Patent Publication Number: US-9850501-B2

Title: Simultaneous site-specific integrations of multiple gene-copies

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application is a continuation of U.S. patent application Ser. No. 14/118,995 filed on Nov. 20, 2013, now U.S. Pat. No. 9,574,199, which is a 35 U.S.C. §371 national application of PCT/EP2012/059597 filed on May 23, 2012, which claims priority or the benefit under 35 U.S.C. §119 of U.S. Provisional. Application No. 61/489,610 filed on May 24, 2011, and European Patent Application No. 11167051.9 filed on May 23, 2011, the contents of which are fully incorporated herein by reference. 
    
    
     REFERENCE TO SEQUENCE LISTING 
     This application contains a Sequence Listing in computer readable form. The computer readable form is incorporated herein by reference. 
     FIELD OF THE INVENTION 
     The present invention relates to a method for the simultaneous site-specific integrations of multiple copies of a polynucleotide of interest into the genome of a fungal host cell using a transiently expressed recombinase together with suitable resident selection markers. 
     BACKGROUND OF THE INVENTION 
     A large number of naturally-occurring organisms have been found to produce useful polypeptide products, e.g., enzymes, the large scale production of which is desirable for research and commercial purposes. Once such a polypeptide product has been identified, efforts are often made to develop manufacturing methods having an improved productivity. One widely used method, which is based on recombinant DNA techniques, is to clone a gene encoding the product and insert the gene into a suitable expression system in order to express the product in a suitable host cell, either integrated in the chromosome or as an extrachromosomal entity, under conditions conducive for the expression of the product. 
     Irrespective of which production method is used, it is normally desirable to increase the production level of a given polypeptide or protein. Thus, efforts are being made to increase the production, e.g., by inserting the gene encoding the product under the control of a strong expression signal, increasing the stability of the transcribed mRNA or by increasing the number of copies of the gene in the production organism in question. This latter approach may be accomplished by inserting the gene into a multicopy plasmid which generally, however, tends to be unstable in the host cell in question, or by integrating multiple copies of the gene into the chromosome of the production organism, an approach which generally is considered more attractive because the stability of the construct tends to be higher. 
     Construction of host cells has been described, wherein a highly expressed chromosomal gene is replaced with a recognition sequence of a site-specific recombinase to allow subsequent insertion of a single product-encoding polynucleotide into that site by the use of a recombinase recognizing said sequence (EP 1 405 908 A1; ProBioGen AG). 
     It has been disclosed to insert DNA at a known location in the genome (O&#39;Gorman et al., 1991 Science, 251:1351-55; Baubonis and Sauer, 1993 Nucl., Acids Res., 21:2025-29; Albert et al., 1995 Plant J., 7:649-59). These methods make use of site-specific recombination systems that are freely reversible. These reversible systems include the following: the Cre-lox system from bacteriophage P1 (Baubonis and Sauer, 1993, supra; Albert et al., 1995 Plant J., 7549-59), the FLP-FRT system of  Saccharomyces cerevisiae  (O&#39;Gorrnan et al., 1991, supra), the R-RS system of  Zygosaccharonzyces rouxii  (Onouchi et al., 1995 Mol. Gen. Genet. 247: 653-660), a modified Gin-gix system from bacteriophage Mu (Maeser and Kahmann, 1991 Mol. Gen. Genet., 230: 170-76), the beta-recombinase-six system from a  Bacillus subtilis  plasmid (Diaz et al., 1999 J. Biol. Chem. 274: 6634-6640), and the delta-gamma-res system from the bacterial transposon Tn1000 (Schwikardi and Dorge, 2000 E B S let. 471: 147-150). Cre, FLP, R, Gin, beta-recombinase and gamma-delta are the recombinases, and lox, FRT, RS, gix, six and res the respective recombination sites (reviewed by Sadowslu, 1993 FASEB J., 7:750-67; Ow and Medberry, 1995 Crit. Rev. Plant Sci. 14: 239-261). Multiplex Cre/lox recombination permits selective site-specific DNA targeting to both a natural and an engineered site in the yeast genome (Sauer, B. Nucleic Acids Research. 1996, Vol. 24(23): 4608-4613). It has been shown that infection of host cells having a natural attachment site, attB as well as an ectopically introduced attB site, with a derivative of the  Streptomyces  phage ΦC31, resulted in the integration of the phage into both attB sites (Smith et al. 2004. Switching the polarity of a bacteriophage integration system. Mol Microbiol 51(6):1719-1728). Multiple copies of a gene can be introduced into a cell comprising multiple attachment sites recognized by the M×9 integrase using the M×9 phage transformation system, (WO 2004/018635 A2). The temperal Lactococcal bacteriophage TP901-1 integrase and recognition sequences are well-characterized (Breüner et al. (1990) Novel Organization of Genes Involved in Prophage Excision Identified in the Temperate Lactococcal Bacteriophage TP901-1. J Bacteriol 181(23): 7291-7297; Breüner et al. 2001. Resolvase-like recombination performed by the TP901-1 integrase. Microbiology 147: 2051-2063). 
     The site-specific recombination systems above have in common the property that a single polypeptide recombinase catalyzes the recombination between two sites of identical or nearly identical sequences. Each recombination site consists of a short asymmetric spacer sequence where strand exchange tales place, flanked by an inverted repeat where recombinases bind. The asymmetry of the spacer sequence gives an orientation to the recombination site, and dictates the outcome of a recombination reaction. Recombination between directly or indirectly oriented sites in cis excises or inverts the intervening DNA, respectively. Recombination between sites in trans causes a reciprocal translocation of two linear DNA molecules, or co-integration if at least one of the two molecules is circular. Since the product-sites generated by recombination are themselves substrates for subsequent recombination, the reaction is freely reversible. In practice, however, excision is essentially irreversible because the probability of an intramolecular interaction, where the two recombination-sites are closely linked, is much higher than an intermolecular interaction between unlinked sites. The corollary is that the DNA molecule inserted into a genomic recombination site will readily excise out. 
     Methods for the replacement, translocation and stacking of DNA in eukaryotic genomes have been disclosed, where multiple genes may be integrated stepwise (WO 02/08409). The simultaneous genomic integration of multiple copies of a promoterless open reading frame or operon by a site-specific and transiently expressed integrase in a microorganism host cell has previously been shown in a  Bacillus  host (WO 2006/042548). 
     SUMMARY OF THE INVENTION 
     The present invention is directed to a process for the integration of two or more copies of a polynucleotide of interest into the chromosome of a fungal host cell, by the steps of: 
     (a) providing a fungal host cell comprising in its chromosome at least two integration sites, each integration site comprising a pair of recognition sequences of a site-specific recombinase, each pair flanking a resident selection marker; 
     (b) introducing into said cell a nucleic acid construct comprising a pair of recognition sequences of the site-specific recombinase, said pair flanking the polynucleotide of interest; 
     (c) transiently expressing the site-specific recombinase in the cell, whereby the chromosomal recognition sequence pairs are recombined with the corresponding recognition sequence pair of the nucleic acid construct by the recombinase so that at the least two integration sites, the resident selection marker in the chromosome is excised while a copy of the polynucleotide of interest is integrated in its place to produce a fungal host cell comprising two or more copies of the polynucleotide of interest integrated into the chromosome of the fungal host cell. 
     As exemplified in the examples section below, the primary aspect of the present invention provides a method for the simultaneous integration of two or more copies of a polynucleotide of interest into the chromosome of a fungal host cell, said method comprising the steps of: 
     (a) providing a fungal host cell comprising in its chromosome at least two pairs of recognition sequences of a site-specific recombinase, each pair flanking a resident negative selection marker; 
     (b) introducing into said cell a nucleic acid construct comprising a pair of recognition sequences of the site-specific recombinase, said pair flanking the polynucleotide of interest; 
     (c) transiently expressing the site-specific recombinase in the cell, whereby the chromosomal recognition sequence pairs are recombined with the corresponding recognition sequence pair of the nucleic acid construct by the recombinase, so that every resident negative selection marker in the chromosome is excised while a copy of the polynucleotide of interest is integrated in its place; and then
 
(d) cultivating the cell in a selective medium and selecting a cell, wherein every negative selection marker has been replaced with two or more copies of the polynucleotide of interest by double homolous recombination.
 
    
    
     
       BRIEF DESCRIPTION OF DRAWINGS 
         FIG. 1  shows the basic scheme of the method of the invention, herein exemplified using the FRT/FLP recombinase system and pyrG as bi-directional selective marker together with the FLP-encoding gene flanked by two copies of the transcriptional terminator, labelled “Term” that enable the excision of the FLP and pyrG genes by double homologous recombination, which allows transient expression of FLP. 
         FIG. 2  shows a plasmid map of pHUda981 (Pgpd, HSV1 tk, TtrpC are described in WO07045248). 
         FIG. 3  shows a plasmid map of pHUda1019. 
         FIG. 4  shows a plasmid map of pHUda1000. 
         FIG. 5A  shows the schematic NA1 locus after the pHUda1000 was introduced correctly in NN059183. 
         FIG. 5B  shows the schematic acid stable amylase locus after the pHUda1000 was introduced correctly in NN059183. 
         FIG. 6  shows a plasmid map of pHUda801. 
         FIG. 7  shows a plasmid map of pHUda1043. 
         FIG. 8  shows a plasmid map of pHUda1078. 
         FIG. 9  shows a plasmid map of pHUda1067. 
         FIG. 10A  shows the schematic NA1 locus in NN059208. 
         FIG. 10B  shows the schematic NA2 locus in NN059208. 
         FIG. 10C  shows the schematic acid stable amylase locus in NN059208. 
         FIG. 11  shows a plasmid map of pRika147. 
         FIG. 12A  shows the schematic NA1 locus after the correct integration of pRika147 in NN059208. 
         FIG. 12B  shows the schematic NA2 locus after the correct integration of pRika147 in NN059208. 
         FIG. 12C  shows the schematic acid stable amylase locus after the correct integration of pRika147 in NN059208. 
         FIG. 13  shows a plasmid map of pHUda1174. 
         FIG. 14  shows the schematic of the PAY loci (upper) in M1146. 
         FIG. 15  shows the plasmid map of pHUda1306. 
         FIG. 16A  shows the schematic NA1 locus when pRika147 was introduced in M1146. 
         FIG. 16B  shows the schematic NA2 locus when pRika147 was introduced in M1146. 
         FIG. 16C  shows the schematic SP288 locus when pRika147 was introduced in M1146. 
         FIG. 16D  shows the schematic PAY locus when pRika147 was introduced in M1146. 
         FIG. 17  shows the plasmid map of pHUda1356. 
         FIG. 18  shows a map of the vector pJfyS147 used to integrate the FRT sites into the  T. reesei  genome at the cbh1 locus. 
         FIG. 19  shows a map of the vector pJfyS150 used to integrate the  A. fumigatus  BG at the cbh1 locus in  T. reesei  strain JfyS147-20B using the FLP/FRT system. 
     
    
    
     DEFINITIONS 
     Cytosine deaminase: Cytosine deaminase (EC 3.5.4.1) catalyzes the deamination of cytosine and 5-fluorocytosine (5FC) to form uracil and toxic 5-fluorouracil (5FU), respectively. When genetically modified cells comprising cytosine deaminase are combined with 5FC it is converted to toxic 5FU, so the cytosine deaminase-encoding gene is potentially a potent negative selection marker. 
     It has also been shown that an inhibitor in the pyrimidine de novo synthesis pathway can be utilized to create a condition in which cells are dependent on the conversion of pyrimidine supplements to uracil by cytosine deaminase. Thus, only cells expressing the cytosine deaminase gene can be rescued in a positive selection medium comprising an inhibitor of the pyrimidine de novo synthesis as well as inosine and cytosine (See FIG. 1 of Wei and Huber, 1996, J Biol Chem 271(7): 3812). The inhibitor is preferably N-(phosphonacetyl)-L-aspartate (PALA), which inhibits aspartate carbamyl transferase. 
     If necessary, cytosine deaminase activity may be quantitated by a genetic assay (Frederico L. A. et al, 1990, Biochemistry 29: 2532-2537). 
     Allelic variant: The term “allelic variant” means any of two or more alternative forms of a gene occupying the same chromosomal locus. Allelic variation arises naturally through mutation, and may result in polymorphism within populations. Gene mutations can be silent (no change in the encoded polypeptide) or may encode polypeptides having altered amino acid sequences. An allelic variant of a polypeptide is a polypeptide encoded by an allelic variant of a gene.
 
Catalytic domain: The term “catalytic domain” means the region of an enzyme containing the catalytic machinery of the enzyme.
 
cDNA: The term “cDNA” means a DNA molecule that can be prepared by reverse transcription from a mature, spliced, mRNA molecule obtained from a eukaryotic or prokaryotic cell. cDNA lacks intron sequences that may be present in the corresponding genomic DNA. The initial, primary RNA transcript is a precursor to mRNA that is processed through a series of steps, including splicing, before appearing as mature spliced mRNA.
 
Coding sequence: The term “coding sequence” means a polynucleotide, which directly specifies the amino acid sequence of a polypeptide. The boundaries of the coding sequence are generally determined by an open reading frame, which begins with a start codon such as ATG, GTG, or TTG and ends with a stop codon such as TAA, TAG, or TGA. The coding sequence may be a genomic DNA, cDNA, synthetic DNA, or a combination thereof.
 
Control sequences: The term “control sequences” means nucleic acid sequences necessary for expression of a polynucleotide encoding a mature polypeptide of the present invention. Each control sequence may be native (i.e., from the same gene) or foreign (i.e., from a different gene) to the polynucleotide encoding the polypeptide or native or foreign to each other. Such control sequences include, but are not limited to, a leader, polyadenylation sequence, propeptide sequence, promoter, signal peptide 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 polynucleotide encoding a polypeptide.
 
Expression: The term “expression” includes any step involved in the production of a polypeptide including, but not limited to, transcription, post-transcriptional modification, translation, post-translational modification, and secretion.
 
Expression vector: The term “expression vector” means a linear or circular DNA molecule that comprises a polynucleotide encoding a polypeptide and is operably linked to control sequences that provide for its expression.
 
Fragment: The term “fragment” means a polypeptide or a catalytic domain having one or more (e.g., several) amino acids deleted from the amino and/or carboxyl terminus of a mature polypeptide or domain; wherein the fragment has cytosine deaminase activity.
 
Host cell: The term “host cell” means any cell type that is susceptible to transformation, transfection, transduction, or the like with a nucleic acid construct or expression vector comprising a polynucleotide of the present invention. The term “host cell” encompasses any progeny of a parent cell that is not identical to the parent cell due to mutations that occur during replication.
 
Isolated or purified: The term “isolated” or “purified” means a polypeptide or polynucleotide that is removed from at least one component with which it is naturally associated. For example, a polypeptide may be at least 1% pure, e.g., at least 5% pure, at least 10% pure, at least 20% pure, at least 40% pure, at least 60% pure, at least 80% pure, at least 90% pure, or at least 95% pure, as determined by SDS-PAGE, and a polynucleotide may be at least 1% pure, e.g., at least 5% pure, at least 10% pure, at least 20% pure, at least 40% pure, at least 60% pure, at least 80% pure, at least 90% pure, or at least 95% pure, as determined by agarose electrophoresis.
 
Negative selection marker: The term “negative selection marker” means a nucleic acid sequence capable of conferring a selection characteristics so that cells which have the negative selection marker are killed or otherwise identified, e.g., by fluorescence. The negative selection marker is preferably substantially incapable of homologous recombination with the target DNA sequence.
 
Nucleic acid construct: The term “nucleic acid construct” means a nucleic acid molecule, either single- or double-stranded, which is isolated from a naturally occurring gene or is modified to contain segments of nucleic acids in a manner that would not otherwise exist in nature or which is synthetic, which comprises one or more control sequences.
 
Operably linked: The term “operably linked” means a configuration in which a control sequence is placed at an appropriate position relative to the coding sequence of a polynucleotide such that the control sequence directs the expression of the coding sequence.
 
Sequence identity: The relatedness between two amino acid sequences or between two nucleotide sequences is described by the parameter “sequence identity”. For purposes of the present invention, the sequence identity between two amino acid sequences is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970 , J. Mol. Biol.  48: 443-453) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000 , Trends Genet.  16: 276-277), preferably version 5.0.0 or later. The parameters used are gap open penalty of 10, gap extension penalty of 0.5, and the EBLOSUM62 (EMBOSS version of BLOSUM62) substitution matrix. The output of Needle labeled “longest identity” (obtained using the -nobrief option) is used as the percent identity and is calculated as follows:
 
(Identical Residues×100)/(Length of Alignment−Total Number of Gaps in Alignment)
 
     For purposes of the present invention, the sequence identity between two deoxyribonucleotide sequences is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, supra) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, supra), preferably version 5.0.0 or later. The parameters used are gap open penalty of 10, gap extension penalty of 0.5, and the EDNAFULL (EMBOSS version of NCBI NUC4.4) substitution matrix. The output of Needle labeled “longest identity” (obtained using the -nobrief option) is used as the percent identity and is calculated as follows:
 
(Identical Deoxyribonucleotides×100)/(Length of Alignment−Total Number of Gaps in Alignment)
 
Simultaneous: The term “simultaneous” as used herein, that is, in reference to the integration of at least two polynucleotides of interest into a host cell, refers to a process by which the integration of at least two copies of the polynucleotide of interest in the the host cell occurs in the same process step that results in the addition of one copy of the polynucleotide of interest, that is, without either the addition of any other materials and/or any additional process steps. Accordingly, the polynucleotide of interest is introduced into the host cell at at least two different integration sites in the same process at the same time or at different times but contemporaneously during the same process.
 
Subsequence: The term “subsequence” means a polynucleotide having one or more (e.g., several) nucleotides deleted from the 5′ and/or 3′ end of a mature polypeptide coding sequence; wherein the subsequence encodes a fragment having cytosine deaminase activity.
 
Variant: The term “variant” means a polypeptide having cytosine deaminase activity comprising an alteration, i.e., a substitution, insertion, and/or deletion of one or more (e.g., several) amino acid residues at one or more positions. A substitution means a replacement of the amino acid occupying a position with a different amino acid; a deletion means removal of the amino acid occupying a position; and an insertion means adding an amino acid adjacent to the amino acid occupying a position.
 
     DETAILED DESCRIPTION OF THE INVENTION 
     A first aspect of the present invention is directed to a process for the integration of two or more copies of a polynucleotide of interest into the chromosome of a fungal host cell, by the steps of: 
     (a) providing a fungal host cell comprising in its chromosome at least two integration sites, each integration site comprising a pair of recognition sequences of a site-specific recombinase, each pair flanking a resident selection marker; 
     (b) introducing into said cell a nucleic acid construct comprising a pair of recognition sequences of the site-specific recombinase, said pair flanking the polynucleotide of interest; 
     (c) transiently expressing the site-specific recombinase in the cell, whereby the chromosomal recognition sequence pairs are recombined with the corresponding recognition sequence pair of the nucleic acid construct by the recombinase so that at the least two integration sites, the resident selection marker in the chromosome is excised while a copy of the polynucleotide of interest is integrated in its place to produce a fungal host cell comprising two or more copies of the polynucleotide of interest integrated into the chromosome of the fungal host cell. 
     In a particular embodiment, the first aspect of the invention relates to a method for the simultaneous integration of two or more copies of a polynucleotide of interest into the chromosome of a fungal host cell, said method comprising the steps of: 
     (a) providing a fungal host cell comprising in its chromosome at least two pairs of recognition sequences of a site-specific recombinase, each pair flanking a resident negative selection marker; 
     (b) introducing into said cell a nucleic acid construct comprising a pair of recognition sequences of the site-specific recombinase, said pair flanking the polynucleotide of interest; 
     (c) transiently expressing the site-specific recombinase in the cell, whereby the chromosomal recognition sequence pairs are recombined with the corresponding recognition sequence pair of the nucleic acid construct by the recombinase, so that every resident negative selection marker in the chromosome is excised while a copy of the polynucleotide of interest is integrated in its place; and then
 
(d) cultivating the cell in a selective medium and selecting a cell, wherein every negative selection marker has been replaced with two or more copies of the polynucleotide of interest by double homolous recombination.
 
     In a preferred embodiment, the polynucleotide of interest comprises an operon or an open reading frame encoding at least one polypeptide of interest. The polypeptide of interest may encode any protein of interest, such as, for example, cytokines (in particular interleukins, interferons, colony stimulating factors (CSF) and growth factors), anticoagulants, enzymes, and enzyme inhibitors. 
     Preferably, the polypeptide of interest comprises an enzyme, preferably a hydrolase, isomerase, ligase, lyase, oxidoreductase, or transferase, e.g., an aminopeptidase, amylase, carbohydrase, carboxypeptidase, catalase, cellobiohydrolase, cellulase, chitinase, cutinase, cyclodextrin glycosyltransferase, deoxyribonuclease, endoglucanase, esterase, alpha-galactosidase, beta-galactosidase, glucoamylase, alpha-glucosidase, beta-glucosidase, invertase, laccase, lipase, mannosidase, mutanase, oxidase, pectinolytic enzyme, peroxidase, phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease, transglutaminase, xylanase, or beta-xylosidase. 
     Site-specific recombination systems that are freely reversible have been described in detail in literature. These reversible systems include the following: the Cre-lox system from bacteriophage P1 (Baubonis and Sauer, 1993, supra; Albert et al., 1995 Plant J., 7549-59), the FLP-FRT system of  Saccharomyces cerevisiae  (O&#39;Gorrnan et al., 1991, supra), the R-RS system of  Zygosaccharonzyces rouxii  (Onouchi et al., 1995 Mol. Gen. Genet. 247: 653-660), a modified Gin-gix system from bacteriophage Mu (Maeser and Kahmann, 1991 Mol. Gen. Genet., 230: 170-76), the beta-recombinase-six system from a  Bacillus subtilis  plasmid (Diaz et al., 1999 J. Biol. Chem. 274: 6634-6640), and the delta-gamma-res system from the bacterial transposon Tn1000 (Schwikardi and Dorge, 2000 E B S let. 471: 147-150). Cre, FLP, R, Gin, beta-recombinase and gamma-delta are the recombinases, and lox, FRT, RS, gix, six and res the respective recombination sites (reviewed by Sadowslu, 1993 FASEB J., 7:750-67; Ow and Medberry, 1995 Crit. Rev. Plant Sci. 14: 239-261). Multiplex Cre/lox recombination permits selective site-specific DNA targeting to both a natural and an engineered site in the yeast genome (Sauer, B. Nucleic Acids Research. 1996, Vol. 24(23): 4608-4613). It has been shown that infection of host cells having a natural attachment site, attB as well as an ectopically introduced attB site, with a derivative of the  Streptomyces  phage ΦC31, resulted in the integration of the phage into both attB sites (Smith et al. 2004. Switching the polarity of a bacteriophage integration system. Mol Microbiol 51(6):1719-1728). Multiple copies of a gene can be introduced into a cell comprising multiple attachment sites recognized by the M×9 integrase using the M×9 phage transformation system, (WO 2004/018635 A2). The temperal Lactococcal bacteriophage TP901-1 integrase and recognition sequences are well-characterized (Breüner et al. (1990) Novel Organization of Genes Involved in Prophage Excision Identified in the Temperate Lactococcal Bacteriophage TP901-1. J Bacteriol 181(23): 7291-7297; Breüner et al. 2001. Resolvase-like recombination performed by the TP901-1 integrase. Microbiology 147: 2051-2063). 
     The site-specific recombination systems above have in common the property that a single polypeptide recombinase catalyzes the recombination between two sites of identical or nearly identical sequences. Each recombination site consists of a short asymmetric spacer sequence where strand exchange tales place, flanked by an inverted repeat where recombinases bind. The asymmetry of the spacer sequence gives an orientation to the recombination site, and dictates the outcome of a recombination reaction. Recombination between directly or indirectly oriented sites in cis excises or inverts the intervening DNA, respectively. Recombination between sites in trans causes a reciprocal translocation of two linear DNA molecules, or co-integration if at least one of the two molecules is circular. Since the product-sites generated by recombination are themselves substrates for subsequent recombination, the reaction is freely reversible. In practice, however, excision is essentially irreversible because the probability of an intramolecular interaction, where the two recombination-sites are closely linked, is much higher than an intermolecular interaction between unlinked sites. The corollary is that the DNA molecule inserted into a genomic recombination site will readily excise out, unless the recombinase is transiently expressed, in which case, the inserted DNA will remain once the recombinase is no longer expressed. 
     Accordingly, it is preferred in the method of the first aspect, that the site-specific recombinase and its pair of recognition sequences are from the the Cre-lox system of bacteriophage P1, the FLP-FRT system of  Saccharomyces cerevisiae , the R-RS system of  Zygosaccharonzyces rouxii , a modified Gin-gix system from bacteriophage Mu, the beta-recombinase-six system from a  Bacillus subtilis  plasmid, the delta-gamma-res system from the bacterial transposon Tn1000, the  Streptomyces  phage ΦC31, the M×9 phage transformation system or the Xis-att system of the temperate Lactococcal bacteriophage TP901-1. 
     In an embodiment, the site-specific recombinase and its pair of recognition sequences are from the FLP-FRT system. In a particular embodiment, the FLP recombinase is an FLP recombinase variant as described in Buchholz, Frank,  Improved properties of FLP recombinase evolved by cycling mutagenesis , Nature Biotechnology Volume: 16 Issue: 7 (1998 Jul. 1) p. 657-662. In another particular embodiment, the FLP recombinase is a thermostable recombinase variant designated “FLPe” having amino acid alterations P2S, L33S, Y108N, S294P. The nucleic acid sequence and corresponding amino acid sequence for FLPe is shown as SEQ ID NO:106 and SEQ ID NO:107, respectively. 
     In a preferred embodiment of the first aspect, the negative selection marker encodes a polypeptide confers resistance to an antibiotic to the host cell and the selective medium comprises an inhibitory concentration of the antibiotic. 
     Alternatively, in another preferred embodiment of the first aspect, the negative selection marker encodes a cytosine deaminase and the selective medium comprises sufficient amounts of 5-fluorocytosin, to be converted to an inhibitory concentration of toxic 5-fluorouracil by said cytosine deaminase. 
     In an embodiment, the negative selection marker encodes a cytosine deaminase polypeptide having a sequence identity to SEQ ID NO:60 of at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%. In one aspect, the polypeptides differ by no more than ten amino acids, e.g., nine amino acids, eight amino acids, seven amino acids, six amino acids, five amino acids, four amino acids, three amino acids, two amino acids, or one amino acid from SEQ ID NO:60. 
     The encoded cytosine deaminase polypeptide of the present invention preferably comprises or consists of the amino acid sequence of SEQ ID NO:60 or an allelic variant thereof; or is a fragment thereof having cytosine deaminase activity. In another aspect, the polypeptide comprises or consists of the polypeptide of SEQ ID NO:60. 
     In another embodiment, the negative selection marker encodes a cytosine deaminase polypeptide and hybridizes under very low stringency conditions, low stringency conditions, medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with (i) the polypeptide coding sequence of SEQ ID NO:59, (ii) the cDNA sequence thereof, or (iii) the full-length complement of (i) or (ii) (Sambrook et al., 1989 , Molecular Cloning, A Laboratory Manual,  2d edition, Cold Spring Harbor, N.Y.). 
     The polynucleotide of SEQ ID NO:59 or a subsequence thereof, as well as the polypeptide of SEQ ID NO:60 or a fragment thereof, may be used to design nucleic acid probes to identify and clone DNA encoding polypeptides having cytosine deaminase activity from strains of different genera or species according to methods well known in the art. In particular, such probes can be used for hybridization with the genomic DNA or cDNA of a cell of interest, following standard Southern blotting procedures, in order to identify and isolate the corresponding gene therein. Such probes can be considerably shorter than the entire sequence, but should be at least 15, e.g., at least 25, at least 35, or at least 70 nucleotides in length. Preferably, the nucleic acid probe is at least 100 nucleotides in length, e.g., at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, at least 500 nucleotides, at least 600 nucleotides, at least 700 nucleotides, at least 800 nucleotides, or at least 900 nucleotides in length. Both DNA and RNA probes can be used. The probes are typically labeled for detecting the corresponding gene (for example, with  32 P,  3 H,  35 S, biotin, or avidin). Such probes are encompassed by the present invention. 
     A genomic DNA or cDNA library prepared from such other strains may be screened for DNA that hybridizes with the probes described above and encodes a polypeptide having cytosine deaminase activity. Genomic or other DNA from such other strains may be separated by agarose or polyacrylamide gel electrophoresis, or other separation techniques. DNA from the libraries or the separated DNA may be transferred to and immobilized on nitrocellulose or other suitable carrier material. In order to identify a clone or DNA that is homologous with SEQ ID NO:59 or a subsequence thereof, the carrier material is preferably used in a Southern blot. 
     For purposes of the present invention, hybridization indicates that the polynucleotide hybridizes to a labeled nucleic acid probe corresponding to (i) SEQ ID NO:59; (ii) the polypeptide coding sequence of SEQ ID NO:59; (iii) the cDNA sequence thereof; (iv) the full-length complement thereof; or (v) a subsequence thereof; under very low to very high stringency conditions. Molecules to which the nucleic acid probe hybridizes under these conditions can be detected using, for example, X-ray film. 
     For probes of at least 100 nucleotides in length, very low stringency conditions are defined as prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 25% formamide, following standard Southern blotting procedures for 12 to 24 hours optimally. The carrier material is finally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at 45° C. 
     For probes of at least 100 nucleotides in length, low stringency conditions are defined as prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 25% formamide, following standard Southern blotting procedures for 12 to 24 hours optimally. The carrier material is finally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at 50° C. 
     For probes of at least 100 nucleotides in length, medium stringency conditions are defined as prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 35% formamide, following standard Southern blotting procedures for 12 to 24 hours optimally. The carrier material is finally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at 55° C. 
     For probes of at least 100 nucleotides in length, medium-high stringency conditions are defined as prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and either 35% formamide, following standard Southern blotting procedures for 12 to 24 hours optimally. The carrier material is finally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at 60° C. 
     For probes of at least 100 nucleotides in length, high stringency conditions are defined as prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 50% formamide, following standard Southern blotting procedures for 12 to 24 hours optimally. The carrier material is finally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at 65° C. 
     For probes of at least 100 nucleotides in length, very high stringency conditions are defined as prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 50% formamide, following standard Southern blotting procedures for 12 to 24 hours optimally. The carrier material is finally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at 70° C. 
     In another embodiment, the negative selection marker of the first aspect has a sequence identity to the polypeptide coding sequence of SEQ ID NO:59 or the cDNA sequence thereof of at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%. 
     In another embodiment, the negative selection marker encodes a variant of the cytosine deaminase polypeptide of SEQ ID NO:60 comprising a substitution, deletion, and/or insertion at one or more (e.g., several) positions. Preferably, amino acid changes are of a minor nature, that is conservative amino acid substitutions or insertions that do not significantly affect the folding and/or activity of the protein; small deletions, typically of one to about 30 amino acids; small amino- or carboxyl-terminal extensions, such as an amino-terminal methionine residue; a small linker peptide of up to about 20-25 residues; or a small extension that facilitates purification by changing net charge or another function, such as a poly-histidine tract, an antigenic epitope or a binding domain. 
     Examples of conservative substitutions are within the groups of basic amino acids (arginine, lysine and histidine), acidic amino acids (glutamic acid and aspartic acid), polar amino acids (glutamine and asparagine), hydrophobic amino acids (leucine, isoleucine and valine), aromatic amino acids (phenylalanine, tryptophan and tyrosine), and small amino acids (glycine, alanine, serine, threonine and methionine). Amino acid substitutions that do not generally alter specific activity are known in the art and are described, for example, by H. Neurath and R. L. Hill, 1979 , In, The Proteins , Academic Press, New York. Common substitutions are Ala/Ser, Val/Ile, Asp/Glu, Thr/Ser, Ala/Gly, Ala/Thr, Ser/Asn, Ala/Val, Ser/Gly, Tyr/Phe, Ala/Pro, Lys/Arg, Asp/Asn, Leu/Ile, Leu/Val, Ala/Glu, and Asp/Gly. 
     Alternatively, the amino acid changes are of such a nature that the physico-chemical properties of the polypeptides are altered. For example, amino acid changes may improve the thermal stability of the polypeptide, alter the substrate specificity, change the pH optimum, and the like. 
     Essential amino acids in a polypeptide can be identified according to procedures known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham and Wells, 1989 , Science  244: 1081-1085). In the latter technique, single alanine mutations are introduced at every residue in the molecule, and the resultant mutant molecules are tested for cytosine deaminase activity to identify amino acid residues that are critical to the activity of the molecule. See also, Hilton et al., 1996 , J. Biol. Chem.  271: 4699-4708. The active site of the enzyme or other biological interaction can also be determined by physical analysis of structure, as determined by such techniques as nuclear magnetic resonance, crystallography, electron diffraction, or photoaffinity labeling, in conjunction with mutation of putative contact site amino acids. See, for example, de Vos et al., 1992 , Science  255: 306-312; Smith et al., 1992 , J. Mol. Biol.  224: 899-904; Wlodaver et al., 1992 , FEBS Lett.  309: 59-64. The identity of essential amino acids can also be inferred from an alignment with a related polypeptide. 
     Single or multiple amino acid substitutions, deletions, and/or insertions can be made and tested using known methods of mutagenesis, recombination, and/or shuffling, followed by a relevant screening procedure, such as those disclosed by Reidhaar-Olson and Sauer, 1988 , Science  241: 53-57; Bowie and Sauer, 1989 , Proc. Natl. Acad. Sci. USA  86: 2152-2156; WO 95/17413; or WO 95/22625. Other methods that can be used include error-prone PCR, phage display (e.g., Lowman et al., 1991 , Biochemistry  30: 10832-10837; U.S. Pat. No. 5,223,409; WO 92/06204), and region-directed mutagenesis (Derbyshire et al., 1986 , Gene  46: 145; Ner et al., 1988 , DNA  7: 127). 
     Mutagenesis/shuffling methods can be combined with high-throughput, automated screening methods to detect activity of cloned, mutagenized polypeptides expressed by host cells (Ness et al., 1999 , Nature Biotechnology  17: 893-896). Mutagenized DNA molecules that encode active polypeptides can be recovered from the host cells and rapidly sequenced using standard methods in the art. These methods allow the rapid determination of the importance of individual amino acid residues in a polypeptide. 
     In an embodiment, the number of amino acid substitutions, deletions and/or insertions introduced into the polypeptide of SEQ ID NO:60 is not more than 10, e.g., 1, 2, 3, 4, 5, 6, 7, 8 or 9. The polypeptide may be a hybrid polypeptide in which a region of one polypeptide is fused at the N-terminus or the C-terminus of a region of another polypeptide. 
     Sources of Polypeptides Having Cytosine Deaminase Activity 
     A polynucleotide encoding a polypeptide having cytosine deaminase activity of the present invention may be obtained from microorganisms of any genus. For purposes of the present invention, the term “obtained from” as used herein in connection with a given source shall mean that the polypeptide encoded by a polynucleotide is produced by the source or by a strain in which the polynucleotide from the source has been inserted. 
     The cytosine deaminase polypeptide may be a fungal polypeptide. For example, the polypeptide may be a yeast polypeptide such as a  Candida, Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces , or  Yarrowia  polypeptide; or a filamentous fungal polypeptide such as an  Acremonium, Agaricus, Alternaria, Aspergillus, Aureobasidium, Botryosphaeria, Ceriporiopsis, Chaetomidium, Chrysosporium, Claviceps, Cochliobolus, Coprinopsis, Coptotermes, Corynascus, Cryphonectria, Cryptococcus, Diplodia, Exidia, Filibasidium, Fusarium, Gibberella, Holomastigotoides, Humicola, Irpex, Lentinula, Leptospaeria, Magnaporthe, Melanocarpus, Meripilus, Mucor, Myceliophthora, Neocallimastix, Neurospora, Paecilomyces, Penicillium, Phanerochaete, Piromyces, Poitrasia, Pseudoplectania, Pseudotrichonympha, Rhizomucor, Schizophyllum, Scytalidium, Talaromyces, Thermoascus, Thielavia, Tolypocladium, Trichoderma, Trichophaea, Verticillium, Volvariella , or  Xylaria  polypeptide. 
     In another aspect, the polypeptide is a  Saccharomyces carlsbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomyces norbensis , or  Saccharomyces oviformis  polypeptide. 
     In another aspect, the polypeptide is an  Acremonium cellulolyticus, Aspergillus aculeatus, Aspergillus awamori, Aspergillus foetidus, Aspergillus fumigatus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Chrysosporium inops, Chrysosporium keratinophilum, Chrysosporium lucknowense, Chrysosporium merdarium, Chrysosporium pannicola, Chrysosporium queenslandicum, Chrysosporium tropicum, Chrysosporium zonatum, 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 sporotrichioides, Fusarium sulphureum, Fusarium torulosum, Fusarium trichothecioides, Fusarium venenatum, Humicola grisea, Humicola insolens, Humicolalanuginosa, Irpex lacteus, Mucor miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium funiculosum, Penicillium purpurogenum, Phanerochaete chrysosporium, Thielavia achromatica, Thielavia albomyces, Thielavia albopilosa, Thielavia australeinsis, Thielavia fimeti, Thielavia microspora, Thielavia ovispora, Thielavia peruviana, Thielavia setosa, Thielavia spededonium, Thielavia subthermophila, Thielavia terrestris, Trichoderma harzianum, Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei , or  Trichoderma viride  polypeptide. 
     It will be understood that for the aforementioned species the invention encompasses both the perfect and imperfect states, and other taxonomic equivalents, e.g., anamorphs, regardless of the species name by which they are known. 
     Those skilled in the art will readily recognize the identity of appropriate equivalents. Strains of these species are readily accessible to the public in a number of culture collections, such as the American Type Culture Collection (ATCC), Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH (DSMZ), Centraalbureau Voor Schimmelcultures (CBS), and Agricultural Research Service Patent Culture Collection, Northern Regional Research Center (NRRL). 
     The polypeptide may be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) using the above-mentioned probes. Techniques for isolating microorganisms from natural habitats are well known in the art. A polynucleotide encoding the polypeptide may then be obtained by similarly screening a genomic DNA or cDNA library of another microorganism or mixed DNA sample. Once a polynucleotide encoding a polypeptide has been detected with the probe(s), the polynucleotide can be isolated or cloned by utilizing techniques that are well known to those of ordinary skill in the art (see, e.g., Sambrook et al., 1989, supra). 
     Nucleic Acid Constructs 
     The present invention also relates to nucleic acid constructs or expression vectors comprising a selection marker and a polynucleotide of interest operably linked to one or more control sequences that direct their expression in a suitable expression host cell. In a particular embodiment, the present invention also relates to nucleic acid constructs or expression vectors comprising a negative selection marker and a polynucleotide of interest operably linked to one or more control sequences that direct their expression in a suitable expression host cell. 
     A polynucleotide may be manipulated in a variety of ways to provide for expression of an encoded polypeptide. Manipulation of the polynucleotide prior to its insertion into a vector may be desirable or necessary depending on the expression vector. The techniques for modifying polynucleotides utilizing recombinant DNA methods are well known in the art. 
     The control sequence may be a promoter sequence, a polynucleotide that is recognized by a host cell for expression of a polynucleotide encoding a polypeptide of the present invention. The promoter sequence contains transcriptional control sequences that mediate the expression of the polypeptide. The promoter may be any polynucleotide that 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 transcription of the nucleic acid constructs of the present invention in a filamentous fungal host cell are promoters obtained from the genes for  Aspergillus nidulans  acetamidase,  Aspergillus niger  neutral alpha-amylase,  Aspergillus niger  acid stable alpha-amylase,  Aspergillus niger  or  Aspergillus awamori  glucoamylase (glaA),  Aspergillus oryzae  TAKA amylase,  Aspergillus oryzae  alkaline protease,  Aspergillus oryzae  triose phosphate isomerase,  Fusarium oxysporum  trypsin-like protease (WO 96/00787),  Fusarium venenatum  amyloglucosidase (WO 00/56900),  Fusarium venenatum  Daria (WO 00/56900),  Fusarium venenatum  Quinn (WO 00/56900),  Rhizomucor miehei  lipase,  Rhizomucor miehei  aspartic proteinase,  Trichoderma reesei  beta-glucosidase,  Trichoderma reesei  cellobiohydrolase I,  Trichoderma reesei  cellobiohydrolase II,  Trichoderma reesei  endoglucanase I,  Trichoderma reesei  endoglucanase II,  Trichoderma reesei  endoglucanase III,  Trichoderma reesei  endoglucanase IV,  Trichoderma reesei  endoglucanase V,  Trichoderma reesei  xylanase I,  Trichoderma reesei  xylanase II,  Trichoderma reesei  beta-xylosidase, as well as the NA2-tpi promoter (a modified promoter from an  Aspergillus  gene encoding a neutral alpha-amylase in which the untranslated leader has been replaced by an untranslated leader from an  Aspergillus  gene encoding a triose phosphate isomerase; non-limiting examples include modified promoters from an  Aspergillus niger  gene encoding neutral alpha-amylase in which the untranslated leader has been replaced by an untranslated leader from an  Aspergillus nidulans  or  Aspergillus oryzae  gene encoding a triose phosphate isomerase); and mutant, truncated, and hybrid promoters thereof. 
     In a yeast host, useful promoters are obtained from the genes for  Saccharomyces cerevisiae  enolase (ENO-1),  Saccharomyces cerevisiae  galactokinase (GAL1),  Saccharomyces cerevisiae  alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH1, ADH2/GAP),  Saccharomyces cerevisiae  triose phosphate isomerase (TPI),  Saccharomyces cerevisiae  metallothionein (CUP1), and  Saccharomyces cerevisiae  3-phosphoglycerate kinase. Other useful promoters for yeast host cells are described by Romanos et al., 1992 , Yeast  8: 423-488. 
     The control sequence may also be a suitable transcription terminator sequence, which is recognized by a host cell to terminate transcription. The terminator sequence is operably linked to the 3′-terminus of the polynucleotide encoding the polypeptide. Any terminator that 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 for  Aspergillus nidulans  anthranilate synthase,  Aspergillus niger  glucoamylase,  Aspergillus niger  alpha-glucosidase,  Aspergillus oryzae  TAKA amylase, and  Fusarium oxysporum  trypsin-like protease. 
     Preferred terminators for yeast host cells are obtained from the genes for  Saccharomyces cerevisiae  enolase,  Saccharomyces cerevisiae  cytochrome C (CYC1), and  Saccharomyces cerevisiae  glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators for yeast host cells are described by Romanos et al., 1992, supra. 
     The control sequence may also be a suitable leader sequence, when transcribed is a nontranslated region of an mRNA that is important for translation by the host cell. The leader sequence is operably linked to the 5′-terminus of the polynucleotide encoding the polypeptide. Any leader sequence that is functional in the host cell of choice may be used. 
     Preferred leaders for filamentous fungal host cells are obtained from the genes for  Aspergillus oryzae  TAKA amylase and  Aspergillus nidulans  triose phosphate isomerase. 
     Suitable leaders for yeast host cells are obtained from the genes for  Saccharomyces cerevisiae  enolase (ENO-1),  Saccharomyces cerevisiae  3-phosphoglycerate kinase,  Saccharomyces cerevisiae  alpha-factor, and  Saccharomyces cerevisiae  alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP). 
     The control sequence may also be a polyadenylation sequence, a sequence operably linked to the 3′-terminus of the polynucleotide and, when transcribed, is recognized by the host cell as a signal to add polyadenosine residues to transcribed mRNA. Any polyadenylation sequence that is functional in the host cell of choice may be used. 
     Preferred polyadenylation sequences for filamentous fungal host cells are obtained from the genes for  Aspergillus oryzae  TAKA amylase,  Aspergillus niger  glucoamylase,  Aspergillus nidulans  anthranilate synthase,  Fusarium oxysporum  trypsin-like protease, and  Aspergillus niger  alpha-glucosidase. 
     Useful polyadenylation sequences for yeast host cells are described by Guo and Sherman, 1995 , Mol. Cellular Biol.  15: 5983-5990. 
     The control sequence may also be a signal peptide coding region that encodes a signal peptide linked to the N-terminus of a polypeptide and directs the polypeptide into the cell&#39;s secretory pathway. The 5′-end of the coding sequence of the polynucleotide may inherently contain a signal peptide coding sequence naturally linked in translation reading frame with the segment of the coding sequence that encodes the polypeptide. Alternatively, the 5′-end of the coding sequence may contain a signal peptide coding sequence that is foreign to the coding sequence. A foreign signal peptide coding sequence may be required where the coding sequence does not naturally contain a signal peptide coding sequence. Alternatively, a foreign signal peptide coding sequence may simply replace the natural signal peptide coding sequence in order to enhance secretion of the polypeptide. However, any signal peptide coding sequence that directs the expressed polypeptide into the secretory pathway of a host cell of choice may be used. 
     Effective signal peptide coding sequences for filamentous fungal host cells are the signal peptide coding sequences obtained from the genes for  Aspergillus niger  neutral amylase,  Aspergillus niger  glucoamylase,  Aspergillus oryzae  TAKA amylase,  Humicola insolens  cellulase,  Humicola insolens  endoglucanase V,  Humicola lanuginosa  lipase, and  Rhizomucor miehei  aspartic proteinase. 
     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 sequences are described by Romanos et al., 1992, supra. 
     The control sequence may also be a propeptide coding sequence that encodes a propeptide positioned at the N-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 an active polypeptide by catalytic or autocatalytic cleavage of the propeptide from the propolypeptide. 
     Where both signal peptide and propeptide sequences are present at the N-terminus of a polypeptide, the propeptide sequence is positioned next to the N-terminus of a polypeptide and the signal peptide sequence is positioned next to the N-terminus of the propeptide sequence. 
     It may also be desirable to add regulatory sequences that regulate expression of the polypeptide relative to the growth of the host cell. Examples of regulatory systems are those that cause 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 include the lac, tac, and trp operator systems. In yeast, the ADH2 system or GAL1 system may be used. In filamentous fungi, the  Aspergillus niger  glucoamylase promoter,  Aspergillus oryzae  TAKA alpha-amylase promoter, and  Aspergillus oryzae  glucoamylase promoter may be used. Other examples of regulatory sequences are those that allow for gene amplification. In eukaryotic systems, these regulatory sequences include the dihydrofolate reductase gene that is amplified in the presence of methotrexate, and the metallothionein genes that are amplified with heavy metals. In these cases, the polynucleotide encoding the polypeptide would be operably linked with the regulatory sequence. 
     Expression Vectors 
     The present invention also relates to recombinant expression vectors comprising a polynucleotide of the present invention, a promoter, and transcriptional and translational stop signals, and as described herein, a pair of recognition sequences of the site-specific recombinase flanking the polynucleotide of interest, the promoter, and the transcriptional and translational stop signals. The various nucleotide and control sequences may be joined together to produce a recombinant expression vector that may include one or more convenient restriction sites to allow for insertion or substitution of the polynucleotide encoding the polypeptide at such sites. Alternatively, the polynucleotide may be expressed by inserting the polynucleotide or a nucleic acid construct comprising the sequence into an appropriate vector for expression. In creating the 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) that can be conveniently subjected to recombinant DNA procedures and can bring about expression of the polynucleotide. 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 vector may be a linear or closed circular plasmid. 
     The vector may be an autonomously replicating vector, i.e., a vector that 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 that, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated. Furthermore, a single vector or plasmid or two or more vectors or plasmids that together contain the total DNA to be introduced into the genome of the host cell, or a transposon, may be used. 
     The vector preferably contains one or more selectable markers that permit easy selection of transformed, transfected, transduced, or the like cells. A selectable marker is a gene the product of which, for example, provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs, and the like. 
     Suitable markers for yeast host cells are ADE2, HIS3, LEU2, LYS2, MET3, TRP1, and URA3. Selectable markers for use in a filamentous fungal host cell include, but are 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 thereof. Preferred for use in an  Aspergillus  cell are  Aspergillus nidulans  or  Aspergillus oryzae  amdS and pyrG genes and a  Streptomyces hygroscopicus  bar gene. 
     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). 
     Host Cells 
     The present invention also relates to recombinant host cells transformed by the methods of the present invention. The present invention also relates to recombinant host cells, suitable for transformation with an integrative nucleic acid construct comprising a polynucleotide of interest flanked by regions of homology to either the cytosine deaminase encoding gene, or regions up and downstream of that gene, respectively, in the host cell genome, which direct chromosomal integration by site-specific double homologous recombination, whereby the polynucleotide of interest is integrated into the genome of the host cell while the cytosine deaminase encoding gene is partially or fully excised and thereby inactivated. The successful inactivation of the residing cytosine deaminase encoding gene is selectable in a medium comprising medium comprising 5-fluorocytosin, which is converted to toxic 5-fluorouracil by cytosine deaminase. So, in such a transformation method, the cytosine deaminase encoding gene functions as a negative selection marker, as outlined in the method of the invention. 
     A host cell with no measurable cytosine deaminase activity is suitable for a transformation method, where the host cell is transformed with a nucleic acid construct comprising at least one expressible cytosine deaminase-encoding polynucleotide, which is then used as a positive selection marker in a growth medium comprising a de novo pyrimidine synthesis inhibitor under conditions conducive for the expression of the cytosine deaminase. Preferably, the de novo pyrimidine synthesis inhibitor is N-(phosphonacetyl)-L-aspartate (PALA), which inhibits aspartate carbamyl transferase. 
     The term “host cell” encompasses any progeny of a parent cell that is not identical to the parent cell due to mutations that occur during replication. The choice of a host cell will to a large extent depend upon the gene encoding the polypeptide and its source. 
     The host cell may be 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&#39;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). 
     The fungal host cell may be a yeast cell. “Yeast” as used herein includes ascosporogenous yeast (Endomycetales), basidiosporogenous yeast, and yeast belonging to the Fungi Imperfecti (Blastomycetes). 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, F. A., Passmore, S. M., and Davenport, R. R., eds,  Soc. App. Bacteriol. Symposium Series  No. 9, 1980). 
     The yeast host cell may be a  Candida, Hansenula, Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces , or  Yarrowia  cell such as a  Kluyveromyces lactis, Saccharomyces carlsbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomyces norbensis, Saccharomyces oviformis , or  Yarrowia lipolytica  cell. 
     The fungal host cell may be 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. 
     The filamentous fungal host cell may be an  Acremonium, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Chrysosporium, Coprinus, Coriolus, Cryptococcus, Filibasidium, Fusarium, Humicola, Magnaporthe, Mucor, Myceliophthora, Neocallimastix, Neurospora, Paecilomyces, Penicillium, Phanerochaete, Phlebia, Piromyces, Pleurotus, Schizophyllum, Talaromyces, Thermoascus, Thielavia, Tolypocladium, Trametes , or  Trichoderma  cell. 
     For example, the filamentous fungal host cell may be an  Aspergillus awamori, Aspergillus foetidus, Aspergillus fumigatus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Bjerkandera adusta, Ceriporiopsis aneirina, Ceriporiopsis caregiea, Ceriporiopsis gilvescens, Ceriporiopsis pannocinta, Ceriporiopsis rivulosa, Ceriporiopsis subrufa, Ceriporiopsis subvermispora, Chrysosporium inops, Chrysosporium keratinophilum, Chrysosporium lucknowense, Chrysosporium merdarium, Chrysosporium pannicola, Chrysosporium queenslandicum, Chrysosporium tropicum, Chrysosporium zonatum, Coprinus cinereus, Coriolus hirsutus, 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 sporotrichioides, Fusarium sulphureum, Fusarium torulosum, Fusarium trichothecioides, Fusarium venenatum, Humicola insolens, Humicola lanuginosa, Mucor miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium purpurogenum, Phanerochaete chrysosporium, Phiebia radiata, Pleurotus eryngii, Thielavia terrestris, Trametes villosa, Trametes versicolor, Trichoderma harzianum, Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei , or  Trichoderma viride  cell. 
     Fungal cells may be transformed by a process involving protoplast formation, transformation of the protoplasts, and regeneration of the cell wall in a manner known per se. Suitable procedures for transformation of  Aspergillus  and  Trichoderma  host cells are described in EP 238023, Yelton et al., 1984 , Proc. Natl. Acad. Sci. USA  81: 1470-1474, and Christensen et al., 1988 , Bio/Technology  6: 1419-1422. 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 Abelson, J. N. and Simon, M. I., editors,  Guide to Yeast Genetics and Molecular Biology, Methods in Enzymology , Volume 194, pp 182-187, Academic Press, Inc., New York; Ito et al., 1983 , J. Bacteriol.  153: 163; and Hinnen et al., 1978 , Proc. Natl. Acad. Sci. USA  75: 1920. 
     Removal or Reduction of Cytosine Deaminase Activity 
     The present invention also relates to methods of producing a mutant of a parent cell, which comprises inactivating, disrupting or deleting a polynucleotide of the first aspect, or a portion thereof, encoding a cytosine deaminase, which results in the mutant cell producing less or none of the encoded cytosine deaminase compared with the parent cell, when cultivated under the same conditions. 
     The mutant cell may be constructed by reducing or eliminating expression of the polynucleotide using methods well known in the art, for example, insertions, disruptions, replacements, or deletions. In a preferred aspect, the polynucleotide is inactivated. The polynucleotide to be modified or inactivated may be, for example, the coding region or a part thereof essential for activity, or a regulatory element required for expression of the coding region. An example of such a regulatory or control sequence may be a promoter sequence or a functional part thereof, i.e., a part that is sufficient for affecting expression of the polynucleotide. Other control sequences for possible modification include, but are not limited to, a leader, polyadenylation sequence, propeptide sequence, signal peptide sequence, transcription terminator, and transcriptional activator. 
     Modification or inactivation of the polynucleotide may be performed by subjecting the parent cell to mutagenesis and selecting for mutant cells in which expression of the polynucleotide has been reduced or eliminated. The mutagenesis, which may be specific or random, may be performed, for example, by use of a suitable physical or chemical mutagenizing agent, by use of a suitable oligonucleotide, or by subjecting the DNA sequence to PCR generated mutagenesis. Furthermore, the mutagenesis may be performed by use of any combination of these mutagenizing agents. 
     Examples of a physical or chemical mutagenizing agent suitable for the present purpose include ultraviolet (UV) irradiation, hydroxylamine, N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), O-methyl hydroxylamine, nitrous acid, ethyl methane sulphonate (EMS), sodium bisulphite, formic acid, and nucleotide analogues. 
     When such agents are used, the mutagenesis is typically performed by incubating the parent cell to be mutagenized in the presence of the mutagenizing agent of choice under suitable conditions, and screening and/or selecting for mutant cells exhibiting reduced or no expression of the gene. 
     Modification or inactivation of the polynucleotide may be accomplished by insertion, substitution, or deletion of one or more nucleotides in the gene or a regulatory element required for transcription or translation thereof. For example, nucleotides may be inserted or removed so as to result in the introduction of a stop codon, the removal of the start codon, or a change in the open reading frame. Such modification or inactivation may be accomplished by site-directed mutagenesis or PCR generated mutagenesis in accordance with methods known in the art. Although, in principle, the modification may be performed in vivo, i.e., directly on the cell expressing the polynucleotide to be modified, it is preferred that the modification be performed in vitro as exemplified below. 
     An example of a convenient way to eliminate or reduce expression of a polynucleotide is based on techniques of gene replacement, gene deletion, or gene disruption. For example, in the gene disruption method, a nucleic acid sequence corresponding to the endogenous polynucleotide is mutagenized in vitro to produce a defective nucleic acid sequence that is then transformed into the parent cell to produce a defective gene. By homologous recombination, the defective nucleic acid sequence replaces the endogenous polynucleotide. It may be desirable that the defective polynucleotide also encodes a marker that may be used for selection of transformants in which the polynucleotide has been modified or destroyed. In an aspect, the polynucleotide is disrupted with a selectable marker such as those described herein. 
     The present invention also relates to methods of inhibiting the expression of a polypeptide having cytosine deaminase activity in a cell, comprising administering to the cell or expressing in the cell a double-stranded RNA (dsRNA) molecule, wherein the dsRNA comprises a subsequence of a polynucleotide of the present invention. In a preferred aspect, the dsRNA is about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex nucleotides in length. 
     The dsRNA is preferably a small interfering RNA (siRNA) or a micro RNA (miRNA). In a preferred aspect, the dsRNA is small interfering RNA for inhibiting transcription. In another preferred aspect, the dsRNA is micro RNA for inhibiting translation. 
     The present invention also relates to such double-stranded RNA (dsRNA) molecules, comprising a portion of the polypeptide coding sequence of SEQ ID NO:59 for inhibiting expression of the polypeptide in a cell. While the present invention is not limited by any particular mechanism of action, the dsRNA can enter a cell and cause the degradation of a single-stranded RNA (ssRNA) of similar or identical sequences, including endogenous mRNAs. When a cell is exposed to dsRNA, mRNA from the homologous gene is selectively degraded by a process called RNA interference (RNAi). 
     The dsRNAs of the present invention can be used in gene-silencing. In one aspect, the invention provides methods to selectively degrade RNA using a dsRNAi of the present invention. The process may be practiced in vitro, ex vivo or in vivo. In one aspect, the dsRNA molecules can be used to generate a loss-of-function mutation in a cell, an organ or an animal. Methods for making and using dsRNA molecules to selectively degrade RNA are well known in the art; see, for example, U.S. Pat. Nos. 6,489,127; 6,506,559; 6,511,824; and 6,515,109. 
     The present invention further relates to a mutant cell of a parent cell that comprises a disruption or deletion of a polynucleotide encoding the cytosine deaminase polypeptide or a control sequence thereof or a silenced gene encoding the polypeptide, which results in the mutant cell producing less of the cytosine deaminase or no cytosine deaminase compared to the parent cell. 
     The cytosine deaminase-deficient mutant cells are particularly useful as host cells for transformation with genes encoding native and heterologous proteins of interest. Therefore, the present invention further relates to methods of producing a native or heterologous polypeptide, comprising: (a) cultivating the mutant cell under conditions conducive for production of the polypeptide; and (b) recovering the polypeptide. The term “heterologous polypeptides” means polypeptides that are not native to the host cell, e.g., a variant of a native protein. The host cell may comprise more than one copy of a polynucleotide encoding the native or heterologous polypeptide. 
     The methods used for cultivation and purification of the product of interest may be performed by methods known in the art. 
     Transient Expression of Recombinase 
     There are numerous well-known and simple ways to bring about the transient expression of the site-specific recombinase of step (c) in the first aspect of the invention. 
     First of all, it could be advantageous to include the polynucleotide encoding the recombinase in the nucleic acid construct introduced into the cell, albeit in such a manner that it could easily be removed from the cell again after its integration, while leaving the remaining integrated polynucleotide of interest in the chromosome. One such method is employed in the examples and also outlined in  FIG. 1 , where a preferred recognition-site pair is indicated, namely FRT-F and FRT-F3, together with the FLP recombinase-encoding gene and the bi-directional pyrG marker as well as the doubled transcriptional terminators (denoted “Term” in  FIG. 1 ), which serve as homology boxes for later excision of the FLP gene and the pyrG marker by double homologous recombination. Of course, the terms in  FIG. 1  are mere examples and are not intended to limit the scope of the invention, the may be substituted for other well-known markers, recognition sequence pairs etc. 
     In a preferred embodiment of the first aspect, the nucleic acid construct further comprises, also flanked by the pair of recognition sequences: an incoming selection marker and a polynucleotide encoding the site-specific recombinase, in turn flanked by a pair of homology-boxes, which is all integrated with the polynucleotide of interest in step (c). Preferably, the incoming selection marker enables positive selection or negative selection or is bi-directional. It is then envisioned, that the method of the first aspect comprises the positively selecting for the integration in step (c) by double homologous recombination of the polynucleotide of interest along with the incoming selection marker and the polynucleotide encoding the site-specific recombinase, wherein the two latter are flanked by homology boxes. Further, the method comprises a step of negatively selecting for the excision of every integrated copy of the incoming selection marker and the polynucleotide encoding the site-specific recombinase by double homologous recombination between the homology boxes flanking them. 
     In another preferred embodiment, a second nucleic acid construct is introduced in said cell in step (b), which is either non-replicating or temperature-sensitively replicating, and which comprises a polynucleotide encoding the site-specific recombinase and a selection marker, which enables positive or negative selection or is bi-directional, and which is maintained in said cell transiently by selective pressure or growth at the permissive temperature, respectively, so that the site-specific recombinase can be transiently expressed in step (c). 
     In a final preferred embodiment, the cell in step (a) comprises in its chromosome at least one copy of a polynucleotide encoding the site-specific recombinase operably linked with a tightly regulated promoter, which can be turned on and off by modifying a growth condition, e.g., by providing a specific carbon source or inducer, so as to enable the transient expression of the site-specific recombinase in step (c). 
     EXAMPLES 
     Molecular cloning techniques are described in Sambrook, J., Fritsch, E. F., Maniatis, T. (1989) Molecular cloning: a laboratory manual (2nd edn.) Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. 
     Enzymes 
     Enzymes for DNA manipulations (e.g., restriction endonucleases, ligases etc.) are obtainable from New England Biolabs, Inc. and were used according to the manufacturer&#39;s instructions. 
     Media and Reagents 
     The following media and reagents were used unless otherwise specified: Chemicals used for buffers and substrates were commercial products of analytical grade. 
     Cove: 342.3 g/L Sucrose, 20 ml/L Cove salt solution, 10 mM acetamide, 30 g/L noble agar. 
     Cove top agar: 342.3 g/L sucrose, 20 ml/L Cove salt solution, 10 mM acetamide, 10 g/L low melt agarose 
     Cove-2: 30 g/L sucrose, 20 ml/L Cove salt solution, 10 mM acetamide, 30 g/L noble agar. 
     Cove-N (tf) plates are composed of 342.3 g sucrose, 20 ml Cove salt solution, 3 g NaNO 3 , and 30 g Noble agar and water to 1 liter. 
     Cove-N plates are composed of 30 g sucrose, 20 ml Cove salt solution, 3 g NaNO 3 , and 30 g Noble agar and water to 1 liter. 
     Cove salt solution is composed of 26 g KCl, 26 g MgSO 4 .7H 2 O, 76 g KH 2 PO 4  and 50 ml Cove trace metals and water to 1 liter. 
     Trace metal solution for COVE is composed of 0.04 g NaB 4 O 7 .10H 2 O, 0.4 g CuSO 4 .5H 2 O, 1.2 g FeSO 4 .7H 2 O, 1.0 g MnSO 4 .H 2 O, 0.8 g Neutral amylase II MoO 2 .2H 2 O, and 10.0 g ZnSO 4 .7H 2 O and water to 1 liter. 
     Cove-N top agarose is composed of 342.3 g sucrose, 20 ml COVE salt solution, 3 g NaNO 3 , and 10 g low melt agarose and water to 1 liter. 
     amyloglycosidase trace metal solution is composed of 6.8 g ZnCl 2 .7H 2 O, 2.5 g CuSO 4 .5H 2 O, 0.24 g NiCl 2 .6H 2 O, 13.9 g FeSO 4 .7H 2 O, 13.5 g MnSO 4 .H 2 O and 3 g citric acid, water to 1 liter. 
     YPG is composed of 4 g yeast extract, 1 g of KH 2 PO 4 , 0.5 g MgSO 4 .7H 2 O and 15 g glucose (pH 6.0) and water to 1 liter. 
     STC buffer is composed of 0.8 M sorbitol, 25 mM Tris (pH 8), and 25 mM CaCl 2  and water to 1 liter. 
     STPC buffer is composed of 40% PEG4000 in STC buffer. 
     MLC is composed of 40 g glucose, 50 g soybean powder, 4 g citric acid (pH 5.0) and water to 1 liter. 
     MSS is composed of 70 g sucrose, 100 g soybean powder (pH 6.0), and water to 1 liter. MU-1 is composed 260 g maltodextrin, 3 g MgSO 4 .7H 2 O, 5 g KH 2 PO 4 , 6 g K 2 SO 4 , amyloglycosidase trace metal solution 0.5 ml and urea 2 g (pH 4.5) and water to 1 liter. 
     KCl plates are composed of 0.6 M KCl, 20 ml of Cove salt solution, 3 g of NaNO 3 , and 30 g of Noble agar and water to 1 liter. 
     5-fluorocytosine stock solution: 1000 mg 5-fluorocytosine dissolved in 1 ml 0.91 NaCl solution. 
     Purchased Material ( E. coli , Plasmid and Kits) 
       E. coli  DH5-alpha (Toyobo) is used for plasmid construction and amplification. The commercial plasmids/vectors TOPO cloning kit (Invitrogen) and pBluescript II SK- (Stratagene #212206) are used for cloning of PCR fragments. Amplified plasmids are recovered with Qiagen® Plasmid Kit (Qiagen). Ligation is done with DNA ligation kit (Takara) or T4 DNA ligase (Boehringer Mannheim). Polymerase Chain Reaction (PCR) is carried out with Expand TM PCR system (Boehringer Mannheim). QIAquick™ Gel Extraction Kit (Qiagen) is used for the purification of PCR fragments and extraction of DNA fragment from agarose gel. 
     Strains 
       Aspergillus oryzae  BECh-2 is described in WO 2000/039322.  Aspergillus nidulans  strain NRRL 1092 was used as a donor strain. 
     The expression host strain  Aspergillus niger  NN059095 was isolated by Novozymes and is a derivative of  Aspergillus niger  NN049184 which was isolated from soil. NN059095 was genetically modified to disrupt expression of amyloglycosidase activities.  Aspergillus oryzae  ToC1512 is described in WO2005/070962, example 11. 
     Plasmids 
     The expression plasmid pHUda440 and the nucleotide sequences of amyloglucosidase from  Trametes cingulata  are described in patent application WO2006/069289. 
     Plasmid pJaL574 and the nucleotide sequences of herpes simplex virus (HSV) thymidine kinase gene (TK),  A. nidulans  glyceraldehyde-3-phosphate dehydrogenase promoter (Pgpd) and  A. nidulans  tryptophane synthase terminator (TtrpC) are described in example 9 in WO07045248. 
     The expression cassette plasmid pJaL790 and the nucleotide sequences of neutral amylase II promoter (Pna2) is described in patent publication WO2005070962. 
     The JA126 amylase expression vector is described in patent application 10729.000-US. 
     Plasmid pDV8 is described in patent WO 2001/068864, example 8. 
     Plasmid pJaL504 is described in example 10. 
     Plasmid pJaL504-delta-BglII is described in example 10. 
     Plasmid pJaL554 is described in patent WO2000/050567A1, example 1. 
     Plasmid pJaL574 is described in example 10. 
     Plasmid pJaL835 is described in example 10. 
     Plasmid pJaL955 is described in example 10. 
     Plasmid pJaL1022 is described in example 10. 
     Plasmid pJaL1025 is described in example 10. 
     Plasmid pJaL1027 is described in example 10. 
     Plasmid pJaL1029 is described in example 10. 
     Plasmid pJaL1120 is described in example 10. 
     Plasmid pJaL1123 is described in example 10. 
     Plasmid pJaL1183 is described in example 10. 
     Plasmid pJaL1194 is described in example 10. 
     Plasmid pJaL1202 is described in example 10. 
     Plasmid pToC65 is described in patent WO 91/17243 
     Plasmid pUC19: The construction is described in Vieira et al, 1982, Gene 19:259-268. 
     Plasmid pCR®4Blunt TOPO® from Invitrogen 
     Transformation of  Aspergillus    
     Transformation of  Aspergillus  species can be achieved using the general methods for yeast transformation. The preferred procedure for the invention is described below. 
     The  Aspergillus niger  host strain was inoculated into 100 ml YPG medium supplemented with 10 mM uridine and incubated for 16 hrs at 32° C. at 80 rpm. Pellets were collected and washed with 0.6 M KCl, and resuspended in 20 ml 0.6 M KCl containing a commercial β-glucanase product (GLUCANEX™, Novozymes A/S, Bagsvrd, Denmark) at a final concentration of 20 mg per ml. The suspension was incubated at 32° C. with shaking (80 rpm) until protoplasts were formed, and then washed twice with STC buffer. The protoplasts were counted with a hematometer and resuspended and adjusted in an 8:2:0.1 solution of STC:STPC:DMSO to a final concentration of 2.5×107 protoplasts/ml. Approximately 4 μg of plasmid DNA was added to 100 μl of the protoplast suspension, mixed gently, and incubated on ice for 30 minutes. One ml of SPTC was added and the protoplast suspension was incubated for 20 minutes at 37° C. After the addition of 10 ml of 50° C. Cove or Cove-N top agarose, the reaction was poured onto Cove or Cove-N (tf) agar plates and the plates were incubated at 32° C. for 5 days. 
     Transformation of other fungal hosts, such as,  Trichoderma  species, can also be achieved using the general methods for fungal transformation. 
     PCR Amplification 
                                            5× PCR buffer (incl. MgCl2)   20 μl            2.5 mM dNTP mix   10 μl            Forward primer (100□ μM)   1 μl           Reverse primer (100 μM)   1 μl           Expand High Fidelity polymerase (Roche)   1 μl           Template DNA (50-100 ng/μl)   1 μl           Distilled water to   100 μl                     
PCR Conditions
 
                                            94 C.   2 min        1 cycle       92 C.   1 min               55 C.   1 min    {close oversize brace}    30 cycles       72 C.   1-2 min                 72 C.   7 min        1 cycle                    
SF Cultivation for Glucoamylase Production
 
     Spores of the selected transformants were inoculated in 100 ml MLC media and cultivated at 30° C. for 2 days. 10 ml of MLC was inoculated to 100 ml of MU-1 medium and cultivated at 30° C. for 7 days. The supernatant was obtained by centrifugation. 
     Southern Hybridization 
     Mycelia of the selected transformants were harvested from overnight culture in 100 ml YPG medium, rinsed with distilled water, dried and frozen at −80° C. Ground mycelia were incubated with Proteinase K and RNaseA at 65° C. for 1 hrs. Genome DNA was recovered by phenol/CHCl3 extraction twice followed by EtOH precipitation and resuspended in distilled water. 
     Non-radioactive probes were synthesized using a PCR DIG probe synthesis kit (Roche Applied Science, Indianapolis Ind.) followed by manufacture&#39;s instruction. DIG labeled probes were gel purified using a QIAquick™ Gel Extraction Kit (QIAGEN Inc., Valencia, Calif.) according to the manufacturer&#39;s instructions. 
     Five micrograms of genome DNA was digested with appropriate restriction enzymes completely for 16 hours (40 μl total volumes, 4 U enzyme/μl DNA) and run on a 0.8% agarose gel. The DNA was fragmented in the gel by treating with 0.2 M HCl, denatured (0.5 M NaOH, 1.5 M NaCl) and neutralized (1 M Tris, pH7.5; 1.5 M NaCl) for subsequent transfer in 20×SSC to Hybond N+ membrane (Amersham). The DNA was UV cross-linked to the membrane and prehybridized for 1 hour at 42° C. in 20 ml DIG Easy Hyb (Roche Diagnostics Corporation, Mannheim, Germany). The denatured probe was added directly to the DIG Easy Hyb buffer and an overnight hybridization at 42° C. was done. Following the post hybridization washes (twice in 2×SSC, roome temperature, 5 min and twice in 0.1×SSC, 68° C., 15 min. each), chemiluminescent detection using the DIG detection system and CPD-Star (Roche) was done followed by manufacture&#39;s protocol. The DIG-labeled DNA Molecular Weight Marker II (Roche) was used for the standard marker. 
     Glucoamylase Activity 
     Glucoamylase activity is measured in AmyloGlucosidase Units (AGU). The AGU is defined as the amount of enzyme, which hydrolyzes 1 micromole maltose per minute under the standard conditions 37° C., pH 4.3, substrate: maltose 23.2 mM, buffer: acetate 0.1 M, reaction time 5 minutes. An autoanalyzer system may be used. Mutarotase is added to the glucose dehydrogenase reagent so that any alpha-D-glucose present is turned into beta-D-glucose. Glucose dehydrogenase reacts specifically with beta-D-glucose in the reaction mentioned above, forming NADH which is determined using a photometer at 340 nm as a measure of the original glucose concentration. 
     Amyloglycosidase Incubation: 
     Substrate: maltose 23.2 mM 
     Buffer: acetate 0.1 M 
     pH: 4.30±0.05 
     Incubation temperature: 37° C.±1 
     Reaction time: 5 minutes 
     Enzyme working range: 0.5-4.0 AGU/mL 
     Color Reaction: 
     GlucDH: 430 U/L 
     Mutarotase: 9 U/L 
     NAD: 0.21 mM 
     Buffer: phosphate 0.12 M; 0.15 M NaCl 
     pH: 7.60±0.05 
     Incubation temperature: 37° C.±1 
     Reaction time: 5 minutes 
     Wavelength: 340 nm 
     Determination of Acid Alpha-Amylase Activity 
     When used according to the present invention the activity of any acid alpha-amylase may be measured in AFAU (Acid Fungal Alpha-amylase Units), which are determined relative to an enzyme standard. 1 FAU is defined as the amount of enzyme which degrades 5.260 mg starch dry matter per hour under the below mentioned standard conditions. Acid alpha-amylase, i.e., acid stable alpha-amylase, an endo-alpha-amylase (1,4-alpha-D-glucan-glucano-hydrolase, E.C. 3.2.1.1) hydrolyzes alpha-1,4-glucosidic bonds in the inner regions of the starch molecule to form dextrins and oligosaccharides with different chain lengths. The intensity of color formed with iodine is directly proportional to the concentration of starch. Amylase activity is determined using reverse colorimetry as a reduction in the concentration of starch under the specified analytical conditions. 
                         
Standard Conditions/Reaction Conditions:
 
Substrate: Soluble starch, approx. 0.17 g/L
 
Buffer: Citrate, approx. 0.03 M
 
Iodine (12): 0.03 g/L
 
CaCl2: 1.85 mM
 
pH: 2.50±0.05
 
Incubation temperature: 40° C.
 
Reaction time: 23 seconds
 
Wavelength: 590 nm
 
Enzyme concentration: 0.025 AFAU/mL
 
Enzyme working range: 0.01-0.04 AFAU/mL
 
     Example 1. Introduction of FRT Sites at the Neutral Amylase I (NAI) Locus in  Aspergillus niger  NN059095 
     Construction of Hygromycin B Resistance Gene Expression Plasmid pHUda966 
     The following primers Tef-F and Tef-R which introduce EcoRI/SpeI and a BamHI site, respectively, were designed to isolate a promoter region of  A. oryzae  tef1 (translation elongation factor 1/Ptef1) based on the nucleotide sequences information in GENBANK (ID#AB007770): 
     
       
         
           
               
               
            
               
                   
                 Tef-F (SEQ ID NO: 1):  
               
               
                   
                 gaattcactagtggggttcaaatgcaaacaa 
               
               
                   
                   
               
               
                   
                 Tef-R (SEQ ID NO: 2):  
               
               
                   
                 ggatcctggtgcgaactttgtagtt 
               
            
           
         
       
     
     A PCR reaction with the genome DNA of the  Aspergillus oryzae  strain BECh2 as template was performed using a primer pair of Tef-F and Tef-R. The reaction products were isolated on a 1.0% agarose gel and 0.7 kb product band was excised from the gel. The 0.7 kb amplified DNA fragment was digested with BamHI and EcoRI, and ligated into the  Aspergillus  expression cassette pHUda440 digested with BamHI and EcoRI to create pHUda440-Ptef. 
     The following primers nia-F and nia-R which introduce an XhoI and an XbaI site, respectively, were designed to isolate a terminator region of  A. oryzae  nitrate reductase (niaD) (Tniad) based on the nucleotide sequences information in EMBL:D49701: 
     
       
         
           
               
               
            
               
                   
                 nia-F (SEQ ID NO: 3):  
               
               
                   
                 ctcgagattatccaagggaatgac 
               
               
                   
                   
               
               
                   
                 nia-R (SEQ ID NO: 4):  
               
               
                   
                 tctagaaagtattttcggtacgatt 
               
            
           
         
       
     
     A PCR reaction with the genome DNA of the  Aspergillus oryzae  strain BECh2 as template was performed using a primer pair of nia-F and nia-R. The reaction products were isolated on a 1.0% agarose gel and 0.5 kb product band was excised from the gel. The 0.5 kb amplified DNA fragment was digested with XhoI and XbaI, and ligated into the  Aspergillus  expression cassette pHUda440-Ptef digested with XhoI and XbaI to create pHUda440-Ptef-Tnia. 
     The following primers hph-F and hph-R which introduce a BamH and an XhoI site, respectively, were designed to isolate a coding region of hygromycin B resistance gene based on the nucleotide sequences information in EMBL:AR109978: 
     hph-F (SEQ ID NO: 5): ggatcctacacctcagcaatgtcgcctgaa 
     hph-R (SEQ ID NO:6): ctcgagctattcctttgccctcggacgagtgct 
     A PCR reaction with pJaL154 harboring the hygromycin B resistance gene (hph) as template was performed using a primer pair of hph-F and hph-R. The reaction products were isolated on a 1.0% agarose gel and 1.0 kb product band was excised from the gel. The 1.0 kb amplified DNA fragment was digested with BamHI and XhoI, and ligated into the  Aspergillus  expression cassette pHUda440-Ptef-Tnia digested with BamHI and XhoI to create pHUda966. The nucleotide sequences of hygromycin B resistance gene (hph) expression parts in pHUda966 are shown in SEQ ID NO:7, with indications of the features positions of the primers used for the construction, the encoded hygromycin B resistance factor is shown in SEQ ID NO:8. 
     Construction of pHUda981 for Introduction of FRT Sites at the NA1 Loci 
     The 2.5 kb DNA fragment containing herpes simplex virus (HSV) thymidine kinase gene (TK) was recovered from pJaL574 by XhoI and EcoRI digestion. The recovered 2.5 kb fragment was ligated to XhoI and EcoRI digested pBluescript II SK-. The ligation mixture was transformed into  E. coli  DH5α to create the expression plasmid pTK. 
     The nucleotide sequences of the FRT-F and FRT-F3 sites are: 
     
       
         
           
               
            
               
                 FRT-F (SEQ ID NO: 9):  
               
               
                 ttgaagttcctattccgagttcctattctctagaaagtataggaacttc 
               
               
                   
               
               
                 FRT-F3 (SEQ ID NO: 10):  
               
               
                 ttgaagttcctattccgagttcctattcttcaaatagtataggaacttca 
               
            
           
         
       
     
     The following primers 3NA1-F and 3NA1-R which introduce an EcoRI and a SpeI site, respectively, were designed to isolate 3′ flanking region of  Aspergillus niger  neutral amylase I (NAI) fused with FRT-F3 recognition site based on the nucleotide sequences information in EMBL:AM270106 and EMBL: DJ052242, respectively: 
     
       
         
           
               
            
               
                 3NA1-F (SEQ ID NO: 11): 
               
               
                 actagtttgaagttcctattccgagttcctattcttcaaatagtatagg 
               
               
                 aacttcaactagagtatatgatggtact 
               
               
                   
               
               
                 3NA1-R (SEQ ID NO: 12):  
               
               
                 gaattcgcattctcctagttactgatgacttt 
               
            
           
         
       
     
     A PCR reaction with the genome DNA of  Aspergillus niger  NN059095 as template was performed using a primer pair of 3NA1-F and 3NA1-R. The reaction products were isolated on a 1.0% agarose gel and 1.0 kb product band was excised from the gel. The 1.5 kb amplified DNA fragment was digested with SpeI and EcoRI, and ligated into the  Aspergillus  expression cassette pTK digested with EcoRI and SpeI to create pHUdaTK-3NA1. 
     The following primers 5NA1-F and 5NA1-R which introduce a NotI and a SpeI site, respectively, were designed to isolate 5′ flanking region of  Aspergillus niger  neutral amylase I (NAI) fused with FRT-F recognition site based on the nucleotide sequences information in EMBL:AM270106 and EMBL: DJ052242, respectively: 
     
       
         
           
               
            
               
                 5NA1-F (SEQ ID NO: 13):  
               
               
                 gcggccgcgtttaaacctatctgttccc 
               
               
                   
               
               
                 5NA1-R (SEQ ID NO: 14):  
               
               
                 actagtgctagcgaagttcctatactttctagagaataggaactcggaat 
               
               
                 aggaacttcaagatgaattcgcggcctacatg 
               
            
           
         
       
     
     A PCR reaction with the genome DNA of  Aspergillus niger  NN059095 as template was performed using a primer pair of 5NA1-F and 5NA1-R. The reaction products were isolated on a 1.0% agarose gel and 1.8 kb product band was excised from the gel. The 1.8 kb amplified DNA fragment was digested with NotI and SpeI, and ligated into the  Aspergillus  expression cassette pTK-3NA1 digested with NotI and SpeI to create pHUdaTK-3NA1-5NA1. 
     The 2.2 kb DNA fragment containing hybromycin B resistance gene driven by  Aspergillus oryzae  tef1 promoter (Ptef) and niaD terminator (Tniad) was recovered from pHUda966 by XbaI and NheI digestion. The recovered 2.2 kb fragment was ligated to SpeI digested pHUdaTK-3NA1-5NA1. The ligation mixture was transformed into  E. coli  DH5α to create the expression plasmid pHUda981. 
     The nucleotide sequence of the NA1-encoding part and flanking regions of pHUda981 is shown in SEQ ID NO:15, the NA1 is shown in SEQ ID NO: 16 and a plasmid map is shown in  FIG. 2 . 
     Introduction of FRT Sites at the NA1 Locus in  A. Niger  NN059095 
     The pHUda981 was introduced into  Aspergillus niger  strain NN059095. Transformants were selected from the Cove-N (tf) supplemented with 10 mM uridine and 1 mM hygromycin B. Randomly selected transformants were inoculated onto Cove-N plates with 10 mM uridine, 1 mM hygromycin B and 2.5 μM 5-Flouro-2-deoxyuridine (FdU), an agent which kills cells expressing the herpes simplex virus (HSV) thymidine kinase gene (TK) harbouring in pHUda981. Strains which grew well on Cove-N plates supplemented with 2.5 μM FdU were purified and subjected to Southern blotting analysis to confirm whether the FRT sites in pHUda981 was introduced correctly or not. 
     The following set of primers to make a non-radioactive probe was used to analyze the selected transformants. For the 5′ NA1 flanking region: 
     
       
         
           
               
               
            
               
                   
                 Forward primer (SEQ ID NO: 17):  
               
               
                   
                 aatccggatcctttcctata 
               
               
                   
                   
               
               
                   
                 Reverse primer (SEQ ID NO: 18):  
               
               
                   
                 gatggagcgcgcctagaagc 
               
            
           
         
       
     
     Genomic DNA extracted from the selected transformants was digested by NcoI and Southern blotting analysis was preformed using the above probe. Strains of interest were identified by the disappearance of a 2.8 kb NcoI band and the appearance of a 3.1 kb NcoI band. Among the strains given the right integration events, a strain denoted NN059180 was selected. 
     Example 2. Introduction of FRT Sites at the Acid Stable Amylase Locus in  A. niger  NN059095 
     Construction of  A. Nidulans  Acetoamidase Gene (amdS) Expression Plasmid pHUda976. 
     The following primers amdS-F and amdS-R which introduce a BamHI and an XhoI site, respectively, were designed to isolate a coding region of amdS gene based on the nucleotide sequences information in EMBL:AF348620: 
     
       
         
           
               
               
            
               
                   
                 amdS-F (SEQ ID NO: 19):  
               
               
                   
                 ggatccaccatgcctcaatcctgg 
               
               
                   
                   
               
               
                   
                 amdS-R (SEQ ID NO: 20):  
               
               
                   
                 ctcgagctatggagtcaccacatttcccag 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus nidulans  strain NRRL 1092 as template was performed using a primer pair of amdS-F and amdS-R. The reaction products were isolated on a 1.0% agarose gel and 1.0 kb product band was excised from the gel. The 1.9 kb amplified DNA fragment was digested with BamHI and XhoI, and ligated into the  Aspergillus  expression cassette pHUda440-Ptef-Tnia digested with BamHI and XhoI to create pHUda976. 
     The nucleotide sequence of the  Aspergillus nidulans  acetoamidase gene (amdS) expression parts in pHUda976 is shown in SEQ ID NO:21 with gene features positions of the primers used, the encoded acetoamidase amino acid sequence is shown in SEQ ID NO:22. 
     Construction of pHUda1019 for Introduction of FRT Sites at the Acid Stable Amylase Locus 
     The following primers 3SP-F and 3SP-R which introduce an EcoRI and a SpeI site, respectively, were designed to isolate 3′ flanking region of  Aspergillus niger  acid stable amylase fused with FRT-F3 recognition site based on the nucleotide sequences information in EMBL:AM270232 and EMBL: DJ052242, respectively: 
     
       
         
           
               
            
               
                 3SP-F (SEQ ID NO: 23):  
               
               
                 actagtttgaagttcctattccgagttcctattcttcaaatagtatagga 
               
               
                 acttcaactagagaatgcaatcataacagaaagta 
               
               
                   
               
               
                 3SP-R (SEQ ID NO: 24):  
               
               
                 gaattcttaattaaatcacggcaagggtttac 
               
            
           
         
       
     
     A PCR reaction with the genome DNA of  Aspergillus niger  NN059095 as template was performed using a primer pair of 3SP-F and 3SP-R. The reaction products were isolated on a 1.0% agarose gel and 1.8 kb product band was excised from the gel. The 1.8 kb amplified DNA fragment was digested with SpeI and EcoRI, and ligated into the  Aspergillus  expression cassette pTK digested with EcoRI and SpeI to create pHUdaTK-3SP. 
     The following primers 5SP-F and 5SP-R which introduce a SaclI and a SpeI site, respectively, were designed to isolate 5′ flanking region of  Aspergillus niger  acid stable amylase fused with FRT-F recognition site based on the nucleotide sequences information in EMBL:AM270232 and EMBL: DJ052242, respectively: 
     
       
         
           
               
            
               
                 5SP-F (SEQ ID NO: 25):  
               
               
                 ccgcggcaacaggcagaatatcttcc 
               
               
                   
               
               
                 5SP-R (SEQ ID NO: 26): 
               
               
                 actagtgaagttcctatactttctagagaataggaactcggaataggaac 
               
               
                 ttcaaacgggatcttggacgcattcca 
               
            
           
         
       
     
     A PCR reaction with the genome DNA of  Aspergillus niger  NN059095 as template was performed using a primer pair of 5SP-F and 5SP-R. The reaction products were isolated on a 1.0% agarose gel and 2.0 kb product band was excised from the gel. The 2.0 kb amplified DNA fragment was digested with SaclI and SpeI, and ligated into the  Aspergillus  expression cassette pTK-3SP digested with SaclI and SpeI to create pHUdaTK-3SP-5SP. 
     The 3.1 kb DNA fragment containing the amdS gene driven by  Aspergillus oryzae  tef1 promoter and niaD terminator was recovered from pHUda976 by XbaI and NheI digestion. The recovered 3.1 kb fragment was ligated to SpeI digested pHUdaTK-3SP-5SP. The ligation mixture was transformed into  E. coli  DH5α to create the expression plasmid pHUda1019. 
     The nucleotide sequence of the  A. niger  acid stable amylase gene with the flanking sequences of pHUda1019 are shown in SEQ ID NO:27 and the encoded amylase amino acid sequence is shown in SEQ ID NO:28; a plasmid map is shown in  FIG. 3 . 
     Introduction of FRT Sites at the Locus in  A. niger  NN059180 
     The pHUda1019 was introduced into  Aspergillus niger  strain NN059180. Transformants were selected from the Cove (tf) supplemented with 10 mM uridine. Randomly selected transformants were inoculated onto Cove-2 plates with 10 mM uridine and 2.5 μM 5-Flouro-2-deoxyuridine (FdU), an agent which kills cells expressing the herpes simplex virus (HSV) thymidine kinase gene (TK) harbouring in pHUda1019. Strains which grew well on Cove-2 plates with 2.5 μM FdU were purified and subjected to Southern blotting analysis to confirm whether the FRT sites in pHUda1019 was introduced correctly or not. 
     The following set of primers to make non-radioactive probe was used to analyze the selected transformants. For 5′ acid stable amylase flanking region: 
     
       
         
           
               
               
            
               
                   
                 Forward primer (SEQ ID NO: 29):  
               
               
                   
                 cgtacaccttgggattatgcgctg 
               
               
                   
                   
               
               
                   
                 Reverse primer (SEQ ID NO: 30):  
               
               
                   
                 cacaaaggcgcaaagcataccatc 
               
            
           
         
       
     
     Genomic DNA extracted from the selected transformants was digested by XhoI. The right integration event were identified by the disappearance of a 6.2 kb XhoI band and the appearance of a 4.1 XhoI band. Among the strains given the right integration events, a strain denoted NN059183 was selected. 
     Example 3. Simultaneous Site Specific-Integration by FLP in the Two Loci 
     Construction of  A. nidulans  pyrG Gene Expression Plasmid pHUda794 
     The following primers pyr-F introducing a PacI site and pyr-R were designed to isolate a promoter and coding region of  A. nidulans  pyrG gene based on the nucleotide sequences information in EMBL:m19132: 
     
       
         
           
               
               
            
               
                   
                 pyr-F (SEQ ID NO: 31):  
               
               
                   
                 ttaattaaactaaatgacgtttgtgaaca 
               
               
                   
                   
               
               
                   
                 pyr-R (SEQ ID NO: 32):  
               
               
                   
                 ctaccgccaggtgtcagtcaccctcaaagtccaactcttttc 
               
            
           
         
       
     
     The following primers Tamg-F and Tamg-R introducing a SphI site were designed to isolate a terminator region of  A. niger  amyloglucosidase (Tamg) gene fused with FRT-F3 recognition site based on the nucleotide sequences information in EMBL:am270061 and DJ052242: 
     
       
         
           
               
            
               
                 Tamg-F (SEQ ID NO: 33):  
               
               
                 agagttggactttgagggtgactgacacctggcggtag 
               
               
                   
               
               
                 Tamg-R (SEQ ID NO: 34): 
               
               
                 gcatgcactagctagttgaagttcctatactatttgaagaataggaactc 
               
               
                 ggaataggaacttcaacctagaggagagagttg 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus nidulans  strain NRRL 1092 as template was performed using a primer pair of pyr-F and pyr-R. The reaction products were isolated on a 1.0% agarose gel and 1.4 kb product band was excised from the gel. 
     A PCR reaction with the genome DNA of  Aspergillus niger  NN059095 as template was performed using a primer pair of Tamg-F and Tamg-R. The reaction products were isolated on a 1.0% agarose gel and 0.8 kb product band was excised from the gel. 
     A PCR reaction with the 1.4 kb and 0.8 kb amplified DNA fragment was performed using a primer pair of pyr-F and Tamg-R. The reaction products were isolated on a 1.0% agarose gel and 2.2 kb product band was excised from the gel. 
     The 2.2 kb amplified DNA fragment was packed into the TOPO cloning vector (pCR2.1 TOPO) provided by Invitrogen followed by the protocol with the kit to create pHUda794. 
     The nucleotide sequence of the  A. nidulans  pyrG gene with flanking sequences in pHUda794 is shown in SEQ ID NO:35 along with features and positions of primers used; the amino acid seqeunce of the encoded PyrG is shown in SEQ ID NO:36. 
     Construction of Synthetic Version of FLP Gene Expression Plasmid pHUda996 
     The following primers xln-F and xln-R introducing a SphI site and a BamHI, respectively, were designed to isolate a promoter region of  A. nidulans  xlnA gene (PxInA) based on the nucleotide sequences information in EMBL:z49892: 
     
       
         
           
               
               
            
               
                   
                 xln-F (SEQ ID NO: 37):  
               
               
                   
                 gcatgcttaattaatggaagtgcgttgatcatt 
               
               
                   
                   
               
               
                   
                 xln-R (SEQ ID NO: 38):  
               
               
                   
                 ggatcccctgtcagttggg 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus nidulans  strain NRRL 1092 as template was performed using a primer pair of xln-F and xln-R. The reaction products were isolated on a 1.0% agarose gel and 0.7 kb product band was excised from the gel. The 0.7 kb amplified DNA fragment was digested with BamHI and SphI, and ligated into the  Aspergillus  expression cassette pHUda966 digested with BamHI and SphI to create pHUda966-PxInA. 
     The 1.3 kb DNA fragment containing synthetic version of FLP gene (sFLP) was recovered from pJaL1008 by BamHI and XhoI digestion. The recovered 1.3 kb fragment was ligated to BamHI and XhoI digested pHUda966-PxInA. The ligation mixture was transformed into  E. coli  DH5α to create the expression plasmid pHUda996. 
     The nucleotide sequences of the synthetic version of FLP expression parts in pHUda996 is shown in SEQ ID NO:39 together with features and positions of the primers used; the amino acid sequence of the encoded sFLP is shown in SEQ ID NO:40. 
     Construction of pHUda1000 for Simultaneous Site Specific-Integration at the Neutral Amylase 1 (NA1) and the Acid Stable Amylase Loci in NN059183 
     The following primers Pna-F and Pna-R introducing an EcoRI site and a BamHI site, respectively, were designed to isolate a promoter region of  A. niger  neutral amylase II (NA2) gene (Pna2) put triple in tandem fused with FRT-F recognition site based on the nucleotide sequences information in pJaL790 and EMBL:DJ052242: 
     
       
         
           
               
            
               
                 Pna-F (SEQ ID NO: 41): 
               
               
                 gaattcatcttgaagttcctattccgagttcctattctctagaaagtat 
               
               
                 aggaacttcgctagccgagagcagcttgaaga 
               
               
                   
               
               
                 Pna-R (SEQ ID NO: 42): 
               
               
                 ggatcccccagttgtgtatatagaggatt 
               
            
           
         
       
     
     A PCR reaction with pJaL790 as template was performed using a primer pair of Pna-F and Pna-R. The reaction products were isolated on a 1.0% agarose gel and 1.7 kb product band was excised from the gel. The 1.7 kb amplified DNA fragment was digested with EcoRI and BamHI, and ligated into the  Aspergillus  expression cassette pHUda440 harboring amyloglucosidase gene from  Trametes cingulata  (T.c. GA) digested with EcoRI and BamHI to create pHUda440-FRT. 
     The 2.2 kb DNA fragment containing  A. nidulans  pyrG gene was recovered from pHUda794 by PacI and SphI digestion. The recovered 2.2 kb fragment was ligated to PacI and SphI digested pHUda440-FRT. The ligation mixture was transformed into  E. coli  DH5α to create the expression plasmid pHUda440-FRT-pyrG. 
     The 2.4 kb DNA fragment containing FLP gene driven by xlnA promoter and niaD terminator was recovered from pHUda996 by PacI and XbaI digestion. The recovered 2.4 kb fragment was ligated to PacI and XbaI digested pHUda440-FRT-pyrG. The ligation mixture was transformed into  E. coli  DH5α to create the expression plasmid pHUda1000. A plasmid map is shown in  FIG. 4 . 
     Simultaneous Site Specific-Integration by FLP 
     The pHUda1000 was introduced into  Aspergillus niger  strain NN059183. Transformants were selected from the Cove-N (tf) supplemented with 1% D-xylose. Randomly selected transformants were inoculated onto Cove-N plates. Strains which grew well on Cove-N plates were purified and subjected to Southern blotting analysis to confirm whether the expression part in pHUda1000 was introduced correctly or not. 
     The following set of primers to make a non-radioactive probe was used to analyze the selected transformants. For T.c.GA coding region: 
     
       
         
           
               
               
            
               
                   
                 Forward primer (SEQ ID NO: 43):  
               
               
                   
                 tcgagtgcggccgacgcgtacgtc 
               
               
                   
                   
               
               
                   
                 Reverse primer (SEQ ID NO: 44):  
               
               
                   
                 cagagagtgttggtcacgta 
               
            
           
         
       
     
     Genomic DNA extracted from the selected transformants was digested by HindIII and Southern blotting analysis was preformed using the above probe. Strains of interest were identified by the disappearance of a 2.8 kb NcoI band and the appearance of a 3.1 kb NcoI band. By the right integration event, two hybridized signals of the size 7.2 kb and 5.7 kb introduced at NA1 and acid stable amylase loci, respectively, were seen. 
       FIG. 5A  shows the schematic NA1 locus and  FIG. 5B  shows the schematic acid stable amylase locus when the pHUda1000 was introduced correctly in NN059183. 
     Example 4.  A. niger  Ku70 Gene Disruption in NN059183 
     Construction of the  A. niger  Ku70 Gene Disruption Vector pHUda801 
     The following primers 3ku-F and 3ku-R introducing an EcoRI site and a SpeI site, respectively, were designed to isolate a 3′ flanking region of  A. niger  ku70 gene based on the nucleotide sequences information in EMBL:am270339: 
     
       
         
           
               
               
            
               
                   
                 3ku-F (SEQ ID NO: 45): 
               
               
                   
                 actagttctagaagccgtgggtatttttatgaa 
               
               
                   
                   
               
               
                   
                 3ku-R (SEQ ID NO: 46):  
               
               
                   
                 gaattcgtttaaacttggcggctgccaagcttcc 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus niger  strain NN059183 as template was performed using a primer pair of 3ku-F and 3ku-R. The reaction products were isolated on a 1.0% agarose gel and 2.0 kb product band was excised from the gel. The 2.0 kb amplified DNA fragment was digested with EcoRI and SpeI, and ligated into the pTK digested with EcoRI and SpeI to create pTK-3ku. 
     The following primers 5ku-F and 5ku-R introducing a NotI site and a SpeI site, respectively, were designed to isolate a 5′ flanking region of  A. niger  ku70 gene based on the nucleotide sequences information in EMBL:am270339: 
     
       
         
           
               
               
            
               
                   
                 5ku-F (SEQ ID NO: 47):  
               
               
                   
                 gcggccgctcattcagagagctacccgt 
               
               
                   
                   
               
               
                   
                 5ku-R (SEQ ID NO: 48):  
               
               
                   
                 actagttaattaagaggaccgcatctttga 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus niger  strain NN059183 as template was performed using a primer pair of 5ku-F and 5ku-R. The reaction products were isolated on a 1.0% agarose gel and 1.3 kb product band was excised from the gel. The 1.3 kb amplified DNA fragment was digested with NotI and SpeI, and ligated into the pTK-3ku digested with NotI and SpeI to create pTK-3ku-5ku. 
     The 2.2 kb DNA fragment containing  A. nidulans  pyrG gene was recovered from pHUda794 by SpeI and XbaI digestion. The recovered 2.2 kb fragment was ligated to SpeI and XbaI digested pTK-3ku-5ku. The ligation mixture was transformed into  E. coli  DH5α to create the expression plasmid pHUda801. 
     The nucleotide sequence of the  A. niger  ku70 gene and flanking sequences of pHUda801 are shown in SEQ ID NO:49; the amino acid sequence of the ku70-encoded polypeptide is shown in SEQ ID NO:50. A plasmid map is shown in  FIG. 6 . 
     The Ku70 Gene Disruption in NN059183 
     The pHUda801 was introduced into  Aspergillus niger  strain NN059183. Transformants were selected from the Cove-N (tf). Randomly selected transformants were inoculated onto Cove-N plates with 2.5 μM 5-Flouro-2-deoxyuridine (FdU), an agent which kills cells expressing the herpes simplex virus (HSV) thymidine kinase gene (TK) harboured in pHUda801. Strains which grew well on Cove-N plates with 2.5 μM FdU were purified and subjected to Southern blotting analysis to confirm whether the ku70 gene was disrupted correctly or not. 
     The following set of primers to make a non-radioactive probe was used to analyze the selected transformants. For the 3′ ku70 flanking region: 
     
       
         
           
               
               
            
               
                   
                 Forward primer (SEQ ID NO: 51):  
               
               
                   
                 acggtatgcgtacaatgatca 
               
               
                   
                   
               
               
                   
                 Reverse primer (SEQ ID NO: 52):  
               
               
                   
                 atttgagggcaccagcacccc 
               
            
           
         
       
     
     Genomic DNA extracted from the selected transformants was digested by SpeI. By the right gene disruption event, a hybridized signal of the size of 8.3 kb by SpeI digestion was shifted to 5.1 kb probed described above. Among the strains given the right integration events, a strain denoted C1997 was selected. 
     Example 5. Simultaneous Site Specific-Integration by FLP in the Two Loci in C1997 
     PyrG Gene Rescue in C1997 
     At first, the introduced pyrG gene at the ku70 loci in C1997 was rescued as follows. The strain C1997 was inoculated once on Cove-N media containing 10 mM uridine and 1 g/L 5-fluoro-orotic acid (5-FOA). Strains in which the pyrG gene has been deleted will grow in the presence of 5-FOA; those that retain the gene will convert 5-FOA to 5-fluoro-UMP, a toxic intermediate. The colonies that grew more quickly were isolated. The isolated strain was named M1117. 
     Simultaneous Site Specific-Integration by FLP in M1117 
     The pHUda1000 was introduced into  Aspergillus niger  strain M1117. Transformants were selected from the Cove-N (tf) supplemented with 1 g/L D-xylose. Randomly selected transformants were inoculated onto Cove-N plates. Strains which grew well on Cove-N plates were purified and subjected to Southern blotting analysis to confirm whether the expression part in pHUda1000 was introduced correctly or not. 
     The following set of primers to make a non-radioactive probe was used to analyze the selected transformants. For the T.c.GA coding region: 
     
       
         
           
               
               
            
               
                   
                 Forward primer (SEQ ID NO: 53):  
               
               
                   
                 tcgagtgcggccgacgcgtacgtc 
               
               
                   
                   
               
               
                   
                 Reverse primer (SEQ ID NO: 54):  
               
               
                   
                 cagagagtgttggtcacgta 
               
            
           
         
       
     
     Genomic DNA extracted from the selected transformants was digested by HindIII. By the right integration event, two hybridized signals at the size of 7.2 kb and 5.7 kb introduced at NA1 and acid stable amylase loci, respectively, were seen. 
     The frequency of the simultaneous integration with the ku70 gene disruption (M1117) was approx. 20% whereas that without ku70 gene disruption (NN059183) was around 4-5%. It suggested that the ku70 gene disruption played a great role in improving the locus specific integration frequency by FLP. 
     Example 6.  A. niger  Fcy1 Gene Disruption in NN059183 
     Construction of the  A. niger  (Cytosine Deaminase) Fcy1 Gene Disruption Vector pHUda1043 
     The following primers 3fcy-F and 3fcy-R introducing a XbaI site and a PmeI site, respectively, were designed to isolate a 3′ flanking region of  A. niger  fcy1 gene based on the nucleotide sequences information in EMBL:am269962: 
     
       
         
           
               
               
            
               
                   
                 3fcy-F (SEQ ID NO: 55):  
               
               
                   
                 tctagaattgaaagctagttctggtcgcat 
               
               
                   
                   
               
               
                   
                 3fcy-R (SEQ ID NO: 56):  
               
               
                   
                 gtttaaactccttgcttcgcatacatgcccac 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus niger  strain NN059183 as template was performed using a primer pair of 3fcy-F and 3fcy-R. The reaction products were isolated on a 1.0% agarose gel and 2.0 kb product band was excised from the gel. The 2.0 kb amplified DNA fragment was digested with XbaI and PmeI, and ligated into the pHUda801 digested with XbaI and PmeI to create pHUda801-3fcy. 
     The following primers 5fcy-F and 5fcy-R introducing a NotI site and a SpeI site, respectively, were designed to isolate a 5′ flanking region of  A. niger  fcy1 gene based on the nucleotide sequences information in EMBL:am269962: 
     
       
         
           
               
               
            
               
                   
                 5fcy-F (SEQ ID NO: 57):  
               
               
                   
                 gcggccgccgccgccgaagaactgagcaaa 
               
               
                   
                   
               
               
                   
                 5fcy-R (SEQ ID NO: 58):  
               
               
                   
                 actagtatatcttcttatcgcagagattg 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus niger  strain NN059183 as template was performed using a primer pair of 5fcy-F and 5fcy-R. The reaction products were isolated on a 1.0% agarose gel and 2.1 kb product band was excised from the gel. The 2.1 kb amplified DNA fragment was digested with NotI and SpeI, and ligated into the pHUda801-3fcy digested with NotI and SpeI to create pHUda1043. 
     The nucleotide sequence of the  A. niger  fcy1 gene and flanking sequences in pHUda1043 is shown in SEQ ID NO:59; the amino acid sequence of the fcy1-encoded polypeptide is shown in SEQ ID NO:60. A plasmid map is shown in  FIG. 7 . 
     The Fcy1 Gene Disruption in NN059183 
     The pHUda1043 was introduced into  Aspergillus niger  strain NN059183. Transformants were selected from the Cove-N (tf). Randomly selected transformants were inoculated onto Cove-N plates with 2.5 μM FdU, an agent which kills cells expressing the herpes simplex virus (HSV) thymidine kinase gene (TK) harbouring in pHUda1043. Strains which grew well on Cove-N plates with 2.5 μM FdU and Cove-N plates with 10 μg/ml 5-fluorocytosine (5FC) were purified and subjected to Southern blotting analysis to confirm whether the fcy1 gene was disrupted correctly or not. 
     The following set of primers to make a non-radioactive probe was used to analyze the selected transformants. For the 3′ fcy1 flanking region: 
     
       
         
           
               
               
            
               
                   
                 Forward primer (SEQ ID NO: 61):  
               
               
                   
                 gaaagctagttctggtcgcattgagc 
               
               
                   
                   
               
               
                   
                 Reverse primer (SEQ ID NO: 62):  
               
               
                   
                 gaagttgaaggagatgggtctgga 
               
            
           
         
       
     
     Genomic DNA extracted from the selected transformants was digested by NheI and XhoI and Southern blotting analysis was preformed using the above probe. Strains of interest were identified by the disappearance of a 3.1 kb NheI-XhoI band and the appearance of a 2.0 kb NheI-XhoI band. Among the strains given the right integration events, a strain NN059186 was selected. 
     Example 7. Introduction of FRT Sites and  A. niger  Fcy1 Gene at the Neutral Amylase II (NA2) Locus in  A. niger  NN059186 
     The pyrG Gene Rescue in NN059186 
     At first, the introduced pyrG gene at the fcy1 loci in NN059186 was rescued as follows. The strain NN059186 was inoculated once on Cove-N media containing 10 mM uridine and 1 g/L 5-fluoro-orotic acid (5-FOA). Strains in which the pyrG gene has been deleted will grow in the presence of 5-FOA; those that retain the gene will convert 5-FOA to 5-fluoro-UMP, a toxic intermediate. The colonies that grew more quickly were isolated. The isolated strain was named NN059200. 
     Construction of pHUda1078 for Introduction of FRT Sites and  A. niger  Fcy1 at the NA2 Loci 
     The following primers 3na2-F and 3na2-R introducing a XbaI site and a PmeI site, respectively, were designed to isolate a 3′ flanking region of  A. niger  NA2 gene fused with FRT-F3 site based on the nucleotide sequences information in EMBL:am270278 and DJ052242: 
     
       
         
           
               
            
               
                 3na2-F (SEQ ID NO: 63): 
               
               
                 tctagattgaagttcctattccgagttcctattcttcaaatagtatagga 
               
               
                 acttcatgtctccatgtttcttgagcggaagtact 
               
               
                   
               
               
                 3na2-R (SEQ ID NO: 64):  
               
               
                 gtttaaacgaagactgatattatggcggaa 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus niger  strain NN059183 as template was performed using a primer pair of 3na2-F and 3na2-R. The reaction products were isolated on a 1.0% agarose gel and 2.1 kb product band was excised from the gel. The 2.1 kb amplified DNA fragment was digested with XbaI and PmeI, and ligated into the pHUda801 digested with XbaI and PmeI to create pHUda801-3na2. 
     The following primers 5na2-F and 5na2-R introducing a NotI site and a SpeI site, respectively, were designed to isolate a 5′ flanking region of  A. niger  NA2 gene fused with FRT-F site based on the nucleotide sequences information in EMBL:am270278 and DJ052242: 
     
       
         
           
               
            
               
                 5na2-F (SEQ ID NO: 65):  
               
               
                 gcggccgcaagagtcaaaagatagcagagc 
               
               
                   
               
               
                 5na2-R (SEQ ID NO: 66): 
               
               
                 actagtgctagcgaagttcctatacttgaataggaactcggaataggaac 
               
               
                 ttcaagatgaattcgcggccggccgcatg 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus niger  strain NN059183 as template was performed using a primer pair of 5na2-F and 5na2-R. The reaction products were isolated on a 1.0% agarose gel and 2.0 kb product band was excised from the gel. The 2.0 kb amplified DNA fragment was digested with NotI and SpeI, and ligated into the pHUda801-3na2 digested with NotI and SpeI to create pHUda801-3na2-5na2. 
     The 4.3 kb DNA fragment containing T.c.GA gene driven by triple tandem NA2 promoter (Pna2) and AMG terminator (Tamg) was recovered from pHUda440-FRT by NheI and XbaI digestion. The recovered 4.3 kb fragment was ligated to NheI and XbaI digested pHUda801-3na2-5na2. The ligation mixture was transformed into  E. coli  DH5α to create the expression plasmid pHUda801-3na2-5na2-TC. 
     The 2.1 kb DNA fragment containing  A. nidulans  pyrG gene was recovered from pHUda794 by SpelI and XbaI digestion. The recovered 2.1 kb fragment was ligated to XbaI partially digested pHUda801-3na2-5na2-TC. The ligation mixture was transformed into  E. coli DH 5α to create the expression plasmid pHUda801-3na2-5na2-TC-pyrG. 
     The following primers fcy-F and fcy-R introducing a NheI site at both sites were designed to isolate an entire region of  A. niger  fcy1 gene based on the nucleotide sequences information in EMBL:am269962: 
     
       
         
           
               
               
            
               
                   
                 fcy-F (SEQ ID NO: 67):  
               
               
                   
                 gctagcgcgaggctatcacggaggctgtgg 
               
               
                   
                   
               
               
                   
                 fcy-R (SEQ ID NO: 68):  
               
               
                   
                 gctagcttctgtggttcttgccatgatcgt 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus niger  strain NN059183 as template was performed using a primer pair of fcy-F and fcy-R. The reaction products were isolated on a 1.0% agarose gel and 1.5 kb product band was excised from the gel. The 1.5 kb amplified DNA fragment was digested with NheI, and ligated into the pHUda801-3na2-5na2-TC-pyrG digested with NheI to create pHUda1078. 
     The nucleotide sequence of the  A. niger  NA2 gene with flanking sequences in pHUda1078 is shown in SEQ ID NO:69; the amino acid sequence of the NA2-encoded polypeptide is shown in SEQ ID NO:70. The nucleotide sequence of  A. niger  fcy1 in pHUda1078 &amp; 1067 (see below) is shown in SEQ ID NO:71 and the fcy1-encoded amino acid sequence in SEQ ID NO:72. A plasmid map of pHUda1078 is shown in  FIG. 8 . 
     Introduction of FRT Sites and  A. niger  Fcy1 Gene Plus T.c. GA at the NA2 Locus in  A. niger  NN059200 
     The pHUda1078 was introduced into  Aspergillus niger  strain NN059200. Transformants were selected from the Cove-N (tf). Randomly selected transformants were inoculated onto Cove-N plates with 2.5 μM 5-Flouro-2-deoxyuridine (FdU). Strains which grew well on Cove-N plates with 2.5 μM FdU and hardly grew on Cove-N plates with 10 μg/ml 5-fluorocytosine (5FC) were purified and subjected to Southern blotting analysis to confirm whether the FRT sites and fcy1/T.c.GA genes were introduced correctly at the NA2 locus or not. 
     The following set of primers to make a non-radioactive probe was used to analyze the selected transformants. For the T.c.GA coding region: 
     
       
         
           
               
               
            
               
                   
                 Forward primer (SEQ ID NO: 73):  
               
               
                   
                 tcgagtgcggccgacgcgtacgtc 
               
               
                   
                   
               
               
                   
                 Reverse primer (SEQ ID NO: 74):  
               
               
                   
                 cagagagtgttggtcacgta 
               
            
           
         
       
     
     Genomic DNA extracted from the selected transformants was digested by SpeI. By the right gene introduction event, a hybridized signal of the size of 4.4 kb by SpeI digestion was observed probed described above. Among the strains given the right integration events, a strain NN059203 was selected. 
     Example 8. Introduction of FRT Sites and the  A. niger  Fcy1 Gene as Well as the T.c.GA Gene at the Neutral Amylase I (NA1) and Acid Stable Amylase Locus in  A. niger  NN059203 
     The pyrG Gene Rescue in NN059203 
     The introduced pyrG gene at the NA2 loci in NN059203 was rescued as follows. The strain NN059203 was inoculated once on Cove-N media containing 10 mM uridine and 1 g/L 5-fluoro-orotic acid (5-FOA). Strains in which the pyrG gene has been deleted will grow in the presence of 5-FOA; those that retain the gene will convert 5-FOA to 5-fluoro-UMP, a toxic intermediate. The colonies that grew more quickly were isolated. The isolates strain was named NN059207. 
     Construction of pHUda1067 for Introduction of FRT Sites and  A. niger  Fcy1 at the NA1 and Acid Stable Amylase Loci 
     The following primers bac-F and bac-R introducing a XbaI site at both sites were designed to isolate a vector sequence of pBluescript II SK-fused with FRT-F and FRT-F3 sites: 
     
       
         
           
               
            
               
                 bac-F (SEQ ID NO: 75):  
               
               
                 tctagagaataggaactcggaataggaacttcaagatgaattcgcggccg 
               
               
                 cg 
               
               
                   
               
               
                 bac-R (SEQ ID NO: 76): 
               
               
                 tctagattgaagttcctattccgagttcctattcttcaaatagtatagga 
               
               
                 acttcagcatgcaagcttggcctccgc 
               
            
           
         
       
     
     A PCR reaction with pBluescript II SK- as template was performed using a primer pair of bac-F and bac-R. The reaction products were isolated on a 1.0% agarose gel and 2.7 kb product band was excised from the gel. The 2.7 kb amplified DNA fragment was digested with XbaI, and ligated into the pHUda1078 digested with XbaI to create pHUda1078-NA2. 
     The following primers FLP-F and FLP-R introducing a PacI site at both sites were designed to isolate a FLP expression cassette driven by  A. nidulans  xylanase promoter (PxInA) and  A. oryzae  niaD terminator (TniaD): 
     
       
         
           
               
               
            
               
                   
                 FLP-F (SEQ ID NO: 77):  
               
               
                   
                 ttaattaatggaagtgcgttgatcattatt 
               
               
                   
                   
               
               
                   
                 FLP-R (SEQ ID NO: 78):  
               
               
                   
                 ttaattaaactagtggagcgaaccaagtga 
               
            
           
         
       
     
     A PCR reaction with pHUda996 as template was performed using a primer pair of FLP-F and FLP-R. The reaction products were isolated on a 1.0% agarose gel and 2.4 kb product band was excised from the gel. The 2.4 kb amplified DNA fragment was digested with PacI, and ligated into the pHUda1078-NA2 digested with PacI to create pHUda1067. A plasmid map is shown in  FIG. 9 . 
     Introduction of FRT Sites and  A. niger  Fcy1 Gene and T.c.GA Gene at the NA1 and Acid Stable Amylase Loci in  A. niger  NN059207 
     The pHUda1067 was introduced into  Aspergillus niger  strain NN059207. Transformants were selected from the Cove-N (tf) supplemented with 1% D-xylose. Randomly selected transformants were inoculated onto Cove-N plates. Strains which grew well on Cove-N plates were purified and subjected to Southern blotting analysis to confirm whether the FRT sites and fcy1 gene in pHUda1067 was introduced at NA1 and acid stable amylase loci correctly or not. 
     The following set of primers to make a non-radioactive probe was used to analyze the selected transformants. For the T.c.GA coding region: 
     
       
         
           
               
               
            
               
                   
                 Forward primer (SEQ ID NO: 79):  
               
               
                   
                 tcgagtgcggccgacgcgtacgtc 
               
               
                   
                   
               
               
                   
                 Reverse primer (SEQ ID NO: 80):  
               
               
                   
                 cagagagtgttggtcacgta 
               
            
           
         
       
     
     Genomic DNA extracted from the selected transformants was digested by HindIII. By the right gene introduction event, hybridized signals of the size of 8.7 kb (NA1), 7.2 kb (acid stable amylase) and 5.6 kb (NA2) by HindIII digestion was observed when probed as described above. Among the strains with the right 3-copy integration events, a strain denoted NN059208 was selected. 
       FIG. 10A  shows the schematic NA1 locus,  FIG. 10B  shows the schematic NA2 locus and  FIG. 10C  shows the schematic acid stable amylase locus in NN059208. 
     NN059203 and NN059208 having 1-copy and 3-copy-T.c.GA genes, respectively, were fermented in shake flasks and their enzyme activities (AGU activities) were measured followed by the materials and methods described above; results are shown in table 1 below. Two-copy T.c. GA strains (1000-7, 18) generated by transformation of either NN059183 or C1997 with pHUda1000 were also fermented. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 The AGU activity of 1-, 2- and 3-copy strains, wherein 
               
               
                 NN059203 is normalized to 1.00. 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                   
                 T.c. GA 
                 AGU 
               
               
                 Strain 
                 Host 
                 plasmid 
                 copies 
                 relative activity 
               
               
                   
               
               
                 NN059203 
                 NN059183 
                 pHUda1078 
                 1 
                 1.00 
               
               
                 1000-7 
                 NN059183 
                 pHUda1000 
                 2 
                 1.98-2.08 
               
               
                 1000-18 
                 C1997 
                 pHUda1000 
                 2 
                 1.96-2.10 
               
               
                 NN059208 
                 NN059203 
                 pHUda1067 
                 3 
                 2.87-3.00 
               
               
                   
               
            
           
         
       
     
     Example 9. Simultaneous Gene Swapping T.c. GA Gene for JA126 Amylase Gene in the 3 Loci (NA1, NA2 and Acid Stable Amylase) in NN059208 by FLP 
     The pyrG Gene Rescue in NN059208 
     At first, the introduced pyrG genes at the NA1 and acid stable amylase loci in NN059208 were rescued as follows. The strain NN059208 was inoculated once on Cove-N media containing 10 mM uridine and 1 g/L 5-fluoro-orotic acid (5-FOA). Strains in which the pyrG gene has been deleted will grow in the presence of 5-FOA; those that retain the gene will convert 5-FOA to 5-fluoro-UMP, a toxic intermediate. The colonies that grew more quickly were isolated. The isolated strain was named NN059209. 
     Construction of pRika147 for Introduction of JA126 Amylase Gene at Three Loci 
     The 1.5 kb DNA fragment containing  A. niger  fcy1 gene was removed from pHUda1067 by NheI digestion. The recovered 1.5 kb fragment was re-ligated. The ligation mixture was transformed into  E. coli  DH5α to create the expression plasmid pHUda1067-fcy. 
     The following primers 126-F and 126-R introducing a BamHI site and a PmII site, respectively, were designed to isolate an encoding region of JA126 amylase comprising the secretion signal sequences of  A. niger  acid stable amylase, catalytic domain of amylase from  Rhizomucor pusillus  and linker and starch binding domain from glucoamylase of  Aspergillus niger : 
     
       
         
           
               
               
            
               
                   
                 126-F (SEQ ID NO: 81):  
               
               
                   
                 ggatccaccatgcggctctccacatcc 
               
               
                   
                   
               
               
                   
                 126-R (SEQ ID NO: 82):  
               
               
                   
                 cacgtgtgattacggacacaatccgttatt 
               
            
           
         
       
     
     The nucleotide sequence of the JA126 amylase gene is shown in SEQ ID NO:83 and the encoded amino acid sequence is shown in SEQ ID NO:84. 
     A PCR reaction with pJA126AN as template was performed using a primer pair of 126-F and 126-R. The reaction products were isolated on a 1.0% agarose gel and 1.9 kb product band was excised from the gel. The 1.9 kb amplified DNA fragment was digested with BamHI and PmII, and ligated into the pHUda1067-fcy digested with BamHI and PmII to create pRika147. A plasmid map is shown in  FIG. 11 . 
     Simultaneous Introduction of JA126 Amylase Gene in the 3 Loci (NA1, NA2 and Acid Stable Amylase) in NN059209 
     The pRika147 was introduced into  Aspergillus niger  strain NN059209. Transformants were selected from the Cove-N (tf) supplemented with 1% D-xylose and 10 μg/ml 5-fluorocytosine (5FC). Randomly selected transformants were inoculated onto Cove-N plates supplemented with 10 μg/ml 5-fluorocytosine (5FC). Strains which grew well on Cove-N plates supplemented with 10 μg/ml 5-fluorocytosine (5FC) were purified and subjected to Southern blotting analysis to confirm whether the JA126 gene in pRika147 was introduced at NA1, NA2 and acid stable amylase loci correctly or not. 
     The following set of primers to make a non-radioactive probe was used to analyze the selected transformants. For the JA126 coding region: 
     
       
         
           
               
               
            
               
                   
                 Forward primer (SEQ ID NO: 85):  
               
               
                   
                 tcgaacttcggcgacgagtcgcagttgaa 
               
               
                   
                   
               
               
                   
                 Reverse primer (SEQ ID NO: 86):  
               
               
                   
                 cccaacatctcggaaatcctggagaaaccc 
               
            
           
         
       
     
     Genomic DNA extracted from the selected transformants was digested by HindIII and PmII. By the right gene introduction event, hybridized signals of the size of 8.0 kb (NA1), 6.5 kb (acid stable amylase) and 4.8 kb (NA2) by HindIII and PmII digestion was observed when probed as described above. 
       FIG. 12A  shows the schematic NA1 locus,  FIG. 12B  shows the schematic NA2 locus and  FIG. 12C  shows the schematic acid stable amylase locus after the correct integration of pRika147 in NN059208. 
     The frequencies of generations of transformants by Cove-N plates supplemented with 10 μg/ml 5-fluorocytosine (5FC) was approx. 1/10,000 of those by Cove-N plates without 5FC. However, 50% of the generated strains by Cove-N plates supplemented with 10 μg/ml 5-fluorocytosine (5FC) gave right integration at 3 loci, whereas all strains selected randomly by Cove-N plates without 5FC gave right integration mostly at 1 loci, whereas no strains generated without 5FC showed the right integration events. It indicated that the counter-selection using the fcy1 gene worked very well. 
     Three strains (R147-17, 26, 34) introducing JA126 amylase gene at 3 loci were fermented in shake flasks and their enzyme activities (AFAU activities) were measured followed by the materials and methods described above; results are shown in table 2 below. As a reference, C2325, a single copy JA126 amylase strain generated by ordinary homologous recombination (not shown) was also fermented. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 The AFAU activity of 1- and 3-copy strains, wherein 
               
               
                 C2325 is normalized to 1.00. 
               
            
           
           
               
               
               
               
            
               
                   
                   
                 JA126 
                   
               
               
                   
                 Strain 
                 copies 
                 AFAU relative activity 
               
               
                   
               
               
                   
                 C2325 
                 1 
                 1.00 
               
               
                   
                 R147-17 
                 3 
                 2.75-2.96 
               
               
                   
                 R147-26 
                 3 
                 2.82-3.00 
               
               
                   
                 R147-34 
                 3 
                 3.15-3.18 
               
               
                   
               
            
           
         
       
     
     Example 10. Introduction of FRT Sites and TK Gene at the Amylase B (amyB) Locus in  A. oryzae  JaL1338 
     Construction of a ligD Disruption Plasmid, pJaL1123 
     Two restriction recognition sites for BamHI and BglII, respectively, were destroyed in pDV8. First pDV8 was digested with BamHI and then the ends were completely filled in by treatment with Klenow enzyme and the four dNTPs. The resulting 6030 bp fragment was re-ligated providing plasmid pJaL504. Secondly pJaL504 was digested with BglII and then the ends were completely filled in by treatment with Klenow enzyme and the 4 dNTPs. The resulting 6034 bp fragment was re-ligated providing plasmid pJaL504-delta-BglII. 
     By PCR with primers 172450 and 172449 a 2522 bp fragment was amplified containing the HSV-TK gene flank by the  A. nidulans  gpd promoter and TrpC terminator. The PCR fragment was then cloned into the plasmid pCR®4Blunt TOPO® vector resulting in pJaL574. 
     
       
         
           
               
            
               
                 Primer 172449 (SEQ ID NO: 87):  
               
               
                 gacgaattccgatgaatgtgtgtcctg 
               
               
                   
               
               
                 Primer 172450 (SEQ ID NO: 88):  
               
               
                 gacgaattctctagaagatctctcgaggagctcaagcttctgtacagtg 
               
               
                 accggtgactc 
               
            
           
         
       
     
     The  A. oryzae  pyrG gene from pJaL554 was isolated as 2403 bp StuI-EcoRI fragment, wherein the EcoRI site was completely filled in by treatment with Klenow enzyme and the 4 dNTPs. The fragment was cloned into the unique PmeI site in pJaL574 resulting in plasmid pJaL1022. 
     Plasmid pJaL1022 was digested with SspB1 and the 8574 bp fragment was isolated and re-ligated, resulting in plasmid pJaL1025. Plasmid pJaL1025 was digested with EcoRI and the 8559 bp fragment was isolated and re-ligated, resulting in plasmid pJaL1027. One of two BamHI sites was destroyed by partial digestion with BamHI following treatment with Klenow enzyme and the four dNTPs, whereby the ends were completely filled in. The 8563 bp fragment was re-ligated resulting in plasmid pJaL1029. 
     From the publicly available  A. oryzae  RIB40 genome sequence (NITE database (http://www.bio.nite.go.jp/dogan/project/view/AO) primers were designed to PCR amplify the 5′ flanking and the 3′ flanking sequences of the ligD gene (AO090120000322). The primers for the 5′ flanking part, X4407C0 and X4407C07, were tailed with BamHI and EcoRI sites, respectively: 
     
       
         
           
               
               
            
               
                   
                 Primer X4407C0 (SEQ ID NO: 89):  
               
               
                   
                 cagggatccgtctaggctgcaataggc 
               
               
                   
                   
               
               
                   
                 Primer X4407C07 (SEQ ID NO: 90):  
               
               
                   
                 ggagaattcggtcacatc 
               
            
           
         
       
     
     The primers for the 3′ flanking part, X7164D09 and X7164D10, were tailed with HindIII and SpeI sites, respectively: 
     
       
         
           
               
               
            
               
                   
                 Primer X7164D09 (SEQ ID NO: 91):  
               
               
                   
                 gacactagtcgtcggcagcaccggtg 
               
               
                   
                   
               
               
                   
                 Primer X7164D10 (SEQ ID NO: 92):  
               
               
                   
                 cagaagcttcagagtgaaatagacgcgg 
               
            
           
         
       
     
     Genomic DNA from ToC1512 was used as template for the PCR reaction. The amplified 5′ and 3′ fragments on 1114 bp and 914 bp were digested with BamHI-EcoRI and HindIII-SpeI, resulting in an 1102 bp fragment and a 902 bp fragment, respectively. The 3′ flanking fragment was cloned into the corresponding sites in pJaL1029 giving pJaL1120. The 5′ flanking fragment was then cloned into the corresponding sites in pJaL1120, resulting in pJaL1123. 
     Construction of a ligD Minus  A. oryzae  Strain, JaL1194. 
     Plasmid pJaL1123 was linearized with SpeI and used to transform  A. oryzae  ToC1512 and transformants were selected on minimal medium supplemented 0.6 mM 5-fluoro-2′-deoxyuridine (FdU) as described in WO 0168864. A number of transformants were re-isolated twice and genomic DNA was prepared. The chromosomal DNA from each of the transformants was digested with Asp718 and analyzed by Southern blotting, using the 1102 bp 32P-labelled DNA EcoRI-BamHI fragment from pJaL1123 containing the 5′ flanks of the  A. oryzae  ligD gene as the probe. Strains of interest were identified by the disappearance of a 3828 bp Asp718 band and the appearance of a 2899 bp Asp718 band. One transformant having the above characteristics was named JaL1194. 
     Isolation of a pyrG Minus  A. oryzae  Strain, JaL1196 
     The  A. oryzae  strain JaL1194 was screened for resistance to 5-flouro-orotic acid (FOA) to identify spontaneous pyrG mutants on minimal plates (Cove D. J. 1966. Biochem. Biophys. Acta. 113:51-56) supplemented with 1.0 M sucrose as carbon source, 10 mM sodiumnitrate as nitrogen source, and 0.5 mg/ml FOA. One strain, JaL1196, was identifying as being pyrG minus. JaL1196 is uridine dependent, therefore it can be transformed with the wild type pyrG gene and transformants selected by the ability to grow in the absence of uridine. 
     Construction of a Aflatrem Gene Cluster (Atm) Deletion Plasmid, pJaL1202 
       A. oryzae  telomere sequences were introduced around the TK expression cassette by PCR with primers T5483H12 and T5483G10 on pJaL574: 
     
       
         
           
               
            
               
                 Primer T5483H12 (SEQ ID NO: 93): 
               
               
                 gcacatatgatttaaatccctaatgttgaccctaatgttgaccctaatgt 
               
               
                 tgagcggccgcgtttaaacgaattcgccc 
               
               
                   
               
               
                 Primer T5483G10 (SEQ ID NO: 94): 
               
               
                 cgtaagcttatttaaatccctaatgttgaccctaatgttgaccctaatgt 
               
               
                 tgagaccggtgactctttctg 
               
            
           
         
       
     
     The amplified fragment of 2595 bp was digested with NdeI and HindIII and the resulting 2582 bp fragment was cloned into the corresponding sites in pU19 giving pJaL835. Plasmid pJaL835 was digested with HindIII, the ends were filled out by treatment with Klenow enzyme and the four dNTPs and then re-ligated to give pJaL955. 
     Plasmid pJaL554 was digested with HindIII and Asp718 and the resulting 1994 bp fragment encoding the  A. oryzae  pyrG gene was cloned into the corresponding sites in pToC65 giving pJaL1183. A 1535 bp fragment 5′ for the atm was amplified from ToC1512 genomic DNA by primers D5831F08 and D5831F09: 
     
       
         
           
               
               
            
               
                   
                 Primer D5831F08 (SEQ ID NO: 95): 
               
               
                   
                 gacgaattcggcgtgggaaattcctgg 
               
               
                   
                   
               
               
                   
                 Primer D5831F09 (SEQ ID NO: 96): 
               
               
                   
                 ccctacacctggggtacc 
               
            
           
         
       
     
     The amplified fragment was digested with EcoRI and Asp718 and the resulting 1514 bp fragment was cloned into the corresponding sites in pJaL1183 giving pJaL1194. The 3529 bp EcoRI-NotI fragment from pJaL1194 containing the atm 5′ flank and the pyrG gene was ligated together with the 3529 bp fragment from pJaL955 containing the TK gene, giving pJaL1202. Plasmid pJaL1202 is a plasmid for deletion of the chromosomal atm gene cluster. 
     Construction of a Atm Minus  A. oryzae  Strain, JaL1268. 
     Plasmid pJaL1202 was linearized with SpeI and used to transform  A. oryzae  JaL1196. Transformants were selected on minimal medium supplemented 0.6 mM 5-fluoro-2′-deoxyuridine (FdU) as described in WO 0168864. A number of transformants were re-isolated twice and genomic DNA was prepared. The chromosomal DNA from each of the transformants was digested with SacI and analyzed by Southern blotting, using the 1514 bp 32P-labelled DNA EcoRI-Asp718 fragment from pJaL1194 containing the 5′ flanks of the  A. oryzae  atm gene cluster as the probe. Strains of interest were identified by the disappearance of a 3230 bp SacI band and the appearance of a 4436 bp SacI band. One transformant having the above characteristics was named JaL1268. 
     Isolation of a pyrG Minus  A. oryzae  Strain, JaL1338 
     The  A. oryzae  strain JaL1268 was screened for resistance to 5-flouro-orotic acid (FOA) to identify spontaneous pyrG mutants on minimal plates (Cove D. J. 1966. Biochem. Biophys. Acta. 113:51-56) supplemented with 1.0 M sucrose as carbon source, 10 mM sodiumnitrate as nitrogen source, and 0.5 mg/ml FOA. One strain, JaL1338, was identifying as being pyrG minus. JaL1338 is uridine dependent, therefore it can be transformed with the wild type pyrG gene and transformants selected by the ability to grow in the absence of uridine. 
     Construction of a Plasmid Containing the TK Gene Flanked by FRT Sites for Integration at the Amylase B Locus, pJaL1258 
     From the publicly available  A. oryzae  RIB40 genome sequence (NITE database (http://www.bio.nite.go.jp/dogan/project/view/AO) primers were designed to amplify the 5′ flanking and the 3′ flanks sequences of the amylase B (amyB) gene (AO090023000944). The primers for the 5′ flanking part, D5775F04 and D5775D07, were tailed with NotI and HindIII sites, respectively: 
     
       
         
           
               
               
            
               
                   
                 Primer D5775F04 (SEQ ID NO: 97): 
               
               
                   
                 gacgcggccgcgctttgctaaaactttgg 
               
               
                   
                   
               
               
                   
                 Primer D5775D07 (SEQ ID NO: 98): 
               
               
                   
                 gacaagcttatgctcgatggaaacgtgcac 
               
            
           
         
       
     
     The primers for the 3′ flanking part, D5775D08 and D5775F05, were tailed with HindIII and NotI sites, respectively: 
     
       
         
           
               
               
            
               
                   
                 Primer D5775D08 (SEQ ID NO: 99): 
               
               
                   
                 gacaagcttacagtagttggactactttac 
               
               
                   
                   
               
               
                   
                 Primer D5775F05 (SEQ ID NO: 100): 
               
               
                   
                 gacgcggccgcgacgagcaactgacggc 
               
            
           
         
       
     
     Genomic DNA from ToC1512 was used as template for the PCR reaction. The amplified 5′ and 3′ fragments on 1307 bp and 511 bp were digested with NotI and HindIII, resulting in a 1294 bp fragment and a 498 bp fragment, respectively. The 5′ and 3′ flanking fragments were then cloned into the NotI sites in pToC65, resulting in pJaL1196. 
     The yeast 2μ plasmid FRT sites F and F3 (Schlake T. and Bode J. Use of mutated FLP recognition target (FRT) sites for the exchange of expression cassettes at defined chromosomal loci. Biochemistry 33: 12746-12751) were cloned into pUC19 by annealing of primers F3-1 and F3-2 to form an adaptor having overhang for cloning into the restriction sites BamHI and PstI of pUC19 giving pJaL952: 
     
       
         
           
               
            
               
                 Primer F3-1 (SEQ ID NO: 101): 
               
               
                 gatccttgaagttcctattccgagttcctattcttcaaatagtataggaa 
               
               
                 cttcactgca 
               
               
                   
               
               
                 Primer F3-2 (SEQ ID NO: 102): 
               
               
                 tgaagttcctatactatttgaagaataggaactcggaataggaacttcaa 
               
            
           
         
       
     
     The insertion of the FRT F3 site into pUC19 was verified by sequencing. Then the primers F-1 and F-2 were annealed together to form an adaptor having overhang for cloning into the restriction site Asp718 of pJaL952: 
     
       
         
           
               
            
               
                 Primer F-1  
               
               
                 (SEQ ID NO: 103) 
               
               
                 gtaccttgaagttcctattccgagttcctattctctagaaagtataggaa 
               
               
                   
               
               
                 cttca 
               
               
                   
               
               
                 Primer F-2  
               
               
                 (SEQ ID NO: 104) 
               
               
                 gtactgaagttcctatactttctagagaataggaagtcggaataggaact 
               
               
                   
               
               
                 tcaa 
               
            
           
         
       
     
     The insertion of the FRT F site in the same orientation as F3 into pJaL952 was verified by sequencing and a correct clone was name pJaL953. 
     The FRT F-F3 sites were inserted between the amyB flanks by taking a 142 bp Sack HindIII fragment from pJaL963 containing the FRT sites F and F3 and cloning that into pJaL1196 digested with SacI-HindIII, resulting in pJaL1249 which contains the 5′ amyB flank followed by the FRT F-F3 sites and the 3′ amyB flank. 
     The pyrG and TK genes were then inserted between the FRT F and FRT F3 sites as follows. A 4838 bp HindIII-SspBI fragment of pJaL1029, where the ends were filled in by treatment with Klenow enzyme and the four dNTP&#39;s, was cloned into the SmaI site of pJaL1249, providing a plasmid with the following arrangement of different elements: 5′ amyB flank-FRT F-pyrG-TK-FTRT F3-3′ amyB flank, which was named pJaL1258. 
     Construction of a  A. oryzae  Strain Having the FRT, pyrG, and TK Integrated at the amyB Locus, JaL1386. 
     Plasmid pJaL1258 was linearized with NotI and used to transform  A. oryzae  JaL1338; transformants were selected on minimal medium. A number of transformants were re-isolated twice and genomic DNA was prepared. The chromosomal DNA from each of the transformants was digested with XhoI and analyzed by Southern blotting, using the 1294 bp 32P-labelled DNA NotI-HindIII fragment from pJaL1196 containing the 5′ flanks of the  A. oryzae  amyB gene as probe. 
     Strains of interest were identified by the disappearance of a 4164 bp XhoI band and the appearance of an 8971 bp XhoI band. One transformant having the above characteristics was named JaL1386. 
     Isolation of a pyrG Minus  A. oryzae  Strain, JaL1394 
     The  A. oryzae  strain JaL1386 was screened for resistance to 5-flouro-orotic acid (FOA) to identify spontaneous pyrG mutants on minimal plates (Cove D. J. 1966. Biochem. Biophys. Acta. 113:51-56) supplemented with 1.0 M sucrose as carbon source, 10 mM sodiumnitrate as nitrogen source, and 0.5 mg/ml FOA. One strain, JaL1394, was identifying as being pyrG minus. JaL1394 is uridine dependent, therefore it can be transformed with the wild type pyrG gene and transformants selected by the ability to grow in the absence of uridine. 
     Example 11. Site Specific-Integration by FLP into the amyB Locus in JaL1394 
     Construction of a the Talaromyce  Emersonii  AMG Expression Cassette pRIKA99 
     A  Talaromyces emersonii  AMG gene containing introns was optimized to provide a synthetic gene (SEQ ID NO:105) for expression in  Aspergillus . For cloning purposes, BamHI and XhoI restriction sites were added to the 5′ end and 3′ end, respectively. The synthesized gene was obtained based on the sequence of plasmid pJ241:13509-Huda2. The 2085 bp BamHI-XhoI fragment encoding the  Talaromyce emersonii  AMG gene and the 9510 bp BamHI-XhoI fragment were isolated from plasmid pJ241:13509-Huda2 and pHUda1000, respectively. The two fragments were ligated together to created pRIKA99. 
     Site Specific-Integration of pRIKA99 in JaL1394 by FLP 
     The pRIKA99 was introduced into  Aspergillus oryzae  strain JaL1394. Transformants were selected on KCl-plates supplemented with 1% D-xylose and 0.6 mM 5-fluoro-2′-deoxyuridine (FdU). Four transformants were re-isolated twice and genomic DNA was prepared. The chromosomal DNA from each of the four transformants was digested with BglII-DraIII and BglII-KspI and analyzed by Southern blotting, first by using a 2095 bp 32P-labelled DNA BamHI-XhoI fragment from pRIKA99 containing the AMG gene and secondly after stripping of the filter by using a 731 bp 32P-labelled DNA AfeI-PacI fragment from pRIKA99 containing the  A. nidulans  xlnA promoter as the probes. 
     The right integration event was identified by giving with: 1) the AMG probe: 7145 bp and 3739 bp bands in the BglII-DraIII digestion and a 6845 bp band in the BglII-KspI digestion; 2) the  A. nidulans  xlnA promoter probe a 6845 bp band in the BglII-DraIII digestion and a 4039 bp band in the BglII-KspI digestion. 
     Example 12.  Aspergillus oryzae  Growth Inhibition by 5-Fluorocytosine (5FC) and Disruption of the Cytosine Aminase 
     To test that  A. oryzae  is growth inhibited by 5-fluorocytosine (5FC), spores of BECh2 were streaked on Cove-N (tf) supplemented with different concentration of 5FC (2.5, 1.5 and 0.625 μg/ml). No growth was detected at the lowest 5FC concentration (0.625 μg/ml) indicating that  A. oryzae  also has a cytosine deaminase. In  A. oryzae  there is only one orthologous gene (AO090003000802 of the public genome sequence) to the  A. niger  fcy1 gene (EMBL:am269962), therefore this has been disrupted to verify that this gene is the cytosine deaminase that causes cell death when growing on 5FC. 
     The AO090003000802 was disrupted by using the bipartite gene-targeting substrate as described in Nielsen et al (2005)  Efficient PCR - based gene targeting with a recyclable marker for Aspergillus nidulans , Fungal Gent Biol 43:54-64. Generation of a fragment on 2145 bp containing the 5′ flank of the  A. oryzae  AO090003000802 gene and a partial pyrG gene (promoter and ⅔ of the encoding region of the pyrG gene) was amplified by PCR. First, a 1036 bp fragment containing the 5′ flank of AO090003000802 was amplified by PCR with primers oJaL132 (CAGATACTGGTTCCTTACGG) (SEQ ID NO:108) and oJaL133 (CGTCCACGCGGGGATTATGCGTAGAATGCAGAGATAGCTG) (SEQ ID NO:109) with BECh2 genomic DNA as template. Then second, a 1129 bp fragment containing the 5′ part of the pyrG was amplified by PCR with primers X1111C07 (GCATAATCCCCGCGTGGACG) (SEQ ID NO:110) and oJaL114 (CCAACAGCCGACTCAGGAG) (SEQ ID NO:111) with pJaL554 as template DNA. The amplified products were isolated on a 1.0% agarose gel and mixed together and PCR was done with primers oJaL132 and oJaL114 resulting in an amplification product on 2145 bp, which was purified on a 1.0 agarose gel. 
     Generation of a fragment on 2436 bp containing the 3′ flank of the  A. oryzae  AO090003000802 gene and a partial pyrG gene (⅔ of the encoding region of the pyrG gene and the terminator) was amplified by PCR. First, a 1011 bp fragment containing the 5′ flank of AO090003000802 was amplified by PCR with primers oJaL134 (CGATAAGCTCCTTGACGGGGTTGAGCACTGCTTTTGGATC) (SEQ ID NO:112) and oJaL135 (GCTCACCCGGCATAAGTTGC) (SEQ ID NO:113) with BECh2 genomic DNA as template. Then second, a 1445 bp fragment containing the 5′ part of the pyrG was amplified by PCR with primers X1111C08 (CCCCGTCAAGGAGCTTATCG) (SEQ ID NO:114) and oJaL113 (GAGCTGCTGGATTTGGCTG) (SEQ ID NO:115)_with pJaL554 as template DNA. The amplified products were isolated on a 1.0% agarose gel and mixed together and PCR was done with primers oJaL1135 and oJaL135 resulting in an amplification product on 2436 bp, which was purified on a 1.0 agarose gel. 
     For disruption of the AO090003000802 gene the above two amplified fragments on 2145 bp and 2436 bp was mixed, transformed into  A. oryzae  JaL1398 strain and transformants was selected from the COVE-N plates. Southern blot analysis was used for verification of the disruption of the AO090003000802 gene. Genomic DNA extracted from 20 transformants was digested with PvuI-SpeI and Southern blotting analysis was performed using the above amplified PCR 1036 bp fragment was 32P-labeled and used as probe. Strains of interest were identified by the disappearance of a 5.5 kb PvuI-SpeI band and the appearance of a 6.9 kb PvuI-SpeI band. At the same time strains were tested for growth on COVE-N plates containing 0.625 μg/ml 5FC and only strains having the expected band on 6.9 kb show growth, which shows that the AO090003000802 gene is a cytosine deaminase. Among these strains one was selected and named JaL1500. 
     Example 13. Introduction of FRT Sites and  A. niger  Fcy1 Gene at the PAY (Putative Alkyl Sulfatase) Locus in  A. niger  NN059209 
     Construction of pHUda1174 ( FIG. 13 ) for Introduction of FRT Sites and  A. niger  Fcy1 at the PAY Locus 
     The following primers 3PAY-F and 3PAY-R introducing a XbaI site and a PmeI site, respectively, were designed to isolate a 3′ flanking region of  A. niger  PAY gene based on the nucleotide sequences information in EMBL:am270278. 
     
       
         
           
               
               
            
               
                   
                 (SEQ ID NO: 116) 
               
            
           
           
               
               
               
            
               
                   
                 3PAY-F: 
                 ttgcttctagacttctatttcctaatat 
               
               
                   
                   
               
            
           
           
               
               
            
               
                   
                 (SEQ ID NO: 117) 
               
            
           
           
               
               
               
            
               
                   
                 3PAY-R: 
                 ttgtttaaacttaattaaccgcgccat 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus niger  strain NN059183 as template was performed using a primer pair of 3PAY-F and 3PAY-R. The reaction products were isolated on a 1.0% agarose gel and 2.1 kb product band was excised from the gel. The 2.1 kb amplified DNA fragment was digested with XbaI and PmeI, and ligated into the pHUda801 digested with XbaI and PmeI to create pHUda801-3PAY. 
     The following primers 5PAY-F and 5PAY-R introducing a NotI site and a SpeI site, respectively, were designed to isolate a 5′ flanking region of  A. niger  PAY gene fused with FRT-F site based on the nucleotide sequences information in EMBL:am270278 and DJ052242. 
     
       
         
           
               
            
               
                 5PAY-F: 
               
               
                 (SEQ ID NO: 118) 
               
               
                 ggtggcggccgcgccgacggtgctggagga 
               
               
                   
               
               
                 5PAY-R: 
               
               
                 (SEQ ID NO: 119) 
               
               
                 tttactagtgaagttcctatactttctagagaataggaactcggaatagg 
               
               
                   
               
               
                 aacttcaagatgaattcctagtcgg 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus niger  strain NN059183 as template was performed using a primer pair of 5PAY-F and 5PAY-R. The reaction products were isolated on a 1.0% agarose gel and 1.3 kb product band was excised from the gel. The 1.3 kb amplified DNA fragment was digested with NotI and SpeI, and ligated into the pHUda801-3PAY digested with NotI and SpeI to create pHUda801-3PAY-5PAY. 
     The 4.3 kb DNA fragment containing T.c.GA gene driven by triple tandem NA2 promoter (Pna2) and AMG terminator (Tamg) was recovered from pHUda440-FRT by NheI and XbaI digestion. The recovered 4.3 kb fragment was ligated to NheI and XbaI digested pHUda801-3PAY-5PAY. The ligation mixture was transformed into  E. coli  DH5α to create the expression plasmid pHUda801-3PAY-5PAY-TC. 
     The following primers pyrG-F and pyrG-R introducing a XbaI site and a SpeI site, respectively, were designed to isolate a  A. nidulans  pyrG gene fused with FRT-F3 site based on the nucleotide sequences information in EMBL: EMBL:M19132 and DJ052242. 
     
       
         
           
               
            
               
                 pyrG-F: 
               
               
                 (SEQ ID NO: 120) 
               
               
                 ttagtactttgaagttcctattccgagttcctattcttcaaatagtatag 
               
               
                   
               
               
                 gaacttcaactagctagtgcatgcctagtggagcg 
               
               
                   
               
               
                 pyrG-R: 
               
               
                 (SEQ ID NO: 121) 
               
               
                 aagtctagaagcaagggcgaattccagca 
               
            
           
         
       
     
     A PCR reaction with genome DNA of pHUda794 as template was performed using a primer pair of pyrG-F and pyrG-R. The reaction products were isolated on a 1.0% agarose gel and 2.1 kb product band was excised from the gel. The 2.1 kb amplified DNA fragment was digested with XbaI and SpeI, and ligated into the pHUda801-3PAY-5PAY-TC digested with XbaI to create pHUda801-3PAY-5PAY-TC-pyrG. 
     The following primers fcy-F and fcy-R introducing a NheI site at both sites were designed to isolate an entire region of  A. niger  fcy1 gene based on the nucleotide sequences information in EMBL:am269962. 
     
       
         
           
               
               
            
               
                   
                 (SEQ ID NO: 122) 
               
            
           
           
               
               
               
            
               
                   
                 fcy-F: 
                 gctagcgcgaggctatcacggaggctgtgg 
               
               
                   
                   
               
            
           
           
               
               
            
               
                   
                 (SEQ ID NO: 123) 
               
            
           
           
               
               
               
            
               
                   
                 fcy-R: 
                 gctagcttctgtggttcttgccatgatcgt 
               
            
           
         
       
     
     A PCR reaction with genome DNA of  Aspergillus niger  strain NN059183 as template was performed using a primer pair of fcy-F and fcy-R. The reaction products were isolated on a 1.0% agarose gel and 1.5 kb product band was excised from the gel. The 1.5 kb amplified DNA fragment was digested with NheI, and ligated into the pHUda801-3PAY-5PAY-TC-pyrG digested with NheI to create pHUda1174 ( FIG. 13 ). 
     Introduction of FRT sites and  A. niger  fcy1 gene at the PAY locus in  A. niger  NN059209 
     The pHUda1174 was introduced into  Aspergillus niger  strain NN059209. Transformants were selected from the Cove-N (tf). Randomly selected transformants were inoculated onto Cove-N plates with 2.5 □M 5-Flouro-2-deoxyuridine (FdU). Strains which grew well on Cove-N plates with 2.5 μM FdU and hardly grew on Cove-N plates with 10 μg/ml 5-fluorocytosine (5FC) were purified and subjected to Southern blotting analysis to confirm whether the FRT sites and fcy1 gene was introduced at PAY loci correctly or not. 
     The following set of primers to make non-radioactive probe was used to analyze the selected transformants. For T.c.GA coding region, forward primer: tcgagtgcggccgacgcgtacgtc (SEQ ID NO:124), reverse primer: cagagagtgttggtcacgta (SEQ ID NO:125) Genomic DNA extracted from the selected transformants was digested by PmII. 
     By the right gene introduction event, a hybridized signal at the size of 7.7 kb by PmII digestion was observed probed described above. Among the strains given the right integration events, a strain NN059280 was selected. 
     Example 14. Competitive Gene Swapping for to Create Strains Having Altered Gene Copies of JA126 Amylase 
     The pyrG gene was rescued in NN059280. 
     The introduced pyrG gene at the PAY loci in NN059280 was rescued as follows. The strain NN059280 was inoculated once on Cove-N media containing 10 mM uridine and 1 g/L 5-fluoro-orotic acid (5-FOA). Strains in which the pyrG gene has been deleted will grow in the presence of 5-FOA; those that retain the gene will convert 5-FOA to 5-fluoro-UMP, a toxic intermediate. The colonies that grew more quickly were isolated. The isolates strain was named M1146. 
     Construction of an Empty Vector pHUda1306 ( FIG. 15 ) 
     The pRika147 was digested with NheI and PmII. The 8.1 kb DNA fragment was filled in by T4 DNA polymerase and re-ligated. The resultant plasmid was termed as pHUda1306 ( FIG. 15 ). 
     Competitive gene swapping using pRika147 and pHUda1306 to create strains having altered gene copies of JA126 amylase; see  FIGS. 16A, 16B, 16C, and 16D . 
     The pRika147 and pHUda1306 were co-introduced into  Aspergillus niger  strain M1146. Transformants were selected from the Cove-N (tf) supplemented with 1% D-xylose and 10 μg/ml 5-fluorocytosine (5FC). Randomly selected transformants were inoculated onto Cove-N plates supplemented with 10 μg/ml 5-fluorocytosine (5FC). Strains which grew well on Cove-N plates supplemented with 10 μg/ml 5-fluorocytosine (5FC) were purified and subjected to Southern blotting analysis to confirm whether the JA126 gene in pRika147 was introduced at NA1, NA2, SP288 or PAY loci correctly or not. 
     The following set of primers to make non-radioactive probe was used to analyze the selected transformants. For JA126 coding region: 
     
       
         
           
               
               
            
               
                 forward primer: 
                   
               
               
                 tcgaacttcggcgacgagtcgcagttgaa 
                 (SEQ ID NO: 126) 
               
               
                   
               
               
                 reverse primer: 
                   
               
               
                 cccaacatctcggaaatcctggagaaaccc 
                 (SEQ ID NO: 127) 
               
            
           
         
       
     
     Genomic DNA extracted from the selected transformants was digested by HindIII and PmII. By the right gene introduction event, hybridized signals at the size of 8.0 kb (NA1), 6.5 kb (SP288), 4.8 kb (NA2) and 4.5 kb (PAY) by HindIII and PmII digestion was observed probed described above. The frequencies of generations of transformants having 0˜4 gene copies of JA126 were mostly identical. Thus, transformants with various copy numbers of the gene in an interest were easily obtained by co-introduction of the expression plasmid and the empty plasmid. 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 Copy numbers 
                 Frequencies (%) 
               
               
                   
               
             
            
               
                   
                 0 
                 20 
               
               
                   
                 1 
                 18 
               
               
                   
                 2 
                 16 
               
               
                   
                 3 
                 18 
               
               
                   
                 4 
                 14 
               
               
                   
                 False integrations: 
                 12 
               
               
                   
               
            
           
         
       
     
     Example 15. Simultaneous Gene Swapping T.c. GA Gene for JA126 Amylase Gene in the 4 Loci (NA1, NA2, SP288 and PAY) in NN059280 by FLP and its Thermostable Variant FLPe 
     Construction of a Thermostable FLP Variant (FLPe) Expression Vector pHUda1352 
     Based on the sequence information on FLPe from literature (Improved properties of FLP recombinase evolved by cycling mutagenesis F. Buchholz, P. O. Angrand, A. F. Stewart. Nat. Biotechnol., 16 (1998), pp. 657-662), the following primers were made. 
     
       
         
           
               
            
               
                 FLPe1: 
               
               
                 (SEQ ID NO: 128) 
               
               
                 ggatctaccatgtcccagttcgatatcctctgcaagaccccccccaaggt 
               
               
                   
               
               
                 cctcgtccgccagttcgtcgagcgcttcgagcgcccctccggcgagaaga 
               
               
                   
               
               
                 tcgcctcctgcgccg 
               
               
                   
               
               
                 FLPe2: 
               
               
                 (SEQ ID NO: 129) 
               
               
                 atgcttctggccgttgtaggggatgatggt 
               
               
                   
               
               
                 FLPe3: 
               
               
                 (SEQ ID NO: 130) 
               
               
                 accatcatcccctacaacggccagaagcat 
               
               
                   
               
               
                 FLPe4; 
               
               
                 (SEQ ID NO: 131) 
               
               
                 ttgatggcgaagatggggtagggggcgttc 
               
               
                   
               
               
                 FLPe5: 
               
               
                 (SEQ ID NO: 132) 
               
               
                 gaacgccccctaccccatcttcgccatcaa 
               
               
                   
               
               
                 FLPe6; 
               
               
                 (SEQ ID NO: 133) 
               
               
                 ttcggatcagatgcggcggttgatgtagga 
               
            
           
         
       
     
     A PCR reaction with pHUda996 as template was performed using a primer pair of FLPe1 &amp; 2, FLPe 3 &amp;4 and FLPe 5 &amp; 6. The reaction products were isolated on a 1.0% agarose gel and 0.3, 0.6 and 0.5 kb product band was excised from the gel. These three fragments were mixed and used for the 2nd PCR reaction using a primer pair of FLPe 1 &amp; 6. The reaction products were isolated on a 1.0% agarose gel and 1.3 kb product band was excised from the gel. 1.3 kb amplified DNA fragment was digested with BamHI and BstBI, and ligated into the pHUda996 digested with BamHI and BstBI to create pHUda1352. 
     Construction of JA126 Amylase Expression Plasmid Carrying a Thermostable FLP Variant (FLPe) expression vector pHUda1356. The pHUda1352 was digested with BamHI and BstBI. The 1.3 kb DNA fragment was ligated into the pRika147 digested with BamHI and BstBI to create pHUda1356 ( FIG. 17 ).
 
Comparison of the Simultaneous Gene Swapping Efficiency Between FLP and FLPe
 
     The pRika147 and pHUda1356 were introduced into  Aspergillus niger  strain M1146. Transformants were selected from the Cove-N (tf) supplemented with 1% D-xylose and 10 μg/ml 5-fluorocytosine (5FC). Randomly selected transformants were inoculated onto Cove-N plates supplemented with 10 μg/ml 5-fluorocytosine (5FC). Strains which grew well on Cove-N plates supplemented with 10 μg/ml 5-fluorocytosine (5FC) were purified and subjected to Southern blotting analysis to confirm whether the JA126 gene in pRika147 was introduced at NA1, NA2, SP288 or PAY loci correctly or not. 
     The following set of primers to make non-radioactive probe was used to analyze the selected transformants. For JA126 coding region: 
     
       
         
           
               
               
            
               
                 forward primer: 
                   
               
               
                 tcgaacttcggcgacgagtcgcagttgaa 
                 (SEQ ID NO: 134) 
               
               
                   
               
               
                 reverse primer: 
                   
               
               
                 cccaacatctcggaaatcctggagaaaccc 
                 (SEQ ID NO: 135) 
               
            
           
         
       
     
     Genomic DNA extracted from the selected transformants was digested by HindIII and PmII. By the right gene introduction event, hybridized signals at the size of 8.0 kb (NA1), 6.5 kb (SP288), 4.8 kb (NA2) and 4.5 kb (PAY) by HindIII and PmII digestion was observed probed described above. The frequency of the simultaneous integration with the FLPe (pHUda1356) was approx. 3 times higher than that with FLP (pRika147), so the thermostable FLP variant FLPe provides an improved locus specific integration frequency. 
     Example 16. Introduction of FRT Sites and TK Genes at the Loci amyB and #13 in  A. oryzae    
     Construction of  A. oryzae  Strain JaL1398 
     Isolation of a niaD Minus  A. oryzae  Strain, JaL828 
     First the  A. oryzae  strain 5-58 (WO20099106488) was screened for resistance to chlorate to identify spontaneous niaD mutants on minimal plates (Cove D. J. 1966. Biochem. Biophys. Acta. 113:51-56) supplemented with 1.0 M sucrose as carbon source, 10 mM Na-glutamate as nitrogen source, and 5% Chlorate. One strain, JaL828, was identifying as being niaD minus. Second, the  A. oryzae  strain JaL828 was screened for resistance to 5-flouro-orotic acid (FOA) to identify spontaneous pyrG mutants on minimal plates (Cove D. J. 1966. Biochem. Biophys. Acta. 113:51-56) supplemented with 1.0 M sucrose as carbon source, 10 mM sodium nitrate as nitrogen source, and 0.5 mg/ml FOA. One strain, COIs454, was identifying as being pyrG minus. COIs454 is uridine dependent, therefore it can be transformed with the wild type pyrG gene and transformants selected by the ability to grow in the absence of uridine. Third the  A. oryzae  COIs454 strain was made ligD minus as described in example 10 resulting in  A. oryzae  strain JaL1390. Fourth the  A. oryzae  strain JaL1390 was made pyrG minus as described above resulting in strain JaL1398. 
     Construction of  A. oryzae  Strain JaL1523 Having the FRT::TK Integrated at the Loci amyB and #13 
     For integration of the TK flanked by FRT sites plasmid pJaL1258 was linearized with NotI and used to transform  A. oryzae  JaL1398; transformants were selected on minimal medium. A number of transformants were re-isolated twice and genomic DNA was prepared. The chromosomal DNA from each of the transformants was digested with XhoI and analyzed by Southern blotting, using the 1294 bp 32P-labelled DNA NotI-HindIII fragment from pJaL1196 containing the 5′ flanks of the  A. oryzae  amyB gene as probe. Strains of interest were identified by the disappearance of a 4164 bp XhoI band and the appearance of an 8971 bp XhoI band. One transformant having the above characteristics was named JaL1450. 
     Isolation of a pyrG Minus  A. oryzae  Strain, JaL1467 
     The  A. oryzae  strain JaL1450 was screened for resistance to 5-flouro-orotic acid (FOA) to identify spontaneous pyrG mutants on minimal plates (Cove D. J. 1966. Biochem. Biophys. Acta. 113:51-56) supplemented with 1.0 M sucrose as carbon source, 10 mM sodium nitrate as nitrogen source, and 0.5 mg/ml FOA. One strain, JaL1467, was identifying as being pyrG minus. JaL1467 is uridine dependent, therefore it can be transformed with the wild type pyrG gene and transformants selected by the ability to grow in the absence of uridine. 
     Construction of a Plasmid Containing the TK Gene Flank by FRT Site for Integration at the #13 Locus, pJaL1313 
     In plasmid pJaL835 (US2010062491) the single HindIII was destroyed by opening of the plasmid with HindIII and then the ends was fill out by treatment with 4dNTP&#39;s and Klenow following re-ligation resulting in plasmid pJaL955. 
     Out from the  A. oryzae  RIB40 genome sequence (www.bio.nite.go.jp/dogan/project/view/AO) primers were designed to amplify the 5′ flanking and the 3′ flanking sequences of the locus #13. The primers for the 5′ flanking part, K6763E12: gacgcggccgccgcgtggaggtctaggac (SEQ ID NO:136) and K6763F01: gacaagcttacaaacccgtgacactcc (SEQ ID NO:137) were tailed with NotI and HindIII sites, respectively. The primers for the 3′ flanking part K6763F02: gacaagcttacgcatgtatgtatgtgtc (SEQ ID NO:138) and K6763F03: gacgtttaaacggatgggtttgccatac (SEQ ID NO:139) were tailed with HindIII and PmeI sites, respectively. Genomic DNA from ToC1512 was used as template for the PCR reaction. The amplified 5′ and 3′ fragments on 1065 bp and 1032 bp were digested with NotI-HindIII and HindIII-PmeI, respectively, resulting in a 1052 bp fragment and a 1021 bp fragment, respectively. The 5′ and 3′ flanking fragments were then clone into the NotI-PmeI sites in pJaL955, resulting in pJaL968. The plasmid pJaL968 was digested with NheI-PmeI and ends were completely filled out by treatment with dNTP&#39;s and Klenow. The 4548 bp fragment was purified and self-ligated resulting in plasmid pJaL1285. 
     The yeast 2μ plasmid FRT sites F and F3 (Schlake T. and Bode J. Use of mutated FLP recognition target (FRT) sites for the exchange of expression cassettes at defined chromosomal loci. Biochemistry 33: 12746-12751) were clone into pUC19 by first annealing of primers F3-1 (SEQ ID NO: 15) and F3-2 (SEQ ID NO: 16) to form an adaptor having overhang for cloning into the restriction sites BamHI and PstI of pUC19 giving pJaL952. The insertion of the FRT F3 site into pUC19 was verified by sequencing. Second the primers F-1 and F-2 was annealed together to form an adaptor having overhang for cloning into the restriction site Asp718 of pJaL952. The insertion of the FRT F site in the right orientation same as F3 into pJaL952 was verified by sequencing and a right clone was name pJaL953. Plasmid pJaL953 was digested with SacI-ScaI and the resulting 1866 bp fragment was ligated to an 920 bp ScaI-SacI fragment from pIC19H, resulting in plasmid pJaL1289. 
     For insertion of the HSV-TK gene between the FRT sites the 4839 bp HindIII-BsrGl, where the ends are completely fill-out bu treatment with dNTP&#39;s and Klenow, where cloned into pJaL1289 digested with SmaI. A plasmid having the different elements in the following way: FRT F_pyrG_HSV-TK_FRT F3 was named pJaL1293. 
     The 4984 bp HindIII fragment harboring the FRT F_pyrG_HSV-TK_FRT F3 part of pJaL1293 was ligated to the 4548 bp HindIII fragment from pJaL1285. A plasmid having the different elements in the following way: 5′ #13 flank_FRT F_pyrG_HSV-TK_FRT F3_3′ #13 flank was named pJaL1313. 
     Construction of an  A. oryzae  Strain Having the FRT, pyrG, and TK Integrated at the #13 Locus, JaL1523. 
     Plasmid pJaL1313 was linearized with NotI and used to transform  A. oryzae  JaL1467 and transformants were selected on minimal medium. A number of transformants were re-isolated twice and genomic DNA was prepared. The chromosomal DNA from each of the transformants was digested with NheI-NdeI and analyzed by Southern blotting, using the 893 bp 32P-labelled DNA NcoI-HindIII fragment from pJaL1313 containing the 3′ flanks of the  A. oryzae # 13 locus as the probe. Strains of interest were identified by the disappearance of a 3896 kb NheI-NdeI band and the appearance of an 5607 kb NheI-NdeI band. One transformant having the above characteristics was named JaL1523. 
     Isolation of a pyrG Minus  A. oryzae  Strain, JaL1540 
     The  A. oryzae  strain JaL1523 was screened for resistance to 5-flouro-orotic acid (FOA) to identify spontaneous pyrG mutants on minimal plates (Cove D. J. 1966. Biochem. Biophys. Acta. 113:51-56) supplemented with 1.0 M sucrose as carbon source, 10 mM sodium nitrate as 4nitrogen source, and 0.5 mg/ml FOA. One strain, JaL1540, was identifying as being pyrG minus. JaL1540 is uridine dependent, therefore it can be transformed with the wild type pyrG gene and transformants selected by the ability to grow in the absence of uridine. 
     Example 17 Utilization of the FRT/FLP Recombination System for Site-Specific Integration in  Trichoderma reesei    
     Media and Reagents 
     The following media and reagents were used: 
     LB broth+100 μg/ml ampicillin: 10 g tryptone, 5 g yeast extract, 5 g NaCl and 1 ml 100 mg/ml ampicillin, per liter. 
     2YT amp: 16 g tryptone, 10 g yeast extract, 5 g NaCl, 15 g bacto agar, 1 ml 100 mg/ml ampicillin, per liter. 
     COVE: 342.3 g sucrose, 20 ml COVE salt solution, 10 ml 1M acetamide, 10 ml 1.5 M CsCl and 25 g Agar Noble, per liter. 
     COVE2+10 mM Uridine: 30 g sucrose, 20 ml COVE salt solution, 10 mM acetamide, 15 mM CsCl and 25 g Agar Noble, per liter. 
     CIM: 20 g Arbocel-natural cellulose fibers (J. Rettenmaier USA LP), 10 g corn steep solids (Sigma), 1.45 g (NH4)2SO4, 2.08 g KH2PO4, 0.28 g CaCl2, 0.42 g MgSO4.7H2O, 0.42 ml  T. reesei  Trace Metals, 2 drops of Pluronic L61 anti-foam. pH 6.0 per liter. 
     COVE Salt Solution: 26 g KCl, 26 g MgSO4 7H20, 76 g KH2PO4, 50 ml COVE trace elements, per liter. 
     Cove trace elements: 0.004 g Na2B4O710H2O, 0.4 g CuSO45H2O, 1.2 g FeSO47H2O, 0.7 g MnSO4H2O, 0.8 g Na2MoO22H2O, 10 g ZnSO4.7H2O, per liter. 
       T. reesei  Trace Metals: 216 g FeCl3.6H2O, 58 ZnSO4.7H2O, 27 g MnSO4.H2O, 10 g CuSO4.5H2O, 2.4 g H3BO, 336 g citric acid. 
     PEG: 500 g polyethylene glycol, 10 ml of 1 M Tris pH7.5, 10 ml of 1 M CaCl2, per liter 
     STC: 0.5 L 1 M Sorbitol, 10 ml of 1 M Tris pH7.5, 10 ml of 1 M CaCl2, per liter 
     TrMM: 30 g glucose, 0.6 g CaCl2, 6 g (NH4)2SO4, 20 ml COVE Salt Solution, 25 g Noble Agar, per liter 
     YPG2%: 10 g yeast extract, 20 g peptone, 20 g glucose, per liter. 
     Plasmid Construction 
     The FRT site integration vector pJfyS147 was constructed and is shown in  FIG. 18 . 
     The FRT/FLP expression vector pjfyS150 containing the beta-glucosidase was constructed and is shown in  FIG. 19 . 
       Trichoderma reesei  protoplasting and transformation 
     Protoplasts of  Trichoderma reesei  strain TV11 were generated as described previously WO 11/075677. Protoplasts were thawed on ice and 5×100 μl protoplast aliquots were transferred to 4×14 ml Falcon 2059 tubes. Pme I-linearized gel purified DNA (˜3 μg) was added to each tube to which 250 μl of 60% PEG were added. 
     The contents of the tubes were gently mixed by inverting gently 5 times and incubating them for 30 minutes at 34° C. To each tube 3 ml STC were added and 1.5 ml were plated to a 150 mm plate containing 50 ml of PDA+1 M Sucrose and spread using a sterile spreader. The plates were incubated at 28° C. for ˜18 hrs after which 20 ml of an overlay of PDA+10 mM uridine+35 μg/ml hygromycin B (Invitrogen cat #10687010) were added. Plates were incubated for 6 days at 28° C. until transformants were picked. 
     Pick Transformants 
     Transformants were picked with a 10 μl inoculating loop and transferred to a 75 mm diameter plate containing PDA agar and incubated for 5 days at 28° C. 
     Shake Flask Analysis of Transformants in CIM Media 
     Spores were collected with a 10 μl inoculation loop and transferred to 125 ml polycarbonate shake flasks, each containing 25 ml CIM media and incubated at 28° C. with shaking for 5 days. 
     Cure Hpt/Tk Markers 
     Spores of 7 day old plate were collected in 0.01% Tween-20 and spore concentrations determined with a hemacytometer. Spores were diluted in sterile diH20 and 104, 105 and 106 were plated to 150 mm TrMM+2% glucose plates+1 μM 5-flourodeoxyuridine (FdU). Plates were incubated for 6 days at 28° C. and spore isolates were picked using a 10 μl inoculation loop and transferred to new PDA plates and incubated at 28° C. 
     Genomic DNA Isolation/Southern Analysis 
     Spores were collected in 5 ml 0.01% Tween-20 and 2 ml were used to inoculate 50 ml of YPG2% medium in 250 ml baffled shake flasks. The cultures were incubated for 40 hours at 28° C. with shaking at 170 rpm. Agar plugs were removed and the cultures were filtered through MIRACLOTH™. Harvested biomass was frozen with liquid nitrogen and the mycelia were ground using a mortar and pestle. 
     Genomic DNA was isolated using a DNEASY® Plant Maxi Kit (QIAGEN, Valencia, Calif., USA) according to the manufacturer&#39;s instructions except that the lytic incubation period at 65° C. was extended to 1.5 hours from 10 minutes. The concentration of the resulting DNA containing solution was determined using a Nanodrop 1000 spectrophotometer (ThermoFischer Scientific, Waltham, Mass., USA). 
     Two and a half μg of genomic DNA were digested with 44 units NdeI in a 50 μl reaction volume at 37° C. for 22 hours. The digestion was subjected to 0.9% agarose gel electrophoresis in TAE buffer. The DNA was fragmented in the gel by treating with 0.25 M HCl, denatured with 1.5 M NaCl-0.5 M NaOH, neutralized with 1.5 M NaCl-1 M Tris pH 8, and then transferred in 20×SSC to a NYTRAN® Supercharge nylon membrane using a TURBOBLOTTER™ Kit (both from Whatman, Kent, UK). The DNA was UV crosslinked to the membrane using a UV STRATALINKER™ (Stratagene, La Jolla, Calif., USA) and prehybridized for 1 hour at 42° C. in 20 ml of DIG Easy Hyb (Roche Diagnostics Corporation, Indianapolis, Ind., USA). 
     A probe hybridizing to the 3′ flank of the  T. reesei  cbh2 gene was generated using a PCR Dig Probe Synthesis Kit (Roche Diagnostics Corporation, Indianapolis, Ind., USA) according to the manufacturer&#39;s instructions with the forward and reverse primers indicated below. The PCR reaction contained 1× HERCULASE® Reaction Buffer (Stratagene, La Jolla, Calif.), 400 nM each primer, 200 μM DIG-labeled dUTP-containing dNTPs, 125 ng TV10 genomic DNA, and 1.5 units HERCULASE® DNA polymerase. The cycling parameters were as follows: 1 cycle at 95° C. for 2 minute; 25 cycles each at 95° C. for 30 seconds, 55° C. for 30 seconds, and 72° C. for 40 seconds; and 1 cycle at 72° C. for 7 minutes. 
     
       
         
           
               
               
            
               
                   
                 (SEQ ID NO: 140) 
               
            
           
           
               
               
               
            
               
                   
                 Forward (069083): 
                 aaaaaacaaacatcccgttcataac 
               
               
                   
                   
               
            
           
           
               
               
            
               
                   
                 (SEQ ID NO: 141) 
               
            
           
           
               
               
               
            
               
                   
                 Reverse (069084): 
                 aacaaggtttaccggtttcgaaaag 
               
            
           
         
       
     
     The probe reaction was subjected to 1% agarose gel electrophoresis in TAE buffer and the band corresponding to the probe was excised and agarose-extracted using a MINELUTE® Gel Extraction Kit (QIAGEN Inc., Valencia, Calif., USA). The probe was boiled for 5 minutes and added to 10 ml of DIG Easy Hyb to produce the hybridization solution. Hybridization was performed at 42 degree C. for 15-17 hours. The membrane was then washed under high stringency conditions in 2×SSC plus 0.1% SDS for 5 minutes at room temperature followed by two washes in 0.1×SSC plus 0.1% SDS for 15 minutes each at 65° C. The probe-target hybrids were detected by chemiluminescent assay (Roche Diagnostics, Indianapolis, Ind., USA) according to the manufacturer&#39;s instructions. 
       Trichoderma reesei  Protoplasting and Transformation of the FLP Vector 
     Protoplasts of  Trichoderma reesei  strain TV11 were generated as described previously (14). Protoplasts were thawed on ice and 5×100 μl protoplasts each were transferred to 4×14 ml Falcon 2059 tubes. Pme I-linearized gel purified DNA (˜2 μg) was added to each tube and 250 μl 60% PEG were added. The contents of the tubes were gently mixed by inverting the tubes gently 5 times and incubated for 30 minutes at 34° C. To each tube 3 ml STC were added and 1.5 ml were plated to a 150 mm plate containing 50 ml of PDA+1 M Sucrose and spread using a sterile spreader. The plates were incubated at 28° C. for ˜18 hrs after which 20 ml of an overlay of PDA+10 mM uridine+35 μg/ml hygromycin B (Invitrogen cat #10687010) were added. Plates were incubated for 6 days at 28° C. until transformants were picked. 
     Spore PCR 
     To screen transformants for the integration of the FLP/FRT vector, transformants were screened by spore PCR. This was accomplished by collecting spores with a sterile 1 μl inoculation loop and transferring them to 25 μl TE buffer in a 0.6 ml Eppendorf tube. Spores were microwaved on high for 1 minute and 1 μl immediately added to an Advantage GC Genomic LA Polymerase PCR mix containing the following components: 1× reaction buffer, 200 μM dNTPs, 400 nM each primer, 1.25 U Polymerase. The PCR products were amplified with the following cycling parameters and the forward and reverse primers indicated below for either the 5′ integration or the 3′ integration: 95° C.—10 min, 30 cycles of 95° C.—30 seconds, 56° C.—30 seconds, 72° C.—1 minute 40 seconds and a final cycle of 72° C.—7 minutes. 
     
       
         
           
               
               
            
               
                   
                 5′ Recombination Forward (#0611526): 
               
            
           
           
               
               
               
            
               
                   
                 ttcccttcctctagtgttgaat 
                 (SEQ ID NO: 142) 
               
               
                   
                   
               
            
           
           
               
               
            
               
                   
                 Reverse No integration (#0611527): 
               
            
           
           
               
               
               
            
               
                   
                 tcgtcgaatactaacatcttgc 
                 (SEQ ID NO: 143) 
               
               
                   
                   
               
            
           
           
               
               
            
               
                   
                 Reverse Integration (#0611528): 
               
            
           
           
               
               
               
            
               
                   
                 cacggacctcgaacctttatat 
                 (SEQ ID NO: 144) 
               
               
                   
                   
               
            
           
           
               
               
            
               
                   
                 3′ Recombination Forward (#999661): 
               
            
           
           
               
               
               
            
               
                   
                 cagcgagagcctgacctattgcatc 
                 (SEQ ID NO: 145) 
               
               
                   
                   
               
            
           
           
               
               
            
               
                   
                 Reverse No integration (#069084): 
               
            
           
           
               
               
               
            
               
                   
                 aacaaggtttaccggtttcgaaaag 
                 (SEQ ID NO: 146) 
               
               
                   
                   
               
            
           
           
               
               
            
               
                   
                 Reverse Integration (#0611648): 
               
            
           
           
               
               
               
            
               
                   
                 gtggctgccgaggtgtgtatacca 
                 (SEQ ID NO: 147) 
               
            
           
         
       
     
     The entire PCR reactions were run on a 1% agarose gel in 50 ml TAE buffer containing 500 ng/ml Ethidium Bromide and products visualized with UV light. 
     Results 
     The FRT site integration vector, pJfyS147 ( FIG. 18 ) was designed so that the sites would be integrated in the genome at the cbh1 locus. The two FRT sites are slightly different in an attempt to prevent unwanted recombination between them and were named FRT-F and FRT-F3 for the 5′ and 3′ sites, respectively. The 5′ cbh1 flank used to target the vector to the locus was chosen so that the cbh1 coding sequence as well as a 1 kb portion of the promoter would also be deleted as the promoter is also incorporated into the expression vector used later and a successful integration would restore the promoter. Since the vector also deletes the cbh1 gene when correctly integrated at the cbh1 locus this allows for a simple proteomic screen since the SDS-PAGE profile would be substantially altered with the removal of CBH1. When protoplasts of strain TV11 were transformed with pJfyS147, one hundred and thirty-three transformants were obtained. All of these transformants were picked and analyzed in shake flasks under cellulase inducing conditions. Of the 133 transformants analyzed, two showed the proteomic profile consistent with deletion of cbh1. 
     The two transformants showing the altered proteomic profile were expected to have the FRT integration plasmid at the cbh1 locus. Two strains JfyS147-20 and -73 were plated to  Trichoderma  minimal media containing 5-fluorodeoxyuridine (FdU) in an attempt to facilitate the excision of the hpt/tk cassettes. Seventy-two FdU resistant colonies were obtained on the plates from strain JfyS147-20 and a lawn was obtained from strain JfyS147-73. Eight colonies were picked from JfyS147-20 named JfyS147-20A to -20H and a section of the lawn was picked from JfyS147-73 and the resulting strain was named JfyS147-73A. Four isolates from JfyS147-20 as well as the one isolated region from JfyS147-73, were analyzed by Southern to determine if the FRT cassette had been cleanly integrated and the hpt/tk markers were correctly excised. 
     Southern analysis showed that one transformant, JfyS47-20, had the deletion cassette at the cbh1 locus as expected and the resulting spore progeny had excised the hpt/tk markers. The other transformant, JfyS147-73, failed to show any hybridization. The region containing the FRTF and FRTF3 sites was PCR amplified from genomic DNA of JfyS147-20B and sequenced to confirm the presence of the two sites. Protoplasts of this stain were generated and transformed with the FLP/FRT integration vector pJfyS150 ( FIG. 19 ). 
     The expression vector pJfyS150 is a derivative of a  Trichoderma  expression vector containing the cbh1 promoter and terminator with the hygromycin phosphotransferase gene for hygromycin resistance. pJfyS150 differs from its parent in that it also contains the FRT-F and FRTF3 sites that reside in the genome of JfyS147-20B and the codon optimized flippase gene (FLP) cassette derived from pRiKa147 (obtained from HuDa). The reporter used was the  A. fumigatus  BG. 
     The vector was linearized with Pme I to remove the bacterial propagation part of the plasmid and the resulting gel-purified fragment used to transform JfyS147-20B protoplasts from which twenty transformants were obtained. The 20 transformants obtained here represented an efficiency of 2.5/μg. 
     The twenty transformants were analyzed by spore PCR to determine if the cassette had been integrated at the desired locus by amplifying the 5′ region of the site of insertion. If the integration of the cassette is ectopic a 1 kb fragment results and if the integration happens with the FRT sites the result is a 1.8 kb PCR product. Of the 20 obtained, 18 appeared to have ectopic integrations while two showed a PCR band consistent with integration at the cbh1 locus but the size was smaller than expected. When the PCR fragments were sequenced the results indicated that the recombination had occurred between the FRTF site present at the locus and two different regions in the cbh1 promoter. 
     1% xylose was added to the protoplast storage solution prior to transformation in an attempt to speed up the required cellular response events. Protoplasts with extra xylose were transformed with the same expression vector as before, pJfyS150, and 19 transformants were obtained. The 19 transformants were analyzed by PCR screen on the 5′ end as before as well as by an additional set of primers hybridizing to the 3′ region of integration. 
     The results indicated that that 5 of the 19 transformants had integrated the cassette at the FRTF site in the 5′ region. Also 2 transformants gave no band in the PCR screen suggesting that region of the locus had been rearranged during transformation, indicating some sort of inexact locus-specific targeting as seen with the previous set of transformants. The PCR screen of the FRTF3 site region on the 3′ end of the transforming integration vector indicated that 5 transformants had undergone the necessary FLP-mediated integration at the 3′ end, and that 3 of the 5 had undergone both necessary recombination. When each region was analyzed separately a few of the transformants had undergone the desired recombination at only one of the FRT sites but a nonspecific recombination at the other. 3 transformants had undergone the required recombination at both FRT sites, which was an improvement compared to the process without the addition of xylose into the protoplast storage media. 
     Accordingly, the FLP/FRT system was successfully utilized in  T. reesei  to introduce an expression plasmid to the cbh1 locus in  T. reesei . In particular strain JfyS147-20B was generated and contained the FRT sites at the cbh1 locus. A new expression vector was also generated incorporating the cbh1 promoter and terminator, the hpt gene as a selection marker, the  A. fumigatus  BG gene as a reporter, as well as the FRT sites and FLP gene required for the system. This new vector, pJfyS150, was used to insert the  A. fumigatus  BG cassette at the cbh1 locus using the FLP/FRT system with an insertion frequency of 15.7% (or at least 10.5% as one of the strains showed instability of the cassette during propagation in shake flasks).