2017 Fiscal Year Annual Research Report
A chemical genomics approach for understanding chemical communication
| Project Area | Frontier research of chemical communications |
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| Project/Area Number |
17H06411
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| Research Institution | Institute of Physical and Chemical Research |
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Principal Investigator |
BOONE CHARLES 国立研究開発法人理化学研究所, 環境資源科学研究センター, チームリーダー (70601342)
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| Co-Investigator(Kenkyū-buntansha) |
八代田 陽子 国立研究開発法人理化学研究所, その他, 研究員 (60360658)
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| Project Period (FY) |
2017-06-30 – 2022-03-31
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| Keywords | chemical genomics / yeast / chemical communication |
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| Outline of Annual Research Achievements |
We developed a high-throughput chemical genomics platform based on a diagnostic set of ~300 viable yeast gene deletion mutants, spanning all major biological processes, within a drug-sensitized genetic background. We also developed a highly multiplexed barcode sequencing protocol, allowing us to decipher rich chemical-genetic profiles on a large-scale. We generated profiles for ~10,000 compounds from the RIKEN Natural Product Depository (NPDepo) and other large compound collections, and, through the profile matching strategy we predicted the cellular targets at the biological process level. From FY2017, we expanded this chemical genomics platform to enable the prediction of precise essential gene targets. To do so, we developed a collection of barcoded conditional, temperature-sensitive alleles of essential genes (TS library) for chemical genomic profiling. In a complementary approach, we deleted a single copy of each essential gene in a diploid yeast (HET library) to enable drug-induced haploinsufficiency profiling (HIP). On the other hand, we started to screen drug-resistant mutants and we so far obtained ~20 mutants for several compounds. We are first approaching detailed target-compound validation by orthogonal genetic approaches. Drug-resistant mutants often identify the precise cellular target. For example, we selected spontaneous drug-resistant mutants to a RIKEN NPDepo compound. In total, we isolated drug-resistant mutants for the compound, one of which showed a nsSNP alteration in the FAS1 gene. HIP validation also suggested the compound targeted to Fas1.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
We already screened bioactive compounds from NPDepo using HET/TS library and obtained several drug resistant mutants as we planned.
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| Strategy for Future Research Activity |
We will continuously do the following project; 1) computational analysis for screening of the HET/TS libraries; 2) identification of mutations of the drug resistant mutants. We are also planning other screening using the MoBY-ORF library and the SUP library. Furthermore, we will validate interactions between ligands and their targets using biochemical assays, for example, for a RIKEN NPDepo compound and Fas1.
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[Journal Article] MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action2018
Author(s)
Nelson J, Simpkins SW, Safizadeh H, Li SC, Piotrowski JS, Hirano H, Yashiroda Y, Osada H, Yoshida M, Boone C, Myers CL.
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Journal Title
Bioinformatics
Volume: 34
Pages: 1251-1252
DOI
Peer Reviewed / Int'l Joint Research
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