Identification of essential genes of Aspergillus fumigatus and methods of use
First Claim
1. A purified or isolated nucleic acid molecule comprising a nucleotide sequence encoding a gene product, wherein said gene product consists essentially of an amino acid sequence of one of SEQ ID NO:
- 3001-3594 or 8001-8603.
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Accused Products
Abstract
The present invention provides nucleotide sequences, methods and compositions that enable the experimental determination as to whether any gene in the genome of Aspegillus fumigatus is essential, and whether that gene is required for virulence or pathogenicity. The methods involve the construction of genetic mutants in which a target 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 Aspergillus fumigatus.
The present invention further provides Aspergillum fumigatus genes that are 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.
59 Citations
43 Claims
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1. A purified or isolated nucleic acid molecule comprising a nucleotide sequence encoding a gene product, wherein said gene product consists essentially of an amino acid sequence of one of SEQ ID NO:
- 3001-3594 or 8001-8603.
- View Dependent Claims (2, 6, 7, 8)
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3. A nucleic acid molecule comprising a fragment of one of SEQ ID NO:
- 1-594, 5001-5603,1001-1594, or 6001-6603, said fragment selected from the group consisting of fragments comprising at least 10, at least 20, at least 25, at least 30, at least 50 and at least 100 consecutive nucleotides of one of SEQ ID NO;
1-594, 5001-5603,1001-1594, or 6001-6603.
- 1-594, 5001-5603,1001-1594, or 6001-6603, said fragment selected from the group consisting of fragments comprising at least 10, at least 20, at least 25, at least 30, at least 50 and at least 100 consecutive nucleotides of one of SEQ ID NO;
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4. A nucleic acid molecule comprising a nucleotide sequence that hybridizes under stringent condition to a second nucleic acid molecule consisting of (a) a nucleotide sequence selected from the group consisting of one of SEQ ID NO:
- 1-594, 5001-5603,1001-1594, or 6001-6603, or (b) a nucleotide sequence that encodes a polypeptide consisting of an amino acid sequence selected from the group consisting of one of SEQ ID NO;
3001-3594 or 8001-8603;
wherein said stringent condition comprises hybridization to filter-bound DNA in 6×
sodium chloride/sodium citrate (SSC) at about 45°
C. followed by one or more washes in 0.2×
SSC/0.1% SDS at about 50-65°
C.
- 1-594, 5001-5603,1001-1594, or 6001-6603, or (b) a nucleotide sequence that encodes a polypeptide consisting of an amino acid sequence selected from the group consisting of one of SEQ ID NO;
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5. A purified or isolated nucleic acid molecule obtained from an organism other than Candida albicans or Saccharomyces cerevisiae comprising a nucleotide sequence having at least 30% identity to a sequence selected from the group consisting of SEQ ID NO:
- 1-594, 5001-5603,1001-1594, or 6001-6603;
fragments comprising at least 25 consecutive nucleotides of SEQ ID NO;
1-594, 5001-5603,1001-1594, or 6001-6603;
the sequences complementary to SEQ ID NO;
1-594, 5001-5603,1001-1594, or 6001-6603; and
the sequences complementary to fragments comprising at least 25 consecutive nucleotides of SEQ ID NO;
1-594, 5001-5603,1001-1594, or 6001-6603, as determined using BLASTN version 2.0 with default parameters.
- 1-594, 5001-5603,1001-1594, or 6001-6603;
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9. A purified or isolated polypeptide comprising an amino acid sequence selected from the group consisting of one of SEQ ID NO:
- 3001-3594, or 8001-8603.
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10. A purified or isolated polypeptide obtained from an organism other than Candida albicans or Saccharomyces cerevisiae comprising an amino acid sequence having at least 30% similarity to an amino acid sequence selected from the group consisting of one of SEQ ID NO:
- 3001-3594 or 8001-8603, as determined using FASTA version 3.0t78 with the default parameters.
- View Dependent Claims (35, 36)
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11. A fusion protein comprising a fragment of a first polypeptide fused to a second polypeptide, said fragment consisting of at least 6 consecutive residues of an amino acid sequence selected from one of SEQ ID NO:
- 3001-3594 or 8001-8603.
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12. A method of producing a polypeptide, said method comprises introducing into a cell, a vector comprising a promoter operably linked to a nucleotide sequence encoding a polypeptide consisting of an amino acid sequence selected from the group consisting of one of SEQ ID NO:
- 3001-3594 or 8001-8603; and
culturing the cell such that the nucleotide sequence is expressed.
- 3001-3594 or 8001-8603; and
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13. A method of producing a polypeptide, said method comprising providing a cell which comprises a heterologous promoter operably linked to a nucleotide sequence encoding a polypeptide consisting of an amino acid sequence selected from the group consisting of one of SEQ ID NO:
- 3001-3594 or 8001-8603; and
culturing the cell such that the nucleotide sequence is expressed.
- 3001-3594 or 8001-8603; and
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14. A method for identifying a compound which modulates the activity of a gene product encoded by a nucleic acid comprising a nucleotide sequence selected from the group consisting of one of SEQ ID NO:
- 2001-2594 or 7001-7603, said method comprising;
(a) contacting said gene product with a compound; and
(b) determining whether said compound modulates the activity of said gene product. - View Dependent Claims (15, 16)
- 2001-2594 or 7001-7603, said method comprising;
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17. A method of eliciting an immune response in an animal, comprising introducing into the animal a composition comprising an isolated polypeptide, the amino acid sequence of which comprises at least 6 consecutive residues of one of SEQ ID NO:
- 3001-3594 or 8001-8603.
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18. An isolated strain of Aspergillus fumigatus wherein the gene comprising a nucleotide sequence selected from the group consisting of one of SEQ ID NO:
- 1-594, 5001-5603,1001-1594, 6001-6603, 2001-2594, and 7001-7603, is inactive or placed under the control of a heterologous promoter.
- View Dependent Claims (20, 37, 38, 39, 40)
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19. An isolated strain of Aspergillus fumigatus comprising a nucleic acid molecule comprising a nucleotide sequence selected from one of SEQ ID NO:
- 1-594, 5001-5603,1001-1594, 6001-6603, 2001-2594, and 7001-7603, under the control of a heterologous promoter.
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21. A method of identifying a compound or binding partner that binds to a polypeptide comprising an amino acid sequence selected from the group consisting of one of SEQ ID NO:
- 3001-3594 or 8001-8603, or a fragment thereof said method comprising;
(a) contacting the polypeptide or fragment thereof with a plurality of compounds or a preparation comprising one or more binding partners; and
(b) identifying a compound or binding partner that binds to the polypeptide or fragment thereof.
- 3001-3594 or 8001-8603, or a fragment thereof said method comprising;
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22. A method for identifying a compound having the ability to inhibit growth or proliferation of Aspergillus fumigatus, said method comprising the steps of:
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(a) reducing the level or activity of a gene product encoded by a nucleic acid selected from the group consisting of SEQ ID NO;
2001-2594 or 7001-7603, in a Aspergillus fumigatus cell relative to a wild type cell, wherein said reduced level is not lethal to said cell;
(b) contacting said cell with a compound; and
(c) determining whether said compound inhibits the growth or proliferation of said cell. - View Dependent Claims (23, 24)
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25. A method for inhibiting growth or proliferation of Aspergillus fumigatus cells comprising contacting the cells with a compound that (i) reduce the level of or inhibit the activity of a nucleotide sequence selected from the group consisting of SEQ ID NO:
- 1-594, 5001-5603,1001-1594, 6001-6603, 2001-2594, and 7001-7603, or (ii) reduce the level of or inhibit the activity of a gene product encoded by a nucleotide sequence selected from the group consisting of SEQ ID NO;
1-594, 5001-5603,1001-1594, 6001-6603, 2001-2594, and 7001-7603,. - View Dependent Claims (26, 27)
- 1-594, 5001-5603,1001-1594, 6001-6603, 2001-2594, and 7001-7603, or (ii) reduce the level of or inhibit the activity of a gene product encoded by a nucleotide sequence selected from the group consisting of SEQ ID NO;
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28. A method for manufacturing an antimycotic compound comprising the steps of:
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(a) screening a plurality of candidate compounds to identify a compound that reduces the activity or level of a gene product encoded by a nucleotide sequence selected from the group consisting of SEQ ID NO;
1-594, 5001-5603, 1001-1594, 6001-6603, 2001-2594, and 7001-7603; and
(b) manufacturing the compound so identified. - View Dependent Claims (29)
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30. A method for treating an infection of a subject by Aspergillus fumigatus comprising administering a pharmaceutical composition comprising a therapeutically effective amount of a compound that reduces the activity or level of a gene product encoded by a nucleic acid comprising a sequence selected from the group consisting of SEQ ID NO:
- 1-594, 5001-5603, 1001-1594, 6001-6603, 2001-2594, and 7001-7603, and a pharmaceutically acceptable carrier, to said subject.
- View Dependent Claims (31, 34)
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32. A method for preventing or containing contamination of an object by Aspergillus fumigatus comprising contacting the object with a composition comprising an effective amount of a compound that reduces the activity or level of a gene product encoded by a nucleic acid comprising a sequence selected from the group consisting of SEQ ID NO:
- 1-594, 5001-5603, 1001-1594, 6001-6603, 2001-2594, and 7001-7603.
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33. A pharmaceutical composition comprising a therapeutically effective amount of an agent which reduces the activity or level of a gene product encoded by a nucleic acid selected from the group consisting of SEQ ID NO:
- 1-594, 5001-5603, 1001-1594, 6001-6603, 2001-2594, and 7001-7603, in a pharmaceutically acceptable carrier.
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41. A nucleic acid molecule microarray comprising a plurality of nucleic acid molecules, wherein each nucleic acid molecule comprises a nucleotide sequence that is hybridizable to a target nucleotide sequence selected from the group consisting of SEQ ID NO:
- 1-594, 5001-5603, 1001-1594, 6001-6603, 2001-2594, and 7001-7603.
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42. A computer or a computer readable medium that comprises at least one nucleotide sequence selected from the group consisting of SEQ ID NO.:
- 1-594, 5001-5603, 1001-1594, 6001-6603, 2001-2594, and 7001-7603, or at least one amino acid sequence selected from the group consisting of SEQ ID NO.;
3001-3594 and 8001-8603.
- 1-594, 5001-5603, 1001-1594, 6001-6603, 2001-2594, and 7001-7603, or at least one amino acid sequence selected from the group consisting of SEQ ID NO.;
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43. A method assisted by a computer for identifying a putatively essential gene of a fungus, comprising detecting sequence homology between a fungal nucleotide sequence or fungal amino acid sequence with at least one nucleotide sequence selected from the group consisting of SEQ ID NO.:
- 1-594, 5001-5603, 1001-1594, 6001-6603, 2001-2594, and 7001-7603, or at least one amino acid sequence selected from the group consisting of SEQ ID NO.;
3001-3594 and 8001-8603.
- 1-594, 5001-5603, 1001-1594, 6001-6603, 2001-2594, and 7001-7603, or at least one amino acid sequence selected from the group consisting of SEQ ID NO.;
Specification