally occurring forms of the polypeptide. These polypeptides may differ in some engineered way from the polypeptide 5 isolated from its native source. For example, it may be of interest to synthesize variants of the polypeptide where the variants differ in specific activity, thermostability, pH optimum, or the like using, e.g.. site-directed mutagenesis. The analogous sequence may be constructed on the basis of a nucleic acid sequence encoding the polypeptide. and/or by introduction of nucleotide substitutions which do not give rise to another amino acid sequence of the o polypeptide encoded by the nucleic acid sequence, but which corresponds to the codon usage of the host organism intended for production of the enzyme, or by introduction of nucleotide substitutions which may give rise to a different amino acid sequence. For a general description of nucleotide substitution, see, e.g., Ford et al.. 1991, Protein Expression and Purification 2: 95-107. 5 The nucleic acid sequence may be modified to produce an expression cassette where the nucleic acid sequence is operably linked to one or more control sequences which direct the expression of the coding sequence in a suitable host cell under conditions compatible with the control sequences. Expression will be understood to include any step involved in the production of the polypeptide including, but not limited to, transcription, post- transcriptional modification, translation, post-translational modification, and secretion.

"Expression cassette" is defined herein as a nucleic acid molecule, either single- or double-stranded, which is isolated from a naturally occurring gene or which has been modified to contain segments of nucleic acid which are combined and juxtaposed in a manner which would not otherwise exist in nature and contains all the control sequences required for expression of a coding sequence. The term "coding sequence^" as defined herein is a sequence which is transcribed into mRNA and translated into a polypeptide. The boundaries of a genomic coding sequence are generally determined by a ribosome binding site (prokaryotes) or by the ATG start codon (eukaryotes) located just upstream of the open reading frame at the 5^" end of the mRNA and a transcription terminator sequence located just downstream of the open reading frame at the 3' end of the mRNA. A coding sequence can include, but is not limited to, DNA, cDNA, and recombinant nucleic acid sequences.

The term "control sequences" is defined herein to include all components which are necessary or advantageous for the expression of a polypeptide. Each control sequence may be native or foreign to the nucleic acid sequence encoding the polypeptide. Such control sequences include, but are not limited to, a leader, polyadenylation sequence, propeptide sequence, promoter, signal sequence, and transcription terminator. At a minimum, the control sequences include a promoter, and transcriptional and translational stop signals. The control sequences may be provided with linkers for the purpose of introducing specific restriction sites facilitating ligation of the control sequences with the coding region of the nucleic acid sequence encoding a polypeptide. The term "operably linked" is defined herein as a configuration in which a control sequence is appropriately placed at a position relative to the coding sequence of the DNA sequence such that the control sequence directs the production of a polypeptide.

The control sequence may be an appropriate promoter sequence, a nucleic acid sequence which is recognized by a host cell for expression of the expression cassette. The promoter sequence contains transcriptional control sequences which mediate the expression of the polypeptide. The promoter may be any nucleic acid sequence which shows transcriptional activity in the host cell of choice including mutant, truncated, and hybrid promoters, and may be obtained from genes encoding extracellular or intracellular polypeptides either homologous or heterologous to the host cell.

Examples of suitable promoters for directing the transcription of the expression cassette in a bacterial host cell are the promoters obtained from the E. coli lac operon, Streptomyces coelicolor agarase gene (dagA), Bacillus subtilis levansucrase gene (sacB), Bacillus licheniformis alpha-amylase gene (amyL), Bacillus stearothermophilus maltogenic amylase gene (amyM), Bacillus amyloliquefaciens alpha-amylase gene (amyQ), Bacillus licheniformis penicillinase gene (penP), Bacillus subtilis xylA and xylB genes, and prokaryotic beta-lactamase gene (Villa-Kamaroff et al., 1978, Proceedings of the National Academy of Sciences USA 75: 3727-3731), as well as the lac promoter (DeBoer et al., 1983, Proceedings of the National Academy of Sciences USA 80: 21-25). Further promoters are described in "Useful proteins from recombinant bacteria" in Scientific American, 1980, 242: 74-94; and in Sambrook et al., 1989, supra.

Examples of suitable promoters for directing the transcription of the expression cassette in a filamentous fungal host cell are promoters obtained from the genes encoding Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, Aspergillus niger neutral alpha-amylase. Aspergillus niger acid stable alpha-amylase. Aspergillus niger or Aspergillus awamori glucoamylase (glaA), Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease. Aspergillus oryzae triose phosphate isomerase. Aspergillus nidulans acetamidase. Fusarium oxysporum trypsin-like protease (U.S. Patent No. 4,288,627), and mutant, truncated, and hybrid promoters thereof, as well as the NA2-tpi promoter (a hybrid of the promoters from the genes encoding Aspergillus niger neutral alpha-amylase and Aspergillus oryzae triose phosphate isomerase).

In a yeast host, useful promoters are obtained from the Saccharomyces cerevisiae enolase (ENO-1) gene. Saccharomyces cerevisiae galactokinase gene (GAL1), Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3 -phosphate dehydrogenase genes (ADH2/GAP), and Saccharomyces cerevisiae 3-phosphoglycerate kinase gene. Other useful promoters for yeast host cells are described by Romanos et al., 1992, Yeast 8: 423-488. In a mammalian host cell, useful promoters include viral promoters such as those from Simian Virus 40 (SV40), Rous sarcoma virus (RSV), adenovirus, bovine papilloma virus (BPV). and human cytomegalovirus (CMV).

The control sequence may also be a suitable transcription terminator sequence, a sequence recognized by a host cell to terminate transcription. The terminator sequence is operably linked to the 3 ' terminus of the nucleic acid sequence encoding the polypeptide. Any terminator which is functional in the host cell of choice may be used in the present invention.

Preferred terminators for filamentous fungal host cells are obtained from the genes encoding Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, Aspergillus niger alpha-glucosidase, and Fusarium oxysporum trypsin-like protease.

Preferred terminators for yeast host cells are obtained from the genes encoding

Saccharomyces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C (CYC1), or Saccharomyces cerevisiae glyceraldehyde-3 -phosphate dehydrogenase. Other useful terminators for yeast host cells are described by Romanos et al.. 1992, supra. Terminator sequences are well known in the art for mammalian host cells. The control sequence may also be a suitable leader sequence, a nontranslated region of an mRNA which is important for translation by the host cell. The leader sequence is operably linked to the 5' terminus of the nucleic acid sequence encoding the polypeptide.

Any leader sequence which is functional in the host cell of choice may be used in the present invention.

Preferred leaders for filamentous fungal host cells are obtained from the genes encoding Aspergillus oryzae TAKA amylase and Aspergillus nidulans triose phosphate isomerase.

Suitable leaders for yeast host cells are obtained from the Saccharomyces cerevisiae enolase (ENO-1) gene, Saccharomyces cerevisiae 3-phosphoglycerate kinase gene, the Saccharomyces cerevisiae alpha-factor, and Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3 -phosphate dehydrogenase genes (ADH2/GAP).

The control sequence may also be a polyadenylation sequence, a sequence which is operably linked to the 3 ' terminus of the nucleic acid sequence and which, when transcribed. is recognized by the host cell as a signal to add polyadenosine residues to transcribed mRNA.

Any polyadenylation sequence which is functional in the host cell of choice may be used in the present invention.

Preferred polyadenylation sequences for filamentous fungal host cells are obtained from the genes encoding Aspergillus oryzae TAKA amylase. Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, and Aspergillus niger alpha- glucosidase.

Useful polyadenylation sequences for yeast host cells are described by Guo and Sherman. 1995, Molecular Cellular Biology 15: 5983-5990. Polyadenylation sequences are well known in the art for mammalian host cells. The control sequence may also be a signal peptide coding region, which codes for an amino acid sequence linked to the amino terminus of the polypeptide that directs the encoded polypeptide into the cell's secretory pathway. The 5' end of the coding sequence of the nucleic acid sequence may inherently contain a signal peptide coding region naturally linked in translation reading frame with the segment of the coding region which encodes the secreted polypeptide. Alternatively, the 5' end of the coding sequence may contain a signal peptide coding region which is foreign to the coding sequence. The foreign signal peptide coding region may be required where the coding sequence does not normally contain a signal peptide coding region. Alternatively, the foreign signal peptide coding region may simply replace the natural signal peptide coding region in order to obtain enhanced secretion of the polypeptide. The signal peptide coding region may be obtained from a glucoamylase or amylase gene from an Aspergillus species, a lipase or proteinase gene from a Rhizomucor species, the gene for the alpha-factor from Saccharomyces cerevisiae, an amylase or protease gene from a Bacillus species, or the calf preprochymosin gene. However, any signal peptide coding region which directs the expressed polypeptide into the secretory pathway of a host cell of choice may be used in the present invention.

An effective signal peptide coding region for bacterial host cells is the signal peptide coding region obtained from the maltogenic amylase gene from Bacillus NCIB 11837, Bacillus stearothermophilus alpha-amylase gene, Bacillus licheniformis subtilisin gene, Bacillus licheniformis beta-lactamase gene. Bacillus stearothermophilus neutral proteases genes (nprT, nprS, nprM), or Bacillus subtilis PrsA gene. Further signal peptides are described by Simonen and Palva, 1993, Microbiological Reviews 57: 109-137.

An effective signal peptide coding region for filamentous fungal host cells is the signal peptide coding region obtained from the Aspergillus oryzae TAKA amylase gene, Aspergillus niger neutral amylase gene. Rhizomucor miehei aspartic proteinase gene, Humicola lanuginosa cellulase gene, or Humicola lanuginosa lipase gene.

Useful signal peptides for yeast host cells are obtained from the genes for Saccharomyces cerevisiae alpha-factor and Saccharomyces cerevisiae invertase. Other useful signal peptide coding regions are described by Romanos et al. 1992, supra.

The control sequence may also be a propeptide coding region, which codes for an amino acid sequence positioned at the amino terminus of a polypeptide. The resultant polypeptide is known as a proenzyme or propolypeptide (or a zymogen in some cases). A propolypeptide is generally inactive and can be converted to a mature active polypeptide by catalytic or autocatalytic cleavage of the propeptide from the propolypeptide. The propeptide coding region may be obtained from the Bacillus subtilis alkaline protease gene (aprE), Bacillus subtilis neutral protease gene (nprT), Saccharomyces cerevisiae alpha-factor gene, Rhizomucor miehei aspartic proteinase gene, or Myceliophthora thermophila laccase gene (WO 95/33836). Where both signal peptide and propeptide regions are present at the amino terminus of a polypeptide. the propeptide region is positioned next to the amino terminus of a polypeptide and the signal peptide region is positioned next to the amino terminus of the propeptide region.

The expression cassette encoding the polypeptide may also comprise one or more other nucleic acid sequences which encode one or more factors that are advantageous for directing the expression of the polypeptide. e.g., a transcriptional activator (e.g., a transacting factor), a chaperone. and a processing protease. Any factor that is functional in the host cell of choice may be used in the present invention. The nucleic acids encoding one or more of these factors are not necessarily in tandem with the nucleic acid sequence encoding the polypeptide.

A transcriptional activator is a protein which activates transcription of a nucleic acid sequence encoding a polypeptide (Kudla et αl, 1990, EMBO Journal 9: 1355-1364; Jarai and Buxton, 1994, Current Genetics 26: 2238-244; Verdier, 1990, Yeast 6: 271-297). The nucleic acid sequence encoding an activator may be obtained from the genes encoding Bacillus stearothermophilus NprA (nprA), Saccharomyces cerevisiae heme activator protein 1 (hapl), Saccharomyces cerevisiae galactose metabolizing protein 4 (gal4), Aspergillus nidulans ammonia regulation protein (areA), and Aspergillus oryzae alpha-amylase activator (amyR). For further examples, see Verdier, 1990, supra and MacKenzie et al, 1993, Journal of General Microbiology 139: 2295-2307.

A chaperone is a protein which assists another polypeptide to fold properly (Hartl et al, 1994, TIBS 19: 20-25; Bergeron et al. 1994, TIBS 19: 124-128: Demolder et al., 1994, Journal of Biotechnology 32: 179-189; Craig, 1993, Science 260: 1902-1903; Gething and Sambrook, 1992, Nature 355: 33-45; Puig and Gilbert. 1994. Journal of Biological Chemistry 269: 7764-7771: Wang and Tsou, 1993, The FASEB Journal 1: 1515-11157; Robinson et al. 1994. Bio/Technology 1 : 381-384; Jacobs et al, 1993. Molecular Microbiology 8: 957-966). The nucleic acid sequence encoding a chaperone may be obtained from the genes encoding Bacillus subtilis GroE proteins. Bacillus subtilis PrsA. Aspergillus oryzae protein disulphide isomerase, Saccharomyces cerevisiae calnexin, Saccharomyces cerevisiae BiP/GRP78. and Saccharomyces cerevisiae Hsp70. For further examples, see Gething and Sambrook. 1992, supra, and Hartl et al, 1994, supra.

A processing protease is a protease that cleaves a propeptide to generate a mature biochemically active polypeptide (Enderlin and Ogrydziak, 1994. Yeast 10: 67-79; Fuller et al, 1989, Proceedings of the National Academy of Sciences USA 86: 1434-1438; Julius et al, 1984, Cell 37: 1075-1089; Julius et al, 1983, Cell 32: 839-852; U.S. Patent No. 5,702,934). The nucleic acid sequence encoding a processing protease may be obtained from the genes encoding Saccharomyces cerevisiae dipeptidylaminopeptidase. Saccharomyces cerevisiae Kex2, Yarrowia lipolytica dibasic processing endoprotease (xprό), and Fusarium oxysporum metalloprotease (p45 gene).

It may also be desirable to add regulatory sequences which allow the regulation of the expression of the polypeptide relative to the growth of the host cell. Examples of regulatory systems are those which cause the expression of the gene to be turned on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound. Regulatory systems in prokaryotic systems would include the lac, tac, and trp operator systems. In yeast, the ADH2 system or GAL1 system may be used. In filamentous fungi, the TAKA alpha-amylase promoter, Aspergillus niger glucoamylase promoter, and Aspergillus oryzae glucoamylase promoter may be used as regulatory sequences. Other examples of regulatory sequences are those which allow for gene amplification. In eukaryotic systems, these include the dihydrofolate reductase gene which is amplified in the presence of methotrexate, and the metallothionein genes which are amplified with heavy metals. In these cases, the nucleic acid sequence encoding the polypeptide would be operably linked with the regulatory sequence. The various nucleic acid and control sequences described above may be joined together to produce a recombinant expression vector which may include one or more convenient restriction sites to allow for insertion or substitution of the nucleic acid sequence encoding the polypeptide at such sites. Alternatively, the nucleic acid sequence may be expressed by inserting the nucleic acid sequence or an expression cassette as described above into an appropriate vector for expression. In creating the recombinant expression vector, the coding sequence is located in the vector so that the coding sequence is operably linked with the appropriate control sequences for expression.

The recombinant expression vector may be any vector (e.g., a plasmid or virus) which can be conveniently subjected to recombinant DNA procedures and can bring about the expression of the nucleic acid sequence. The choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector is to be introduced. The vectors may be linear or closed circular plasmids. The vector may be an autonomously replicating vector, i. e.. a vector which exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a plasmid. an extrachromosomal element, a minichromosome, or an artificial chromosome. The vector may contain any means for assuring self-replication. Alternatively, the vector may be one which, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated. The vector system may be a single vector or plasmid or two or more vectors or plasmids which together contain the total DNA to be introduced into the genome of the host cell, or a transposon.

The vectors preferably contain one or more selectable markers which permit easy selection of transformed cells. A selectable marker is a gene the product of which provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs. and the like. Examples of bacterial selectable markers are the dal genes from Bacillus subtilis or Bacillus licheniformis. or markers which confer antibiotic resistance such as ampicillin (amp), kanamycin (kari), chloramphenicol (cam), or tetracycline (tet) resistance. Suitable markers for mammalian cells are the dihydrofolate reductase (dfhr), hygromycin phosphotransferase (hygB), aminoglycoside phosphotransferase II. and phleomycin resistance genes. Suitable markers for yeast host cells are ADE2, HIS3. LEU2, LYS2, MET3, TRP1, and URA3. Suitable selectable markers for filamentous fungal host cells may be selected from the group including, but not limited to, amdS (acetamidase), argB (ornithine carbamoyltransferase). bar (phosphinothricin acetyltransferase), hph (hygromycin phosphotransferase). niaD (nitrate reductase), pyrG (orotidine-5^" -phosphate decarboxylase), sC (sulfate adenyltransferase), and trpC (anthranilate synthase). as well as equivalents from other species. The vectors preferably contain an element(s) that permits integration of the vector into the host cell genome or autonomous replication of the vector in the cell independent of the genome of the cell.

For integration into the host cell genome, the vector may rely on the nucleic acid sequence encoding the polypeptide or any other element of the vector for integration of the vector into the genome by homologous or nonhomologous recombination. Alternatively, the vector may contain additional nucleic acid sequences for directing integration by homologous recombination into the genome of the host cell. The additional nucleic acid sequences enable the vector to be integrated into the host cell genome at a precise location(s) in the chromosome(s). To increase the likelihood of integration at a precise location, the integrational elements should preferably contain a sufficient number of nucleic acids, such as at least 100 to 10.000 base pairs, preferably at least 400 to 10.000 base pairs, and most preferably at least 800 to 10,500 base pairs, which are highly homologous with the corresponding target sequence to enhance the probability of homologous recombination. The integrational elements may be any sequence that is homologous with the target sequence in the genome of the host cell. Furthermore, the integrational elements may be non-encoding or encoding nucleic acid sequences. On the other hand, the vector may be integrated into the genome of the host cell by non-homologous recombination.

For autonomous replication, the vector may further comprise an origin of replication enabling the vector to replicate autonomously in the host cell in question. Examples of bacterial origins of replication are the origins of replication of plasmids pBR322, pUC19, pACYC177. and pACYC184 permitting replication in E. coli. and pUBHO, pE194, pTA1060, and pAMBl permitting replication in Bacillus. Examples of origins of replication for use in a yeast host cell are the 2 micron origin of replication. ARSl, ARS4, the combination of ARSl and CEN3. and the combination of ARS4 and CEN6. The origin of replication may be one having a mutation which makes its functioning temperature-sensitive in the host cell (see. e.g., Ehrlich, 1978, Proceedings of the National Academy of Sciences USA 75: 1433).

The procedures used to ligate the elements described above to construct the recombinant expression vectors of the present invention are well known to one skilled in the art (see. e.g.. Sambrook et al, 1989, supra).

Cells

The methods of the present invention may be used with any cell containing a nucleic acid sequence encoding a polypeptide of interest including prokaryotic cells such as bacteria, or eukaryotic cells such as mammalian, insect, plant, and fungal cells. The cell may be wild- type or a mutant cell. For example, the mutant cell may be a cell which has undergone classical mutagenesis or genetic manipulation. Furthermore, the cell may be a recombinant cell, comprising a nucleic acid sequence encoding a polypeptide which is a heterologous polypeptide as defined herein, which is advantageously used in the recombinant production of the heterologous polypeptide.

Useful prokaryotic cells are bacterial cells such as gram positive bacteria including, but not limited to, a Bacillus cell, e.g., Bacillus alkalophilus. Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus coagulans, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus stearothermophilus. Bacillus subtilis, and Bacillus thuringiensis; or a Streptomyces cell, e.g., Streptomyces lividans and Streptomyces murinus, or gram negative bacteria such as E. coli and Pseudomonas sp. In a preferred embodiment, the bacterial cell is a Bacillus lentus, Bacillus licheniformis. Bacillus stearothermophilus. or Bacillus subtilis cell.

In a preferred embodiment, the cell is a fungal cell. "Fungi^" as used herein includes the phyla Ascomycota. Basidiomycota, Chytridiomycota, and Zygomycota (as defined by Hawksworth et al.. In, Ainsworth and Bisby 's Dictionary of The Fungi, 8th edition, 1995, CAB International. University Press, Cambridge, UK) as well as the Oomycota (as cited in Hawksworth et al, 1995, supra, page 171) and all mitosporic fungi (Hawksworth et al, 1995, supra). Representative groups of Ascomycota include, e.g., Neurospora, Eupenicillium (=Penicillium), Emericella (= Aspergillus), Eurotium (=Aspergillus), and the true yeasts. Examples of Basidiomycota include mushrooms, rusts, and smuts. Representative groups of Chytridiomycota include, e.g., Allomyces, Blastocladiella, Coelomomyces, and aquatic fungi. Representative groups of Oomycota include, e.g., Saprolegniomycetous aquatic fungi (water molds) such as Achlya. Examples of mitosporic fungi include Alternaria, Aspergillus, Candida, and Penicillium. Representative groups of Zygomycota include, e.g., Mucor and Rhizopus. In a preferred embodiment, the fungal cell is a yeast cell. "Yeast" as used herein includes ascosporogenous yeast (Endomycetales), basidiosporogenous yeast, and yeast belonging to the Fungi Imperfecti (Blastomycetes). The ascosporogenous yeasts are divided into the families Spermophthoraceae and Saccharomycetaceae. The latter is comprised of four subfamilies, Schizosaccharomycoideae (e.g., genus Schizosaccharomyces), Nadsonioideae, Lipomycoideae, and Saccharomycoideae (e.g., genera Kluyveromyces,

Pichia. and Saccharomyces). The basidiosporogenous yeasts include the genera Filobasidiella, Filobasidium, Leucosporidim, Rhodosporidium. and Sporidiobolus. Yeast belonging to the Fungi Imperfecti are divided into two families. Sporobolomycetaceae (e.g., genera Bullera and Sporobolomyces) and Cryptococcaceae (e.g., genus Candida). Since the classification of yeast may change in the future, for the purposes of this invention, yeast shall be defined as described in Biology and Activities of Yeast (Skinner et al. , 1980, Soc. App. Bacteriol. Symposium Series No. 9, 1980. The biology of yeast and manipulation of yeast genetics are well known in the art (see, e.g., Biochemistry and Genetics of Yeast, Bacil. M., Horecker, B.J., and Stopani. A.O.M., editors, 2nd edition, 1987: The Yeasts (Rose, A.H., and Harrison, J.S.. editors), 2nd edition, 1987; and The Molecular Biology of the Yeast Saccharomyces, Strathern et al, editors, 1981).

In a more preferred embodiment, the yeast cell is a cell of a species of Candida, Hansenula, Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces, or Yarrowia.

In a most preferred embodiment, the yeast cell is a Saccharomyces carlsbergensis,

Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii,

Saccharomyces kluyveri, Saccharomyces norbensis, or Saccharomyces oviformis cell. In another most preferred embodiment, the yeast cell is a Kluyveromyces lactis cell. In another most preferred embodiment, the yeast cell is a Yarrowia lipolytica cell.

In another preferred embodiment, the fungal cell is a filamentous fungal cell. "Filamentous fungi^" include all filamentous forms of the subdivision Eumycota and Oomycota (as defined by Hawksworth et al, 1995, supra). The filamentous fungi are generally characterized by a mycelial wall composed of chitin. cellulose, glucan. chitosan, mannan, and other complex polysaccharides. Vegetative growth is by hyphal elongation and carbon catabolism is obligately aerobic. In contrast, vegetative growth by yeasts such as Saccharomyces cerevisiae is by budding of a unicellular thallus and carbon catabolism may be fermentative. In a more preferred embodiment, the filamentous fungal cell is a cell of a species of, but not limited to, Acremonium, Aspergillus, Fusarium, Humicola, Mucor, Myceliophthora, Neurospora, Penicillium, Scytalidium, Thielavia, Tolypocladium, and

Trichoderma.

In an even more preferred embodiment, the filamentous fungal cell is an Aspergillus, Acremonium, Fusarium. Humicola, Mucor, Myceliophthora. Neurospora, Penicillium, Thielavia, Tolypocladium. or Trichoderma cell. In a most preferred embodiment, the filamentous fungal cell is an Aspergillus awamori, Aspergillus foetidus, Aspergillus japonicus. Aspergillus nidulans, Aspergillus niger, or Aspergillus oryzae cell. In another most preferred embodiment, the filamentous fungal cell is a Fusarium bactridioides, Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum. Fusarium graminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi. Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum,

Fusarium sambucinum. Fusarium sarcochroum. Fusarium sporotricioides, Fusarium sulphureum, Fusarium torulosum. Fusarium trichothecioides, or Fusarium venenatum cell. In another most preferred embodiment, the filamentous fungal cell is a Humicola insolens, Humicola lanuginosa. Mucor miehei. Myceliophthora thermophila, Neurospora crassa, Penicillium purpurogenum, or Thielavia terrestris cell. In another most preferred embodiment, the filamentous fungal cell is a Trichoderma harzianum, Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei, or Trichoderma viride cell. Useful mammalian cells include Chinese hamster ovary (CHO) cells. HeLa cells, baby hamster kidney (BHK) cells. COS cells, or any number of immortalized cells available, e.g., from the American Type Culture Collection.

Nucleic Acid Constructs

In the methods of the present invention, a nucleic acid construct is introduced into the genome of a parent cell at a locus which is not within the nucleic acid sequence(s) encoding a polypeptide of interest. Alternatively, a nucleic acid construct is introduced into the genome of a parent cell at a locus which is within one of the tandem copies of the nucleic acid sequence or within the nucleic acid sequence comprising repeats.

The nucleic acid constructs may be any nucleic acid molecule, either single- or double-stranded, which is synthetic DNA, isolated from a naturally occurring gene, or has been modified to contain segments of nucleic acid which are combined and juxtaposed in a manner which would not otherwise exist in nature. The nucleic acid constructs may be circular or linear. Furthermore, the nucleic acid constructs may be contained in a vector, may be a restriction enzyme cleaved linearized fragment, or may be a PCR amplified linear fragment.

The nucleic acid constructs may contain any nucleic acid sequence of any size. In one embodiment, the nucleic acid constructs are between about 10 - 20,000 bp in length, preferably about 100 - 15,000 bp in length, more preferably about 500 - 15,000 bp in length, even more preferably about 1,000 - 15,000 bp in length, and most preferably about 1,000 - 10,000 bp in length.

The nucleic acid construct can be introduced into a cell as two or more separate fragments. In the event two fragments are used, the two fragments share sufficient nucleic acid sequence homology (overlap) at the 3' end of one fragment and the 5" end of the other, so upon introduction into the cell the two fragments can undergo homologous recombination to form a single fragment. The product fragment is then in a form suitable for recombination with the cellular sequences. More than two fragments can be used, designed such that they will undergo homologous recombination with each other to ultimately form a product suitable for recombination with a cellular sequence.

It will be further understood that two or more nucleic acid constructs may be introduced into the cell as circular or linear fragments in the methods of the present invention, wherein the fragments do not contain overlapping regions as described above. It is well known in the art that for some organisms, the introduction of multiple constructs into a cell may result in their integration at the same locus.

The nucleic acid constructs can contain coding or non-coding DNA sequences. Coding sequences are defined herein. In a preferred embodiment, the nucleic acid constructs contain a selectable marker. Examples of such selectable markers are described supra.

In another preferred embodiment, the constructs comprise vector sequences alone or in combination with a selectable marker, including vector sequences containing an origin of replication, e.g., E. coli vector sequences such as pUC19, pBR322. or pBluescript. For example, an E. coli vector sequence containing an origin of replication can facilitate recovery of the construct from the host genome after integration due to the E. coli origin of replication. The construct can be recovered from the host genome by digestion of the genomic DNA with a restriction endonuclease followed by ligation of the recovered construct and transformation of E. coli.

In another preferred embodiment, the nucleic acid constructs do not contain the coding sequence of the nucleic acid sequence for the polypeptide or portions thereof. In another preferred embodiment, the nucleic acid constructs contain a sequence which is not homologous to the nucleic acid sequence encoding the polypeptide in order to block the construct from integrating or disrupting the nucleic acid sequence.

Preferably, the nucleic acid constructs have less than 40% homology. preferably less than 30% homology, more preferably less than 20%) homology. even more preferably less than 10%) homology, and most preferably no homology with the nucleic acid sequence encoding the polypeptide of interest. For purposes of the present invention, the degree of homology between two nucleic acid sequences is determined by the Wilbur-Lipman method (Wilbur and Lipman, 1983, Proceedings of the National Academy of Science USA 80: 726- 730) using the LASERGENE™ MEGALIGN™ software (DNASTAR. Inc., Madison, WI) with an identity table and the following multiple alignment parameters: Gap penalty of 10 and gap length penalty of 10. Pairwise alignment parameters are Ktuple=3. gap penalty=3. and windo ws=20.

In another preferred embodiment, the nucleic acid constructs contain at least one copy of the nucleic acid sequence for the polypeptide or portions thereof. In another preferred embodiment, the nucleic acid constructs contain a sequence which is homologous to the nucleic acid sequence encoding the polypeptide. When the nucleic acid construct containing one or more copies of a nucleic acid sequence encoding a polypeptide of interest is introduced into a cell, the increase in copy number is greater than the sum of the copy number of the nucleic acid sequence present in the cell before the introduction of the construct and the copy number of the nucleic acid sequence in the construct introduced into the cell. Alternatively, when the nucleic acid construct containing one or more copies of a nucleic acid sequence encoding a polypeptide of interest is introduced into a cell, the decrease in copy number is greater than the sum of the copy number of the nucleic acid sequence present in the cell before the introduction of the construct and the copy number of the nucleic acid sequence in the construct introduced into the cell. However, it may be necessary to label the nucleic acid (s) contained in the construct in a manner, e.g., unique restriction site(s), so the number of copies of the sequence from the construct which actually integrate into the genome of the cell can be identified.

In another preferred embodiment, the nucleic acid constructs contain transposable elements, i.e., transposons. A transposon is a discrete piece of DNA which can insert itself into many different sites in other DNA sequences within the same cell. The proteins necessary for the transposition process are encoded within the transposon. A copy of the transposon may be retained at the original site after transposition. The ends of a transposon are usually identical but in inverse orientation with respect to one another. In another preferred embodiment, the nucleic acid constructs may contain one or more control sequences, e.g., a promoter alone or in combination with a selectable marker, where the control sequences upon integration are not operably linked to the nucleic acid sequence encoding the polypeptide of interest. Such control sequences may be a promoter, a signal sequence, a propeptide sequence, a transcription terminator, a polyadenylation sequence, an enhancer sequence, an attenuator sequence, and an intron splice site sequence. Each control sequence may be native or foreign to the cell or to the polypeptide-coding sequence.

In another preferred embodiment, the nucleic acid constructs contain a control sequence other than a promoter.

In another preferred embodiment, the nucleic acid constructs do not contain control sequences.

In a more preferred embodiment, the nucleic acid construct is pDSY82, pDSY112, pMT1612, pMT1936, pLRF2, pDSY153, or pHB218.

Introduction of Nucleic Acid Constructs into Cells The nucleic acid construct(s) may be introduced into a cell by a variety of physical or chemical methods known in the art including, but not limited to. transfection or transduction, electroporation, microinjection, microprojectile bombardment, alkali salts, or protoplast- mediated transformation.

The introduction of a nucleic acid construct into a bacterial host cell may, for instance, be effected by protoplast transformation (see, e.g.. Chang and Cohen. 1979,

Molecular General Genetics 168: 111-115), by using competent cells (see. e.g., Young and Spizizin, 1961, Journal of Bacteriology 81 : 823-829, or Dubnau and Davidoff-Abelson, 1971. Journal of Molecular Biology 56: 209-221), by electroporation (see, e.g., Shigekawa and Dower, 1988. Biotechniques 6: 742-751), or by conjugation (see. e.g., Koehler and Thome, 1987, Journal of Bacteriology 169: 5771-5278).

Suitable procedures for transformation of Aspergillus cells are described in EP 238 023 and Yelton et al, 1984, Proceedings of the National Academy of Sciences USA 81 : 1470- 1474. Suitable methods for transforming Fusarium species are described by Malardier et al, 1989, Gene 78: 147-156. and WO 96/00787.

Yeast may be transformed using the procedures described by Becker and Guarente, In Guide to Yeast Genetics and Molecular Biology, Methods of Enzymology 194: 182-187; Ito et al., 1983, Journal of Bacteriology 153: 163; and Hinnen et al. 1978, Proceedings of the National Academy of Sciences USA 75: 1920.

Mammalian cells may be transformed by direct uptake using the calcium phosphate precipitation method of Graham and Van der Eb, 1978, Virology 52: 546. Other processes, e.g., electroporation, known to the art, may be used. When the nucleic acid construct is a vector, integration into the cell's genome occurs randomly by homologous and/or non-homologous recombination depending on the cell of choice.

The nucleic acid construct may be introduced into the parent cell by restriction enzyme-mediated integration (REMI). REMI, which is described in Schiestl and Petes, 1991, Proceedings of the National Academy of Sciences USA 88: 7585-7589, is the introduction of plasmid DNA digested with a restriction enzyme along with the restriction enzyme into a cell which subsequently leads to integration of the plasmid DNA into the genome often at a site specified by the restriction enzyme added. The advantage of REMI is it can generate mutations whose molecular basis can be easily identified. In another preferred embodiment, the nucleic acid construct is introduced into the parent cell as a circularized molecule.

In another preferred embodiment, the nucleic acid construct is introduced into the parent cell as part of a vector.

In another preferred embodiment, the nucleic acid construct is introduced into the parent cell as a linear fragment.

Screening of Mutant Cells

Following the introduction of a nucleic acid construct into a cell, the next step is to isolate from a population of presumptive mutant cells the mutant cell with the modified copy number of the nucleic acid sequence of interest where the mutant cell produces more or less of the polypeptide than the parent cell when both cells are cultivated under the same conditions. The isolation of the mutant cell preferably relies initially on measurement of the production of the polypeptide by the mutant cell relative to the parent cell when the mutant cell and the parent cell are cultured under the same conditions. The isolation of a mutant cell may involve screening methods known in the art specific to the polypeptide and/or methods for determining the copy number of the nucleic acid sequence. Methods for determining the copy number of a gene are will known in the art and include Southern analysis, quantitative PCR, or real time PCR. The population of presumptive mutants obtained by introducing a nucleic acid construct into the cells of an organism are first purified using standard plating techniques such as those used in classical mutagenesis (see, for example. Lawrence, C.W., 1991, In Christine Guthrie and Gerald R. Fink, editors, Methods in Enzymology, Volume 194, pages 273-281, Academic Press, Inc., San Diego), single spore isolation, or enrichment techniques. The standard plating techniques are preferably conducted in combination with a means of detecting the desired polypeptide. However, whether or not a means for identifying the mutant cell with respect to the polypeptide of interest can be incorporated into a plating medium, the purified presumptive mutants are preferably further characterized to confirm the increase or decrease in the production of the polypeptide encoded by the nucleic acid sequence. Furthermore, determination of the copy number of the nucleic acid sequence is also desirable to confirm the increase or decrease in the production of the polypeptide is a result of the modification of the copy number of the nucleic acid sequence.

A mutant cell with increased production of a specific polypeptide may be identified by using a detection method known in the art that is specific for the polypeptide. Detection methods for polypeptides may include, but are not limited to. use of specific antibodies, enzymatic activity by measuring formation of an enzyme product or disappearance of an enzyme substrate, clearing zones on agar plates containing an enzyme substrate, and biological activity assays. In a preferred embodiment, the polypeptide is produced by the mutant cell in an amount which is at least 20%, preferably at least 50%>, more preferably at least 75%o, more preferably at least 100%. more preferably at least 100%-1000%. even more preferably at least

200%- 1000%, and most preferably at least 500%-1000% greater or more than the parent cell.

A mutant cell which is no longer capable or has a diminished capability of producing a specific polypeptide may be identified using the same methods described above for polypeptides, but where no or diminished production is measured relative to the parent cell.

In another preferred embodiment, the polypeptide is produced by the mutant cell in an amount which is at least 20%, more preferably at least 50%o, even more preferably at least 15%, and most preferably 100%) lower than the parent cell.

Locus

In the methods of the present invention, the nucleic acid constructs may be introduced at a "locus not within the nucleic acid sequence of interest" which means that the nucleic acid construct is not introduced into the polypeptide-coding sequence, the control sequences thereof, or any intron sequences within the coding sequence of the nucleic acid sequence.

Where intervening sequences are present between tandem copies of a nucleic acid sequence, the construct may be introduced into these intervening sequences. Alternatively, in the methods of the present invention, the nucleic acid constructs may be introduced at a "locus within the nucleic acid sequence of interest" which means that the nucleic acid construct is introduced into the polypeptide-coding sequence, the control sequences thereof, or any intron sequences within the coding sequence of the nucleic acid sequence.

Control sequences include all components which are operably linked to the nucleic acid sequence and involved in the production of the polypeptide. Such control sequences include, but are not limited to, a promoter, signal sequence, propeptide sequence, transcription terminator, leader, and polyadenylation sequence as described herein. Each of the control sequences may be native or foreign to the coding sequence.

Where the locus is not within the nucleic acid sequence of interest, the locus may be noncontiguous or contiguous with the above-noted control sequences. Preferably the locus is noncontiguous. The locus may be on the same chromosome or the same extrachromosomal element or on a different chromosome or a different extrachromosomal element as that of the nucleic acid sequence of interest. Furthermore, the locus may be native or foreign to the cell.

In a preferred embodiment, the locus is at least 100 bp or less, preferably at least 1,000 bp, more preferably at least 2,000 bp, and even more preferably at least 3.000 bp, even more preferably at least 4,000 bp, even more preferably at least 5.000 bp. and most preferably at least 10,000 bp from the 5' or 3' terminus of the nucleic acid sequence.

In another preferred embodiment, the locus is on a different chromosome than the nucleic acid sequence encoding the polypeptide of interest. In another preferred embodiment, the locus encodes a polypeptide different from the polypeptide encoded by the nucleic acid sequence.

In another preferred embodiment, the locus is the nucleic acid sequence which encodes the polypeptide.

Rescue of a Locus with the Inserted Nucleic Acid Construct and Use of a Targeting Construct

The present invention further relates to methods for rescuing a locus with the inserted nucleic acid construct comprising isolating from the identified mutant cell (i) the nucleic acid construct and (ii) the 3' and 5' flanking regions of the locus of the genome where the nucleic acid construct has been integrated; and identifying the 3' and 5' flanking regions of the locus.

The nucleic acid construct and flanking regions can be isolated or rescued by methods well known in the art such as cleaving with restriction enzymes and subsequent ligation and transformation of E. coli, inverse PCR, random primed gene walking PCR, or probing a library of the mutant cell. The isolated nucleic acid construct with either or both the 3' and 5' flanking regions is defined herein as a "targeting construct".

The targeting construct includes between 100 - 9,000 bp, preferably 200 - 9,000 bp, more preferably 500 - 7.000 bp, even more preferably 1,000 - 7,000 bp, and most preferably 1.000 - 3,000 bp upstream and or downstream of the integration site of the nucleic acid construct.

The targeting construct of the invention may be introduced into a different cell to modify the production of a polypeptide similar or identical to or completely different from the polypeptide modified in the original cell. The other cell may be of the same or a different species or of a different genera as the original cell. If the original cell was a fungal cell, the other cell is preferably a fungal cell. If the original cell was a bacterial cell, the other cell is preferably a bacterial cell. If the original cell was a mammalian cell, the other cell is preferably a mammalian cell. When the cell is a different cell, integration of the targeting construct preferably occurs at a target locus which is homologous to the locus sequence of the original cell from which the targeting construct was obtained, i.e., identical or sufficiently similar such that the targeting sequence and cellular DNA can undergo homologous recombination to produce the desired mutation. The sequence of the targeting construct is preferably, therefore, homologous to a preselected site of the cellular chromosomal DNA with which homologous recombination is to occur. However, it will be understood by one of ordinary skill in the art that the likelihood of a targeting construct reinserting at a target locus will depend on the cell since homologous recombination frequencies range from almost 100% in the yeast Saccharomyces cerevisiae to as low as 1% in Aspergillus. The targeting construct may integrate by non-homologous recombination at a non-target locus which results in the modification of the copy number of a nucleic acid sequence encoding a polypeptide of interest.

Preferably, the target locus includes DNA sequences that have greater than 40% homology, preferably greater than 60% homology, more preferably greater than 70% homology, even more preferably greater than 80%) homology, and most preferably greater than 90%) homology with the flanking sequences of the targeting construct. The degree of homology between two nucleic acid sequences is determined by the Wilbur-Lipman method as described herein.

The targeting construct may contain either or both of the 3^" and 5' regions depending on whether a single cross-over or a replacement is desired. Furthermore, the targeting construct may be modified to correct any aberrant events, such as rearrangements, repeat sequences, deletions, or insertions, which occurred during the introduction and integration of the original nucleic acid construct into the cell's genome at the locus from which it was originally rescued. The targeting construct described above may be used as is, i.e., a restriction enzyme cleaved linear nucleotide sequence, or may be circularized or inserted into a suitable vector. For example, a circular plasmid or DNA fragment preferably employs a single targeting sequence. A linear plasmid or DNA fragment preferably employs two targeting sequences. The targeting construct upon introduction into a cell, in which the cell comprises a nucleic acid sequence encoding a polypeptide of interest, integrates into the genome of the cell at a target locus or at a nontarget locus, but preferably at a target locus, which may be within or not within the nucleic acid sequence encoding the polypeptide of interest. The target locus may be on the same chromosome or the same extrachromosomal element or on a different chromosome or a different extrachromosomal element as that of the DNA sequence of interest. The integration modifies the copy number of the nucleic acid sequence encoding the polypeptide by the mutant cell relative to the parent cell when the mutant cell and the parent cell are cultured under the same conditions. In a preferred embodiment, the targeting construct contains a selectable marker.

Optionally, the targeting construct can be introduced into a cell as two or more separate fragments. For example when two fragments are used, the fragments share DNA sequence homology (overlap) at the 3' end of one fragment and the 5^' end of the other, while one carries a first targeting sequence and the other carries a second targeting sequence. Upon introduction into a cell, the two fragments can undergo homologous recombination to form a single fragment with the first and second targeting sequences flanking the region of overlap between the two original fragments. The product fragment is then in a form suitable for homologous recombination with the cellular target sequences. More than two fragments can be used, designed such that they will undergo homologous recombination with each other to ultimately form a product suitable for homologous recombination with the cellular target sequences.

Upon introduction of the targeting construct into a cell, the targeting construct may be further amplified by the inclusion of an amplifiable selectable marker gene which has the property that cells containing amplified copies of the selectable marker gene can be selected for by culturing the cells in the presence of the appropriate selectable agent.

In a preferred embodiment, one or more targeting constructs are introduced into target loci. In another preferred embodiment, each targeting construct modifies the copy number of another nucleic acid sequence encoding a different polypeptide. In another preferred embodiment, two or more targeting constructs together when introduced into target loci act additively or synergistically to modify the copy number of a nucleic acid sequence encoding a polypeptide.

Methods for Cultivation of a Mutant Cell and Recovery of the Polypeptide

Mutant cells selected for increased or decreased production of a desired polypeptide are cultivated in a nutrient medium suitable for production of the polypeptide using methods known in the art. For example, the cell may be cultivated by shake flask cultivation, or small-scale or large-scale fermentation (including continuous, batch, fed-batch, or solid state fermentations) in laboratory or industrial fermentors performed in a suitable medium and under conditions allowing the polypeptide to be expressed and/or isolated. The cultivation takes place in a suitable nutrient medium comprising carbon and nitrogen sources and inorganic salts, using procedures known in the art (see, e.g., Bennett. J.W. and LaSure, L., editors, More Gene Manipulations in Fungi, Academic Press, CA. 1991). Suitable media are available from commercial suppliers or may be prepared according to published compositions (e.g.. in catalogues of the American Type Culture Collection). If the polypeptide is secreted into the nutrient medium, the polypeptide can be recovered directly from the medium. If the polypeptide is not secreted, it is recovered from cell lysates.

The polypeptides may be detected using methods known in the art that are specific for the polypeptides such as those methods described earlier or the methods described in the Examples.

The resulting polypeptide may be recovered by methods known in the art. For example, the polypeptide may be recovered from the nutrient medium by conventional procedures including, but not limited to, centrifugation, filtration, extraction, spray-drying, evaporation, or precipitation.

The polypeptides may be purified by a variety of procedures known in the art including, but not limited to, chromatography (e.g., ion exchange, affinity, hydrophobic, chromatofocusing, and size exclusion), electrophoretic procedures (e.g., preparative isoelectric focusing), differential solubility (e.g., ammonium sulfate precipitation), or extraction (see, e.g.. Protein Purification, J.-C. Janson and Lars Ryden, editors, VCH Publishers, New York. 1989).

Methods for Obtaining a Mutant Cell

The present invention also relates to methods for obtaining a mutant cell. In a first embodiment, the methods for obtaining a mutant cell, comprise:

(a) introducing a nucleic acid construct into a parent cell, wherein the parent cell comprises at least two tandem copies of a nucleic acid sequence encoding a polypeptide, under conditions in which the nucleic acid construct integrates into the genome of the parent cell at a locus not within the copies of the nucleic acid sequence to produce a mutant cell, wherein the integration of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence, the modification of the copy number is not under selective pressure, and the mutant cell produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions; and

(b) identifying the mutant cell which produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions.

In a second embodiment, the methods for obtaining a mutant cell, comprise: (a) introducing a nucleic acid construct into a parent cell, wherein the parent cell comprises at least two tandem copies of a nucleic acid sequence encoding a polypeptide. under conditions in which the nucleic acid construct integrates into the genome of the parent cell at a locus not within the copies of the nucleic acid sequence to produce a mutant cell. wherein the integration of the nucleic acid construct into the locus decreases the copy number of the nucleic acid sequence, the modification of the copy number is not under selective pressure, and the mutant cell produces less of the polypeptide than the parent cell when both cells are cultivated under the same conditions; and

(b) identifying the mutant cell which produces less of the polypeptide than the parent cell when both cells are cultivated under the same conditions.

In a third embodiment, the methods for obtaining a mutant cell, comprise: (a) introducing a nucleic acid construct into a parent cell, wherein the parent cell comprises at least two tandem copies of a nucleic acid sequence encoding a polypeptide. under conditions in which the nucleic acid construct integrates into the genome of the parent cell at a locus within one of the copies of the nucleic acid sequence to produce a mutant cell, wherein the integration of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence, the modification of the copy number is not under selective pressure, and the mutant cell produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions; and

(b) identifying the mutant cell which produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions. In a fourth embodiment, the methods for obtaining a mutant cell, comprise:

(a) introducing a nucleic acid construct into a parent cell, wherein the parent cell comprises at least two tandem copies of a nucleic acid sequence encoding a polypeptide. under conditions in which the nucleic acid construct integrates into the genome of the parent cell at a locus within one of the copies of the nucleic acid sequence to produce a mutant cell, wherein the integration of the nucleic acid construct into the locus decreases the copy number of the nucleic acid sequence, the modification of the copy number is not under selective pressure, and the mutant cell produces less of the polypeptide than the parent cell when both cells are cultivated under the same conditions; and

In a fifth embodiment, the methods for obtaining a mutant cell, comprise: (a) introducing a nucleic acid construct into a parent cell, wherein the parent cell comprises a nucleic acid sequence encoding a polypeptide, which nucleic acid sequence comprises repeat sequences at the 5' and 3' ends of the nucleic acid sequence, under conditions in which the nucleic acid construct integrates into the genome of the parent cell at a locus not within the nucleic acid sequence to produce a mutant cell, wherein the integration of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence, the modification of the copy number is not under selective pressure, and the mutant cell produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions; and

The present invention is further described by the following examples which should not be construed as limiting the scope of the invention.

EXAMPLES

Strains and Media

The starting strains were pyrG-minus Aspergillus oiyzae HowB425. Aspergillus oryzae JaL250, E. coli DH5α (GIBCO-BRL, Gaithersburg, MD), and E. coli HB101 (GIBCO-BRL, Gaithersburg, MD). PDA plates contained 39 g/1 Potato Dextrose Agar (Difco) and were supplemented with 10 mM uridine for pyrG auxotrophs unless otherwise indicated.

MY25 medium at pH 6.5 was composed per liter of 25 g of maltose. 2.0 g of MgS0₄-7H₂O, 10 g of KH₂PO₄, 2.0 g of citric acid, 10 g of yeast extract, 2.0 g of K₂S0₄, 2.0 g of urea, and 0.5 ml of trace metals solution. MY25 shake-flask medium was diluted 1:100 or 1 :1000 with glass distilled water for use in microtiter growth experiments (MY25/100 or MY25/1000). Cultures were grown at 34°C.

2X MY Salts pH 6.5 solution was composed per liter of 4 g of MgS0₄-7H₂O. 4 g of K₂SO₄, 20 g of KH₂P0₄, 4 g of citric acid, 1 ml of trace metals, and 2 ml of CaCl₂-2H₂0 (100 g/1 stock solution. Minimal medium transformation plates were composed per liter of 6 g of NaN0₃,

0.52 g of KC1, 1.52 g of KH₂P0₄, 1 ml of trace metals solution. 1 g of glucose. 500 mg of MgSCy7H₂O, 342.3 g of sucrose and 20 g of Noble agar per liter (pH 6.5). Minimal medium transfer plates (pH 6.5) were composed per liter of 6 g of NaNO,, 0.52 g of KC1. 1.52 g of KH₂P0₄, 1 ml of trace elements, 1 g of glucose, 500 mg of MgS0₄-7H₂O, and 20 g Noble agar.

The trace metals solution (1000X) was composed per liter of 22 g of ZnS0₄-7H₂0, 11 g of H₃BO₃, 5 g of MnCl₂4H₂O. 5 g of FeSO₄-7H₂O, 1.6 g of CoCl₂-5H₂0, 1.6 g of (NH₄)₆Mo₇O₂₄, and 50 g of Na₄EDTA.

COVE plates were composed per liter of 343.3 g of sucrose. 20 ml of COVE salts solution, 10 ml of 1 M acetamide, 10 ml of 3 M CsCl, and 25 g of Nobel agar. The COVE salts (50X) solution was composed per liter of 26 g of KC1, 26 g of MgSO₄-7H₂0, 76 g of KH₂P0₄, and 50 ml of COVE trace metals solution. COVE trace metals solution was composed per liter of 0.04 g of NaB₄O₇ 10H₂O, 0.040 g of CuS0₄-5H₂0. 0.70 g of FeSO₄-H₂O, 0.80 g of Na₂MoO₂-2H₂O, and 10 g of ZnS0₄.

YEG medium was composed per liter of 5 g yeast extract and 20 g dextrose.

BASTA plates contained per liter 342.3 g sucrose, 20 ml COVE salts solution, 10 ml 1 M urea, 25 g Noble agar and 5 mg/ml final BASTA concentration for selection of transformants. The overlay for the BASTA transformation had the same composition as the

BASTA plates above. BASTA transfer plates were as above but contained 10 mg/ml

BASTA.

Example 1: Construction of Aspergillus oryzae HowB430

Aspergillus oryzae HowB430 was constructed to contain a lipase gene from Humicola lanuginosa (LIPOLASE™ gene. Novo Nordisk A/S, Bagsvasrd. Denmark). pBANeδ was constructed as described below to contain the TAKA NA2-tpi leader hybrid promoter, the lipase gene from Humicola lanuginosa. the AMG terminator, and the full-length Aspergillus nidulans amdS gene as a selectable marker.

PCR was employed to insert Nsil sites flanking the full-length amdS gene of pToC90 (Christensen et al, 1988. Biotechnology 6: 1419-1422) using primers 1 and 2 below and to insert an EcoRI site at the 5' end and a Swa site at the 3^" end of the NA2-tpi leader hybrid promoter of pJaL292 (Figure 1) using primers 3 and 4 below. The primers were synthesized with an Applied Biosystems Model 394 DNA RNA Synthesizer (Applied Biosystems, Inc.,

Foster City, CA) according to the manufacturer's instructions. Primer 1 : 5'-ATGCATCTGGAAACGCAACCCTGA-3' Primer 2: 5'-ATGCATTCTACGCCAGGACCGAGC-3' Primer 3: 5'-TGGTGTACAGGGGCATAAAAT-3' Primer 4: 5"-ATTTAAATCCAGTTGTGTATATAGAGGATTGTGG-3'

Amplification reactions (100 μl) were prepared using approximately 0.2 μg of either pToC90 or pJaL292 as the template. Each reaction contained the following components: 0.2 μg of plasmid DNA, 48.4 pmol of the forward primer, 48.4 pmol of the reverse primer, 1 mM each of dATP. dCTP, dGTP, and dTTP, 1 x Taq DNA polymerase buffer, and 2.5 U of Taq DNA polymerase (Perkin-Elmer Corp., Branchburg, NJ). The reactions were incubated in an

Ericomp Thermal Cycler programmed as follows: One cycle at 95°C for 5 minutes followed by 30 cycles each at 95°C for 1 minute, 55°C for 1 minute and 72°C for 2 minutes.

The PCR products were electrophoresed on a 1%> agarose gel to confirm the presence of a 2.7 kb amdS fragment and a 0.6 kb NA2-tpi fragment. The PCR products were subsequently subcloned into pCRII using a TA Cloning Kit

(Invitrogen, San Diego. CA) according to the manufacturer's instructions. The transformants were then screened by extracting plasmid DNA from the transformants using a QIAwell-8 Plasmid Kit (Qiagen. Inc.. Chatsworth, CA) according to the manufacturer's instructions, and restriction digesting the plasmid DNA with either Nsil or EcoKl/Swal followed by agarose electrophoresis to confirm the presence of the correct size fragments, 2.7 kb and 0.6 kb, respectively, for the Nsil amdS fragment and Swal/EcoKl NA2-tpi fragment. In order to confirm the PCR products, the products were sequenced with an Applied Biosystems Model 373A Automated DNA Sequencer (Applied Biosystems, Inc.. Foster City, CA) on both strands using the primer walking technique with dye-terminator chemistry (Giesecke et al, 1992, Journal of Virol. Methods 38: 47-60) using the Ml 3 reverse (-48) and Ml 3 forward (-20) primers (New England Biolabs, Beverly, MA) and primers unique to the DNA being sequenced. The plasmids from the correct transformants were then digested with the restriction enzymes for which the plasmids were designed, separated on a 1% agarose gel, and purified using a FMC SpinBind Kit (FMC, Rockland. ME) according to the manufacturer^'s instructions. pKS6 (Figure 2). which contains the TAKA amylase promoter, a polylinker, the AMG terminator, and the Aspergillus nidulans pyrG gene, was digested with EcoRI and Swαl to remove a portion of the TAKA amylase promoter. This region was replaced with the NA2-tpi PCR product to produce pBANel3 (Figure 3). pBANel3 was digested with NM to remove the Aspergillus nidulans pyrG gene. This region was then replaced with the full length amdS gene PCR product described above to produce pBAΝeό (Figure 4). PCR was used to insert Svrøl and Pad flanking sites on the full-length Humicola lanuginosa lipase gene of pMHan37 (Figure 5) using primers 5 and 6 below. Primers 5 and 6 were synthesized as described above.

Primer 5: 5^'-ATTTAAATGATGAGGAGCTCCCTTGTGCTG-3^" Primer 6: 5'-TTAATTAACTAGAGTCGACCCAGCCGCGC-3^' The amplification reaction (100 μl) contained the following components: 0.2 μg of pMHan37, 48.4 pmol of primer 5, 48.4 pmol of primer 6, 1 mM each of dATP. dCTP, dGTP, and dTTP, 1 x Taq DΝA polymerase buffer, and 2.5 U of Taq DΝA polymerase. The reaction was incubated in an Εricomp Thermal Cycler programmed as follows: One cycle at 95°C for 5 minutes followed by 30 cycles each at 95°C for 1 minute. 55°C for 1 minute, and 72°C for 2 minutes. Two μl of the reaction was electrophoresed on an agarose gel to confirm the amplification of the lipase gene product of approximately 900 bp.

The PCR amplified lipase gene product was then subcloned into pCRII using a TA

Cloning Kit. The transformants were screened by extracting plasmid DΝA from the transformants using a QIAwell-8 Plasmid Kit, restriction digesting the plasmid DΝA with Swal/Pacl, and sequencing the DΝA according to the method described above to confirm the

PCR product. The lipase gene was excised from the pCRII plasmid by digesting with Swαl and Pad and subsequently subcloned into Swal/Pacl digested pBANeό to produce pBANe8 (Figure 6). pBANe8 was digested with Pmel and the linear Pmel fragment containing the NA2- 5 tpi promoter, the lipase gene from Humicola lanuginosa. and the AMG terminator was isolated by preparative agarose electrophoresis using 40 mM Tris-acetate-1 mM disodium EDTA (TAE) buffer.

Aspergillus oryzae HowB430 was generated by transformation of Aspergillus oryzae HowB425 with the linear Pmel fragment according to the following procedure. o Aspergillus oryzae HowB425 was grown in 100 ml of 1% yeast extract-2% peptone-

1% glucose at 32°C for 16-18 hours with agitation at 150 rpm. The mycelia were recovered by filtration through a 0.45 mm filter until approximately 10 ml remained on the filter, washed with 25 ml of 1.0-1.2 M MgSO₄-10 mM sodium phosphate pH 6.5. filtered as before, washed again as before until 10 ml remained, and then resuspended in 10 ml of 5 mg/ml s NOVOZYM 234™ (Novo Nordisk A S, Bagsv-erd. Denmark) in 1.2 M MgSO₄-10 mM sodium phosphate pH 6.5 (0.45 μm filtered) in a 125 ml Ehrlenmeyer flask. The suspension was incubated with gentle agitation at 50 rpm for approximately one hour at 37°C to generate protoplasts. A volume of 10 ml of the protoplast/mycelia preparation was added to a 30 ml Corex centrifuge tube, overlaid with 5 ml of 0.6 M sorbitol- 10 mM Tris-HCl pH 7.5, and 0 centrifuged at 3600 x g for 15 minutes in a swinging bucket rotor to recover the protoplasts.

The protoplasts were recovered from the buffer interface with a Pasteur pipet. The protoplasts were then washed with five volumes of STC, centrifuged. and then rewashed and centrifuged as before. The protoplasts were resuspended in STC to a final concentration of 2 x 10⁷ protoplasts per ml. 5 Transformation of Aspergillus oryzae HowB425 for amdS selection was conducted with protoplasts at a concentration of 2x10⁷ protoplasts per ml. Ten μg of DNA were added to 100 ml of protoplasts. A volume of 250 ml of PEG solution (60% PEG 4000-10 mM CaCl₂-10 mM Tris-HCl pH 8.0) was then added and the mixture was placed at 37°C for 30 minutes. Three ml of 1 M sorbitol-10 mM CaCl₂-10 mM Tris pH 7.5 (STC) was added and o the mixture was plated on Cove plates supplemented with 10 mM uridine selecting for amdS.

The plates were incubated 7-10 days at 34°C. Transformants were transferred to plates of the same medium and incubated 3-5 days at 37°C. The transformants were purified by streaking spores and picking isolated colonies using the same plates of the same medium without sucrose under the same conditions. 5

Example 2: Construction of plasmids pSO122, pDSY81, and pDSY82 pS0122 was constructed as described below to contain a 1.5 kb fragment of the Aspergillus oryzae pyrG gene. pSO2 (Figure 7) was constructed from a genomic library of Aspergillus oryzae 1560. The genomic library of Aspergillus oryzae 1560 was constructed by first partially digesting Aspergillus oryzae 1560 genomic DNA with Sau3A (New England Biolabs, Beverly, MA). Four units of Sau3A were used to digest 10 μg of Aspergillus oryzae 1560 genomic DNA using conditions recommended by the manufacturer. The reaction was carried out at 65°C, and samples were taken at 5 minute intervals (from 0 to 50 minutes). The samples were placed on ice and stopped by the addition of EDTA to 10 μM. These digests were then run on a 1% agarose gel with ethidium bromide, and the region of the gel containing DNA from 3 kb to 9 kb was excised. The DNA was then purified from the gel slice using Beta-Agarase I using a protocol provided by the manufacturer (New England Biolabs, Beverly, MA). The size-selected DNA was then ligated into EMBL 4 arms according to the manufacturer's instructions (Clontech. Palo Alto, CA) at 16°C overnight using conditions recommended by the manufacturer. The ligation reaction was packaged and titered using a Gigapack II Packaging Kit (Stratagene, La Jolla, CA) according to the manufacturer's protocol. A total of 16.000 recombinant plaques were obtained, and the library was amplified using a protocol provided by the manufacturer.

Appropriate dilutions of the genomic library were made to obtain 7000 plaques per 150 mm petri plate as described in the protocols provided with the EMBL 4 arms. The plaques were lifted to Hybond-N plus circular filters (Amersham. Cleveland. OH) using standard protocols (Sambrook et al, 1989, supra). The filters were fixed using UV crosslinking, and prehybridized at 42°C (5X SSPE, 35%> formamide). The genomic library was probed at low stringency (35%) formamide, 5X SSPE at 42°C) with a 500 bp fragment consisting of the Aspergillus niger pyrG gene which was labeled with ³²P using a random prime DNA labeling kit (Boehringer Mannheim, Indianapolis. IN). A 3.8 kb Hindlϊl fragment was isolated from one phage and subcloned into a pUC 1 18 cloning vector to produce pSO2.

PCR was used to generate pS0122 by introducing a BamHl restriction site at the 5' end of the pyrG gene of pSO2 using primers 7 and 8 shown below. Primers 7 and 8 were synthesized with an Applied Biosystems Model 394 DNA/RNA Synthesizer according to the manufacturer^'s instructions.

Primer 7: 5'-GCGGGATCCCTAGAGTAGGGGGTGGTGG-3' Primer 8: 5'-GCGGGATCCCCCCTAAGGATAGGCCCTA-3'

The amplification reaction (50 μl) contained the following components: 2 ng of pS02. 48.4 pmoles of the forward primer, 48.4 pmoles of the reverse primer, 1 mM each of dATP. dCTP, dGTP. and dTTP, 1 x Taq DNA polymerase buffer, and 2.5 U of Taq DNA polymerase. The reaction was incubated in an Ericomp Thermal Cycler programmed as follows: One cycle at 95°C for 5 minutes followed by 30 cycles each at 95°C for 1 minute,

52 55°C for 1 minute, and 72°C for 2 minutes. The PCR product was isolated by electrophoresis on a 1% agarose gel.

The isolated PCR product was digested with BamHl and cloned into the BamHl site of pBluescript SK^" (Stratagene, La Jolla, CA) to yield pSO122 (Figure 8). The only homology between the genome of Aspergillus oryzae HowB430 and pSO122 was in the 5' end of the pyrG insert since the rest of the pyrG fragment was deleted from Aspergillus oryzae HowB430 as described in Example 1.

In order to reduce the frequency of targeting to this homologous region in the genome and since pSO122 contains two BamHl sites, two derivatives of pSO122, pDSY81 and pDSY82 (Figure 8), were constructed in which one of the BamHl sites was destroyed. The plasmids pDSY81 and pDSY82 were constructed by partially digesting pSO122 with BamHl, filling-in the 5^' overhangs with the Klenow fragment, closing down the plasmid by ligation and subsequent transformation into E. coli DH5α (Sambrook et al, 1989, supra). The transformants were then screened by extracting plasmid DNA from the transformants using a QIAwell-8 Plasmid Kit and restriction digesting the plasmid DNA with BamHl to determine if one of the BamHl sites had been destroyed. Plasmids with one of the BamHl sites destroyed were digested with Nsil/BamHl to determine which BamHl site had been destroyed.

Example 3: Aspergillus oryzae HowB430 transformation with pSO122, pDSY81, or pDSY82

Protoplasts of Aspergillus oryzae HowB430 were prepared as described in Example 1. A 5-15 μl aliquot of DNA (circular pSO122, pDSY81 linearized with 4 to 12 U of EcoRI, or pDSY82 linearized with 15 U of BamHl) was added to 0.1 ml of the protoplasts at a concentration of 2 x 10 protoplasts per ml in a 14 ml Falcon polypropylene tube followed by

250 μl of 60% PEG 4000-10 mM CaCl₂-10 mM Tris-HCl pH 7. gently mixed, and incubated at 37°C for 30 minutes. The transformations were made either with 5 μg of circular pSO122, 6 μg of linearized pDSY81, or 6 μg of linearized pDSY82. Three ml of SPTC (1.2 M sorbitol- 10 mM CaCl₂-10 mM Tris pH 8) were then added and the suspension was gently mixed. The suspension was mixed with 12 ml of molten overlay agar (IX COVE salts, 1%

NZ amine. 0.8 M sucrose, 0.6% Noble agar) or 3 ml of STC medium and the suspension was poured onto a Minimal medium plate. The plates were incubated at 37°C for 3-5 days.

The transformation frequencies of the circular pSO122 transformations ranged from about 100 to 200 transformants/μg. A library of -120,000 transformants of Aspergillus oryzae HowB430 was obtained.

The transformation frequencies of the EcoRI RΕMI pDSY81 transformations ranged from about 60 to 100 per μg. An EcoRI RΕMI library of -28,000 transformants of Aspergillus oryzae HowB430 was generated. The transformation frequencies of the BamHl REMI pDSY82 transformations ranged from about 80 to 110 transformants/μg. A BamHl REMI library of -27.000 transformants of Aspergillus oryzae HowB430 was obtained.

Hindlll and Sail REMI libraries of Aspergillus oryzae HowB430 were also prepared using pDSY81 as described above.

The transformation frequencies of the Hindlll REMI pDSY81 transformations ranged from about 80 to 120 per μg. A Hindlll REMI library of 35,000 transformants of Aspergillus oryzae HowB430 was generated.

The transformation frequencies of the Sail REMI pDSY81 transformations ranged from about 80 to 120 per μg. A Sail REMI library of 25,000 transformants of Aspergillus oryzae HowB430 was generated.

The Aspergillus oryzae HowB430 library pools were designated "h" for pSO122; "e" for pDSY81 digested with EcoRI with subsequent transformation in the presence of EcoRI; "b" for pDSY82 digested with BamHl with subsequent transformation in the presence of BamHl; "hill" for pDSY81 digested with Hindlll with subsequent transformation in the presence of Hindlll: and "s" for pDSY81 digested with Sail with subsequent transformation in the presence of Sail. There were 123 "h" pools, 28 "e" pools. 23 "b" pools, 55 "hill" pools, and 25 "s^" pools.

The libraries described above were pooled into groups of -1000 transformants and stored in 10% glycerol at -80°C.

Example 4: Lipase expression screening

The Aspergillus oryzae HowB430 mutant library "h", "e". "b". "s", and "hill" pools described in Example 3 were assayed for lipase expression. For 96-well plate screens. MY25 medium was diluted 1000-fold using a diluent made of equal volumes of sterile water and 2X MY Salts pH 6.5 solution. For 24-well plate methods, MY25 medium was diluted 100-fold using a diluent made of equal volumes of sterile water and 2X MY Salts pH 6.5 solution.

Primary 96-well plate screens involved the dilution of spores from distinct pools into MY25/1000 so that one spore on average was inoculated per well when 50 ml of medium was dispensed into the wells. After inoculation, the 96-well plates were grown for 7 days at 34°C under static conditions. Cultures were then assayed for lipase activity as described below. Mutants of interest were inoculated directly into 24-well plates containing MY25/100 and were grown for 7 days at 34°C. Cultures were then assayed for lipase activity as described below. Mutants of interest were then plated on COVE plates to produce spores, spread on PDA plates to produce single colonies, and then 4 single colonies from each isolate were tested in the 24-well plate method described above. The lipase assay substrate was prepared by diluting 1 :50 a p-nitrophenylbutyrate stock substrate (21 μl of p-nitrophenylbutyrate/ml DMSO) into MC buffer (4 mM CaCl₂-100 mM MOPS pH 7.5) immediately before use. Standard lipase (LIPOLASE™. Novo Nordisk A S, Bagsv-erd. Denmark) was prepared to contain 40 LU/ml of MC buffer containing 0.02% alpha olefin sulfonate (AOS) detergent. The standard was stored at 4°C until use. Standard lipase was diluted 1/40 in MC buffer just before use. Broth samples were diluted in MC buffer containing 0.02% AOS detergent and 20 μl aliquots were dispensed to wells in 96-well plates followed by 200 μl of diluted substrate. Using a plate reader, the absorbance at 405 nm was recorded as the difference of two readings taken at approximately 1 minute intervals. Lipase units/ml (LU/ml) were calculated relative to the lipase standard.

The results of the 96-well screen followed by the 24-well screen identified for further evaluation 360 transformants from the pSO122 transformations and 44 transformants from the pDSY81 or pDSY82 REMI transformations. These identified transformants produced higher levels of lipase than the control strains Aspergillus oryzae HowB427 and Aspergillus oryzae HowB430.

Example 5: Shake flask, fermentation, and lipase gene copy number evaluation

The highest lipase-producing mutants described in Example 4 were then plated onto COVE plates to produce spores for shake flask and fermentation evaluations. Shake flask evaluations were performed by inoculating 300-500 ml of a spore suspension (0.02%) Tween-80 plus spores from the COVE plates) into 25 ml of MY25 medium at pH 6.5 in a 125 ml shake flask. The shake flasks were incubated at 34°C for 3 days at 200 rpm. Samples were taken at day 2 and day 3 and lipase activity was measured as described in Example 4. The same mutants were grown in a 2 liter lab fermentor containing medium composed of Nutriose. yeast extract. (NH₄)₂HP0₄, MgS0 -7H₂0. citric acid, K₂S0₄. CaCl₂Η,0, and trace metals solution at 34°C, pH 7, 1000-1200 rpm for 8 days. Lipase activity was measured as described in Example 4.

Lipase copy number in the Aspergillus oryzae mutants was determined by real time PCR analysis using an Applied Biosystems Prism Model 7700 Sequence Detector (Applied Biosystems, Inc.. Foster City, CA) according to the manufacturer^'s instructions. Real time PCR reactions were performed on each genomic DNA preparation for both lipase and a single copy gene control oliC. Spores of the mutants were grown in 5 ml of YEG medium for 24 hours at 34°C in a small Petri plate. Mycelia were then collected from each culture by filtration through Whatman filter paper No. 1 (Whatman, Springfield Mill, England) and transferred to a 1.7 ml centrifuge tube. The mycelial preparations were frozen in liquid nitrogen and dried in a SpeedVac (Savant Instruments, Inc.. Farmingdale. NY) overnight at room temperature. Genomic DNA was obtained using the DNeasy Kit (Qiagen, Chatsworth. CA) according to the manufacturer^'s instructions. The average lipase copy number for each strain was calculated by taking a ratio of lipase amplicon quantity to oliC amplicon quantity. Standard curves for the analysis were generated using genomic DNA from Aspergillus oryzae HowB430. The following set of primers and probes were used for real time amplification of the lipase gene:

Lipase gene probe: 6FAM-5'-TGGCCAGTCCTATTCGTCGAGAGGTC-3'-TAMRA Lipase gene forward primer (lipo 9F): 5^'-CTCCCTTGTGCTGTTCTTTGTCT-3' Lipase gene reverse primer (lipol 11R): 5'-CTGTGCAAAGAGATTGAACTGGTTA-3' The following set of primers and probe were used for real time amplification of oliC: oliC probe: 6FAM-5^'-TGGGTATGGGTTCCGCCGCC-3'-TAMRA oliC forward primer (oliC4F): 5'-GATGGTCCAGGTCTCCCAGAA-3' oliC reverse primer (oliC122R): 5'-CAGGGTTGCGGGAGACA-3'

6FAM is an abbreviation for the fluorescent reporter 6-carboxyfluorescein which is covalently linked to the 5' end of the probes, and TAMRA is an abbreviation for 6- carboxvtetramethvlrhodamine which is a quencher which is attached via a linker arm to the 3' end of the probe.

For the standard curve, Aspergillus oryzae HowB430 genomic DNA was serially diluted 1 : 10, 1 : 100. 1 : 1000 and 1 : 10000, and real time PCRs were run for both primers/probe sets. For analysis of other strains, genomic DNA was diluted either 1:50 and 1 :100 or 1 :100 and 1 :200, and real time amplifications were run with both primers/probe sets. The real time amplification reactions were set up using TaqMan PCR Reagent kits (Applied Biosystems, Inc.. Foster City, CA) according to the manufacturer's instructions. The reactions contained IX TaqMan Buffer A. 3.5 mM MgC 200 μM each of dATP, dCTP, dGTP and dUTP, 0.025 U/ml AmpliTaq Gold, 0.01 U/ml AmpErase, and either the lipase gene or oliC probes at 100 nM. Lipase primers were added at a final concentration of 0.9 μM each. The oliC primers were added at a final concentration of 0.3 μM. The reactions were run using the following cycling conditions on the Applied Biosystems Prism Model 7700 Sequence Detector: 1 cycle at 50°C for 2 minutes, 1 cycle at 95°C for 10 minutes, and 40 cycles each at 95°C for 15 seconds and 60°C for 1 minute. The raw data was analyzed using the Sequence Detector v 1.6.

The results obtained are shown in Table 1 below where the lipase yield of either Aspergillus oryzae HowB427 or Aspergillus oryzae HowB430 as a control was normalized to 1.0 and the average iipase gene copy number of Aspergillus oryzae HowB430 was normalized to 1.0. Table I - Lipase Expression and Lipase Gene Copy Number of Mutants Strain Construct Library Shake Flask Results Average Relative

Copy #

HowB430 HowB425-pBANe8 NA 1.0 1.0

HowL371.3 pS0122 h 2.5 1.56

HowL500.1 pS0122 h 2.7 1.25

HowL795.4 pS0122 h 3.8 1.75

HINL981 pDSY81 hill 5.9 5.62

HINL949 pDSY81 hill 5.7 5.81

HINL917 pDSY81 hill 5.6 5.38

HINL980 pDSY81 hill 4.6 3.81

SALL678 pDSY81 s 3.7 2.19

SALL714 pDSYδl s 3.4 2.56

BAML5 pDSY82 b 3.0 1.62

HI L985 pDSY81 hill 2.9 1.56

ECOL56 pDSY82 e 2.7 1.50

HINL990 pDSY81 hill 2.4 1.62

HI L955 pDSY81 hill 2.4 2.37

HINL933 pDSYδl hill 2.3 1.75

As shown in Table I, the mutants produced approximately 2- to 6-fold more lipase than the control strain Aspergillus oryzae HowB430 when grown in shake flasks. The mutants tested in fermentors produced approximately 2- to 5 -fold more lipase than the control strain Aspergillus oryzae HowB427 when grown in fermentors (not all were tested).

Example 6: Construction of pMT1936 pMT1936 was constructed to contain a disruption cassette of the palB gene of Aspergillus oryzae A1560 described in WO 98/1 1203 using the following primers synthesized with an Applied Biosystems Model 394 DNA RNA Synthesizer according to the manufacturer^'s instructions.

100752: 5^'-GGTTGCATGCTCTAGACTTCGTCACCTTATTAGCCC-3' 100753 : 5 '-TTCGCGCGCATCAGTCTCGAGATCGTGTGTCGCGAGTACG-3 ' 100754 : 5 ^" -GATCTCGAGACTAGTGCGCGCGAACAGAC ATCAC AGGAACC-3 ' 100755: 5 ^' -C AAC ATATGCGGCCGCGAATTCACTTCATTCCC ACTGCGTGG-3 '

The Aspergillus oryzae palB 5' flanking sequence and the sequence encoding the N- terminal part of the palB product were PCR amplified from genomic DNA of Aspergillus oryzae A 1560 obtained according to the method described in Example 1. Approximately 0.05 μg of DNA template and 5 pmole of each of the two primers 100755 and 100754 were used. Amplification was performed with the polymerase Pwo as described by the manufacturer (Boehringer Mannheim, Indianapolis. IN). Amplification proceeded through 40 cycles. Part of the reaction product was phenol extracted, ethanol precipitated, digested with restriction enzymes EcoRI and Xhόl and a fragment of approximately 1.05 kb was isolated by agarose gel electrophoresis.

The Aspergillus oryzae palB 3' flanking sequence and the sequence encoding the C- terminal part of the palB gene product were obtained as described above except that primers 100753 and 100752 were used for amplification and the PCR product was digested with restriction enzymes Xhόl and Xbal before gel electrophoresis to recover a fragment of approximately 1.50 kb.

The two digested and purified PCR fragments described above were ligated in a three part ligation with the purified 2.7 kb EcoRI -Xbal fragment from the vector pJaL400 (Figure 9) to produce pMT1935 (Figure 10). ThepalB 5' and 3' flanks of pMT1935 are separated by

BssHll, Spel, and Xhol sites introduced via PCR primers 100754 and 100753.

To insert an Aspergillus oryzae pyrG gene between the pal B 5' flank and the 3' flank of pMT1935, the 3.5 kb Hindlll fragment of pJaL394 (Figure 11) containing the repeat flanked pyrG gene was cloned into Hindlll cut, dephosphorylated and purified pBluescript II SK^". Plasmids with inserts in either orientation were obtained. One plasmid, pMT1931

(Figure 12), was selected in which the S el site of the pBluescript polylinker was downstream of the pyrG gene and the Xhol site was upstream of the pyrG gene. The pyrG gene was isolated as a 3.5 kb Spel-Xhol fragment and inserted in Spel and Xhol digested and purified pMT1935 to produce the disruption plasmid pMT1936 (Figure 13). The pyrG selectable palB disruption cassette can be isolated from pMT1936 as a 5.5 kb Asel-Pvul fragment (Asel and Pvul cutting within the actual palB 5' and 3' flanking sequences).

Example 7: Aspergillus oryzae transformation with AsellPvul palB disruption cassette from pMT1936 and lipase screening

Aspergillus oryzae HowB430 was transformed using the same transformation procedure described in Example 3 with a 5.5 kb AsellPvul fragment obtained from pMT1936. The linear fragment for transformation was isolated by digestion of pMT1936 with Asel and Pvul and separation of the fragment on a 1% agarose gel using a QIAquick Gel Extraction Kit according to the manufacturer's instructions. The transformants were then tested for growth on Minimal medium plates at pH 6.5 or pH 8.0. The average lipase gene copy number was determined as described in Example 5.

The results showed that 13 of the 128 transformants tested possessed the palB minus phenotype as indicated by the inability to grow at pH 8.0. The 13 palB minus strains and 13 of the transformants that were able to grow at pH 8.0 were spore purified and then evaluated in shake flask cultures for lipase production using the methods described in Examples 4 and 5, respectively. The average lipase gene copy number was determined as described in Example 5. The results are shown in Table 2 below where the lipase yield and average lipase gene copy number of Aspergillus oryzae HowB430 were normalized to 1.0. The 5 palB minus strains which did not produce more lipase than Aspergillus oryzae HowB430 had all lost 50% or more of the copies of the lipase expression cassette. Table 2

Strain palB phenotype Shake flask results Average Relative Copy

Number

HowB430 plus 1.0 1.0

DEBY10.3 minus 2.2 1.0 palB24-l minus 1.7 0.38 palB29-l minus 1.0 0.31 palB46-l minus 0.6 0.31 palB78-l minus 1.6 0.44 palB91-l minus 1.3 0.38

Example 8: Aspergillus oryzae transformation with Ndel linearized pDSY138 and lipase expression screening

Aspergillus oryzae HowB430 was transformed with NM digested pDSY138 isolated from Aspergillus oryzae DEBY932 (WO 98/11203) and the transformants were recovered using the methods described in Example 3. Totally, 180 recovered transformants were grown in 24 well microtiter plates in 1/100 strength MY25, and samples were taken at 4 and 6 days for lipase assays as described in Example 4. The top 1 1 highest lipase producing transformants and 1 average lipase producing transformant were spore purified and retested in 24 well microtiter cultures. These purified transformants were also evaluated in shake flasks in full-strength MY25 as described in Example 5. The top two producers were also grown in a 2 liter fermentor as described in Example 5. Lipase activity was measured as described in Example 4. The average lipase gene copy number was determined as described in Example 5.

The results obtained are shown in Table 3 below where the lipase yield and average lipase gene copy number of Aspergillus oryzae HowB430 were normalized to 1.0. The top two lipase producers produced essentially the same amount of lipase activity as Aspergillus oryzae DEBY932. but also had increases in the copy number of the lipase gene.

Table 3

Strain Fermentation Results Average Relative Copy

Number

HowB430 1.0 1.0

138T83.1.1 2.2 1.81 138T102.1.1 1.9 1.81

Example 9: Construction of Aspergillus oryzae HowB432

Aspergillus oryzae HowB432 was generated by transformation of Aspergillus oryzae JaL250 with a linear fragment containing the NA2-tpi promoter, a cellulase gene from Humicola lanuginosa (CAREZYME™ gene, Novo Nordisk A/S. Bagsv-erd, Denmark), and the AMG terminator obtained from plasmid pGAG3 (Figure 14).

Aspergillus oryzae JaL250 was constructed from Aspergillus oryzae JaL142 (Christensen et al.. 1988. Bio/Technology 6: 1419-1422) by deleting the neutral protease I gene (npl). The npl deletion plasmid was constructed by exchanging a 1.1 kb Ball fragment coding for the central part of the npl gene in plasmid pJaL389 (Figure 15), which contained a 5.5 kb Sαcl genomic fragment encoding the npl gene, with a 3.5 kb Hindlll fragment from pJaL335 (Figure 16) containing the pyrG gene flanked by repeat sequences, thereby creating plasmid pJaL399 (Figure 17). Aspergillus oryzae JaL142 was transformed with the 7.9 kb Sαcl fragment. Transformants were selected by relief of the uridine requirement on Minimal medium plates. The transformants were analyzed by Southern analysis as described in Example 7 and by IEF protease profile analysis according to standard methods.

Two out of 35 transformants possessed an altered Southern profile compared to the parent strain and displayed no neutral protease I activity by IEF. Furthermore, Southern analysis showed that one of the two transformants had a clean deletion of the npl gene and was designated Aspergillus oryzae JaL228.

Totally, 2.3 x 10⁷ conidiospores of Aspergillus oryzae JaL228 were spread on Minimal medium plates supplemented with 0.1 %> 5-fluoro-orotic acid (FOA) and 10 mM uridine. Eight FOA resistant colonies were obtained. A Southern blot of BamHl digested genomic DNA from the eight colonies probed with a 401 bp pyrG repeated region demonstrated that the pyrG gene had been excised by recombination at the repeated regions. Aspergillus oryzae JaL228 showed two bands of the expected size of 2.7 and 3.1 kb originating from the two copies of the repeated region. If the pyrG gene had been lost by recombination between the repeated regions, the 3.1 kb band would have disappeared and only the 2.7 kb would have remained. All 8 FOA resistant colonies showed this pattern of bands. Sequencing of a PCR fragment covering the junctions between the npl gene and the copy of the 401 bp repeat remaining in the 8 colonies confirmed that the pyrG gene was excised by recombination between the repeat sequences. One of the colonies was designated Aspergillus oryzae JaL250. pGAG3 was constructed by isolating from pDM176 (Figure 18) a Swal/Pacl fragment containing the Humicola lanuginosa cellulase gene and ligating the fragment into Swal/Pacl digested pBANeό. The Swal/Pacl fragment from pDM176 and Swal/Pacl digested pBANeό were separated on a 1% agarose gel, and isolated using a QIAquick Gel Extraction Kit (Qiagen Inc., Chatsworth. CA) according to the manufacturer^'s instructions prior to ligation. The ligation was used to transform E. coli DH5α cells, and the transformants were then screened by extracting plasmid DNA from the transformants using a QIAwell-8 Plasmid Kit according to the manufacturer's instructions, restriction digesting the plasmid DNA to confirm the presence of the correct size fragment, and sequencing the DNA according to the method described in Example 1. pGAG3 was then digested with Pmel and the linear expression cassette was isolated by preparative agarose electrophoresis using TAE buffer. The linear cassette was then used to transform Aspergillus oryzae JaL250. Transformation of Aspergillus oryzae JaL250 for amdS selection was conducted with protoplasts at a concentration of 2x10⁷ protoplasts per ml prepared as described in Example 1. Ten μg of the linear fragment described above were added to 100 μl of protoplasts. A volume of 250 μl of PEG (60% PEG 4000-10 mM CaCl₂-10 mM Tris-HCl pH 8.0) was then added, and the mixture was placed at 37°C for 30 minutes. Three ml of STC medium was added and the mixture was plated on Cove plates supplemented with 10 mM uridine for amdS selection. The plates were incubated 7-10 days at 34°C. Transformants were then transferred to plates of the same medium and incubated 3-5 days at 37°C. The transformants were purified by streaking spores and picking isolated colonies using the plates of the same medium without sucrose.

Example 10: Aspergillus oryzae transformation with Ndel linearized pDSY138 and cellulase expression screening

Aspergillus oryzae HowB432 was transformed with Ndel digested pDSY138 (WO 98/11203) using the method described in Example 3. Totally, 240 transformants were recovered which were grown in 24 well microtiter plates in 1/4 strength MY25 as described in Example 4 except samples were taken at days 3 and 5 and assayed for cellulase activity as described below.

Cellulase activity was measured according to the following protocol. A substrate solution containing 2% azo-carboxymethylcellulose was prepared by dissolving the material in 100 mM MOPS pH 7.0 buffer at 80°C for 10 minutes. CAREZYME™ (Novo Nordisk A S, Bagsvaerd, Denmark) was used as a standard. Stock solutions of 2.5 to 25 ECU per ml were prepared to construct a standard curve by diluting accordingly CAREZYME™ in 100 mM MOPS pH 7.0 buffer. Five μl aliquots of the standards and samples (diluted for shake flasks and fermentations) were pipetted into individual wells of a 96 well plate. A volume of 65 μl of the 2% azo-carboxymethylcellulose solution was pipetted into each of the wells and mixed. The reactions were incubated at 45°C for 30 minutes and then stopped by the addition of 215 μl of stop reagent followed by mixing. The stop reagent was prepared by first suspending 0.2 g of ZnC in 20 ml of 250 mM MOPS pH 7.0 and adding the suspension to 80 ml of acidified ethanol containing 1.1 ml of concentrated HC1 per liter of ethanol. The plate containing the stopped reaction was then centrifuged at 3000 rpm for 10 minutes. A 100 μl aliquot of each supernatant was pipetted into a 96 well plate and the absorbance measured at 600 nm. Using linear regression, the slope, intercept, and correlation coefficient were determined for the standards and samples.

The top 20 cellulase producing transformants were spore purified and retested in 24 well microtiter cultures. The top 8 cellulase producing once purified transformants were spore purified a second time and tested in shake flasks in full-strength MY25 as described in Example 5. The top 2 producers were also grown in a 2 liter lab fermentor using the same medium and conditions described in Example 5. Cellulase activity was measured as described above. Cellulase copy number was determined using the same procedure described in Example 5 using the following primers and Aspergillus oryzae HowB432 genomic DNA for a standard. Cellulase gene copy number for each strain was calculated by taking a ratio of the cellulase amplicon quantity to the oliC amplicon quantity. Cellulase gene probe: 6FAM-CAGCCTGTCTTTTCCTGCAACGCC-TAMRA Cellulase gene forward primer (CARE119F): CCAAGAAGGCTCCCGTGAA Cellulase gene reverse primer (CARE186R): GAAGTCCGTGATACGCTGGAA

The results obtained shown in Table 4 below where the cellulase yield and average cellulase gene copy number of Aspergillus oryzae HowB432 were normalized to 1.0 demonstrated that Aspergillus oryzae C138T205.1.1 had 50%> more copies of the cellulase gene than Aspergillus oryzae HowB432 which correlated with the 50% increase in cellulase yield in fermentation.

Table 4 Strain Fermentation Results Average Relative Copy Number

HowB432 1.0 1.0

C138T205.1.1 1.5 1.56

C138T21.1.1 1.15 1.0

Example 11: Construction of glucose transporter gene overexpression plasmids pHB218 and pDSY153 and stop control plasmids pDSY152 and pDSY155

Plasmids to overexpress the glucose transporter gene from Aspergillus oryzae DEBY599.3 (WO 98/11203) were constructed to determine if over-expression of the glucose transporter would lead to an increase in the yields of Humicola lanuginosa lipase and cellulase. The glucose transporter open reading frame was PCR amplified to place Swαl and Pad sites at the 5^' and 3^' end of the ORF, respectively. The following primers synthesized with an Applied Biosystems Model 394 DNA RNA Synthesizer according to the manufacturer^'s instructions were used in combination with 0.2 mg of pDSY112 (WO 98/11203) in the amplification:

961176: 5'-ATTTAAATGGTCCTCGGTGGATCAAGC-3^' 961177: 5'-TTAATTAATTAGTCCTGTCTGCGCTGGT-3' The conditions and parameters used for the amplification are described in Example 1.

Ten ml of the PCR reaction was electrophoresed on an agarose gel. and a 1.5 kb product was obtained as expected. The PCR product was cloned using a pPCR-Script™ Kit (Stratagene, La Jolla, CA) according to the manufacturer's protocols. The ligation reaction was used to transform E. coli DH5α cells, and plasmid DNA was isolated from several of the tramsformants using the QIAWell-8 Plasmid Kit. The plasmids were digested with Notl and EcoRI to determine which clones had the 1.5 kb insert. Six of the 1 1 clones analyzed had the correct size insert as determined by electrophoreses on an agarose gel. One of the clones. pDSYl 19, was digested with Eαcl and Swal, and the digest was run on an agarose gel. The 1.5 kb Swal/Pac I band was excised from the gel, and DΝA was purified from the gel slice using the QIAQuick Gel Extraction Kit. The 1.5 kb fragment was ligated with Swal/Pacl cut pBAΝel3 (Figure 3) using standard conditions (Sambrook et al, 1989, supra). The ligation was used to transform E. coli DH5α cells, and plasmid DNA was isolated from several of the transformants. The plasmids were digested with Swal/Pacl to determine which clones had the expected 1.5 kb insert. The final plasmid was designated pHB218 (Figure 19). A version of pHB218 in which the selectable marker was the bar gene were constructed for transformation of strains which are pyrG plus. The Swal/Pacl insert from pHB218 were isolated by restriction digestion, electrophoresed on an agarose gel, and purified using QIAQuick Gel Extraction Kit. The insert were ligated into pSE39 (Figure 20) and digested with Swal/Pacl. The ligation reaction was used to transform E. coli DH5α, and plasmid DNA was isolated from the colonies as described above. The plasmids were digested with Swal/Pacl to determine which clones contained the expected 1.5 kb insert. The plasmids were sequenced as described in Example 1 to confirm the absence of the stop codon at amino acid 9 pDSY153 (Figure 21).

Example 12: Transformation of Aspergillus oryzae HowB430 with pHB218 and lipase screening

Aspergillus oryzae HowB430 was transformed with pHB218. and the transformants were recovered using the methods described in Example 3. One hundred and twenty transformants with pHB218 were recovered, grown in shake flasks in MY25 medium as described in Example 5 and assayed for lipase activity after 2 and 3 days as described in

Example 4. The lipase gene copy number was determined as described in Example 5.

The results are shown in Table 5 where the lipase yield and average lipase gene copy number of Aspergillus oryzae HowB430 were normalized to 1.0. As seen in Table 5, transformants with an increase in lipase gene copy number produced higher yields of lipase in shake flasks, and Aspergillus oryzae 218T95 which had lost copies of the lipase gene produced less lipase.

Table 5 Strain Sha ⁷lask . Results Average Relative Copy Number

HowB430 1.0 1.0

218T56 1.8 5.33

218T87 1.7 4.00

218T18 1.8 2.87

218T43 1.6 2.53

218T95 0.9 0.47

Example 13: Transformation of Aspergillus oryzae DEBY10.3 with pDSY153 and lipase screening

Aspergillus oryzae DEBY10.3 was transformed with pDSY153, and the transformants were recovered using the methods described in Example 3. Two hundred sixteen transformants with pDSY153 were recovered, grown in shake flasks in MY25 medium as described in Example 5. and assayed for lipase activity on days 2 and 3 as described in Example 4. Lipase copy number was determined as described in Example 5.

The results as shown in Table 6 where the lipase yield and average lipase gene copy number of Aspergilus oryzae DEB Yl 0.3 were normalized to 1.0 demonstrated that transformants with an increase in copy number also had an increase in lipase yield in shake flasks while those transformants that had a decrease in lipase copy number had a decrease in lipase yield.

Table 6 Strain Sha ⁷lask Results Average Relative Copy Number

DEBY10.3 1.0 1.0

153T208 1.43 2.87

153T214 1.35 2.93

153T171 1.25 1.19

153T90 0.4 0.56

153T11 0.2 0.44

Example 14: Construction of pLRF2 pLRF2, a derivative of pMT1612 (BASTA resistance), was constructed to contain the palB promoter, open reading frame and terminator. The genomic fragment of the palB gene was amplified from Aspergillus oryzae genomic DNA using the following oligonucleotides: 5'-CATATGCACAATACTCACACCAGTAGGCGACCAC-3' 5'-CATATGCTGGTTGTGATCACAGCGACTGGGATGG-3' The product was amplified using Aspergillus oryzae HowB430 genomic DNA as template and a Clontech Advantage Genomic PCR Kit (Clontech. Palo Alto. CA) according to the manufacturer^'s instructions. The reaction conditions were 94°C for 1 minute; 35 cycles each at 94°C for 30 seconds and 68°C for 6 minutes: and 1 cycle at 68°C for 6 minutes. The expected product of -4.7 kb was obtained, and 3^' A^'s were added to the product using Taq DNA polymerase at 72°C for 10 minutes using a TA Cloning Kit according to the manufacturer's instructions.

The product was subcloned into pCR2.1 using an Invitrogen Topo TA Cloning Kit and E. coli transformants were screened for inserts. The nucleotide sequences of the palB fragment from three of the subclones pLRFl were determined by primer walking. All 3 subclones had 3 base pair changes: T to C at position 1910 (wobble position so it would be silent), A to G in the terminator -110 bp from the stop codon. and A to T at position 3885 which would change the amino acid residue. In order to correct the A to T at position 3885, the oligonucleotide below was used for site-directed mutagenesis using a Morph Site Directed Mutagenesis Kit (Five Prime-Three Prime, Inc., Boulder, CO) according to the manufacturer's instructions from 5' to 3'.

5'-CCTGGCGACTTCGGAAGATGGAACTCACAG-3'

The template for the site-directed mutagenesis was pLRF2. pLRF2 was constructed by digesting pLRFl with Ndel, isolating the 4.6 kb palB fragment and subcloning it into pMT1612 (WO 98/11203) which had been digested with NJel and phosphatased using shrimp alkaline phosphatase. Following mutagenesis, the nucleotide sequence of several E. coli clones was determined to identify clones in which the T at position 3385 had been changed to an A. In addition, the nucleotide sequence of the palB fragment of one of the site- directed mutagenesis clones of pLRF2 containing the desired T to A change was determined by primer walking to be sure no other changes had been introduced.

Example 15: Complementation of the palB minus phenotype and screening of the transformants for lipase production

Linkage of the palB minus phenotype to the increase in lipase production was demonstrated by complementation of the palB minus phenotype with the wild-type palB gene in Aspergillus oryzae strain DEBY10.3 and one of the Aspergillus oryzae HowB430 palB disrupted transformants described in Examples 5 and 7, respectively. This complementation would lead to a decrease in lipase production. Aspergillus oryzae DEBY10.3 or one of the palB disrupted Aspergillus oryzae HowB430 strains, Aspergillus oryzae palB76-l-l, was transformed with pLRF2 selecting for resistance to BASTA according to the protocol described in Example 3. The strains were also transformed with just pMT1612 to BASTA resistance as a control. In Aspergillus oryzae DEBY10.3, 26 and 11 transformants were obtained with pLRF2 and pMT1612, respectively. In Aspergillus oryzae HowB430 palB76-l-l, 28 and 14 transformants were obtained with pLRF2 and pMT1612, respectively.

All of the transformants were spore purified and tested for the palB phenotype on Minimal medium pH 6.5 and pH 8.0 plates. The results are presented in Tables 7 and 8 below for Aspergillus oryzae DEBY10.3 and Aspergillus oryzae HowB430 palB76-l-l, respectively. All of the pLRF2 Aspergillus oryzae DEBY10.3 transformants were palB plus while all of the pMT1612 Aspergillus oryzae DEBY10.3 transformants were palB minus. In the Aspergillus oryzae HowB430 palB76-l-l populations, 27 of the 28 pLRF2 transformants were palB plus, and 13 of the 14 pMT1612 transformants were palB minus.

The lipase production capability of the transformants was determined by inoculating each transformant into 24 well microtiter plates containing 1/100 th strength MY25 pH 6.5 medium as described in Example 4. Each transformant was inoculated into 3 wells each, and the plates were incubated at 34°C with shaking at 150 rpm. Supernatant samples were taken at 3 and 5 days and were assayed as described in Example 4. The average lipase gene copy was determined as described in Example 5.

The results are shown in Tables 7 and 8 for Aspergillus oryzae DEBY10.3 and Aspergillus oryzae HowB430 palB76-l-l, respectively. Results are normalized to 1.0 for these strains.

Table 7

Relative Average I

Strain palB phenotype LU/ml microtiter u

DEBY10.3 minus 1 1 pLRF2-l plus 0.9 1.17 pLRF2-2 plus 0.8 1.19 pLRF2-3 plus 1.3 3.5 pLRF2-4 plus 0.5 0.61 pLRF2-5 plus 0.7 0.94 pLRF2-6 plus 1.1 1.61 pLRF2-7 plus 0.69 0.67 pLRF2-8 plus 0.85 0.89 pLRF2-9 plus 0.63 0.56 pLRF2-10 plus 1.1 1.44 pLRF2-l l plus 0.8 0.83 pLRF2-12 plus 0.6 0.56 pLRF2-13 plus 1.1 1.21 pLRF2-14 plus 0.5 0.39 pLRF2-15 plus 0.6 0.67 pLRF2-16 plus 0.5 0.39 pLRF2-17 plus 0.8 1 pLRF2-18 plus 0.8 0.89 pLRF2-19 plus 0.7 0.78 pLRF2-20 plus 0.7 1.06 pLRF2-21 plus 0.8 0.9 pLRF2-22 plus 1 1.17 pLRF2-23 plus 0.9 0.89 pLRF2-24 plus 0.8 0.89 pLRF2-25 plus 0.5 0.56 pLRF2-26 plus 0.6 0.67

pMT1612-l minus 1.3 1.05 pMT1612-2 minus 1.3 1.05 pMT1612-3 minus 0.73 0.39 pMT1612-4 minus 1.1 1 pMT1612-5 minus 1.1 0.94 pMT1612-7 minus 1.2 1.5 pMT1612-8 minus 1.1 0.94 pMT1612-9 minus 1 0.94 pMT1612-10 minus 1.3 1.39 pMT1612-l l minus 1.3 1.44 pMT1612-12 minus 1.1 1.05

Table 8

Relative Average Relative

Strain palB phenotype LU/ml Copy Number

HowB430 plus 1 1 pLRF2-l plus 0.95 1 pLRF2-2 plus 1.4 2.13 pLRF2-3 plus 1.2 1.53 pLRF2-4 plus 1.4 2 pLRF2-5 plus 1.2 1.2 pLRF2-6 minus 1.7 1.47 pLRF2-7 plus 0.9 1 pLRF2-8 plus 1.2 1.47 pLRF2-9 plus 1.1 1.2 pLRF2-10 plus 1 1.13 pLRF2-l l plus 0.9 0.87 pLRF2-12 plus 1.3 1.53 pLRF2-13 plus 0.7 0.5 pLRF2-14 plus 0.9 0.87 pLRF2-16 plus 0.7 0.6 pLRF2-17 plus 1.1 1.53 pLRF2-18 plus 1.29 2 pLRF2-19 plus 1.1 1.27 pLRF2-20 plus 0.6 0.6 pLRF2-21 plus 0.9 0.87 pLRF2-22 plus 1.2 1.33 pLRF2-24 plus 0.8 0.87 pLRF2-25 plus 1.2 1.67 pLRF2-26 plus 0.8 1.07 pLRF2-27 plus 0.7 0.87 pLRF2-28 plus 1.4 1.33 pLRF2-29 plus 1.3 2.27 pLRF2-32 plus 0.8 0.93

pMT1612-l minus 1.4 0.93 pMT1612-2 minus 1.6 1.27 pMT1612-3 minus 1.3 0.93 pMT1612-4 plus 1.3 1.2 pMT1612-5 minus 1.6 2.2 pMT1612-6 minus 1.5 1 pMT1612-8 minus 1.6 1.27 pMT1612-10 minus 1.6 1.2 pMT1612-l l minus 1.8 1.13 pMT1612-12 minus 1.2 0.73 pMT1612-13 minus 1.4 1.13

76-1-1 minus 1.4 1 There were several strains that had either lost or gained copies of the lipase gene. The frequencies of copy number changes were quite high in all 4 populations ranging from 45 to 66%o. The loss or gain of copy numbers correlated well with either a decrease or an increase in lipase expression, respectively.

The invention described and claimed herein is not to be limited in scope by the specific embodiments herein disclosed, since these embodiments are intended as illustrations of several aspects of the invention. Any equivalent embodiments are intended to be within the scope of this invention. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims.

All publications mentioned herein are incorporated herein by reference for the purpose of describing and disclosing the particular information for which the publication was cited. The publications discussed above are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention.

It is to be understood that this invention is not limited to the particular methods and compositions described as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting since the scope of the present invention will be limited only by the appended claims.

Unless defined otherwise all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any materials or methods similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are described.

Claims

ClaimsWhat is claimed is:

1. A method for producing a polypeptide, comprising:

(i) the mutant cell is related to a parent cell, which parent cell comprises at least two tandem copies of a nucleic acid sequence encoding the polypeptide. by the introduction of a nucleic acid construct into the genome of the parent cell at a locus not within the copies of the nucleic acid sequence to produce the mutant cell, wherein the introduction of the nucleic acid construct into the locus modifies the copy number of the nucleic acid sequence and the modification in the copy number is not a result of selective pressure; and (ii) the mutant cell produces more or less of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for the production of the polypeptide; and

(b) recovering the polypeptide from the cultivation medium.

2. The method of claim 1, wherein the introduction of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence and the mutant cell produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for the production of the polypeptide.

3. The method of claim 1. wherein the introduction of the nucleic acid construct into the locus decreases the copy number of the nucleic acid sequence and the mutant cell produces less of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for the production of the polypeptide.

4. A method for producing a polypeptide, comprising:

(i) the mutant cell is related to a parent cell, which parent cell comprises at least two tandem copies of a nucleic acid sequence encoding the polypeptide, by the introduction of a nucleic acid construct into the genome of the parent cell at a locus within one of the copies of the nucleic acid sequence to produce the mutant cell, wherein the introduction of the nucleic acid construct into the locus modifies the copy number of the nucleic acid sequence and the modification in the copy number is not a result of selective pressure; and

(b) recovering the polypeptide from the cultivation medium.

5. The method of claim 4. wherein the introduction of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence and the mutant cell produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide.

6. The method of claim 4, wherein the introduction of the nucleic acid construct into the locus decreases the copy number of the nucleic acid sequence and the mutant cell produces less of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide.

7. A method for producing a polypeptide, comprising:

(a) cultivating a mutant cell under conditions conducive for production of the 0 polypeptide. wherein

(i) the mutant cell is related to a parent cell, which parent cell comprises a nucleic acid sequence encoding the polypeptide, which nucleic acid sequence comprises repeat sequences at the 5' and 3' ends of the nucleic acid sequence, by the introduction of a nucleic acid construct into the genome of the parent cell at a locus 5 not within the nucleic acid sequence to produce the mutant cell, wherein the introduction of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence and the modification of the copy number is not a result of selective pressure; and

(ii) the mutant cell produces more of the polypeptide than the parent cell o when both cells are cultivated under the same conditions conducive for production of the polypeptide: and

(b) recovering the polypeptide from the cultivation medium.

8. The method of any of claims 1-7, wherein the nucleic acid construct has less than 5 40%) homology with the nucleic acid sequence.

9. The method of any of claims 1-8, wherein the locus is on a different chromosome than the nucleic acid sequence or on the same chromosome as the nucleic acid sequence.

10. The method of any of claims 1-9, wherein the nucleic acid construct is contained in a vector.

11. The method of any of claims 1-9. wherein the nucleic acid construct is a circular molecule.

12. The method of any of claims 1-9. wherein the nucleic acid construct is a linear fragment.

13. The method of any of claims 1-12, wherein the nucleic acid construct comprises a selectable marker.

14. The method of claim 13, wherein the selectable marker is dal. amp. kan. cam. let. dfhr). hygB. ADE2, HIS3. LEU2, LYS2. MET3, TRPl. URA3. amdS. argB. bar, hygB. niaD, pyrG. sC. or trpC.

15. The method of any of claims 1-14, wherein the parent cell is a prokaryotic cell or a eukaryotic cell.

16. The method of claim 15. wherein the prokaryotic cell is a bacterial cell.

17. The method of claim 16, wherein the bacterial cell is selected from the group consisting of a Bacillus. Streptomyces. and Pseudomonas cell.

18. The method of claim 15. wherein the eukaryotic cell is a mammalian cell.

19. The method of claim 15. wherein the eukaryotic cell is a fungal cell.

20. The method of claim 19. wherein the fungal cell is a filamentous fungal cell.

21. The method of claim 20, wherein the filamentous fungal cell is an Acremonium, Aspergillus. Fusarium. Humicola, Mucor, Myceliophthora, Neurospora. Penicillium. Scytalidium. Thielavia. Tolypocladium. or Trichoderma cell.

22. The method of claim 19. wherein the fungal cell is a yeast cell.

23. The method of claim 22, wherein the yeast cell is selected from the group consisting of Candida, Kluyveromyces, Hansenula, Pichia, Saccharomyces. Schizosaccharomyces, and Yarrowia.

24. The method of any of claims 1-23, wherein the polypeptide is a recombinant polypeptide.

25. The method of any of claims 1-24, wherein the polypeptide is a heterologous polypeptide.

26. The method of any of claims 1-25. wherein the polypeptide is an antibody or portion thereof, antigen, clotting factor, enzyme, hormone or variant thereof, receptor or portion thereof, regulatory protein, structural protein, reporter, or transport protein.

27. The method of claim 26, wherein the enzyme is an oxidoreductase. transferase, hydrolase, lyase, isomerase, or ligase.

28. The method of claim 27, wherein the enzyme is an aminopeptidase, amylase, carbohydrase, carboxypeptidase. catalase, cellulase. chitinase, cutinase, deoxyribonuclease, 0 esterase, alpha-galactosidase, beta-galactosidase, glucoamylase. alpha-glucosidase, beta- glucosidase, invertase, laccase, lipase, mannosidase, mutanase, oxidase, pectinolytic enzyme, peroxidase, phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease. or xylanase.

29. The method of any of claims 1-28, wherein the nucleic acid construct is pDSY82, 5 pDSYl 12, pMT1612, pMT1936. pLRF2. pDSY153, or pHB218.

30. A method for producing a polypeptide, comprising:

(a) forming a mutant cell by introducing a nucleic acid construct into the genome of the parent cell, which parent cell comprises at least two tandem copies of a nucleic acid o sequence encoding the polypeptide. at a locus which is not within the copies of the nucleic acid sequence or is within one of the copies of the nucleic acid sequence, wherein the integration of the nucleic acid construct into the locus modifies the copy number of the nucleic acid sequence, the modification of the copy number is not under selective pressure, and the mutant cell produces more or less of the polypeptide than the parent cell when both 5 cells are cultivated under the same conditions conducive for production of the polypeptide;

(b) isolating the mutant cell which produces more or less of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide: (c) identifying the locus wherein the nucleic acid construct has been integrated;

(d) producing a cell in which a corresponding locus has been disrupted;

(e) culturing the cell under conditions conducive for production of the polypeptide; and

5 (f) recovering the polypeptide from the cultivation medium.

31. A method for producing a polypeptide, comprising:

(a) forming a mutant cell by introducing a nucleic acid construct into the genome of the parent cell, which parent cell comprises a nucleic acid sequence encoding the 0 polypeptide. which nucleic acid sequence comprises repeat sequences at the 5' and 3' ends of the nucleic acid sequence, at a locus which is not within the nucleic acid sequence, wherein the integration of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence, the modification of the copy number is not under selective pressure, and the mutant cell produces more of the polypeptide than the parent cell when both cells are 5 cultivated under the same conditions conducive for production of the polypeptide;

(b) isolating the mutant cell which produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide;

(c) identifying the locus wherein the nucleic acid construct has been integrated; o (d) producing a cell in which a corresponding locus has been disrupted;

(f) recovering the polypeptide from the cultivation medium.

5 32. A method for obtaining a mutant cell, comprising::

(a) introducing a nucleic acid construct into a parent cell, wherein the parent cell comprises at least two tandem copies of a nucleic acid sequence encoding a polypeptide, under conditions in which the nucleic acid construct integrates into the genome of the parent cell at a locus not within the copies of the nucleic acid sequence to produce a mutant cell, o wherein the integration of the nucleic acid construct into the locus modifies the copy number of the nucleic acid sequence, the modification of the copy number is not under selective pressure, and the mutant cell produces more or less of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide; and 5 (b) identifying the mutant cell which produces more or less of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide.

A mutant cell produced by the method of claim 32.

34. A method for obtaining a mutant cell, comprising::

(a) introducing a nucleic acid construct into a parent cell, wherein the parent cell comprises at least two tandem copies of a nucleic acid sequence encoding a polypeptide, under conditions in which the nucleic acid construct integrates into the genome of the parent cell at a locus within one of the copies of the nucleic acid sequence to produce a mutant cell, wherein the integration of the nucleic acid construct into the locus modifies the copy number of the nucleic acid sequence, the modification of the copy number is not under selective pressure, and the mutant cell produces more or less of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide; and

(b) identifying the mutant cell which produces more or less of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for s production of the polypeptide.

35. A mutant cell produced by the method of claim 34.

36. A method for obtaining a mutant cell, comprising:: 0 (a) introducing a nucleic acid construct into a parent cell, wherein the parent cell comprises a nucleic acid sequence encoding a polypeptide, which nucleic acid sequence comprises repeat sequences at the 5' and 3' ends of the nucleic acid sequence, under conditions in which the nucleic acid construct integrates into the genome of the parent cell at a locus not within the nucleic acid sequence to produce a mutant cell, wherein the integration 5 of the nucleic acid construct into the locus increases the copy number of the nucleic acid sequence, the increase of the copy number is not under selective pressure, and the mutant cell produces more of the polypeptide than the parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide; and

(b) identifying the mutant cell which produces more of the polypeptide than the o parent cell when both cells are cultivated under the same conditions conducive for production of the polypeptide.

37. A mutant cell obtained by the method of claim 36.