A chemical genomics approach for understanding chemical communication

2020 Fiscal Year Annual Research Report

• Project Area: Frontier research of chemical communications
• Project/Area Number: 17H06411
• Research Institution: Institute of Physical and Chemical Research
• 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)
• Co-Investigator(Kenkyū-buntansha): 八代田 陽子 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, 副チームリーダー (60360658)
• Project Period (FY): 2017-06-30 – 2022-03-31
• Keywords: chemical genomics / yeast / chemical communication / HAP1

Outline of Annual Research Achievements

We conducted a yeast (Saccharomyces cerevisiae) chemical genomics (CG) approach for bioactive NPDepo compounds and compounds provided by domestic and foreign collaborators. In our S. cerevisiae CG pipeline, the set of ~1000 yeast essential genes was analyzed with three different strain collections including a set of temperature sensitive (TS) mutants, a set of heterozygous diploid (HET) deletion mutants, and a set of yeast strains each carrying an essential gene on a high-copy plasmid (MoBY; Molecular Barcoded Yeast). The nonessential gene set consisting of ~5000 viable haploid deletion mutants (WG; whole genome) was also analyzed. Based on our CG profiling, we have carried out the prediction of targets for several compounds (e.g., fatty acid synthase, aminoacyl-tRNA synthetase, cell wall synthesis, glycosylation, etc.). Especially, we focused on a clionamine analog which inhibits Mycobacterium tuberculosis (Mtb) survival in macrophages. Our CG analysis predicted a phosphatidylinositol 4-kinase (PI4K) as a target of the clionamine analog, which was supported by a pull-down assay and an in vivo inhibition assay. Finally, using mammalian cells, we validated PI4K as a viable host directed therapy cellular target against Mtb.
In collaboration with the Moffat Lab in University of Toronto, we developed a CRISPR-Cas9-based CG analysis method using human cell line HAP1 in suspension culture, which increased throughput. We launched to screen the compounds whose targets were successfully predicted by the yeast CG pipeline as well as our collaborators’ compounds.

Current Status of Research Progress

1: Research has progressed more than it was originally planned.

Reason

We already established S. cerevisiae version of CG pipeline that is our main goal of this project. Moreover, we established the human cell version of CG analysis pipeline.

Strategy for Future Research Activity

We will conduct yeast and human chemical genomics (CG) analysis for bioactive compounds provided from the NPDepo and the collaborators in the groups A01 and A02. We will validate the compound-target interactions that are predicted by the CG pipeline. We will also start to establish the S. pombe version of CG pipeline.

Research Products

• [Int'l Joint Research] University of Toronto/The University of British Columbia(カナダ)
  • Country Name: CANADA
  • Counterpart Institution: University of Toronto/The University of British Columbia
• [Int'l Joint Research] University of Minnesota(米国)
  • Country Name: U.S.A.
  • Counterpart Institution: University of Minnesota
• [Journal Article] Genetic profiling of protein burden and nuclear export overload. (2020)
  • Author(s): Kintaka R, Makanae K, Namba S, Kato H, Kito K, Ohnuki S, Ohya Y, Andrews BJ, Boone C, Moriya H.
  • Journal Title: Elife Volume: 9 Pages: e54080
  • DOI: 10.7554/eLife.54080.
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability (2020)
  • Author(s): Mattiazzi Usaj M, Sahin N, Friesen H, Pons C, Usaj M, Masinas MPD, Shuteriqi E, Shkurin A, Aloy P, Morris Q, Boone C, Andrews BJ.
  • Journal Title: Mol Syst Biol Volume: 16 Pages: e9243
  • DOI: 10.15252/msb.20199243.
  • Peer Reviewed / Open Access / Int'l Joint Research