Selection in fungi

Patent metadata

Field	Value
Publication number	US-10351863-B2
Application number	US-201816018726-A
Country	US
Kind code	B2
Filing date	Jun 26, 2018
Priority date	May 31, 2012
Publication date	Jul 16, 2019
Grant date	Jul 16, 2019

Abstract

The present invention relates to methods for constructing a recombinant fungal host cell comprising one or more copies of a polynucleotide construct integrated in its genome, said method comprising transforming a fungal host cell with an integrative polynucleotide construct comprising a first polynucleotide encoding a selectable marker, wherein the first polynucleotide, a 5′ untranslated region thereof and/or a riboswitch operably linked therewith comprises a spliceosomal intron which has 5 nucleotides or less between its branch site and its acceptor site; and a second polynucleotide encoding a polypeptide of interest; as well as suitable polynucleotide constructs, resulting fungal host cells and methods of manufacture.

First claim

The invention claimed is:

1. A method for constructing a recombinant fungal host cell comprising one or more copies of a polynucleotide construct integrated in its genome, said method comprising:
a) providing a fungal host cell transformed with an integrative polynucleotide construct, said construct comprising a first polynucleotide encoding a selectable marker, wherein the first polynucleotide, a 5′ untranslated region thereof and/or a riboswitch operably linked therewith comprises a spliceosomal intron which has 5 or less nucleotides between its branch site and its acceptor site; and a second polynucleotide encoding a polypeptide of interest;
b) cultivating the transformed fungal host cell under conditions conducive for expressing the selectable marker; and
c) isolating a recombinant fungal host cell comprising one or more copies of the polynucleotide construct integrated in its genome.

2. The method of claim 1 , wherein the fungal host cell in step a) has a growth deficiency and the integrative polynucleotide construct complements said growth deficiency when integrated into the genome of the host cell.

3. The method of claim 2 , wherein the fungal host cell in step a) lacks a functional nitrate reductase or nitrite reductase and the integrative polynucleotide construct comprises a gene encoding a functional nitrate reductase, or a gene encoding a functional nitrite reductase, or wherein the fungal host cell in step a) lacks a functional enolase and the integrative polynucleotide construct comprises a gene encoding a functional enolase.

4. The method of claim 2 , wherein the integrative polynucleotide construct in step a) is flanked on one or both side(s) by a homology box of sufficient size and sequence homology to a specific locus in the fungal host cell genome to enable site-specific integration of the integrative polynucleotide construct into said genome by homologous recombination after transformation.

5. The method of claim 1 , wherein the spliceosomal intron has 4 nucleotides or less between its branch site and its acceptor site.

6. The method of claim 1 , wherein the spliceosomal intron comprises a nucleotide sequence selected from the group of intron nucleotide sequences consisting of SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO:30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39 and SEQ ID NO: 40.

7. The method of claim 1 , wherein the first polynucleotide of the integrative polynucleotide construct has a riboswitch operably linked therewith.

8. The method of claim 1 , wherein the isolated recombinant fungal host cell comprises two or more copies of the polynucleotide construct integrated in its genome.

9. The method of claim 1 , wherein the isolated recombinant fungal host cell comprises three or more copies of the polynucleotide construct integrated in its genome.

10. The method of claim 1 , wherein the isolated recombinant fungal host cell comprises four or more copies of the polynucleotide construct integrated in its genome.

11. The method of claim 1 , wherein the first polynucleotide of the integrative polynucleotide construct encodes the selectable marker orotidine-5′-phosphate decarboxylase or PyrG.

12. The method of claim 1 , wherein the enzyme is a hydrolase, isomerase, ligase, lyase, oxidoreductase, or transferase.

13. The method of claim 1 , wherein the enzyme is an aminopeptidase, amylase, carbohydrase, carboxypeptidase, catalase, cellobiohydrolase, cellulase, chitinase, cutinase, cyclodextrin glycosyltransferase, deoxyribonuclease, endoglucanase, esterase, alpha-galactosidase, beta-galactosidase, glucoamylase, alpha-glucosidase, beta-glucosidase, invertase, laccase, lipase, mannosidase, mutanase, oxidase, pectinolytic enzyme, peroxidase, phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease, transglutaminase, xylanase, or beta-xylosidase.

14. The method of claim 1 , wherein the fungal host cell is a filamentous fungal host cell.

15. The method of claim 14 , wherein the filamentous fungal host cell is an Acremonium, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Chrysosporium, Coprinus, Coriolus, Cryptococcus, Filibasidium, Fusarium, Humicola, Magnaporthe, Mucor, Myceliophthora, Neocallimastix, Neurospora, Paecilomyces, Penicillium, Phanerochaete, Phiebia, Piromyces, Pleurotus, Schizophyllum, Talaromyces, Thermoascus, Thielavia, Tolypocladium, Trametes , or Trichoderma cell.

16. The method of claim 1 , wherein the fungal host cell is a yeast host cell.

17. The method of claim 16 , wherein the yeast host cell is a Candida, Hansenula, Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces, or Yarrowia cell.

18. The method of claim 16 , wherein the yeast host cell is a Kluyveromyces lactis, Saccharomyces carisbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomyces norbensis, Saccharomyces oviformis, or Yarrowia lipolytica cell.

19. The method of claim 2 , wherein the integrative polynucleotide construct is randomly integrated in the genome by non-homologous recombination after transformation.

20. The method of claim 3 , wherein the gene encoding a functional nitrate reductase is niaD.

21. The method of claim 3 , wherein the gene encoding a functional nitrite reductase is niiA.

22. The method of claim 3 , wherein the gene encoding a functional enolase is acuN.

23. The method of claim 5 , wherein the spliceosomal intron has 3 nucleotides or less between its branch site and its acceptor site.

24. The method of claim 5 , wherein the spliceosomal intron has 2 nucleotides or less between its branch site and its acceptor site.

25. The method of claim 5 , wherein the spliceosomal intron has 1 nucleotide between its branch site and its acceptor site.

26. The method of claim 5 , wherein the branch site and the acceptor site of the spliceosomal intron overlap by at least one nucleotide.

27. The method of claim 7 , wherein the riboswitch is derived from the thiA gene in Aspergillus oryzae.

28. The method of claim 7 , wherein the riboswitch is derived from the nmtA gene in Aspergillus oryzae.

Assignees

• Novozymes As

Inventors

• Olsen Carsten Lillelund

Classifications

• C12P21/00

  Preparation of peptides or proteins (single cell protein C12N1/00) · CPC title

• C12N9/0044

  acting on other nitrogen compounds as donors (1.7) · CPC title

• C12N9/88

  Lyases (4.) · CPC title

• C12Y107/01004

  Nitrite reductase [NAD(P)H] (1.7.1.4) · CPC title

• C12Y402/01011

  Phosphopyruvate hydratase (4.2.1.11), i.e. enolase · CPC title