Microarray-based method for monitoring yeast overexpression strains reveals small-molecule targets in TOR pathway (original) (raw)

References

  1. Harding, M.W., Galat, A., Uehling, D.E. & Schreiber, S.L. A receptor for the immunosuppressant FK506 is a cis-trans peptidyl-prolyl isomerase. Nature 341, 758–760 (1989).
    Article CAS Google Scholar
  2. Sigal, N.H., Dumont, F.J. Cyclosporin A FK-506, and rapamycin: pharmacologic probes of lymphocyte signal transduction. Annu. Rev. Immunol. 10, 519–560 (1992).
    Article CAS Google Scholar
  3. Heitman, J., Movva, N.R. & Hall, M.N. Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science 253, 905–909 (1991).
    Article CAS Google Scholar
  4. Brown, E.J. et al. A mammalian protein targeted by G1-arresting rapamycin-receptor complex. Nature 369, 756–758 (1994).
    Article CAS Google Scholar
  5. Chiu, M.I., Katz, H. & Berlin, V. RAPT1, a mammalian homolog of yeast Tor, interacts with the FKBP12/rapamycin complex. Proc. Natl. Acad. Sci. USA 91, 12574–12578 (1994).
    Article CAS Google Scholar
  6. Sabatini, D.M., Erdjument-Bromage, H., Lui, M., Tempst, P. & Snyder, S.H. RAFT1: a mammalian protein that binds to FKBP12 in a rapamycin-dependent fashion and is homologous to yeast TORs. Cell 78, 35–43 (1994).
    Article CAS Google Scholar
  7. Jacinto, E. & Hall, M.N. Tor signalling in bugs, brain and brawn. Nat. Rev. Mol. Cell Biol. 4, 117–126 (2003).
    Article CAS Google Scholar
  8. Crespo, J.L. & Hall, M.N. Elucidating TOR signaling and rapamycin action: lessons from Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 66, 579–591 (2002).
    Article CAS Google Scholar
  9. Shamji, A.F., Nghiem, P. & Schreiber, S.L. Integration of growth factor and nutrient signaling: implications for cancer biology. Mol. Cell 12, 271–280 (2003).
    Article CAS Google Scholar
  10. Inoki, K., Corradetti, M.N. & Guan, K.L. Dysregulation of the TSC-mTOR pathway in human disease. Nat. Genet. 37, 19–24 (2005).
    Article CAS Google Scholar
  11. Huang, J. et al. Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc. Natl. Acad. Sci. USA 101, 16594–16599 (2004).
    Article CAS Google Scholar
  12. Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391 (2002).
    Article CAS Google Scholar
  13. Winzeler, E.A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999).
    Article CAS Google Scholar
  14. Giaever, G. et al. Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat. Genet. 21, 278–283 (1999).
    Article CAS Google Scholar
  15. Lum, P.Y. et al. Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell 116, 121–137 (2004).
    Article CAS Google Scholar
  16. Giaever, G. et al. Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc. Natl. Acad. Sci. USA 101, 793–798 (2004).
    Article CAS Google Scholar
  17. Rine, J., Hansen, W., Hardeman, E. & Davis, R.W. Targeted selection of recombinant clones through gene dosage effects. Proc. Natl. Acad. Sci. USA 80, 6750–6754 (1983).
    Article CAS Google Scholar
  18. Chan, T.F., Carvalho, J., Riles, L. & Zheng, X.F. A chemical genomics approach toward understanding the global functions of the target of rapamycin protein (TOR). Proc. Natl. Acad. Sci. USA 97, 13227–13232 (2000).
    Article CAS Google Scholar
  19. Xie, M.W. et al. Insights into TOR function and rapamycin response: chemical genomic profiling by using a high-density cell array method. Proc. Natl. Acad. Sci. USA 102, 7215–7220 (2005).
    Article CAS Google Scholar
  20. Parsons, A.B. et al. Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat. Biotechnol. 22, 62–69 (2004).
    Article CAS Google Scholar
  21. Mulsch, A., Busse, R., Liebau, S. & Forstermann, U. LY 83583 interferes with the release of endothelium-derived relaxing factor and inhibits soluble guanylate cyclase. J. Pharmacol. Exp. Ther. 247, 283–288 (1988).
    CAS PubMed Google Scholar
  22. Mulsch, A., Luckhoff, A., Pohl, U., Busse, R. & Bassenge, E. LY 83583 (6-anilino-5,8-quinolinedione) blocks nitrovasodilator-induced cyclic GMP increases and inhibition of platelet activation. Naunyn Schmiedebergs Arch. Pharmacol. 340, 119–125 (1989).
    CAS PubMed Google Scholar
  23. Kiser, G.L. & Weinert, T.A. GUF1, a gene encoding a novel evolutionarily conserved GTPase in budding yeast. Yeast 11, 1311–1316 (1995).
    Article CAS Google Scholar
  24. Hughes, T.R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109–126 (2000).
    Article CAS Google Scholar
  25. Leinders-Zufall, T. & Zufall, F. Block of cyclic nucleotide-gated channels in salamander olfactory receptor neurons by the guanylyl cyclase inhibitor LY83583. J. Neurophysiol. 74, 2759–2762 (1995).
    Article CAS Google Scholar
  26. Prasad, R.K., Behrooz, A. & Ismail-Beigi, F. LY-83583 stimulates glucose transporter-1-mediated glucose transport independent of changes in cGMP levels. Eur. J. Pharmacol. 366, 101–109 (1999).
    Article CAS Google Scholar
  27. Marchler-Bauer, A. et al. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res. 33, D192–D196 (2005).
    Article CAS Google Scholar
  28. Hardwick, J.S., Kuruvilla, F.G., Tong, J.K., Shamji, A.F. & Schreiber, S.L. Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins. Proc. Natl. Acad. Sci. USA 96, 14866–14870 (1999).
    Article CAS Google Scholar
  29. Liu, C.L., Schreiber, S.L. & Bernstein, B.E. Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics 4, 19 (2003).
    Article CAS Google Scholar
  30. Gollub, J. et al. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res. 31, 94–96 (2003).
    Article CAS Google Scholar

Download references