# Patent

## Title
Method for the targeted integration of multiple copies of a gene of interest in a yarrowia strain

## Abstract

This invention concerns a method for the targeted integration of at least three copies of a gene of interest in the genome of a Yarrowia strain including the steps of: (a) cultivating a Yarrowia strain, said strain including a deletion among at least three genes, the phenotype associated with each of these deletions corresponding to an auxotrophy or to a dominant character for this strain; (b) transforming said Yarrowia strain thus obtained with at least three recombinant vectors that include selection markers allowing, for this strain, the complementation of auxotrophy and, potentially, of the dominant character resulting from each of these deletions; and (c) selecting, on a minimum medium, the yeasts having integrated said at least three recombinant vectors. This invention also includes a method for producing a polypeptide of interest using this method as well as a method for obtaining a modified Yarrowia strain including a deletion among at least three genes, the phenotype associated with each of these deletions corresponding to an auxotrophy or to a dominant character for this strain.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a U.S. National Stage of international application PCT/EP2009/051332, filed Feb. 5, 2009, which designates the U.S. and which was not filed or published in English and claims priority to French patent application FR 0850736, filed Feb. 5, 2008. Each of these applications is incorporated by reference herein in its entirety.
This invention concerns a method for the targeted integration of at least three copies of a gene of interest in the genome of a Yarrowia strain that includes the steps of (a) cultivating a Yarrowia strain, said strain including a deletion among at least three genes, the phenotype associated with each of said deletions corresponding to an auxotrophy or to a dominant character for said strain; (b) transforming the Yarrowia strain thus obtained using at least three recombinant vectors, including selection markers enabling, for this Yarrowia strain, the complementation of auxotrophy and, potentially, the dominant character resulting from each of the deletions; and (c) selecting, on a minimum medium, yeasts having integrated these at least three recombinant vectors. This invention also includes a method for producing a polypeptide of interest using said method as well as a method for obtaining a modified Yarrowia strain including a deletion among at least three genes, the phenotype associated with each of these deletions corresponding to an auxotrophy or to a dominant character for this strain.
Yarrowia lipolytica yeast is now increasingly used as expression host for genes of interest. This yeast has the specific characteristic of producing and secreting high molecular weight proteins such as alkaline proteases, acid proteases or RNase with great effectiveness in the culture medium, these proteins then being easily recovered from the culture medium. In order to permit the expression of these genes of interest, various technologies were developed early such as those described more particularly in patent EP 0 138 508 B1 or EP 0 220 864 B1. These different technologies have in common that they use “integrative” vectors that allow the insertion of a DNA segment carrying the gene of interest in the chromosomal DNA; this gene of interest is then expressed. Nevertheless, none of these technologies have completely satisfied the requirements of industrial production, namely a large yield and great stability over time.
New technologies have been developed to better satisfy these industrial requirements.
Thus, patent application PCT WO 00/12729 describes a technology that uses integrative vectors comprising a sequence of interest flanked by zeta sequences corresponding to the LTRs of the retrotransposon Ylt1 of Yarrowia lipolytica. When they are used in Yarrowia lipolytica strains devoid of zeta sequences, these integrative vectors allow multicopy, random integrations in the genome of these strains. This particular technology was used in particular to produce acid-resistant extracellular lipase LIP2 (see patent application PCT WO 01/83773).
However, it appeared that the majority of the Yarrowia lipolytica strains transformed by LIP2 had mediocre genetic stability, generally below 50%. Furthermore, since these transformed strains are obtained as a result of random integration events, monitoring the genetic stability of the strains via sequencing of the insertion sites is extremely tedious.
Added to the problems relating to the stability of the obtained strains and the difficulty in identifying the precise integration site of the exogenous sequence are the additional problems associated with the absence of Yarrowia lipolytica strains lacking multiple selection markers due to the instability of these strains.
Among the expression cassette integration methods, we can cite those using homologous transformation methods, but these methods use few markers (LEU2, URA3, LYS5) and few multimarked strains and have deletions allowing a sharp decrease in conversion rates. The strains often have genome markers corresponding to mutations and few markers corresponding to deletions. The only genome markers known with deletions are: ura3-302 (deletion of 695 pb), ura3-41 (deletion of 41 pb), leu2-270 (StuI deletion of 681 pb). MADZAK et al. (J. of Biotech., vol. 109, p: 63-81, 2004) thus describes the markers ura3-302 and leu2-270.
Among the vectors, we can cite those that allow targeted integration, but by integrating the plasmid portion, i.e., integration of plasmids in a pBR322 (Madzak et. al., Fems yeast research, vol. 5, p: 635-646, 2005) or zeta (Bordes et al., J. Microbiol Methods Vol. 70, p. 493-502, 2007) platform. There are autocloning vectors for integration and amplification. However these vectors are dispersed and random.
To produce therapeutic proteins, no plasmid DNA is necessary and targeted integration is necessary to identify the insertion and verify its sequence. It is also necessary to be able to increase the number of copies of the gene to increase expression.
The inventors have devised a method that allows targeted integration thanks to “integration vectors” that were constructed to release the integration cassette (rare site 1) and eliminate the vector portion, which have rare sites for introducing the selection markers quickly (rare site 2) and for cloning the expression cassettes (rare site 3). Combinations of integration vectors with a different locus/marker combination.
The inventors have also:

    
    
        optimized transformation conditions to increase the transformation rates, particularly for the ADE2 and GUT2 markers; and
        achieved the association of integration and a phenotype to quickly identify the interesting clones that have integrated the integration cassettes in the desired locus.
    
    


Thus, the inventors have produced here a method for integrating an expression cassette at a locus that makes it possible to introduce a new selection marker at the same time (e.g., new genome marker, new auxotrophy) to allow a new integration with a new integration cassette possessing the corresponding selection marker.
Due to the possibility of good transformation effectiveness, a low conversion rate, and insertion identification screening (lipase for LIP2, brown for ADE2, SUC− for URA3), it is thus possible to achieve cointegration (transforming with two integration cassettes). This makes it possible to reduce the time necessary to obtain the production strain. Likewise, insertion at defined sites allows rapid characterization of the production strains. The final strain being prototrophic
The final strain no longer expresses the major proteins secreted (AEP protease, LIP2p lipase); it has stable deletions, weak cell lysis and a clean supernatant (few secreted proteins).
The inventors have also demonstrated the possibility of obtaining the general excision of the markers with these excisable markers making it possible to regenerate the markers and thus to be able once again to integrate new copies.
To obtain multi-marked strains, a genome marker can be inserted via different methods.
For example, the POP IN/POP OUT method is used in Yarrowia lipolytica to construct the leu2-270, ura3-302 and xpr2-322 markers and is described in the publication by G. Barth et al.: Yarrowia lipolytica. in: Nonconventional Yeasts in Biotechnology A Handbook (Wolf, K., Ed.), Vol. 1, 1996, pp. 313-388. Springer Verlag. It consists in integrating a vector possessing a deletion of the gene at the locus then in selecting the excision of this vector and identifying a clone that, through recombination, eliminated the wild-type gene and retained the mutated gene. This is a lengthy, inefficient method that also requires the use of a counter-selection marker. For example, the counter-selection of Ura+clones with 5FOA. This counter-selection can introduce secondary mutations.
The SEP method (Maftahi, N, Nicaud, J-M., Gaillardin, C., 1996. Sticky-end polymerase chain reaction method for systematic gene disruption in Saccharomyces cerevisiae. Yeast, vol. 12, p: 859-868) can also be used. This method was adapted in Yarrowia lipolytica for the successive disruption of the POX genes (Wang, H. J., Le Dall, M-T., Waché, Y., Belin, J-M., Gaillardin, C. Nicaud, J-M., 1999. Evaluation of Acyl CoA oxidase (Aox) isozymes function in the n-alkanes-assimilating yeast Yarrowia lipolytica. J. Bacteriol., vol. 181, p. 5140-5148). This method is faster, but still requires the use of a counter-selection marker.
It is also possible to use the SEP/cre method developed by Fickers et al., (Fickers, P., Le Dall, M. T., Gaillardin, C., Thonart, P., Nicaud, J-M., New disruption cassettes for rapid gene disruption and marker rescue in the yeast Yarrowia lipolytica. J. Microbiol. Methods vol. 55, p: 727-737, 2003). This is a fast method that does not require the use of a counter-selection marker. This method consists in 1) selecting the gene of interest that is to be deleted, 2) constructing a disruption cassette via PCR (“Polymerase Chain Reaction) or via cloning, 3) introducing a selection marker containing on both sides a recombination sequence (advantageously a loxP or loxR sequence or derivative) allowing
a recombination between it for the elimination of the marker (advantageously a loxP type sequence that allows recombination under the action of the cre recombinase), 4) selecting the strains with the gene of interest deleted (transformation and selection of the transformants) and verifying the disruption, 5) transforming with a vector allowing the expression of the recombinase (advantageously the cre recombinase, which allows the recombination of the loxP/loxR sequences and the elimination of the marker), and 6) the isolation of a clone having the deletion of the gene of interest and having lost the recombinase expression plasmid. However, it is necessary to optimize the deletions and the markers in order to minimize the gene conversions during transformation.
It is clear from the preceding that there are no existing transformation technologies making it possible to integrate the sequence of a gene of interest specifically and stably in the genome of Yarrowia lipolytica in order to obtain a significant expression of this gene.
The inventors have now shown that the stability of the Yarrowia strains obtained by transformation was highly dependent on the number of integrated copies. Thus, a strain with 8 integrated copies of the LIP2 gene has 70% stability; this stability increases to 98% for 7 copies and to 100% for 6 copies.
Similarly, the inventors have succeeded in developing new, viable strains of Yarrowia lipolytica displaying auxotrophy and, potentially, a dominant character associated with at least three distinct selection markers chosen in particular from among the selection markers Ura3, Leu2, Lut 2 and Ade2. The viable strains developed also have broad deletions (Ura3-302, Leu2-270, Gut2-744 and Ade2-844), particularly with the new Gut2-744 and Ade2-844 deletions, which make it possible to considerably limit the frequency of gene conversion (cf. examples).
The use of these types of strains in integration methods, particularly targeted integration methods, makes it possible to obtain transformed strains containing multiple integrations of a gene of interest much more quickly and simply.
Finally, the inventors have succeeded in developing a new method for transforming strains of Yarrowia lipolytica making it possible to obtain stable transformed strains with an interesting production level of a polypeptide of interest.
PURPOSE OF THE INVENTION
The purpose of the invention is to remedy the disadvantages of the prior art and quickly obtain strains that overproduce a gene or genes of interest for the production of heterologous proteins and to be able to quickly verify the expression cassettes and characterize the production strain.
Strains possessing selection markers allowing a low conversion level and high transformation effectiveness are used as microorganisms.
A set of vectors allowing the construction of vectors containing the expression cassettes and of vectors containing the integration cassettes are used;
Quick methods for identifying the transformants containing the integration of the integration cassettes at the defined loci are also used.
Finally, the method according to the invention allows the production of a heterologous protein.
In more detailed fashion, the invention proposes sets of strains, vectors, selection markers, and phenotype and characterization assays for the insertion of insertion cassettes to quickly obtain strains that overproduce a gene or genes of interest for the production of heterologous proteins and for the quick verification of the expression cassettes and characterization of the production strain that includes:

    (a) Receiver strains containing deletions of genes conferring an auxotrophy or a growth defect on certain media;
    (b) A set of cloning vectors allowing the construction of “expression vectors” that contain the expression cassettes; a set of “integration vectors” allowing the construction of integration vectors;
    (c) Methods for obtaining transformants and for identifying the transformants containing the integration of the integration cassettes at the defined locus; and
    (d) A method for producing the heterologous protein.

As a result, the first purpose of the invention concerns a method for the targeted integration of at least three copies of a gene of interest in the genome of a Yarrowia strain including the steps of: 2 a deletion in at least three genes and characterized in that it is independent of any of these three genes; the phenotype associated with each of these deletions corresponds to an auxotrophy or to a dominant character for this strain;

    b) transformation of this auxotrophic or dominant character Yarrowia strain with at least three recombinant vectors that contain selection markers enabling, for this Yarrowia strain, the complementation of the auxotrophy and/or the dominant phenotype resulting from each of the deletions, these recombinant vectors each containing:
    i) the sequence of the gene of interest,
    ii) a selection marker, and
    iii) two DNA sequences framing the sequence of the gene of interest and the selection marker; these two DNA sequences are homologous to the sequences corresponding to the ends of the targeted integration site in the genome of the Yarrowia strain in order to allow the targeted integration of this recombinant vector via homologous recombination;
    c) selection on a minimum medium of the yeasts having integrated at least three recombinant vectors.


In a preferred embodiment, the targeted integration method according to the invention is characterized in that the genes having a deletion and associated with an auxotrophic phenotype or a dominant character phenotype are chosen from among:

    
    
        for the auxotrophy markers, the URA3, LEU2, GUT2, ADE2, HIS and LYS5 genes; and
        for the dominant characters, the hygromycin-resistance gene HYG4, and the MDR3, KanMX, HPH and Tn5ble genes.
    
    


Preferably, the genes with a deletion are associated with an auxotrophic phenotype, UFA3, LEU2, GUT2 and ADE2 genes being the most preferred genes.
Advantageously, the URA3 deletion corresponds to the Ura3-302 deletion, which is well known to the person skilled in the art and described in particular in MADZAK et al. (2004).
Advantageously, the LEU2 deletion corresponds to the Leu2-270 deletion also well known to one with ordinary skill in the art and described in particular in MADZAK et al. (2004).
Advantageously, the GUT2 deletion corresponds to the Gut2-744 deletion described in the examples. Gut2-744 corresponds to a complete deletion of the ORF of the GUT 2 gene (SEQ ID NO: 4), of which deletion is present in the mutant FF-Lug (CNCM-3911) and FF-luga (CNCM-3913) strains. After excision, the sequence SEQ ID NO: 11 remains on the Yarrowia genome between the GUT2 promoter and terminator sequences.
Advantageously, the ADE2 deletion corresponds to the Ade2-844 deletion described in the examples. Ade2-844 corresponds to a complete deletion of the ORF of the ADE2 gene (SEQ ID NO: 3), of which deletion is present in the FF-Lua (CNCM-3912) and FF-luga (CNCM -3913) strains. After excision, the sequence SEQ ID NO: 12 remains on the Yarrowia genome between the ADE2 promoter and terminator sequences.
Minimal medium, as used here, means a medium that does not contain the elements for which the Yarrowia strain is auxotrophic or one potentially allowing for the selection of the strain.
Yarrowia strains are well known to the one with ordinary skill in the art. We can cite the Yarrowia lipolytica strains as preferred examples of these strains.
The technique for transforming a yeast via targeted integration of a gene is a frequently used molecular biology technique. In this technique, a DNA fragment is cloned in a vector and inserted in the cell to be transformed; this DNA fragment is then integrated through homologous recombination in a targeted region of the receiver genome (ORR-WEAVER et al., Proc. Natl. Acad. Sci. USA, vol. 78, p: 6354-6358, 1981). These transformation methods are well known to one with ordinary skill in the art and are described in particular in ITO et al. (J. Bacteriol., vol. 153, p: 163-168, 1983), in KLEBE et al., (Gene, vol. 25, p: 333-341, 1983) and in GYSLER et al. (Biotechn. Techn., vol. 4, p: 285-290, 1990). Inasmuch as this recombination event is rare, selection markers are inserted between the sequences ensuring recombination in order to make it possible, after transformation, to isolate the cells where the integration of the fragment took place through the revelation of the corresponding markers.
The selection markers allowing auxotrophy complementation, also commonly called auxotrophic markers, are well known to one with ordinary skill in the art.
The selection marker URA3 is well known to one with ordinary skill in the art. More specifically, a Yarrowia strain whose URA3 gene (SEQ ID No. 1 for Yarrowia lipolytica, this sequence is also accessible via the accession number Yali0E2679g, encoding for orotidine-5′-phosphate decarboxylase, is inactivated (for example, by deletion) and will not be able to grow on a medium that is not supplemented with uracil. The integration of the URA3 selection marker in this strain of Yarrowia will then make it possible to restore the growth of this strain on a medium devoid of uracil.
The LEU2 selection marker described more particularly in U.S. Pat. No. 4,937,189 is also well known to the one with ordinary skill in the art. More specifically, a Yarrowia strain whose LEU2 gene (Yali0E26719g; SEQ ID No. 2 for Yarrowia lipolytica), encoding for 13-isopropylmalate dehydrogenase, is inactivated (for example by deletion) will not be able to grow on a medium not supplemented with leucine. As before, the integration of the LEU2 selection marker in this strain of Yarrowia will thus make it possible to restore the growth of this strain on a medium not supplemented with leucine.
The ADE2 selection marker is also well known to the one with ordinary skill in the field of yeast transformation. A Yarrowia strain whose ADE2 gene (SEQ ID No. 3 for Yarrowia lipolytica, YALI0B23188g), encoding for phosphoribosylaminoimidazole carboxylase, is inactivated (for example by deletion) will not be able to grow on a medium not supplemented with adenine. Here again, the integration of the ADE2 selection marker in this strain of Yarrowia will then make it possible to restore the growth of this strain on a medium not supplemented with adenine.
The GUT2 gene encodes for glycerol-3-phosphate dehydrogenase (SEQ ID No. 4, for Yarrowia lipolytica, YALI0B13970g) and its inactivation (for example by deletion) leads to the inability of the resulting mutant to grow on a non-fermentable medium whose carbon source corresponds to glycerol.
Among the resistance genes that may be used as a selection marker to give the Yarrowia strain a phenotype having a dominant character, we can cite:

    
    
        The mouse MDR3 gene encodes for P-glycoprotein and, when it is expressed in a strain of Yarrowia, confers resistance to FK520 (antifungal agent and immunosuppressor; RAYMOND et al., Mol. Cell. Biol., vol. 14, p: 277-286, 1994).
        The KanMX module, which contains the kanr sequence coming from the transposon Tn903 of Escherichia coli fused with the transcriptional sequences of the TEF gene of the filamentous fungus Ashbya gossypii or with any functional transcription promoter or terminator gives a Yarrowia strain resistance to geneticin (G418; WACH et al., Yeast, vol. 10, p: 1793-1808, 1994).
        The HPH gene (HYG), originally from an Escherichia coli plasmid, allows resistance to hygromycin B (GRITZ & DAVIES, Yeast, vol. 8, p: 667-668, 1992; CORDERO OTERO & GAILLAIRDIN, Applied Microbiol and Biotechnologies, vol. 46, p: 143-148, 2004).
        The Escherichia coli Tn5ble gene allows transformed yeast to acquire resistance to phleomycin (WENZEL et al., Yeast, vol. 8, p: 667-668, 1992).
    
    


Other selection markers that can be used in the method according to the invention are also described by BARTH & GAILLARDIN (The dimoorphic fungus Yarrowia lipolytica. In: Non conventional yeasts in biotechnology (Wolf K, Ed.). Springer-Verlag, Berlin, p: 313-388, 1996).
In an embodiment that is also preferred, the targeted integration method according to the invention is characterized in that in step b), the targeted integration site in the genome of this strain of Yarrowia is chosen from among the URA3, LEU2, ADE2, LIP2, LIP7, LIP8, AXP, GUT2 and XPR2 genes.
Preferably, the targeted integration method is characterized in that in step b), the integration site in the genome of this Yarrowia strain is chosen from among the genes, therefore the disruption confers an easily detectable phenotype (visualizable, measurable) particularly from among the URA3, ADE2, LIP2, LIP8 and AXP genes.
The LIP2 gene (SEQ ID NO. 5 for Yarrowia lipolytica) may be used as insertion locus. The LIP2 gene encodes for an extracellular lipase (PIGNEDE et al., J. Bacteriol., vol. 182(10), p: 2802-10, 2000) which preferentially hydrolyzes the long chain triglycerides of the oleic residues. A Yarrowia strain whose LIP2 gene is inactivated (for example by deletion), will have reduced lipase activity (weak extracellular lipase activity, weak hydrolysis halo in a Petri dish of tributyrin).
The LIP8 gene (SEQ ID No. 6 for Yarrowia lipolytica) may be used as insertion locus. The LIP8 gene encodes for a triaclyglycerol hydrolase. A Yarrowia strain whose LIP8 gene is inactivated (after having inactivated LIP2) will not show any tributyrin hydrolysis halo on a dish of YNBT medium and no lipase activity (FICKERS et al., Fungal Genetics and Biology, vol. 42, P; 264-274, 2005).
The AXP gene (SEQ ID No. 7 for Yarrowia lipolytica) may be used as insertion locus. The AXP gene encodes for an extracellular acid protease normally expressed when the pH of the medium is lower than 4. A Yarrowia strain whose AXP gene is inactivated (for example by deletion) will present on a dish of YNBcaseine at an acid pH a diminished caseine hydrolysis halo and reduced protease activity (GLOVER et al., Microbiology, vol. 143, p: 3045-54, 1997).
The XPR2 gene encodes for an extracellular alkaline protease expressed when the pH of the medium is higher than 6. A Yarrowia strain whose XPR2 gene (SEQ ID No. 8 for Yarrowia lipolytica) is inactivated (for example by deletion) will show a reduced caseine hydrolysis halo and reduced protease activity on a dish of YNBcaseine at pH6 (DAVIDOW et. al., J. Bacteriol., vol. 169, p. 4621-9, 1987).
Preferably, this auxotrophic Yarrowia strain will include at least one deletion among the URA3, LEU2 and ADE2 or URA3, LEU2 and GUT2 genes.
For example, we can cite the strain of Yarrowia lipolytica deposited on Feb. 4, 2008 in accordance with the Budapest Treaty with the Collection nationale de Culture de Microorganismes (CNCM), PASTEUR INSTITUTE, 25 rue du Docteur Roux, 75724 PARIS CEDEX 15, France under the number CNCM-3912.
For example, we can cite the strain of Yarrowia lipolytica deposited on Feb. 4, 2008 in accordance with the Budapest Treaty with the Collection nationale de Culture de Microorganismes (CNCM), PASTEUR INSTITUTE, 25 rue du Docteur Roux, 75724 PARIS CEDEX 15, France under the number CNCM-3911.
Advantageously, the auxotrophic Yarrowia strain used in step a) in the method according to the invention includes a deletion among four genes resulting in an auxotrophic phenotype for the four genes of the group including URA3, LEU2, ADE2 and GUT2.
[Text illegible] the Yarrowia lipolytica strain deposited on Feb. 4, 2008, in accordance with the Budapest Treaty with the Collection nationale de Culture de Microorganismes (CNCM), PASTEUR INSTITUTE, 25 rue du Docteur Roux, 75724 PARIS CEDEX 15, France under the number CNCM-3913.
According to a preferred embodiment of the method according to the invention, this embodiment allows the targeted integration of from 3 to 10 copies of the gene of interest, preferably from 4 to 8 copies and more preferably still from 5 to 7 copies of this gene of interest.
Advantageously, the method according to the invention includes the transformation of this auxotrophic Yarrowia strain with from three to ten recombinant vectors, preferably from 4 to 8 recombinant vectors and, more preferably still, from 5 to 7 recombinant vectors.
The recombinant vectors used in step b) may also include one or more selection markers distinct from those allowing for this Yarrowia strain complementation of the auxotrophy and, potentially, of the dominant character resulting from the deletions among the at least three genes.
The encoding sequences for the selection marker and those for the gene of interest also include the elements necessary for their expression in a strain of Yarrowia. 
These elements correspond in particular to active promoter and terminator sequences in a strain of Yarrowia. Preferably, the promoter and terminator sequences used belong to different genes in order to minimize the risks of undesired recombination in the genome of the Yarrowia strain.
These promoter sequences are well known to one with ordinary skill in the art and may correspond in particular to inducible or constitutive promoters. For examples of promoters that may be used in the method according to the invention, we can cite in particular the promoter of a gene of Yarrowia lipolytica that is strongly repressed by glucose and that is inducible by fatty acids or triglycerides such as the POX2 promoter of the acyl CoA oxidase 2 gene of Yarrowia lipolytica and the promoter of the LIP2 gene described in patent application PCT WO 01/83773. We can also use the promoter of the FBA1 gene of the fructose-bisphosphate aldolase gene (US 2005/0130280), the promoter of the YAT1 gene of the ammonium transporter gene (US 2006/0094102 A1), the promoter of the GPAT gene of the glycerol-3-phosphate O -acyltransferase gene (US 2006/0057690 A1), the TEF gene promoter (US 2001/6265185) and the hp4d hybrid promoter (WO9641889).
These terminator sequences are also well known to one with ordinary skill in the art, and we can cite as examples of terminator sequences that can be used in the method according to the invention the terminator sequence of the PGK1 gene and the terminator sequence of the LIP2 gene described in application PCT WO 01/83773.
When the product of the gene of interest is intended to be secreted by the host cell, this insert also includes secretion control signals for this product. To this end, functional signal sequences in Yarrowia strains can be used, for example all or part of the prepro sequence of the LIP2 gene described in application PCT WO 01/83773.
The gene of interest encodes for a polypeptide to be produced in large quantity in the transformed Yarrowia strain. This polypeptide preferably corresponds to a heterologous polypeptide like Erwinia chrysanthemi L-asparaginase (SEQ ID No. 9) or Escherichia coli (SEQ ID No. 10), however it may also correspond to an autologous peptide like the Yarrowia lipolytica LIP2 lipase described earlier.
According to a particular embodiment of the method according to the invention, steps b) transformation of the Yarrowia strain and c) selection on minimum medium are performed separately for each of the at least three recombinant vectors.
According to a more preferred embodiment, the targeted integration method according to the invention is characterized in that, in step b), transformations with at least three recombinant vectors are carried out independently and successively with each of the recombinant vectors or simultaneously with all of these recombinant vectors, and in that all of these transformations are followed by a step c) involving selection on a minimal medium of yeasts that have integrated all of these recombinant vectors.
According to another preferred embodiment, the method according to the invention is characterized in that the selection marker is framed by sequences allowing its excision to follow the targeted integration of this recombinant vector.
According to a fourth preferred embodiment of the method according to the invention, the selection marker is framed by sequences allowing its excision following the targeted integration of this recombinant vector.
The method according to the invention thus makes it possible to reuse a same selection marker, particularly an auxotrophic marker, for another targeted integration during a new transformation step.
Such sequences allowing the excision and elimination of a framed sequence in a Yarrowia strain are well known to one with ordinary skill in the art.
For example, we can cite the use of two identical or similar sequences, called direct repeat sequences (DRS), in order to obtain a recombination event as described in patent EP 0994192 B1 or in patent EP 0635574 B1.
For example, we can also cite the “Cre-lox” system as described in patent EP 0220009 B1, in which the sequences equivalent to the direct repeat sequences are in this case specific sequences called “lox,” and the excision of the DNA sequence included between the two “lox” sequences is done in the presence of a “Cre” recombinase expressed by an expression vector. Other equivalent systems using other specific recombinases are also known to one of ordinary skill in the art, particularly the method described in patent EP 0814165 B1.
From another perspective, this invention concerns a method for producing a polypeptide encoded by a gene of interest, characterized in that it includes:

    A) a targeted integration method according to the invention;
    B) a step d) cultivation of the Yarrowia strain in a liquid culture medium containing assimilable sources of carbon, nitrogen and inorganic salts in order to allow the growth of this transformed strain of Yarrowia and
    C) the recovery of this expressed polypeptide of interest from the Yarrowia cells or from the culture medium obtained in step B).


Advantageously, the method according to the invention includes a step e) after step C) involving purification of this polypeptide encoded by the gene of interest.
This purification step e) can be performed either after cell lysis or, advantageously, using the culture medium in which it is secreted by the cells, using standard known techniques, for example by fractionated precipitation followed by one or more chromatography steps.
The transformed Yarrowia cells likely to be obtained via the method according to the invention are also part of this invention.
In another aspect, this invention relates to a method for obtaining a modified strain of Yarrowia, characterized in that it includes a step in which this Yarrowia strain is transformed with at least three vectors resulting in a Yarrowia strain including a deletion in at least three genes and characterized by the independence of these three genes from one another. The phenotype associated with each of these deletions corresponds to an auxotrophy or to a dominant character for this strain.
Preferably here, the deletion of at least three genes is associated with an auxotrophic or dominant character phenotype which are selected from among:

    
    
        for auxotrophic markers, the URA3, LEU2, GUT2, ADE2, HIS and LYS5 genes, and preferably from among the URA3, LEU2, GUT2 and ADE2 genes; and
        for dominant characters, the hygromycin-resistance gene HPH (HYG), and the MDR3, KanMX and Tn5ble genes, the HYG gene also being the most preferred of the resistance genes.
    
    


In an embodiment that is also preferred, the method for obtaining a modified Yarrowia strain according to the invention is characterized in that the genes having a deletion are associated with an auxotrophic phenotype and are preferably chosen from among the URA3, LEU2, GUT2 and ADE2 genes.
According to a final aspect, this invention concerns an auxotrophic strain of Yarrowia potentially having an acquired dominant character likely to be obtained via the method for obtaining a modified Yarrowia strain according to the invention. The strain includes a deletion in at least three genes of its genome and is characterized in the independence of these three genes from one another; the phenotype associated with each of these deletions corresponds to an auxotrophy or to a dominant character for this strain. Each of the preferences defined for the number of genes deleted, the genes chosen for the deletion as defined
for step a) of the integration method according to the invention is also preferred for this method.
Advantageously, the strain of Yarrowia obtained via this method is a strain of Yarrowia lipolytica. 
Preferably, this auxotrophic strain of Yarrowia will include at least one mutation among the URA3, LEU2 and ADE2 or URA3, LEU2 and GUT2 genes.
For example, we can cite the Yarrowia lipolytica strains deposited on Feb. 4, 2008 in accordance with the Budapest Treaty with the Collection nationale de Culture de Microorganismes (CNCM), PASTEUR INSTITUTE, 25 rue du Docteur Roux, 75724 PARIS CEDEX 15, France under the numbers CNCMI-3911 and CNCM I-3912.
According to a second preferred embodiment, the auxotrophic strain of Yarrowia used in the method according to the invention includes a mutation among four genes necessary for the growth of this strain, of which three genes are chosen from the group containing URA3, LEU2, ADE2, LIP2, LIP7, LIP8, AXP, GUT2 and XPR2.
Preferably, this auxotrophic strain of Yarrowia will include at least one mutation among the URA3, LEU2, ADE2 and GUT2 genes.
For example, we can cite the Yarrowia lipolytica strain deposited on Feb. 4, 2008 in accordance with the Budapest Treaty with the Collection nationale de Culture de Microorganismes (CNCM), PASTEUR INSTITUTE, 25 rue du Docteur Roux, 75724 PARIS CEDEX 15, France under the number CNCM I-3913.
This invention will be better understood by means of the figures and their legend and the additional description that will follow, which refers to non-limiting examples for obtaining transformed strains of Yarrowia lipolytica according to the invention.



FIGURE LEGENDS
FIG. 1: Schematic representation of the construction of a targeted “integration cassette” of an “expression cassette.” 1) The gene of interest is cloned in an expression vector, 2) the expression cassette is released via I-SceI digestion, 3) then cloned in different integration vectors, 4) the integration cassettes are released via NotI digestion, purified and used to transform an integration strain.
FIG. 2: Schematic representation of the cloning vector. 1) The cloning vector includes a strong promoter followed by unique restriction sites for the cloning of the gene of interest, a transcription terminator and on either site a rare site to allow the excision of the expression cassette. 2) the base pVC vector contains a multisite composed of the ClaI, BamHI, KpnI and AvrII sites, the terminator sequence of the LIP2 gene (LIP2term) with on either side the rare site I-CeuI, 3) the expression vector contains the pPOX2 promoter cloned at the ClaI and BamHI sites, 4) The expression cassette is obtained by multiple site cloning of the gene of interest, for example BamHI-AvrII, then digestion of the expression vector by I-CeuI.
FIG. 3: Schematic representation of the integration vector and obtaining the targeted integration cassette. 1) The integration vector contains a region upstream of the insertion locus (region P, for promoter) and a region downstream of the insertion locus (region T for terminator) with on either side a rare site 1 for the excision of the integration cassette. Between P and T regions are two rare sites, rare site 2 for the insertion of the selection marker and rare site 3 for the insertion of the expression cassette.
FIG. 4: Schematic representation of the integration vectors for random integration. I) schematic representation of the vector that includes a rare site I usable for releasing the expression cassette from the plasmid part, a rare site 2 for cloning the selection marker for Y. lipolytica. It contains a promoter between the ClaI and BamHI sites (here the pPOX2 promoter), the terminator of the LIP2 gene and the Zeta regions for random integration (see amplification patent). The JMP61 series has the addressing sequence of the Lip2 lipase. II) Schematic representation of the integration vectors for random integration constructed with the NotI site as rare site 1 and the I-SceI site as rare site 2 used for the insertion of the URA3, LEU2, Hyg, GUT2 and ADE2 markers.
FIG. 5: Expression of the asparaginase in the strains containing different number of copies of the gene. A) Analysis on 10% NuPAGE electrophoresis gel and staining with colloidal blue (equivalent to 30 μl of supernatant), B) Analysis on 10% NuPAGE electrophoresis gel, transfer and detection by Western blot with an anti-Asparaginase antibody (equivalent to 10 μl of supernatant). Band a corresponds to the nonglycosylated protein and band b corresponds to the monoglycosylated protein. L1, receiving strain FF-luga; L2, strain 5LAsp1:ade2::GUT2-Asp, 1 copy; L3, strain 6LAsp1:ade2::GUT2-Asp, 1 copy; L4, strain 15LAsp2:ade2::GUT2-Asp lip2::URA3-Asp, 2 copies; L5 strain 21LAsp2:ade2::GUT2-Asp lip2::URA3-Asp:2 copies; L6, strain 1LAsp3:ade2::GUT2-Asp lip2::URA3-Asp leu2::ADE2-Asp:3 copies; L7, strain 2LAsp4:ade2::GUT2-Asp lip2::URA3-Asp leu2::ADE2-Asp ura3::Leu2-Asp:4 copies.
FIG. 6: Suc+/Suc− phenotype analysis to verify the insertion at the URA3 locus. The transformants obtained with the targeted integration cassette in the URA3 locus are streak tested on a dish of glucose-rich (YPD) and saccharose (YPS) medium. The receiver strains Suc+ FF-lug, FF-lua and FF-luga are used as control.
FIG. 7: Lip+/Lip− phenotype analysis to verify the insertion at the LIP2 locus. The transformants obtained with the targeted integration cassette at the LIP2 locus are cultivated in an oleic acid rich medium (YPD2O2). The lipase activity in the supernatant of the strains containing different copies of the asparaginase. The receiver strain Lip+ FF-luga is used as control. Strains with 1 copy at the ADE2 locus (ade2::GUT2-Asp):5LAsp1 and 6LAsp1; strains with 1 copy at the ADE2 locus (ade2::GUT2-Asp):5 LAsp1 and 6LAsp1; strains with 1 copy at the ADE2 locus and 1 copy at the LIP2 locus (ade2::GUT2-Asp, lip2::URA3-Asp): 14LAsp2, 15LAsp2, 16LAsp2, 17LAsp2 and 21LAsp2.
FIG. 8: Determination of the number of copies of the LIP2 gene and Asp via RT-qPCR in the transformants.



EXAMPLES
Example 1
Strains Used in the Examples
The strains used in the method according to the invention are derived from a wild-type strain of Yarrowia lipolytica, in particular the wild-type strain Yarrowia lipolytica W29 (atcc 20460, indexed under CLIB89 in the Collection of the CIRM (Centre International de Ressources Microbiennes).
Thus, we can use new mutant strains derived from the Yarrowia lipolytica strain ATCC 20460 through the intermediary of the strain Po1d [auxotrophic strain got leucine (Leu−) and uracil (Ura−)], described in the publication of G. Barth et al.: Yarrowia lipolytica. in Nonconventional Yeasts in Biotechnology: A Handbook (Wolf, K., Ed.), Vol. 1, 1996, pp. 313-388. Springer-Verlag. It is indexed under CLBI139 in the CIRM.
Obtaining these new receiver strains (FF-lu, FF-lug (CNCM I-3911), FF-lua (CNCM I-3912), FF-luga (CNCM I-3913)) will be described later.
Obtaining the Strains
The mutant receiver strains usable in the method according to the invention can be obtained from the Po1d strain, which is derived from the wild-type strain Yarrowia lipolytica W29. The Po1d is an auxotrophic strain for leucine (leu−) and uracil (ura−). It is described in the publication of G. Barth et al.: Yarrowia lipolytica in: Nonconventional Yeasts in Biotechnology: A Handbook (Wolf, K., Ed.) Vol. 1, 1996, pp. 313-388. Springer-Verlag, Berlin, Heidelberg, N.Y. It is listed as CLIB139 in the CIRM collection. Mutant strains usable in the method according to the invention can be obtained by the insertion of the gene deletion, thereby conferring auxotrophy or a growth defect in certain media, in which the gene has a deletion, if possible a deletion that cannot be reversed, which advantageously corresponds to a complete deletion of the gene. The corresponding gene can be used as selection markers for the selection of transformants having integrated the integration cassettes. The deletions will have a significant deletion compared to the corresponding cassette used for the construction of the selection markers in order to reduce the conversion rate.
1. Deletion of the GUT2 gene (Δgut2-744), construction of the GUT2 marker and obtaining the mutant strain FF-lug (CNCM I-3911).
1.1 Deletion of the GUT2 gene (Δgut2-744)
To obtain this strain, the procedure is as follows:

    1) selection of the gene of interest that is to be deleted;
    2) construction of a disruption cassette by cloning or by PCR (“Polymerase Chain Reaction”) by amplifying the upstream region of the gene (“promoter” region, symbolized by P) and the downstream region of the gene (terminator” region symbolized by T);
    3) introduction of a selection marker containing on either side a recombination sequence (advantageously a loxP or loxR sequence or derivative) allowing a recombination between it for the elimination of the marker (advantageously a loxP type sequence that allows recombination under the action of the cre recombinase);
    4) transformation with the disruption cassette and selection of the strains with the gene of interest deleted (transformation and selection of the transformants) and verification of the disruption of the gene;
    5) transformation with a vector allowing the expression of the recombinase (advantageously the cre recombinase, which allows the recombination of the loxP/loxR sequences and elimination of the marker);
    6) isolation of a clone having the deletion of the gene of interest and having lost the recombinase expression plasmid.


Using the auxotrophic mutant FF-lu (Leu−, Ura−), we constructed a mutant Y. lipolytica FF-lug auxotrophic for leucine and uracil (Leu−, Ura−) and incapable of using glycerol as carbon source (gly−). The first step is the construction of the FF-lug::URA3 strain prototrophic for uracil (Leu−, Ura+) through deletion of the GUT2 gene via the gut2::URA3ex disruption cassette by transforming the PCR GUT2-PUexT (JME744) fragment and selecting the Ura+ on YNBcasa. We select the auxotrophs for uracil (Leu+, Ura−) by excision of the URA3ex marker by transforming with the replicative vector pRRQ2 containing the Cre recombinase and the LEU2 marker (Cre-LEU2) and by selecting the auxotrophic transformants for uracil, Leu+. The loss of the pRRQ2 plasmid is achieved by cultivation on YPD rich medium and by isolation of a clone (Leu−, Ura−, Gly−).
The schematic representation of the construction of these mutants is summarized in Table I below.







TABLE 1







Transformation steps required for the production of the FF-lug mutant









Transformation operations











Mutant to be
Transformation



Step
transformed
cassette
Transformed mutant





1
FF-lu, PO1d,
Gut2-PUexT
JMY1202, Leu−, Ura+,



Leu−, Ura−

Gly− gut2-PUexT


2
JMY1202, Leu−,
pRRQ2 vector
JMY1202, Leu−, Ura+,



Ura+, Gly−,
(pKS Cre
Gly− gut2-PUexT



Gut2-PUexT
ARS68 LEU2)









The disruption cassette for the GUT2 gene was constructed by amplification of the upstream region (P region; Yali0B: 1873518 . . . 1872400, reverse direction, 1119 bp) and the downstream T region; Yali0B:1870468 . . . 1869652 complementary, 817 bp), which allows the deletion of the ORF of the GUT2 gene (YaliOB1870469 . . . 1872401) and leaves a homology with the selection marker GUT2ex-0.5 (485 bp with the P region and 56 bp in the T region) in order to minimize gene conversions. The ex selection markers are presented in Table 11.
The P and T regions were amplified with the primers G3PD-P1, G3PD-P2, G3PD-T1 and G3PD-T2 (Table 9).
The primers G3PD-P2 and G3PD-T1 contain the rare site I-SceI for the insertion of the excisable URA3ex selection marker. The PT fragment was cloned in pGEM-T (Invitrogen) to produce the pGEM-GUT2-PT (JME743) plasmid. The pGEM-GUT2-PUexT (JME744) disruption plasmid was obtained by insertion of the URA3ex marker at the I-SceI site coming from the JME507 plasmid.
The disruption cassette (3245 pb) was obtained by PCR with the primers G3PD-P1 and G3PD-T2. The PCR product was purified on agarose gel using the Qiagen gel extraction kit. The strains were transformed using the lithium acetate method. The Ura+ transformants were selected on YNBcasa medium.
The Ura+ transformants are obtained with a typical transformation rate (Fickers, 2003). Disruption of the GUT2 gene was verified by PCR with the 5′ primers of the P region (G3PDver1) and the 3′ primes of the T region (G3PDver2). The JMY1202 gut2::URA3ex mutant was then transformed by the replicative plasmid pRRQ2 (pKS Cre ARS68 LEU 2; JME461). The transformants obtained are screened for excision of the URA3 marker and loss of the cre recombinase replicative expression plasmid achieved by cultivation on YPD rich medium and by isolation of a clone (Leu−, Ura−, Gly−). The JMY1346 mutant (FF-lug) was selected. The sequence of the gut2-844 locus of the JMY1346 mutant was amplified with the primers G3PDver1 and G3PDver2. The PCR product (size 2415 pb) was sequenced. The obtained sequence shows the absence of the Ura3 marker sequence. After excision, the following sequences remain on the genome between P and T of the GUT2 locus:







TGCAGCTTTCGAGAACCGACGCCTGGGACCTGTGTCTGTAGGGATAA


 


CAGGGTAATTCGCTTCGGATAACTCCTGCTATAACGAAGTTATGTAG


 


GGATAACAGGGTAAT


(SEQ ID NO: 11; or site I-SceI-sequence LoxR-


site I-SceI).






1.2 Construction of the GUT2ex marker
For the construction of the GUT2ex marker, the genome sequence of the GUT2 locus was amplified with the primers G3PTS and G3PTR (Table 8) and cloned in the pKs-LPR vector (Fickers et al., 2003, Journal of Microbiological Methods, vol. 55, p: 727-737) at the EcoRI site. It contains 492 bp of promoter, the ORF of the GUT2 gene, (ORF Yali0B:1870546 . . . 1872384) and 132 bp of the terminator and corresponds to the sequence Yali0B:1872876 . . . 1870417. This ORF contains 2 BamHI sites and 1 EcoRI site that were eliminated by mutagenesis directed by introducing silent mutations. We used the following primers: G3PB1S and G3PB1R for the first BamHI site (ggAtcc in ggCtcc), G3PB2S and G3PB2R for the second BamHI site (ggatcC into ggatcT) and G3PE1S and G3PE1R for the EcoRI site (gaAttc into gaGttc) (Table 9).
The marker may be inserted in both directions. For this GUT2ex0.5 marker, only direction 1 was obtained in the pKS-LPR. After verification by sequencing, the plasmid containing the modified GUT2ex0.5 marker is JME792.
Two other markers GUT2ex 1.0 and GUT2ex 1.5 containing 1 kb and 1.5 kb of promoter respectively were constructed as a result of the difficulty in obtaining transformants using the GUT2ex0.5 marker (paragraph 1.3). These promoters were amplified using DNAg (E150 Yarrowia lipolytica strain) with the primers P1KB and PNHE1 and P15KB and PNHE1, respectively. Cloning was done by 3-way ligation between the pKS-LPR (dephosphorylated EcoRI), the PCR product (EcoRI and NheI) and the rest of the modified GUT2ex marker resulting from JME792 (NheI and EcoRI). The GUT2ex 1.0 marker in direction 1 corresponds to JME919 and in direction 2 corresponds to JME920. The GUT2ex1.5 marker in direction 1 corresponds to JME921 and in direction 2 corresponds to JME922.
1.3 Transformation with the GUT2ex0.5, GUT2×1.0 and GUT2ex1.5 markers.
To validate the use of the GUT2ex marker, the GUT2ex0.5 marker was isolated from the JME792 plasmid (pKS-LPR-GUT2ex0.5) by I-SceI digestion and inserted at the I -SceI site of the JMP62 I-SceI (JME801) plasmid to produce the plasmid JMP62Gut2-ex0.5 (JME805).
The JME805 plasmid was digested by NotI and used to transform the FF-lug strain using the lithium acetate method. The transformants were selected on YNBcasa (1% Glycerol) medium supplemented with uracil (100 mg/L). After several attempts, this marker did not make it possible to obtain transformants.
Initially, we hypothesized that the promoter part (492 pb) was too defective. We therefore constructed 2 other markers containing longer promoter parts (cf. paragraph 1.2), i.e., the GUT2x1.0 and GUT2ex1.5 markers. The same results were obtained.
A repression of the use of glucose in the presence of glycerol has been described in Saccharomyces cerevisiae yeast for Δgut2 strains. In fact, the FF-lug strain is incapable of growing in the presence of the 2 carbon sources cited earlier. By modifying our transformation method, we obtained transformants. This new transformation method remains identical to the lithium acetate method and to the polyethylene glycol method (Gaillardin et al. 1985) to which an expression phase is added before spreading the transformation on the selective media. This expression phase is carried out as follows: following thermal shock at 42° C. for 10 minutes. The product of the transformation is centrifuged at 2000 rpm for 3 minutes and the cells are washed with 2 mL of TE buffer pH8. This washing is repeated twice. The cells are then taken up with the nutritive medium 1% Yeast Extract 1% Peptones and 0.2% dextrose. They are incubated for 16 hours at 28 degrees, without stirring. Once again, the product is centrifuged at 2000 rpm for 3 minutes and the cells are washed with 2 mL of TE buffer pH8. This washing is repeated twice. The cells are then taken up with 2 mL of TE and are spread over selective media containing 1% glycerol as sole carbon source.
The results of the transformation of the GUT2ex1.0 marker in the FF-lug strain are presented in table 2 below:







TABLE 2







Transformation effectiveness depending on the transformation method














Standard

New





method without

method with




expression

expression



Type of
phase

phase













Integration
random
targeted
random
targeted

















Number of
0
14
133
615



transformants



Transformation rate
0
187
266
8215



per μg of DNA



% of integration
ND
75%
ND
100%










2. Deletion of the ADE2 (Δade2-844) gene, construction of the ADE2 marker and obtaining mutant FF-lua (CNCM I-3912) and FF-lug (CNCM I-3913) strains.
2.1 Deletion of the ADE2 (Δade2-844) gene
To obtain these strains, it is possible to proceed as follows: using the FF-lu mutant, we constructed the FF-lua Leu−, Ura−, Ade− strain and from the FF-lug mutant we constructed the FF-luga Leu−, Ura−, Ade−, Gly− strain.
2.1a Using the auxotrophic FF-lu (Leu−, Ura−) mutant we constructed an FF-lua mutant Y. lipolytica strain auxotrophic for leucine, uracil and adenine (Leu−, Ura−, Ade−). The first step is the construction of the FF-lua::URA3 strain prototrophic for uracil (Leu−, Ura+, Ade−) by deletion of the ADE2 gene via the Ade2::URA3ex disruption cassette by transforming the NotI PTAde2-Ura3EX (JME844) cassette and by selecting the Ura+ on YNBcasa, supplemented with adenine (800 mg/L). The uracil auxotrophs (Leu+, Ura−, ade−) are selected by excision of the URA3ex marker by transforming with the replicative vector pRRQ2 containing the Cre recombinase and the LEU2 marker (Cre-LEU2) and by selecting the transformants auxotrophic for uracil, Leu+. The loss of the cre recombinase replicative expression plasmid pRRQ2 is achieved by cultivation on a YPD rich medium and by isolation of a clone (Leu−, Ura−, Ade−). The JMY1409 (FF-lua) mutant was selected.
2.1.b Using the auxotrophic FF-lug mutant (leu−, Ura−) incapable of using glycerol as a carbon source (Gly−), we constructed a mutant FF-luga Y. lipolytica strain auxotrophic for leucine, uracil and adenine (Leu−, Ura−, Ade−) and incapable of using glycerol as carbon source (Gly−). The first step is the construction of the FF-luga::URA3 strain auxotrophic for leucine and adenine (Leu−, Ade−, Ura+) by deletion of the ADE2 gene via the ade2::URA3dx disruption cassette by transforming the NotI PTAde2-PUra3ExT (JME844) cassette and by selecting the Ura+ on YNBcasa supplemented with adenine (800 mg/L). We select the uracil auxotrophs (Leu+, Ura−) by excision of the URA3ex marker via transformation with the replicative vector pRRQ2 containing the Cre recombinase and the LEU2 (Cre-LEU2) marker and by selecting the uracil auxotrophic transformants, Leu+. The loss of the pRRQ2 plasmid is achieved by cultivation on YPD rich medium and by isolation of a clone (Leu−, Ura−, Ade−, Gly−). The JMY1404 (FF-luga) mutant was selected.
The schematic representation of the construction of these mutants is summarized in Table 3 below.







TABLE 3







Transformation steps required for the production of the


FF-lua and FF-luga mutants









Transformation operations











Mutant to be




Step
transformed
Transformation cassette
Transformed mutant





1
PO1d, Leu−,
PTade2-Ura3Ex
JMY1407, Leu−,



Ura−

Ura+ ade2-





PUexT


2
JMY1407,
pRRQ2 vector,
JMY1409, Leu−,



Leu−, Ura+
Leu+ selection,
Ura−, Ade−



Ade2-PUexT
Gly− verification, loss of
Ade2-844




the pRRQ2 plasmid on
FF-lua




YPD, isolation of Leu−


1b
JMY1346, Leu−,
PTade2-Ura3Ex
JMY1396, Leu−,



Ura−, Gly−

Ura+ Gly− ade2-



Gut2-744

PUexT


2b
JMY1396, Leu−,
pRRQ2 vector,
JMY1404, Leu−,



Ura+, Gly−
Leu+ selection,
Ura−, Ade−, Gly−,



Ade2-844
Gly− verification, loss of
Ade2-844




the pRRAQ2 vector on
FF-luga




YPD, isolation of Leu−









The disruption cassette for the ADE2 gene (Yali0B23188g; highly similar to tr|Q9P4V1 Candida boidinii), which encodes for phosphoribosyl-5-aminoimidazole carboxylase, protein deduced from 565 aa (Yali0B:3030460 . . . 3032157, forward direction) was constructed by amplification of the upstream region (P region; Yali0B:3029011 . . . 3029931, 920 bp) and of the downstream region (T region; 792 pb, Yali0B:3031871 . . . 3032662) which allows the deletion of the ADE2 gene ORF (Yali0B:3030460 . . . 3032157). The region eliminated is 1939 pb (Yali0B:3029932 . . . 3031870) and only leaves a very weak homology with the ADE2ex selection marker (O by with the P region and 415 bp in the T region) in order to minimize gene conversions. The ADE2ex marker corresponds to the region Yali0B:3029961 . . . 3032280 fragment of 2319 pb. The ex selection markers are presented in Table 11.
The P and T regions were amplified with the following primers: P1ADE2, P2AD2, T12ADE2 and T2AD2 (Table 9).
The primers P2 and T1 contain the rare site I-SceI for insertion of the excisable selection marker URA3ex. Primer T1 also contains the rare site I-CeuI for the insertion of the expression cassette. Primers P1 and T2 contain the rare site NotI for cloning in pHSS6-NotI (JME800). The PT fragment was cloned in the JME800 digested by NotI and dephosphorylated to produce the plasmid pADE2-PT in orientation 1 (direction 1, JME813) or in orientation 2 (direction 2, JME814). The Direction is defined according to the orientation of the site I-SceI: either direction 1 with the I-SceI site directional or direction 2 with the I-SceI site complementary. The disruption plasmid pPTAde2-Ura3Ex (JME844) was obtained by insertion of the URA3ex marker at the I-SceI site of the JME813 plasmid.
The disruption cassette was obtained by NotI digestion and purification of the 3,089 pb band. The Po1d strain was transformed using the lithium acetate method. The Ura+ transformants were selected on YNBcasa medium supplemented with adenine (100 mg/L). The typical concentrations necessary for complementation of an auxotrophy that are used are generally between 100 and 200 mg/L. The Ura+ transformants are obtained with a low transformation rate, around 50 transformants per microgram of DNA, the analysis of the transformants revealed that they contained a conversion of the ura3-302 marker and not the deletion of the ADE2 gene. We performed several disruption assays with increasing concentrations of adenine. To obtain transformation rates of higher than 103 transformants per μg of DNA, it is necessary to have an adenine concentration higher than 400 mg/L in the media. The concentration used for complementation was 800 mg/L. It is only with these conditions that we obtained transformants with a disruption of the ADE2 gene. Contrary to S. cerevisiae, the Ade− strains do not show any pink color. On the other hand, the Ade− clones of Y. lipolytica have a brown color after several days in a Petri dish and a brown supernatant in liquid medium. Phenotype usable to identify the transformants or the integration of the expression cassette was indeed integrated at the ADE2 locus (sic).
Verification of the sequence of the ade2-844 locus. The sequence of the ade2-844 locus was amplified with the primers ver1ade2 and ver2ade2 (Table 9). The PCR product of size 2204 pb was sequenced. The sequence obtained shows the absence of the URA3 marker sequence. Furthermore, this verification shows the absence of the integration of the 5′ and 3′ NotI sites of the PUexT disruption cassette. After excision, the following sequences remain on the genome between P and T of the ade2 locus:







(SEQ ID NO.: 12)


TAGGATAACAGGGTAATTATCGCTTCGGATAACTCCTGCTATACGAA


 


GTTATGTAGGGATAACAGGGTAATTAACTATAACGGTCCTAAGGTAG


 


CGA


or the following sites I-SceI-LoxR-I-SceI-I-CeuI.






2.2 Construction of the ADE2ex marker
For the construction of the ADE2ex marker, the genome sequence of the ADE2 locus was amplified using the primers ADE2S and ADE2R and cloned in the pKS-LPR vector (Fickers et al., 2003, Journal of Microbiological Methods, vol. 55, p: 727-737) at the site EcoRI. It contains 500 bp of promoter, the ORF of the ADE2 gene (Yali0B23188g) and 125 bp of the terminator and that corresponds to the sequence Yali0B:3029961 . . . 3032280 or 2319 pb. The EcoRI site present in the ORF of the ADE2 gene was eliminated by modifying the gaatTc into gaatCc via mutagenesis directed with the primers ADE2ES and ADE2ER (Table 9). This modified base creates a silent mutation ATT into ATC.
The marker can be inserted in both directions. The ADE2ex marker in direction 1 corresponds to JME798 and in direction 2 to JME799.
2.3 Transformation with the ADE2ex marker
To test the use of the ADE2ex marker, the ADE2ex marker was isolated from the plasmid JME798 (pKS-LPR-ADE2) by I-SceI digestion and inserted at the I-SceI site of the plasmid JMP631-SceI (JME793) to obtain the plasmid JMP62 ADE2ex (JME862). The JME862 plasmid was digested by NotI and used to transform the FF-lua strain using the lithium acetate method. The transformants were selected on YNBcasa medium with uracil (100 mg/L) and adenine. In the bibliography, regarding Ade-mutants of different species of yeasts, selective media are described that are supplemented with adenine at a concentration of 100 to 200 mg/L. In our case for the Ade− mutants mentioned above, the concentration necessary for proper growth of the transformants is 800 mg/L. Under these conditions, we obtain transformation rates similar to the transformation rates obtained with the URA3 marker.
3. Deletion of the LEU2 gene (Δleu2-958 marker), obtaining the FF2-lu, FF-2lug, FF2-lua and FF2-luag mutant strains and construction of the LEU2ΔBamHI marker.
3.1 Deletion of the LEU2 gene (Δleu2-958)
To obtain these strains, we can proceed as follows: using the FF-lu mutant, we constructed the FF2-lu Leu−, Ura− strain. In similar fashion it is possible to construct strains derived from FF-lua, FF-lug and FF-luag having the Δleu2-958 deletion. Using the FF-lug mutant, we can construct the FF2-lug Leu−, Ura−, gly− strain, using the FF-lua mutant we can construct the FF2-lua Leu−, Ura−, ade− strain and using the FF-luag mutant, we can construct the FF2-luang Leu−, Ura−, ade−, gly− strain.
For example, using the FF-lu mutant, we constructed the corresponding Y. lipolytica mutant strain having a larger deletion of the LEU2 gene than for the genetic marker leu2-270. The first step is the construction of the FF2-lu::URA3 strain prototrophic for uracil (Leu−, Ura+) by deletion of the leu2-270 gene via the leu2::URA3ex disruption cassette by transforming the NotI cassette resulting from the pPTLeu2-Ura3EX (JME958) plasmid containing this marker and by selecting the Ura+ on YNBcasa. We select uracil auxotrophs (Leu−, Ura−) by excision of the URA3ex marker transforming with the replicative vector pRRQ2 containing the Cre recombinase and the LEU2 marker (Cre-LEU2) and by selecting the uracil auxotrophic transformants, Leu+. The loss of the pRRQ2 plasmid is achieved by cultivation on YPD rich medium and by isolation of a clone (Leu−, Ura−). The same method may be used to obtain the FF2-lua, FF2-lug and FF2-luga mutants.
The schematic representation of the construction of the FF2-lu mutant is summarized in Table 4 below.







TABLE 4







Transformation steps required for the production of the FF2-lu mutant









Transformation operations











Mutant to be

Transformed


Step
transformed
Transformation cassette
mutant





a1
FF-lu, Leu−, Ura−
PTLeu2-Ura3Ex
FF-IU+, leu−,



JMY195, Po1d

Ura+





Leu2-PUexT


a2
FF-IU+, Leu−,
pRRQ2 vector,
JMY1516, Leu−,



Ura+, leu2-
Leu+ selection,
Ura−, leu2-958



URA3
Ura− verification, loss of
FF2-lu




the pRRQ2 plasmid on




YPD, isolation of Leu−









The disruption cassette for the LEU2 gene was constructed by amplification of the upstream region (P region; Yali0C44989 . . . Yali0C46081, 1092 pb) and of the downstream region (T region; Yali0C47036 . . . Yali0C47932, 897 pb), which allows the deletion of the ORF of the LEU2 gene (Yali0C46082 . . . Yali0C47035, 954 pb) and that leaves only a very weak homology with the LEU2ex selection marker (O bp with the P region and 207 bp in the T region) in order to minimize gene conversions. The Leu2Ex selection marker was strongly homologous with the genetic marker leu2-270 (401 bp with the P region and 710 bp in the T region) because this marker corresponds to a simple StuI deletion of 681 bp of the LEU2 gene. The ex selection markers are presented in Table 11.
The P and T regions were amplified with the primers P1Leu2, P2Leu2, T1Leu2 and T2Leu2 (Table 9).
The P2 and T1 primers contain the rare site I-SceI for the insertion of the Ura3ex excisable selection marker. The T1 primer also contains the rare site I-CeuI for the insertion of the expression cassette. The primers P1 and T2 contain the rare site NotI for cloning in pHSS6-NotI (JME800). The PT fragment was cloned in the JME800 digested by NotI and dephosphorylated to produce the pLeu2-PT plasmid in orientation 1 (direction 1, JME811) or in orientation 2 (direction 2, JME812). The Direction is defined according to the orientation of the I-SceI site: either direction 1 with the I-ScI site in the forward orientation or direction 2 with the I-SceI site in the reverse orientation. The pPTLeu2-Ura3Ex (JME958) disruption plasmid was obtained by insertion of the Ura3ex marker at the I-SceI site of the JME811 plasmid.
The disruption cassette was obtained by NotI digestion and purification of the 3351 pb band. The strains were transformed using the lithium acetate method. The Ura+ transformants were selected on YNBcasa medium.
3.2 Construction of the LEU2n (LEU2exΔBamHI) marker
For the construction of the expression cassettes and of the integration cassettes, the selection markers must not contain the unique sites used for cloning the genes of interest (BamHI, HindIII, KpnI and AvrII). For the construction of the LEU2n (LEU2exΔBamHI) marker, the Leu2-L1 and Leu2-L2 primers were used to create a linker providing the modification ggaatT into ggaatC and possessing the ApaI site (Table 9). The pKS-LPR-Leu2 (JME509) plasmid was digested on the one hand by ApaI and ScaI and, on the other, by BamHI and ScaI. The ApaI-ScaI band of 1471 pb and BamHI-ScaI band of 3300 pb were purified on agarose gel. A 3-way ligation was performed with these 2 bands plus the Leu2L1/Leu2L2 linker. We obtained a plasmid containing the new modified LEU2n marker LEU2exΔBamHI (JME790).
4. Development of the random monocopy integration system with different excisable markers.
The construction was done using different existing excisable markers and markers obtained in this invention (Table 11).
First, we constructed the 2 base vectors named I-SceI or JMP61 I-SceI and JMP62 I-SceuI. Using the JMP61 leu2Ex and JMP62 leu2Ex vectors containing the excisable LEU2 marker, we performed PCT for the entire plasmid with a primer couple: 62claS and 62claR (Table 9). We used the Stratagene “QuikChange® Site-Directed Mutagenesis Kit,” which makes it possible to perform directed mutations. The principle, based on PCR amplification, uses primers constructed specifically to force the mutation of the PCR product. Usually used for short insertions/deletions or specific mutations, we used this principle in order to eliminate the Leu2Ex marker by recircularization of the plasmid at the I-SceI site. These 2 primers were also constructed to eliminate the BamHI and AvrII sites contained in the JMP61 Leu2Ex plasmid upstream of the I-SceI site and to restore the ClaI site in order to allow the exchange of the promoter by this unique site. The PCR product obtained is then digested by the restriction enzyme DpnI, which makes it possible to eliminate the parental strand. This parental strand, coming from a strain of E. coli dam+ is methylated and, contrary to the newly formed strand, it will be recognized and digested specifically by the DpnI enzyme. After transformation and screening, we obtained the vectors JMP61 I-SceI and JMP62 I-SceI (Table 12).
The other constructions (Table 12) were accomplished using these 2 plasmids. The ligations were performed with the plasmids digested by I-SceI and dephosphorylated and the purified I-SceI purified of the different excisable markers using the corresponding pKS-LPR plasmids (Table 11). For the excisable marker Leu2, we used the plasmid JME790 containing the marker LEU2n (Leu2ΔBamHI).







TABLE 5







Strains obtained:









Strain
Collection No.
Genotype





FF-lu
JMY195, Po1d
xpr2-322, leu2-270, ura3-302


FF2-lu

xpr2-322, leu2-958, ura3-302



JMY1202
xpr2-322, leu2-270, ura3-302, gut2-PUext


FF-lug
JMY1346
xpr2-322, leu2-270, ura3-302, gut2-744



JMY1407
xpr2-322, leu2-270, ura3-302, ade2-PUexT


FF-lua
JMY1409
xpr2-322, leu2-270, ura3-302, ade2-844



JMY1396
xpr2-322, leu2-270, ura3-302, gut2-744,




ade2-PUexT


FF-luga
JMY1404
xpr2-322, leu2-270, ura3-302, ade2-744,




ade2-844


5LAsp1
1 copy
ade2 ::GUT2-Asp


6LAsp1
1 copy
ade2 ::GUT2-Asp


14LAsp2
2 copies
ade2 ::GUT2-Asp lip2 ::URA3-Asp


15LAsp2
2 copies
ade2 ::GUT2-Asp lip ::URA3-Asp


16LAsp2
2 copies
ade2 ::GUT2-Asp lip2 ::URA3-Asp


17LAsp2
2 copies
ade2 ::GUT2-Asp lip ::URA3-Asp


21LAsp2
2 copies
ade2 ::GUT2-Asp lip ::URA3-Asp


1LAsp3
3copies
ade2 :: GUT2-Asp lip2 ::URA3-Asp




leu2 ::ADE2-Asp


2LAsp4
4 copies
ade2 :: GUT2-Asp lip2 ::URA3-Asp




leu2 ::ADE2-Asp ura3




::LEU2-Asp









5. Construction of the base, cloning and expression vectors.
5.1 Base and cloning vectors.
The base vector was constructed using the JMP62 vector by retaining only the E. coli shuttle portion coming from the pHSS6 plasmid. After digestion of the JMP62 vector by NotI, the 2210 pb band containing the origin of replication for E. coli and the resistance to Kanamycin was isolated and purified then religated to thus form the base vector named pHSS6-NotI (JME800). Using this base vector, we constructed the cloning vector (FIG. 2) through the ligation of 2 linkers and a PCR fragment containing the terminal sequences of the LIP2 lipase of Y. lipolytica contained in the JMP62 vector. The linkers were made via couple synthesis of the 5′ phosphorylated primer, i.e., the linker 1 with the primers link 1 and link 11 and the linker 2 with the primers link 2 and link 22 (Table 10). These linkers create a cloning multisite containing respectively the sites ClaI and BamHI for the insertion of a promoter and the sites BamHI/HindIII and SacII/KpnI/AvrII for the insertion of the gene of interest. We also introduced a “consensus” sequence in −4 and −1 of the ATG: C−4 A C A−1. This sequence is present for the Y. lipolytica genes that encode for strongly expressed proteins. Thus, for an expression with this sequence, the cloning of the gene of interest is done by HindIII and without this sequence by BamHI in the 5′ position. The PCR fragment (840 pb) containing the terminal sequences of LIP2 was obtained with the primers PDX2Xho and Lip2Thc. This fragment was digested by AvrII and NotI to obtain the 179 pb fragment containing only the terminal sequences of LIP2. We added a unique HindIII site in order to allow the exchange of these terminal sequences by AvrII and HindIII. We introduced 2 rare sites of the restriction enzyme I-CeuI on either side of the multisite and the terminal sequences. This I-CeuI double site makes it possible to isolate and purify the expression cassette for cloning in integration vectors.
A 3-way ligation was performed with the 2 linkers, the 179 pbAvrII/NotI band pb and the dephosphorylated base vector pHXX6 NotI to obtain the cloning vector named pVC (JME829).
5.2 Expression vector
The expression vector was constructed using the pVC cloning vector digested by ClaI and BamHI. The reduced promoter pPOX2 (1017 pb) was isolated and purified after digestion by ClaI and BamHI of the JMP62 vector (Table 12). A ligation of the pVC and the pPOX2 promoter was carried out to obtain the expression vector named pVC-pPOX2 (JME830), Table 6.







TABLE 6







Vectors used to construct the expression vector











Description
Vector name
Collection No.







Base vector
pHSS6-NotI
JME800



Cloning vector
pVC
JME829



Expression vector
pVC-pPOX2
JME830










6. Selection of the insertion loci and construction principle for the integration vectors. We chose the following different loci:
6.1 Leu2-270 locus
This locus has often been used as homologous integration target via simple “crossing over” (eg. Bordes et al., 2007), but with this genome marker we obtain a high conversion rate (it corresponds to a small StuI deletion of 681 pb that leaves a 5′ region of 401 pb (Yali0C:46411 . . . 46537) and a 3′ region of 710 pb (Yali0C:46528 . . . 46948) that allows a double recombination with the LEU2 selection marker used in our vectors. Thus, a high conversion rate is generally observed during transformations of expression cassettes containing this marker. To reduce the conversion rate, as a first step, we chose to insert an expression cassette at the leu2-270 locus in order to eliminate these homology regions in 5′ and 3′ regions. Thus, during an insertion of a new expression cassette containing the LEU2 marker at another locus, the conversion rate is sharply reduced. Alternatively, it is possible to construct a strain with the marker leu2-958 as described in chapter 3.
6.2 Ura3-320 locus
The deletion was performed via double crossing-over leaving only 21 pb in 5′ position (Yali0E:3171873 . . . 3171893) and 108 pb in 3′ position (Yali0E:3175134 . . . 3175241). The deleted fragment (695 pb) was replaced with the following expression cassette: promoter of the XPR2 gene and the SUC2 gene encoding for the invertase of Saccharomyces cerevisiae in the reverse direction (3240 pb, Yali0E:3171894 . . . 3175133). Integration in this Ura3-320 makes it possible to eliminate the SUC2 gene coming from S. cerevisiae in the production strain and to simply and quickly screen the Suc− transformants (absence of any growth on medium containing only saccharose as sole carbon source) as described in FIG. 6.
6.2 Lip2 locus
The LIP2 gene encodes for the Lip2p lipase of Y. lipolytica. Its expression is induced in the presence of fatty acids and triglycerides (Pignede et al., 2000). In this invention, the expression of the proteins of interest is placed under the strong and inducible promoter pPOX2. This promoter is also inducible by fatty acids like oleic acid. Integration at the LIP2 locus makes it possible to invalidate the LIP2 gene and to obtain the absence of expression of the Lip2P lipase in the culture supernatants at the time of production. Furthermore, this makes it possible to simply and quickly screen the Lip2− transformants (absence of any degradation of a tributyrin emulsion visible on gelosed medium or absence of any lipase activity in the culture supernatant as described in FIG. 7).
6.4 Ade2 locus
In this invention, new Ade− strains were constructed, as well as the Ade2ex selection marker. For the disruption of the ADE2 gene the P and T sequences were amplified. These same sequences were thus used in the integration vectors. Thus, no additional construction was necessary for this locus. If the receiver strain used is FF-lug, insertion at the ADE2 locus renders the Ade− strain, which creates a new auxotrophy, which may be used to introduce an additional copy of the gene of interest. This disruption is also associated with a quickly identifiable phenotype (brown coloration of the disrupted colonies on rich medium in a Petri dish, brown coloration of the culture medium).
This list or these Locus/Marker combinations is not exhaustive. All other combinations are possible, preferably with a locus whose disruption creates a rapidly visualizable phenotype that allows rapid screening of the transformants having correctly integrated the expression cassette at the locus. Other loci and other markers can be chosen or other combinations can be produced.
6.5 Construction principle for the integration vectors. The construction principle for the integration vectors is described in FIG. 3. The different integration cassettes at defined loci were constructed using an identical methodology. Using the DNAg of the E150 strain, we amplified the promoter part named P and the terminator part named T of the gene to be disrupted. The P and T fragments must preferably have a size between 800 and 1000 pb to achieve effective homologous double recombination in Y. lipolytica. The primers used are named P1/P2 for the P fragment and T1/T2 for the T fragment followed by the name of the locus (Table 9). The primers P1 and P2 contain a rare site 1, here the NotI site, to allow cloning in the base vector pHSS6-NotI and also to release the expression cassette. The primers P2 and T1 contain two other rare sites, rare site 2 and rare site 3, here the sites I-SceI and I-CeuI, respectively, which allow the fusion via PCR of the 2 fragments and the subsequent cloning of the selection marker at rare site 2, here the site I-SceI, and of the expression cassette at rare site 3, here the site I-CeuI. PCR fusion is therefore achieved using a purified mixture of the 2 P and T fragments and of the P1/T2 primer couple. The PT fragment obtained is digested by NotI and is then cloned by ligation in the vector pHSS6 digested by NotI and dephosphorylated. The integration vectors are named pPT followed by the name of the locus (Table 7).
Description of the P and T fragments of the different loci:
Leu2-270 locus: The regions amplified for homologous double recombination are 1092 pb for the P region (Yali0C:44989 . . . 46081) and 897 pb for the T region (Yali0C:47036 . . . 47932). The region that will be eliminated is 954 pb (Yali0C:46082 . . . 47035). This region eliminates the entire 5′ region of the marker Leu2 (401 pb) and a portion of the 3′ region (503 pb). A homology of 207 pb of the 3′ region of the Leu2 marker remains.
Ura3-302 locus: The regions amplified for the homologous double recombination are 1197 pb for the P region (Yali0E:3170698 . . . 3171894) and 1013 pb for the T region
(Yali0E:3175412 . . . 3176424). The region that will be eliminated is 3516 pb
(Yali0E:3171895 . . . 3175411). This region eliminates the entire expression cassette pXPR2+SUC2 and the 3′ region of the Ura3 marker (280 pb). A homology of 200 pb of the 5′ region of the Ura3 marker remains.
Lip2 locus: The regions amplified for homologous double recombination are 1123 pb for the P region (Yali0A:2185897 . . . 2187019) and 961 pb for the T region (Yali0A:2187883 . . . 2188843). The region that will be eliminated is 863 pb (Yali0C:2187020 . . . 2187882). This region eliminates almost all of the LIP2 gene. A homology of the 3′ region of 148 pb of the LIP2 gene remains. Ade2 Locus: The regions amplified for homologous double recombination are 920 pb for the P region (Yali0B:3029011 . . . 3029931) and 792 pb for the T region (Yali0B:3031871 . . . 3032662). The region that will be eliminated is 1939 pb (Yali0B:3029932 . . . 3031870), which leaves only a very weak homology with the selection marker ADE2ex (O bp with the P region and 415 bp in the T region) in order to minimize gene conversions.
For each locus, the P and T regions were amplified using the primer couple named P1/P2 and T1/T2 followed by the name of the locus (Table 9). Then the PT fusion was performed with the P1/T2 couple.
Using these pPT vectors, different excisable markers were introduced by cloning at the I-SceI site. This site allows oriented cloning of the marker. We chose to orient the marker in the reverse direction of the expression cassette. The integration vectors obtained are named pPT followed by the name of the locus followed by the name of the excisable marker inserted (Table 7).
The Locus/Marker combinations are given only as examples; different combinations are possible.







TABLE 7







list of integration vectors














Vector
I-Scel
Collection

Vector
Collection


Locus
name
orientation
No.
Marker
name
No.





LIP2
pPTLip2


URA3ex
pPTLip2-Ura3ex
JME815




Direction 1
JME806
GUT2-0.5ex
pPTLip2-Gut2-0.5ex
JME816




Direction 2
JME807


URA3
pPTUra3
Direction 1
JME809
LEU2nex
pPTUra3-Leu2nex
JME817




Direction 2
JME810


LEU2
pPTLeu2
Direction 1
JME811
ADE2ex
pPTLeu2-Ade2ex
JME818






URA3ex
pPTLeu2-Ura3ex
JME958




Direction 2
JME812


ADE2
pPTAde2


GUT2-0.5ex
pPTAde2-Gut2-0.5ex
JME819




Direction 1
JME813
URA3ex
pPTAde2-Ura3ex
JME844




Direction 2
JME814









7. Construction principle for integration vectors for the expression of a protein of interest. Cloning of a gene of interest is achieved in only 2 cloning steps. The first step is a subcloning in the pVC expression vector to obtain the pVC-gene of interest vector under the control of the PDX2 promoter (other strong promoters may be used such as the promoter hp4d or inducible promoters). This pVC-gene of interest vector is digested by I-CeuI to isolate and purify the expression cassette. The second step is the cloning of this I-CeuI expression cassette in the integration vectors. The integration cassette/expression cassette vector is isolated and purified after digestion by NotI before transformation in Y. lipolytica (FIG. 3).
Example 2
Construction and Use of an Integration/Expression Cassette for the Targeted Insertion of a Gene Encoding for a Therapeutic Protein of Interest not Produced by Y. lipolytica 
We took as example the L-asparaginase protein of Erwinia chyrsanthemi. The gene encoding for this protein was introduced into the vector pVC-pPOX2 at the HindIII/AvrII site. To do this, a fusion PCR was performed between the preproLIP2 sequence and the portion of the sequence of the gene encoding for the mature form of the L-asparaginase protein. PCR was performed with the primers preproLip2 and Lip2KR to amplify the pre-pro-LIP2 sequence and with the Laspens and Lasprev primers to amplify the sequence encoding for the mature protein. Then, by mixing the 2 PCR products obtained, the fusion with the preproLIP2 and pLasprev primers was carried out.
The preproLip2 primer contains the HindIII site and the Lasprev primer the AvrII site for cloning the fusion product in the pCV-pPOX2. The vector pVC-pPOX2-preproLip-LAsp (JME898) containing the expression cassette of the L asparaginase protein is thus obtained (Table 8). From this vector, the expression cassette is extracted through digestion by the restriction enzyme I-CeuI and purified. This cassette is then cloned in the different integration vectors at the I -CeuI site. The different integration/expression vectors obtained are described in Table 8.







TABLE 8







Integration/expression vectors obtained:









Descriptions
Vector name
Collection No.





Expression vector
pVC-pPOX2-LAsp
JME898


Int. vector Ura3 locus
pPTUra3-Leu2nEx-LAsp
JME923


Int. vector Ade2 locus
pPTAde2-Gut2-0.5Ex-LAsp
JME924


Int. vector Ade2 locus
pPTAde2-Ura3Ex-LAsp
JME925


Int. vector Leu2 locus
pPTLeu2-Ade2Ex-LAsp
JME926


Int. vector Lip2 locus
pPTLip2-Ura3Ex-LAsp
JME927


Int. vector Ade2 locus
pPTAde2-Gut2-1.0Ex(d1)-LAsp
JME941


Int. vector Ade2 locus
pPTAde2-Gut2-1.0Ex(d2)-LAsp
JME942


Int. vector Ade2 locus
pPTAde2-Gut2-1.5Ex(d1)-LAsp
JME943


Int. vector Ade2 locus
pPTAde2-Gut2-1.5Ex(d2)-LAsp
JME944









The integration/expression cassettes are obtained by digestion of the restriction enzyme NotI of the different integration/expression vectors. These cassettes are then extracted and purified in order to eliminate the E. coli exogenous DNA sequences.
Example 3
Transformation of the Integration/Expression Cassettes of the L-asparaginase Protein in Y. lipolytica 
It is possible, for example, to introduce successively 4 copies of the expression cassette of L-asparaginase in the 4 loci mentioned earlier in the FF-luga strain.
1 Insertion of the First Copy at the ADE2 Locus.
The first expression cassette was introduced by transformation of the FF-luga strain at the ADE2 locus using the integration/expression cassette PTAde2-Gut2-1.0Ex-LAsp from the vector JME941. The transformants are selected on selective YNBcasa medium supplemented with uracil and adenine and containing 1% glycerol as sole carbon source. The transformants obtained are isolated on this same selective medium and integration at the locus is verified by PCR using the primers Ver1ade2 and Ver2ade2 located upstream and downstream of the integration sequences.
The transformation rate obtained is 8.2 103 transformants per μg of DNA transformed.
Verification of integration at the Ade2 locus via PCR showed that 100% of the transformants integrated the LAsp expression cassette at this locus.
We retained 2 transformants named 5LAsp1 and 6LAsp1 (Table 5). The first figure at the start of the name give the number of the transformant and the second figure at the end of the name gives the number of copies of the LAsp expression cassette.
2 Insertion of the Second Copy at the LIP2 Locus.
The second expression cassette was introduced by transformation of the transformant 5LAsp1 at the LIP2 locus using the integration/expression cassette PTLip2-Ura3Ex-LAsp resulting from the vector JME927. The transformants were selected on selective YNBcasa medium supplemented with adenine and containing 1% glucose as sole carbon source. The transformants obtained are isolated on this same selective medium and integration at the locus is verified by PCR using the Ver1lip2 and Ver2lip2 primers located upstream and downstream of the integration sequences. The transformation rate obtained is 1.1 104 transformants per μg of DNA transformed. Verification by PCR of integration at the LIP2 locus showed that 75% of the transformants integrated the LAsp expression cassette at this locus. Alternatively, verification of integration of the expression cassette at the LIP2 locus can be accomplished by measuring the lipase activity as demonstrated in FIG. 7.
We retained 5 transformants named 14LAsp2, 15LAsp2, 16LAsp2, 17LAsp2 and 21LAsp2 (Table 5).
3 Insertion of the Third Copy at the LEU2 Locus.
The third expression cassette was introduced by transformation of the transformant 15LAsp2 at the LEU2 locus using the integration/expression cassette PTLeu2-Ade2Ex-LAsp resulting from the vector JME926. The transformants were selected on selective YNBcasa medium containing 1% glucose as sole carbon source. The transformants obtained are isolated on this same selective medium and integration at the locus is verified by PCR using the Ver1leu2 and Ver21leu2 primers located upstream and downstream of the integration sequences.
The transformation rate obtained is 1.6 104 transformants per μg of DNA transformed.
Verification by PCR of integration at the LEU2 locus showed that 20% of the transformants integrated the LAsp expression cassette at this locus.
We retained 1 transformant named 1LAsp3 (Table 5).
4 Insertion of the Fourth Copy at the URA3 Locus.
The fourth expression cassette was introduced by transformation of the transformant 1 LAsp3 at the URA3 locus using the integration/expression cassette PTUra3-Leu2nEx-LAsp resulting from the JME923 vector. The transformants were selected on selective YNB medium containing 1% glucose as sole carbon source. The transformants obtained were isolated on this same selective medium and integration at the locus was verified by PCR using the Ver1Ura3 and Ver2Ura3 primers located upstream and downstream of the integration sequences.
The transformation rate obtained is 5.25 103 transformants per μg of DNA transformed. PCR verification of integration at the URA3 locus showed that 87% of the transformants integrated the LAsp expression cassette at this locus, 87% of the transformants are Ura− (FIG. 6).
We retained 1 transformant named 2LAsp4 (Table 5).
This last strain indeed contains at least one supplemental copy (see FIG. 5 (electrophoresis gel) and FIG. 8 RT-qPRC quantification.
5 Insertion Procedure Variant:
The invention may also be implemented according to the following steps: First, the 4 (for example) transformations are carried out one after the other. Then the insertions are screened using different markers. This explains the interest, if the Cre-lox system is not used, of having as many different screening systems as copies to be integrated.
Example 4
Analysis of the Expression of L-Asparaginase Based on the Number of Copies Integrated
The expression of L-Asparaginase was analyzed in production using the different transformants obtained containing 1 to 4 copies. Production was carried out in a 250 mL flask containing 25 mL of rich medium composed of 1% Yeast Extract, 2% Bacto Tryptone, 1% Glucose, 50 mM of sodium phosphate buffer pH16.8 and a 2% oleic acid emulsion (called Y1T2D1O2). The oleic acid serves as inducer of the pPOX2 promoter. The expression is analyzed by gel electrophoresis under denaturing and reducing conditions using the supernatant of the cultures. Gel electrophoresis is revealed by colloidal blue staining and by western blot using polyclonal rabbit antibodies directed against L-Asparaginase. The results of this analysis are presented in FIG. 5.
Example
Dish Screening of the Transformants Obtained by Insertion of the Integration/Expression Cassette at the URA3 Locus
As described previously, insertion at the URA3 locus makes it possible to eliminate the heterologous gene SUC2 encoding for invertase from S. cerevisiae. The transformants having integrated the expression cassette then become Suc2−. They are no longer able to grow on saccharose as sole carbon source. The transformants are streaked onto 2 rich media: YPD (1% glucose) and YPS (1% saccharose). The results of this analysis are presented in FIG. 6. Through this screening we confirm the results obtained by PCR analysis with the Ver1Ura3 and Ver2Ura3 primers.
Example 6
Screening of the Transformants Obtained by Insertion of the Integration/Expression Cassette at the LIP2 Locus
As described previously, insertion at the LIP2 locus makes it possible to eliminate the LIP2 gene encoding for the extracellular lip2p lipase of Y. lipolytica. The transformants having integrated the expression cassette then become Lip2−. During production in a medium containing an inducer like oleic acid, the transformants no longer secrete lipase in the culture supernatant. Screening is performed by cultivation in production medium Y1T2D1O2 for 48 hours at 28° C. and stirring at 180 rpm. The presence of lipase in the supernatant is detected by a microplate enzyme assay from 20 μL of supernatant. The results of this analysis are presented in FIG. 7. Through this screening, we confirm the results obtained by PCR analysis with the Ver1Lip2 and Ver2Lip2 primers.
Example 7
Analysis of the Transformants Obtained by RT-qPCR
The number of copies integrated can be analyzed via real time quantitative PCR via specific amplification of an amplicon (150 pb) of the gene encoding for L-Asparaginase. Using the DNAg of the transformants obtained, we performed RT-qPCR using the specific primers LAsp1 and LAsp2 of the gene encoding for L-Asparaginase and the specific primers Act4 and Act5 of the gene encoding for the actin of Y. lipolytica. This RT-qPCR was performed using the LightCycler Faststart DNA Master SyBR Green I Kit (Roche). The actin amplicon makes it possible to be a so-called household gene whose expression is known in order not to be modified between the conditions assayed and in our case a gene present in a single copy in the genome. Thus, the results are standardized with this amplicon. We also performed RT-qPCR with the help of specific Lip2-1 and Lip2-2 primers of the gene encoding for the Lip2p lipase of Y. lipolytica to verify the absence of the gene as of the second expression cassette integrated at the LIP2 locus. The results of this analysis are presented in FIG. 8.







TABLE 9







Lists of primers used for the disruption cassettes,


the verifications and the construction of new markers.












Primer
5′-3′
F/R
Sites





Leu2EX
LEU2-L1
GATCTGCTAGTGTATAAGACTCTATAAAAAGGGCC
F
ΔBamHI



LEU2-L2
CTTTTTATAGAGTCTTATACACTAGCA
R
ΔBamHI


 


GUT2 marker
PG3PTS
CCGGAATTCCTGACCAGTCTCACATCCGACC
F
EcoRI



PG3PTR
CCGGAATTCTAAAGCAGATACTCAACAACTCAGCAATAGTC
R
EcoRI



G3PB1S
GGAGCTACCGGCTCCGGTATCGC
F
ΔBamHI



G3PH1R
GCGATACCGGAGCCGGTAGCTCC
R
ΔBamHI



G3PB2S
CGGAAACGCTGGATCTTTCAACATCAAGGCC
F
ΔBamHI



G3PB2R
GGCCTTGATGTTGAAAGATCCAGCGTTTCCG
R
ΔBamHI



G3PES
GGAGCAGGAGTTCAACACCGGTGTCG
F
ΔEcoRI



G3PER
CGACACCGGTGTTGAACTCCTGCTCC
R
ΔEcoRI


 


AGUT2
G3PD-P1
GCAGATCCACTGTCAAGCCG
F




G3PD-P2
GCTAGGGATAAACAGGGTAATGCGGTAGGAAAGAGAAGTTCCGCG
R
I-SceI



G3PD-T1
GCATTACCCTGTTATCCCTAGCCGGACTATTTCCCCGCAGC
F
I-SceI



G3PD-T2
GCAGCCAGCAGCACGTAGTAG
R




G3PD-Ver1
GAATGACGGGGGCAACGCAG
F




G3PD-Ver2
CAGCAGCCACAAATAGCAGACTGCC
R



 


pGUT2-1.0 and 
P1KB
CCGGAATTCCGTGACAACGGATGATGCTGTCACATGACG
F
EcoRI


1.5
P15KB
CCGGAATTCCTGTTGCCATGCACAGCTCCACTCAACG
F
EcoRI



PNHE1
TCCCGCTAGCCGAGGTATGCAAGGACGAGTGC
R
NHeI


 


ADE2 locus
P1ADE2
ATAAGAATGCGGCCGCGCGAGTGAGAGCCGATACCAAGGGATGCGAG
F
NotI



P2ADE2
CATTACCCTGTTATCCCTACAGACACAGGTCCCAGGCGTCGGTTCTCG
R
I-SceI



T1ADE2
CTAGGGATAACAGGGTAATTAACTATAACGGTCCTAAGGTAGCGACCTCG
F
I-SceI/




GAAACCACTCTGCCAGTCATCGGTGTC

CeuI



T2ADE2
ATAGTTTAGCGGCCGCGGAAGCGTGTCAACGACATGTTCCCTCTTCATACC
R
NotI



Ver1Ade2
CGACGATAGAGCAGGTCTCACTGTTGGGAATGCTG
F




Ver2Ade2
CTACACTGACGAAGTGGACATCCCGGCTTGGACTG
R



 


ADE2 marker
ADE2S
CGCGAATTCGCCTGCTTGAAAGAAGTGAGTGGTATGCTCGG
F
EcoRI



ADE2R
CGCGAATTCCATTGCCACGACCTGTTAAAAGACAAGATGACC
R
EcoRI



ADE2ES
GCTGGCCATCCGAATCCTGGCTGCTTACGACGCC
F
AEcoRI



ADE2ER
GGCGTCGTAAGCAGCCAGGATTCGGATGGCCAGC
R
AEcoRI


 


Lip2 locus
P1Lip2
ATAAGAATGCGGCCGCGTGGTACGTTTCGTCGCATCGGACGAG
F
NotI



P2Lip2
CATTACCCTGTTATCCCTAGAGAGCTGGTACTTGGGTATCAATTGAGG
R
I-SceI



T1Lip2
CTACCGATAACAGGGTAATTAACTATAACGCTCCTAAGGTAGCGACCTGA
F
I-SceI/




TCCACCCTCCTCTCTCCAACG

CeuI



T2Lip2
ATAGTTTAGCGGCCGCGTGGACACAAGGAAGTATGCGGTCGTCGTCG
R
NotI



Lip2Ver1
CTCTGTCAGTGTTCGGATAAGTCCTTAGATCACC
F




Lip2Ver2
CCTCACTTCTGTCACAGATGATGCATTCAACAC
R



 


Leu2 locus
P1Leu2
ATAAGAATGCGGCCGCGACACTACTCTGGCTACAGCTTGCGGTACTG
F
NotI



P2Leu2
CATTACCCTGTTATCCCTAGCTCGAATAACATTCACAGGCTTGGTG
R
I-SceI



T1Leu2
CTAGGGATAACAGGGTAATTAACTATAACGGTCCTAAGGTAGCGAGGTGT
F
I-SceI/




GTTTGTAGTGGAGGACAGTGGTACG

I-CeuI



T2 Leu2
ATAGTTTAGCGGCCGCGTACTGAACCGACTTTGGTGCTTGCACTC
R
NotI



Leu2Ver1
CTCCACGCTAATGCCCATCATACTCTGTTTGGC
F




Leu2Ver2
CCTGGCGTTACAAAGCCGAGGGAGACAGCCTTGAC
R



 


Ura3 locus
P1Ura3
ATAAGAATGCGGCCGCGGTGACACTGCACTATTGGTTTGCTTCTGATG
F
NotI



P2Ura3
CATTACCCTGTTATCCCTAGTCGAGCTTCGTAGGAGGGCATTTTGGTGG
R
I-SceI



T1Ura3
CTAGGGATAACAGGGTAATTAACTATAACGGTCCTAAGGTAGCGATACGG
F
I-SceI/




AGATGCTGGGTACAAGTAGC

CeuI



T2Ura3
ATAGTTTAGCGGCCGCCTATGCTACGAGCGTCGGATTCACCACAG
R
NotI



Ura3Ver1
GGCACACTGCTCACTATCGCAGGCTGCAACAATG
F




Ura3Ver2
CCTGACTCGTCTCGATACTCAAGACCTCATTGACGC
R





[F = forward direction/ R = reverse direction] 













TABLE 10







List of primers used to construct the pVC vector and quantitative PCR, RT-qPCR.












Primer
5′-3′
F/R
Sites





pVC 
Link1
GGCCGCTAACTATAACGGTCCTAAGGTAGCG
F



polylinker
Link11
CCGAATCGATTCGCTACCTTAGGACCGTTATAGTTAGC
R




Link2
AATCGATTCGGATCCCACAATGAAGCTTCCCCGCGGTAC
F




Link22
CTAGGTACCGCGGGGAAGCTTCATTGTGGGAT
R




Lip2Thc
TATCAAATGCGGCCGCTTCGCTACCTTAGGACCGTTATAGT
R
NotI




TAACACGATTCGATTTGTCTTAGAGGAACGC





PDX2Xho
GAGTAATGCTCGAGTATCGAAGTCTTGTACC
F
XhoI


 


JMP62
62claS
GCGATATTACCCTGTTATCCCTAGAATCGATTCCCACAAGACGAACAAGT
F



ISceI

G





62claR
CACTTGTTCGTCTTGTGGGAATCGATTCTAGGGATAACAGGGTAATATCGC
R



 


LAsp gene
preproLip2
CGCGGATCCCACAATGAAGCMCCACCATCCTTTTCACAGCCTGCGCTAC
F
BamHI






HindIII



Lip2KR
TCGCTTCTGGAGAACTGCGGCCTC
R




LAspsens
GAGGCCGCAGTTCTGCAGAAGCGAGCCGACAAGCTGCCCAACATTGTGAT
F





TC





LAsprev
CCACCTAGGCTAGTAGGTGTGGAAGTACTCCTGGATG
R
AvrII


 


qPCR
LIP2-1
TACTCTTGGTCAGCCCAT
F



Lip2
LIP2-2
AGAAGGGCACTTGAGGGA
R



 


qPCR
Act4
TATTGCCGAGCGAATGC
F



Act
Act5
CTTGGAGATCCACATCTGC
R



 


qPCR
LAsp1
GCTGAACGACCGAATTGG
F



LAsp
LAsp2
GTGGTGTGCAGCTTGTC
R





[F = forward direction/R = reverse direction] 













TABLE 11







List of excisable markers constructed.









Marker
Vector name
Collection No.





ADE2
pKS-LPR-Ade2 (direction 1)
JME798



pKS-LPR-Ade2 (direction 2)
JME799


GUT2-0.5
pKS-LPR-Gut2-0.5 (direction 1)
JME792


GUT2-1.0
pKS-LPR-Gut2-1.0 (direction 1)
JME919



pKS-LPR-Gut2-1.0 (direction 2
JME920


GUT2-1.5
pKS-LPR-Gut2.1.5 (direction 1)
JME921



pKS-LPR-Gut2-1.5 (direction 2)
JME922


LEU2
pKS-LPR-Leu2 (direction 2)*
JME509


LEU2n
pKS-LPR-Leu2ΔBamHI (direction 2)
JME790


URA3
pKS-LPR-Ura3 (direction 1)
JME507


HYG
pKS-LPR-hph (direction 2)*
JME508





*Fickers et al., Journal of Microbiological Methods 55 (2003) 727-737













TABLE 12







List of random integration vectors, JMP61 and JMP62 series.










Vector name
Collection No.







JMP61-SceI
JME793



JMP61 Leu2nEx
JME794



JMP61 Ura3Ex
JME795



JMP61HygEx
JME796



JMP61 Gut2-0.5Ex
JME797



JMP61 Ade2Ex
JME861



JMP62 I-SceI
JME801



JMP62 Leu2nEx
JME802



JMP62 Ura3Ex
JME803



JMP62 HygEx
JME804



JMP62 Gut2-0.5Ex
JME805



JMP62 Ade2Ex
JME862

## Claims

1. A method for the targeted integration of at least three copies of a gene of interest in the genome of a Yarrowia strain including the following steps:
a) cultivation of a Yarrowia strain comprising a deletion in at least three genes wherein the deletion is a deletion in URA3, a deletion in LEU2 and the specific deletion GUT2-744 or wherein the deletion is a deletion in URA3, a deletion in LEU2 and the specific deletion Ade2-844 and wherein independent of the at least three genes, the phenotype associated with each of the deletions corresponds to an auxotrophy or to a dominant character for the strain;
b) transformation of the auxotrophic and/or dominant character Yarrowia strain with at least three recombinant vectors that include selection markers allowing, for the Yarrowia strain, complementation of the auxotrophy and/or of the dominant phenotype resulting from each of the deletions, the recombinant vectors each including:
i) the sequence of the gene of interest,
ii) a selection marker, and
iii) two DNA sequences framing the sequence of the gene of interest and the selection marker, the two DNA sequences are homologous to the sequences corresponding to the ends of the targeted integration site in the genome of the Yarrowia strain in order to allow the targeted integration of the recombinant vector via homologous recombination; and

c) selection on minimum medium of the yeasts having integrated the at least three recombinant vectors.

2. The targeted integration method as claimed in claim 1, wherein the genes having a dominant character phenotype are chosen from among:
the hygromycin-resistance gene HPH (HYG), the MDR3 gene, the Kan MX gene and the Tn5ble gene.

3. The targeted integration method as claimed in claim 1, wherein in step b), the targeted integration site in the genome of the Yarrowia strain is chosen from among the genes URA3, LEU2, ADE2, LIP2, LIP7, LIP8, AXP, GUT2 or XPR2.

4. The targeted integration method as claimed in claim 3, wherein in step b), the targeted integration site in the genome of the Yarrowia strain is chosen from among the genes URA3, LEU2, ADE2, LIP2, LIP8 or AXP.

5. The targeted integration method as claimed in claim 1, wherein the step b) transformation of the Yarrowia strain and the step c) selection on minimum medium are carried out separately for each of the at least three recombinant vectors.

6. The targeted integration method as claimed in claim 1, wherein in step b), the transformations with at least the three recombinant vectors are carried out independently and successively with each of the recombinant vectors or simultaneously with all of the recombinant vectors and in that all of the transformations are followed by a step c) selection on a minimum medium of the yeasts having integrated the recombinant vectors.

7. The targeted integration method as claimed in claim 1, wherein the Yarrowia strain is a strain of Yarrowia lipolytica.

8. The targeted integration method as claimed in claim 1, wherein the Yarrowia strain includes four genes having independent of one another a deletion associated with an auxotrophic or dominant character phenotype chosen from among the genes URA3, LEU2, GUT2 or ADE2.

9. The targeted integration method as claimed in claim 1, wherein the step b) transformation is carried out with three to ten recombinant vectors.

10. The targeted integration method as claimed in claim 1, wherein the selection marker is framed by sequences allowing its excision after the targeted integration of the recombinant vector.

11. A method for producing a polypeptide encoded by a gene of interest from a Yarrowia strain, which includes:
i) targeted integration of at least three copies of a gene of interest in the genome of the Yarrowia strain as claimed in claim 1;
ii) cultivation of the Yarrowia strain in a liquid culture medium containing assimilable sources of carbon, nitrogen and inorganic salts in order to allow the growth of the transformed Yarrowia strain and expression of the polypeptide of interest; and
iii) recovery of the expressed polypeptide of interest from the Yarrowia cells or from the culture medium obtained in step ii).

12. A method for obtaining a modified Yarrowia strain, which includes a step in which the Yarrowia strain is transformed with at least three vectors to produce a Yarrowia strain comprising at least three deletions wherein the deletion is a deletion in URA3, a deletion in LEU2 and the specific deletion GUT2-744 or wherein the deletion is a deletion in URA3, a deletion in LEU2 and the specific deletion Ade2-844 and wherein the phenotype associated with each of the deletions corresponds to an auxotrophy or to a dominant character for the strain.

13. The method as claimed in claim 12, wherein the deletion of at least three genes is further associated with a dominant character phenotype selected from among:
the hygromycin-resistance gene HPH (HYG), the MDR3 gene, the KanMX gene, or the Tn5ble gene.

14. An auxotrophic Yarrowia strain, which strain includes a deletion in at least three genes of its genome wherein the deletion is a deletion in URA3, a deletion in LEU2 and the specific deletion GUT2-744 or wherein the deletion is a deletion in URA3, a deletion in LEU2 and the specific deletion Ade2-844 and the phenotype associated with each of the deletions corresponds to an auxotrophy or to a dominant character for the strain.

15. The auxotrophic Yarrowia strain of claim 14, which includes a deletion in at least four genes of its genome chosen from among the genes URA3, LEU2, GUT2, ADE2, HIS and LYS5.

16. The auxotrophic Yarrowia strain as claimed in claim 14, which is selected from the group consisting of the Yarrowia lipolytica strains deposited on Feb. 4, 2008 in accordance with the Budapest Treat with the Collection nationale de Culture de Microorganismes (CNCM), PASTEUR INSTITUTE, 25 rue du Docteur Roux, 75724 PARIS CEDEX 15, France, under the numbers CNCM 1-3911 and CNCM 1-3912.

17. The auxotrophic Yarrowia strain as claimed in claim 14, which corresponds to the Yarrowia lipolytica strain deposited on Feb. 4, 2008 in accordance with the Budapest Treaty with the Collection nationale de Culture de Microorganismes (CNCM), PASTEUR INSTITUTE, 25 rue du Docteur Roux, 75724 PARIS CEDEX 15, France under the number CNCM I-3913.

18. The targeted integration method as claimed in claim 1 wherein the deletion in at least three genes is selected from the deletions Ura3-302, Leu2-270, Gut2-744 or Ade2-844.

19. The targeted integration method as claimed in claim 1 further comprising a an auxotrophic marker selected from the HIS and LYS5 genes.

20. The targeted integration method as claimed in claim 2 wherein the gene having a dominant character phenotype is the hygromycin-resistance gene HPH (HYG).

21. A method for the targeted integration of at least three copies of a gene of interest in the genome of a Yarrowia strain including the following steps:
a) cultivation of a Yarrowia strain comprising a deletion in at least three genes wherein the deletion is selected from a deletion in URA3, a deletion in LEU2, and the deletion Gut2-744 or the deletion Ade2-844 and wherein at least one deletion is Gut2-744 and wherein independent of the at least three genes, the phenotype associated with each of the deletions corresponds to an auxotrophy or to a dominant character for the strain;
b) transformation of the auxotrophic and/or dominant character Yarrowia strain with at least three recombinant vectors that include selection markers allowing, for the Yarrowia strain, complementation of the auxotrophy and/or of the dominant phenotype resulting from each of the deletions, the recombinant vectors each including:
i) the sequence of the gene of interest,
ii) a selection marker, and
iii) two DNA sequences framing the sequence of the gene of interest and the selection marker, the two DNA sequences are homologous to the sequences corresponding to the ends of the targeted integration site in the genome of the Yarrowia strain in order to allow the targeted integration of the recombinant vector via homologous recombination; and

c) selection on minimum medium of the yeasts having integrated the at least three recombinant vectors.

22. The auxotrophic Yarrowia strain as claimed in claim 14 which strain includes the deletion Gut2-744.

23. The auxotrophic Yarrowia strain as claimed in claim 14 which strain includes the deletions Ura3-302, Leu2-958, Gut2-744 or Ade2-844.