Gene disruption methodologies for drug target discovery

• US 6,783,985 B1
• Filed: 02/20/2001
• Issued: 08/31/2004
• Est. Priority Date: 02/18/2000
• Status: Expired due to Fees

• Current Assignee: Merck & Co., Inc.
• Original Assignee: Elitra Pharmaceuticals, Inc. (Merck & Co., Inc.)
• Inventors: Roemer, Terry, Jiang, Bo, Boone, Charles, Bussey, Howard
• Primary Examiner(s): Ketter, James
• Assistant Examiner(s): Lambertson, David
• Application Number:
  US09/792,024
• Time in Patent Office: 1,288 Days
• Field of Search: 435/4, 435/6, 435/29, 435/34, 435/440, 435/471, 435/243, 435/254.1, 435/254.11, 435/254.22, 435/254.3, 435/254.7, 435/254.8, 435/254.9, 435/255.1, 435/255.3, 435/255.4, 435/256.1, 435/256.2, 435/256.6
• US Class Current: 435/440
• CPC Class Codes: A61K 39/00 Medicinal preparations containing antigens or antibodies materials for immunoassay G01N33/53
• CPC Class Codes: C07K 14/37 from fungi
• CPC Class Codes: C07K 14/40 from Candida
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• CPC Class Codes: C12N 1/145 Fungal isolates
• CPC Class Codes: C12N 1/165 Yeast isolates
• CPC Class Codes: C12N 15/1034 Isolating an individual clone by screening libraries
• CPC Class Codes: C12N 15/65 using markers enzymes used as markers C12N15/52
• CPC Class Codes: C12N 15/80 for fungi
• CPC Class Codes: C12N 15/90 Stable introduction of foreign DNA into chromosome
• CPC Class Codes: C12R 2001/645 Fungi ; Processes using fungi
• CPC Class Codes: C12R 2001/725 Candida albicans

Abstract

The present invention provides methods and compositions that enable the experimental determination as to whether any gene in the genome of a diploid pathogenic organism is essential, and whether it is required for virulence or pathogenicity. The methods involve the construction of genetic mutants in which one allele of a specific gene is inactivated while the other allele of the gene is placed under conditional expression. The identification of essential genes and those genes critical to the development of virulent infections, provides a basis for the development of screens for new drugs against such pathogenic organisms. The present invention further provides Candida albicans genes that are demonstrated to be essential and are potential targets for drug screening. The nucleotide sequence of the target genes can be used for various drug discovery purposes, such as expression of the recombinant protein, hybridization assay and construction of nucleic acid arrays. The uses of proteins encoded by the essential genes, and genetically engineered cells comprising modified alleles of essential genes in various screening methods are also encompassed by the invention.

Claims

1. A method for constructing a strain of diploid fungal cells in which both alleles of a gene are modified, the method comprising the steps of:

(a) modifying a first allele of a gene in diploid fungal cells by recombination using a gene disruption cassette comprising a first nucleotide sequence encoding a first expressible selectable marker, thereby providing heterozygous diploid fungal cells in which the first allele of the gene is inactivated; and

(b) modifying the second allele of the gene in the diploid fungal cells by recombination using a promoter replacement fragment comprising a second nucleotide sequence encoding a second expressible selectable marker and a heterologous promoter, such that expression of the second allele of the gene is regulated by the heterologous promoter

wherein at least one of the first and the second expressible selectable marker is a drug-resistance marker,

thereby constructing a strain of diploid fungal cells in which both alleles of a gene are modified.

3. The method of claim 1, wherein the diploid fungal cells are cells of fungal species selected from the group consisting of Aspergillus fumigatus, Aspergillus niger, Aspergillus flavis, Candida albicans, Candida tropicalis, Candida parapsilopsis, Candida krusei, Cryptococcus neoformans, Coccidioides immitis, Exophalia dermatiditis, Fusarium oxysporum, Histoplasma capsulatum, Phneumocystis carinii, Trichosporon beigelii, Rhizopus arrhizus, Mucor rouxii, Rhizomucor pusillus, Absidia corymbigera, Botrytis cinerea, Erysiphe graminis, Magnaporthe grisea, Puccinia recodita, Septoria triticii, Tilletia controversa, and Ustilago maydis.

4. The method of claim 1, wherein the diploid fungal cells are cells of Candida.

5. The method of claim 1, wherein the first and/or second expressible selectable marker is selected from the group consisting of CaHIS3, CaSAT1, CaBSR1, CaURA3, CaLEU2, CaTRP1, and combinations thereof.

6. The method of claim 1 or 2, wherein the method further comprises

(c) introducing a nucleotide sequence encoding a transactivation fusion protein that is expressible in the diploid fungal cell, said transactivation fusion protein comprising a DNA binding domain and a transcription activation domain; and

wherein the heterologous promoter in the promoter replacement fragment comprises at least one copy of a nucleotide sequence which is bound by the DNA binding domain of the transactivation fusion protein, such that binding of the transactivation fusion protein increases transcription from the heterologous promoter.

7. The method of claim 1 or 2, wherein the first selectable marker in the gene disruption cassette is disposed between a first region and a second region, wherein the first region and the second region hybridize separately to non-contiguous regions of the first allele of the gene in the diploid fungal cells.

8. The method of claim 7, wherein the first selectable marker is selected from the group consisting of CaSAT1, CaBSR1, CaURA3, CaHIS3, CaLEU2, CaTRP1, and combinations thereof.

9. The method of claim 7, wherein the second selectable marker is selected from the group consisting of CaSAT1, CaBSR1, CaURA3, CaHIS3, CaLEU2, CaTRP1, and combinations thereof.

2. A method of assembling a collection of diploid fungal cells each of which comprises modified alleles of a different gene, the method comprising the steps of:

(a) modifying a first allele of a first gene in diploid fungal cells by recombination using a gene disruption cassette comprising a first nucleotide sequence encoding a first expressible selectable marker, thereby providing heterozygous diploid fungal cells in which the first allele of the gene is inactivated;

(b) modifying a second allele of the first gene in the heterozygous diploid fungal cells by recombination using a promoter replacement fragment comprising a second nucleotide sequence encoding a second expressible selectable maker and a heterologous promoter, such that expression of the second allele of the gene is regulated by the heterologous promoter, wherein at least one of the first and the second expressible selectable marker is a drug-resistance selectable marker, thereby providing a first strain of diploid fungal cells comprising a modified allelic pair of the first gene; and

(c) repeating steps (a) and (b) a plurality of times, wherein a different gene is modified with each repetition, thereby providing the collection of diploid fungal cells each comprising the modified alleles of a different gene.

10. A method for constructing a strain of diploid fungal cells in which both alleles of a gene are modified, the method comprising the steps of:

(a) providing diploid fungal cells wherein a first allele of the gene is inactivated; and

(b) modifying a second allele of the gene in the diploid fungal cells by recombination using a promoter replacement fragment comprising a second nucleotide sequence encoding an expressible drug-resistance selectable marker and a heterologous promoter, such that expression of the second allele of the gene is regulated by the heterologous promoter,

thereby constructing a strain of diploid fungal cells in which both alleles of a gene are modified.

11. A method for constructing a strain of diploid fungal cell in which both alleles of a gene are modified, the method comprising the steps of:

(a) providing diploid fungal cells wherein expression of a first allele of the gene is regulated by a heterologous promoter; and

(b) inactivating a second allele of the gene in the diploid fungal cells by recombination using a gene disruption cassette comprising a nucleotide sequence encoding an expressible drug-resistance selectable marker,

thereby constructing a strain of diploid fungal cells in which both alleles of a gene are modified.

12. A strain of diploid fungal cells comprising modified alleles of a gene, wherein the first allele of the gene is inactivated by recombination using a gene disruption cassette comprising a nucleotide sequence encoding a first expressible selectable marker the second allele of the gene is modified by recombination using a promoter replacement fragment comprising a second nucleotide sequence encoding a second expressible selectable marker and a heterologous promoter such that expression of the second allele of the gene is regulated by the heterologous promoter that is operably linked to the coding region of the second allele of the gene;

wherein the first modified allele of the gene in the strain is linked with the first expressible selectable marker and the second modified allele of the gene in the strain is linked with the second expressible selectable marker; and

wherein at least one expressible selectable marker in the strain is a drug-resistance selectable marker.

13. A strain of diploid fungal cells according to claim 12, wherein the diploid fungal cells are cells of fungal species selected from the group consisting of Aspergillus fumigatus, Aspergillus niger, Aspergillus flavis, Candida albicans, Candida tropicalis, Candida parapsilopsis, Candida krusei, Cryptococcus neoformans, Coccidioides immitis, Exophalia dermatiditis, Fusarium oxysporum, Histoplasma capsulatum, Phneumocystis carinii, Trichosporon beigelii, Rhizopus arrhizus, Mucor rouxii, Rhizomucor pusillus, Absidia corymbigera, Botrytis cinerea, Erysiphe graminis, Magnaporthe grisea, Puccinia recodita, Septoria triticii, Tilletia controversa, and Ustilago maydis.

14. A strain of diploid fungal cells according to claim 12, wherein the diploid fungal cells are cells of Candida.

15. The diploid fungal cells of claim 12 further comprising a nucleotide sequence encoding a transactivation fusion protein that is expressible in the diploid fungal cell, said transactivation fusion protein comprising a DNA binding domain and a transcription activation domain;

and wherein the heterologous promoter in the promoter replacement fragment comprises at least one copy of a nucleotide sequence which is bound by the DNA binding domain of the transactivation fusion protein, such that binding of the transactivation fusion protein increases transcription from the heterologous promoter.

16. The strain of diploid fungal cells of claim 12 or 15, wherein the gene is a gene essential for the growth and/or survival of the cells.

17. The strain of diploid fungal cells of claim 12 or 15, wherein the gene is a gene that contributes to the virulence and/or pathogenicity of the fungal cells against a host organism.

18. A strain of diploid fungal cells according to claim 17, wherein the diploid fungal cells are cells of fungal species selected from the group consisting of Aspergillus fumigatus, Aspergillus niger, Aspergillus flavis, Candida albicans, Candida tropicalis, Candida parapsilopsis, Candida krusei, Cryptococcus neoformans, Coccidioides immitis, Exophalia dermatiditis, Fusarium oxysporum, Histoplasma capsulatum, Phneumocystis carinii, Trichosporon beigelii, Rhizopus arrhizus, Mucor rouxii, Rhizomucor pusillus, Absidia corymbigera, Botrytis cinerea, Erysiphe graminis, Magnaporthe grisea, Puccinia recodita, Septoria triticii, Tilletia controversa, and Ustilago maydis.

19. A strain of diploid fungal cells according to claim 17, wherein the diploid fungal cells are cells of Candida.

20. A collection of diploid fungal strains of claim 12 each comprising the modified alleles of a different gene, wherein each gene is essential for the growth and/or survival of the cells.

21. The collection of diploid fungal strains of claim 20, wherein substantially all of the essential genes in the genome of the fungus are modified and present in the collection.

22. A collection of diploid fungal strains of claim 12 each strain comprising the modified alleles of a different gene, wherein each gene contributes to the virulence and/or pathogenicity of the cells to a host organism.

23. The collection of diploid fungal strains of claim 22, wherein substantially all of the genes in the genome of the diploid fungus that contribute to the virulence and/or pathogenicity of the fungal cells against a host organism are modified and present in the collection.

24. A collection of diploid fungal strains of claim 12 wherein each strain comprises modified alleles of a different gene, and wherein substantially all the different genes in the genome of the fungus are modified and represented in the collection.

25. The collection of diploid fungal strains according to claim 24, wherein the diploid fungal cells are cells of fungal species selected from the group consisting of Aspergillus fumigatus, Aspergillus niger, Aspergillus flavis, Candida albicans, Candida tropicalis, Candida parapsilopsis, Candida krusei, Cryptococcus neoformans, Coccidioides immitis, Exophalia dermatiditis, Fusarium oxysporun, Histoplasma capsulatum, Phneumocystis carinii, Trichosporon beigelii, Rhizopus arrhizus, Mucor rouxii, Rhizomucor pusillus, Absidia corymbigera, Botrytis cinerea, Erysiphe graminis, Magnaporthe grisea, Puccinia recodita, Septoria triticii, Tilletia controversa, and Ustilago maydis.

26. The collection of diploid fungal strains according to claim 24, wherein the diploid fungal cells are cells of Candida.

27. The collection of diploid fungal strains of claim 24, wherein the essential genes present in the collection all share a characteristic selected from the group consisting of:

similar biological activity, similar intracellular localization, structural homology, sequence homology, cidal terminal phenotype, static terminal phenotype, sequence homology to human genes, and exclusivity with respect to the organism.

28. The collection of claim 24, 20, 22, or 27 wherein the cells of each strain further comprise a molecular tag of about 20 nucleotides, the sequence of which is unique to each strain.

29. The collection of claim 28, wherein the molecular tag is disposed within the gene disruption cassette.