Drug discovery using yeast as a model system: A functional genomic and proteomic view

Current Proteomics

Volumn 2, Issue 1, 2005, Pages 1-13

  Auerbach, Daniel ^a   Arnolde, Anthony ^b   Bogdan, Boris ^b   Fetchko, Michael ^b   Stagljar, Igor ^b  

^a DUALSYSTEMS BIOTECH AG   (Switzerland)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Drug discovery; Genomics; Proteomics; Yeast two hybrid system

Indexed keywords

EUKARYOTA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

EID: 19944375491     PISSN: 15701646     EISSN: None     Source Type: Journal    
DOI: 10.2174/1570164053507790     Document Type: Review

References (73)

1. Abedi, M.R., Caponigro, G. and Kamb, A. (1998). Green fluorescent protein as a scaffold for intracellular presentation of peptides. Nucleic Acids Res. 26: 623-30.
2. Auerbach, D., Fetchko, M.J. and Stagljar, I. (2003). Protemic approaches for generation of protein-protein interaction maps. Targets 2: 85-92.
3. Auerbach, D., Thaminy, S., Hottiger, M.O. and Stagljar, I. (2002). The post-genomic era of interactive proteomics: facts and perspectives. Proteomics 2: 611-23.
4. Bach, S., Talarek, N., Andrieu, T., Vierfond, J. M., Mettey, Y., Galons, H., Dormont, D., Meijer, L., et al. (2003). Isolation of drugs active against mammalian prions using a yeast-based screening assay. Nat. Biotechnol. 21: 1075-81.
5. Baetz, K., McHardy, L., Gable, K., Tarling, T., Reberioux, D., Bryan, J. Andersen, R.J., Dunn, T., et al. (2004). Yeast genome-wide drug-induced haploinsufficiency screen to determine drug mode of action. Proc. Natl. Acad. Sci. USA 101: 4525-30.
6. Bedalov, A., Gatbonton, T., Irvine, W.P., Gottschling, D.E. and Simon, J.A. (2001). Identification of a small molecule inhibitor of Sir2p. Proc. Natl. Acad. Sci. USA 98: 15113-8.
7. Benhar, I. (2001). Biotechnological applications of phage and cell display. Biotechnol. Adv. 19: 1-33.
8. Borisy, A.A., Elliott, P.J., Hurst, N.W., Lee, M.S., Lehar, J., Price, E.R., Serbedzija, G., Zimmermann, G.R., et al. (2003). Systematic discovery of multicomponent therapeutics. Proc. Natl. Acad. Sci. USA 100: 3977-82.
9. Bouwmeester, T., Bauch, A., Ruffner, H., Angrand, P.O., Bergamini, G., Croughton, K., Cruciat, C., Eberhard, D., et al. (2004). A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat. Cell Biol. 6: 97-105.
10. Chene, P. (2003). Inhibiting the p53-MDM2 interaction: an important target for cancer therapy. Nat. Rev. Cancer 3: 102-9.
11. Colas, P., Cohen, B., Jessen, T., Grishina, I., McCoy, J. and Brent, R. (1996). Genetic selection of peptide aptamers that recognize and inhibit cyclin-dependent kinase 2. Nature 380: 548-50.
12. Colas, P., Cohen, B., Ko Ferrigno, P., Silver, P.A. and Brent, R. (2000). Targeted modification and transportation of cellular proteins. Proc. Natl. Acad. Sci. USA 97: 13720-5.
13. DiMasi, J.A., Hansen, R.W. and Grabowski, H.G. (2003). The price of innovation: new estimates of drug development costs. J. Health Econ. 22: 151-85.
14. Duncan, S.J., Gruschow, S., Williams, D.H., McNicholas, C., Purewal, R., Hajek, M., Gerlitz, M., Martin, S., et al. (2001). Isolation and structure elucidation of Chlorofusin, a novel p53-MDM2 antagonist from a Fusarium sp. J. Am. Chem. Soc. 123: 554-60.
15. Dykxhoorn, D.M., Novina, C.D. and Sharp, P.A. (2003). Killing the messenger: short RNAs that silence gene expression. Natl. Rev. Mol. Cell Biol. 4: 457-67.
16. Fang, Y., Frutos, A.G. and Lahiri, J. (2002). G-protein-coupled receptor microarrays. Chembiochem 3: 987-91.
17. Fields, S. and Song, O. (1989). A novel genetic system to detect protein-protein interactions. Nature 340: 245-6.
18. Freedman, D.A., Epstein, C.B., Roth, J.C. and Levine, A.J. (1997). A genetic approach to mapping the p53 binding site in the MDM2 protein. Mol. Med. 3: 248-59.
19. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., et al. (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-7.
20. Giaver, G., Shoemaker, D.D., Jones, T.W., Liang, H., Winzeler, E.A., Astromoff, A. and Davis, R.W. (1999). Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat. Genet. 21: 278-83.
21. Giaver, G., Flaherty, P., Kumm, J., Proctor, M., Nislow, C., Jaramillo, D.F., Chu, A.M., Jordan, M.I., et al. (2004). Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast. Proc. Natl. Acad. Sci. USA 101: 793-8.
22. Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y.L., Ooi, C. E., et al. (2003). A protein interaction map of Drosophila melanogaster. Science 302: 1727-36.
23. Goffeau, A., Barrell, B., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., et al. (1996). Life with 6000 genes. Science 274: 546-51.
24. Hartman, J.L., Garvik, B. and Hartwell, L. (2001). Principles for the buffering of genetic variation. Science 291: 1001-4.
25. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., et al. (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-3.
26. Howbrook, D.N., van der Valk, A.M., O'Shaughnessy, M.C., Sarker, D.K., Baker, S. C. and Lloyd, A.W. (2003). Developments in microarray technologies. Drug Discov. Today 8: 642-51.
27. Huang, J. and Schreiber, S.L. (1997). A yeast genetic system for selecting small molecule inhibitors of protein-protein interactions in nanodroplets. Proc. Natl. Acad. Sci. USA 94: 13396-401.
28. Hubsman, M., Yudkovsky, G. and Aronheim, A. (2001). A novel approach for the identification of protein-protein interaction with integral membrane proteins. Nucleic Acids Res. 29: E18.
29. Hudson, J.R.J., Dawson, E.P., Rushing, K.L., Jackson, C.H., Lockshon, D., Conover, D., Lanciault, C., Harris, J.R., et al. (1997). The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form. Genome Res. 7: 1169-73.
30. Hughes, T. R. (2002). Yeast and drug discovery. Funct., Integr. Genomics 2: 199-211.
31. International human genome sequencing consortium (2001). Initial sequencing and analysis of the human genome. Nature 409: 860-921.
32. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. and Sakaki, Y. (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98: 4569-74.
33. Kato-Stankiewicz, J., Hakimi, I., Zhi, G., Zhang, J., Serebriiskii, I., Guo, L., Edamatsu, H., Koide, H., et al. (2002). Inhibitors of Ras/Raf-1 interaction identified by two-hybrid screening revert Ras-dependent transformation phenotypes in human cancer cells. Proc. Natl. Acad. Sci. USA 99: 14398-403.
34. Kaur, R. and Bachhawat, A.K. (1999). The yeast multidrug resistance pump, Pdr5p, confers reduced drug resistance in erg mutants of Saccharomyces cerevisiae. Microbiology 145: (Pt 4), 809-18.
35. Kolaczkowski, M., Kolaczowska, A., Luczynski, J., Witek, S. and Goffeau, A. (1998). In vivo characterization of the drug resistance profile of the major ABC transporters and other components of the yeast pleiotropic drug resistance network. Microb. Drug Resist. 4: 143-58.
36. Kubbutat, M.H., Jones, S.N. and Vousden, K.H. (1997). Regulation of p53 stability by Mdm2. Nature 387: 299-303.
37. Kussie, P.H., Gorina, S., Marechal, V., Elenbaas, B., Moreau, J., Levine, A.J. and Pavletich, N.P. (1996). Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274: 948-53.
38. Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.O., Han, J. D., et al. (2004). A map of the interactome network of the metazoan C. elegans. Science 303:, 540-3.
39. MacBeath, G. and Schreiber, S.L. (2000). Printing proteins as microarrays for high-throughput function determination. Science 289: 1760-3.
40. Mantripragada, K.K., Buckley, P.G., de Stahl, T.D. and Dumanski, J.P. (2004). Genomic microarrays in the spotlight. Trends Genet. 20: 87-94.
41. Marton, M.J., DeRisi, J.L., Bennett, H.A., Iyer, V.R., Meyer, M.R., Roberts, C.J., Stoughton, R., Burchard, J., et al. (1998). Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat. Med. 4: 1293-301.
42. Melese, T. and Hieter, P. (2002). From genetics and genomics to drug discovery: yeast rises to the challenge. Trends Pharmacol. Sci. 23: 544-7.
43. Michaud, G.A., Salcius, M., Zhou, F., Bangham, R., Bonin, J., Guo, H., Snyder, M., Predki, P. F., et al. (2003). Analyzing antibody specificity with whole proteome microarrays. Nat. Biotechnol. 21: 1509-12.
44. Oliner, J.D., Pietenpol, J.A., Thiagalingam, S., Gyuris, J., Kinzler, K.W. and Vogelstein, B. (1993). Oncoprotein MDM2 conceals the activation domain of tumour suppressor p53. Nature 362: 857-60.
45. Parsons, A.B., Brost, R.L., Ding, H., Li, Z., Zhang, C., Sheikh, B., Brown, G.W., Kane, P.M., et al. (2004). Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat. Biotechnol. 22: 62-9.
46. Pierce, K.L., Premont, R.T. and Lefkowitz, R.J. (2002). Seven-transmembrane receptors. Nat. Rev. Mol. Cell Biol. 3: 639-50.
47. Reiter, L.T., Potocki, L., Chien, S., Gribskov, M. and Bier, E. (2001). A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster. Genome Res. 11: 1114-25.
48. Serebriiskii, I.G., Mitina, O., Pugacheva, E.N., Benevolenskaya, E., Kotova, E., Toby, G.G., Khazak, V., Kaelin, W.G., et al. (2002). Detection of peptides, proteins and drugs that selectively interact with protein targets. Genome Res. 12: 1785-91.
49. Snyder, M. and Kumar, A. (2002). Yeast genomics: past, present and future promise. Funct. Integr. Genomics 2: 135-7.
50. Stagljar, I., Korostensky, C., Johnsson, N. and te Heesen, S. (1998). A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. Proc. Natl. Acad. Sci. USA 95: 5187-92.
51. Stoll, R., Renner, C., Hansen, S., Palme, S., Klein, C., Belling, A., Zeslawski, W., Kamionka, M.,et al. (2001). Chalcone derivatives antagonize interactions between the human oncoprotein MDM2 and p53. Biochemistry 40: 336-44.
52. Tewari, M., Hu, P.J., Ahn, J.S., Ayivi-Guedehoussou, N., Vidalain, P.O., Li, S., Milstein, S., Armstrong, C.M., et al. (2004). Systematic interactome mapping and genetic pertubation analysis of a C. elegans TGF-beta signaling network. Mol. Cell 13: 469-82.
53. Thaminy, S., Auerbach, D., Arnoldo, A. and Stagljar, I. (2003). Identification of novel ErbB3-interacting factors using the split-ubiquitin membrane yeast two-hybrid system. Genome Res. 13: 1744-53.
54. Tong, A.H., Evangelista, M., Parsons, A.B., Xu, H., Bader, G.D., Page, N., Robinson, M., Raghibizadeh, S., et al. (2001). Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-8.
55. Tong, A.H., Lesage, G., Bader, G.D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G. F., et al. (2004). Global mapping of the yeast genetic interaction network. Science 303: 808-81.
56. Toogood, P.L. (2002). Inhibition of protein-protein association by small molecules: approaches and progress. J. Med. Chem. 45: 1543-58.
57. Tucker, C.L. (2002). High-throughput cell-based assays in yeast. Drug Discov. Today 7: S125-30.
58. Tucker, C.L. and Fields, S. (2001). A yeast sensor of ligand binding. Nat. Biotechnol. 19: 1042-6.
59. Tucker, C.L. and Fields, S. (2004). Quantitative genome-wide analysis of yeast deletion strain sensitivities to oxidative and chemical stress. Comp. Funct. Genom. 5: 216-24.
60. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., et al. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-7.
61. Urech, D.M., Lichtlen, P. and Barberis, A. (2003). Cell growth selection system to detect extracellular and transmembrane protein interactions. Biochim. Biophys. Acta 1622: 117-27.
62. Vassilev, L.T., Vu, B.T., Graves, B., Carvajal, D., Podlaski, F., Filipovic, Z., Kong, N., Kammlott, U., et al. (2004). In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 303: 844-8.
63. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., et al. (2001). The sequence of the human genome. Science 291: 1304-51.
64. Vidal, M., Brachmann, R.K., Fattaey, A., Harlow, E. and Boeke, J.D. (1996). Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc. Natl. Acad. Sci. USA 93: 10315-20.
65. Wang, L.F. and Yu, M. (2004). Epitope identification and discovery using phage display libraries: applications in vaccine development and diagnostics. Curr. Drug Targets 5: 1-15.
66. Wittke, S., Lewke, N., Muller, S. and Johnsson, N. (1999). Probing the molecular environment of membrane proteins in vivo. Mol. Biol. Cell 10: 2519-30.
67. Yang, M., Wu, Z. and Fields, S. (1995). Protein-peptide interactions analyzed with the yeast two-hybrid system. Nucleic Acids Res. 23: 1152-6.
68. Young, K., Lin, S., Sun, L., Lee, E., Modi, M., Hellings, S., Husbands, M., Ozenberger, B., et al. (1998). Identification of a calcium channel modulator using a high throughput yeast two-hybrid screen. Nat. Biotechnol. 16: 946-50.
69. Zewail, A., Xie, M.W., Xing, Y., Lin, L., Zhang, P.F., Zou, W., Saxe, J.P. and Huang, J. (2003). Novel functions of the phosphatidylinositol metabolic pathway discovered by a chemical genomics screen with wortmannin. Proc. Natl. Acad. Sci. USA 100: 3345-50.
70. Zhao, J., Wang, M., Chen, J., Luo, A., Wang, X., Wu, M., Yin, D. and Liu, Z. (2002). The initial evaluation of non-peptidic small-molecule HDM2 inhibitors based on p53-HDM2 complex structure. Cancer Lett. 183: 69-77.
71. Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., et al. (2001). Global analysis of protein activities using proteome chips. Science 293: 2101-5.
72. Zhu, H., Bilgin, M. and Snyder, M. (2003). Proteomics. Annu. Rev. Biochem. 72: 783-812.
73. Zhu, H. and Snyder, M. (2003). Protein chip technology. Curr. Opin. Chem. Biol. 7: 55-63.