We use cookies to improve your experience. By continuing to browse this site, you accept our cookie policy.×
ReviewOpen Accesscc iconby icon

Resolving the network of cell signaling pathways using the evolving yeast two-hybrid system

    Vladimir Ratushny

    Fox Chase Cancer Center

    Drexel University College of Medicine, Philadelphia, PA, USA

    &
    Erica A. Golemis

    *Address correspondence to Erica A. Golemis, Fox Chase Cancer Center, W406, 333 Cottman Avenue, Philadelphia, PA 19111 USA. e-mail:

    E-mail Address: EA_Golemis@fccc.edu

    Fox Chase Cancer Center

    Published Online:https://doi.org/10.2144/000112797

    In 1983, while investigators had identified a few human proteins as important regulators of specific biological outcomes, how these proteins acted in the cell was essentially unknown in almost all cases. Twenty-five years later, our knowledge of the mechanistic basis of protein action has been transformed by our increasingly detailed understanding of protein-protein interactions, which have allowed us to define cellular machines. The advent of the yeast two-hybrid (Y2H) system in 1989 marked a milestone in the field of proteomics. Exploiting the modular nature of transcription factors, the Y2H system allows facile measurement of the activation of reporter genes based on interactions between two chimeric or “hybrid” proteins of interest. After a decade of service as a leading platform for individual investigators to use in exploring the interaction properties of interesting target proteins, the Y2H system has increasingly been applied in high-throughput applications intended to map genome-scale protein-protein interactions for model organisms and humans. Although some significant technical limitations apply, Y2H has made a great contribution to our general understanding of the topology of cellular signaling networks.

    References

    • 1. McCoy, M.S., J.J. Toole, J.M. Cunningham, E.H. Chang, D.R. Lowy, and R.A. Weinberg. 1983. Characterization of a human colon/lung carcinoma oncogene. Nature 302:79–81.
    • 2. Schwab, M., K. Alitalo, K.H. Klempnauer, H.E. Varmus, J.M. Bishop, F. Gilbert, G. Brodeur, M. Goldstein, and J. Trent. 1983. Amplified DNA with limited homology to myc cellular oncogene is shared by human neuroblastoma cell lines and a neuroblastoma tumour. Nature 305:245–248.
    • 3. Capon, D.J., E.Y. Chen, A.D. Levinson, P.H. Seeburg, and D.V. Goeddel. 1983. Complete nucleotide sequences of the T24 human bladder carcinoma oncogene and its normal homologue. Nature 302:33–37.
    • 4. Schwab, M., K. Alitalo, H.E. Varmus, J.M. Bishop, and D. George. 1983. A cellular oncogene (c-Ki-ras) is amplified, overexpressed, and located within karyotypic abnormalities in mouse adrenocortical tumour cells. Nature 303:497–501.
    • 5. Fields, S. and O. Song. 1989. A novel genetic system to detect protein-protein interactions. Nature 340:245–246.
    • 6. Chevray, P.M. and D. Nathans. 1992. Protein interaction cloning in yeast: identification of mammalian proteins that react with the leucine zipper of Jun. Proc. Natl. Acad. Sci. USA 89:5789–5793.
    • 7. Chien, C.T., P.L. Bartel, R. Sternglanz, and S. Fields. 1991. The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. Proc. Natl. Acad. Sci. USA 88:9578–9582.
    • 8. Durfee, T., K. Becherer, P.L. Chen, S.H. Yeh, Y. Yang, A.E. Kilburn, W.H. Lee, and S.J. Elledge. 1993. The retinoblastoma protein associates with the protein phosphatase type 1 catalytic subunit. Genes Dev. 7:555–569.
    • 9. Estojak, J., R. Brent, and E.A. Golemis. 1995. Correlation of two-hybrid affinity data with in vitro measurements. Mol. Cell. Biol. 15:5820–5829.
    • 10. Gyuris, J., E. Golemis, H. Chertkov, and R. Brent. 1993. Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2. Cell 75:791–803.
    • 11. Vojtek, A.B., S.M. Hollenberg, and J.A. Cooper. 1993. Mammalian Ras interacts directly with the serine/threonine kinase Raf. Cell 74:205–214.
    • 12. Brent, R. and M. Ptashne. 1981. Mechanism of action of the lexA gene product. Proc. Natl. Acad. Sci. USA 78:4204–4208.
    • 13. Zervos, A.S., J. Gyuris, and R. Brent. 1993. Mxi1, a protein that specifically interacts with Max to bind Myc-Max recognition sites. Cell 72:223–232.
    • 14. Golemis, E.A. (Ed.) 2005. Protein-Protein Interactions. CSH Laboratory Press, Cold Spring Harbor, NY.
    • 15. Du, W., M. Vidal, J.E. Xie, and N. Dyson. 1996. RBF, a novel RB-related gene that regulates E2F activity and interacts with cyclin E in Drosophila. Genes Dev. 10:1206–1218.
    • 16. Marsolier, M.C., M.N. Prioleau, and A. Sentenac. 1997. A RNA polymerase III-based two-hybrid system to study RNA polymerase II transcriptional regulators. J. Mol. Biol. 268:243–249.
    • 17. Marsolier, M.C. and A. Sentenac. 1999. RNA polymerase III-based two-hybrid system. Methods Enzymol. 303:411–422.
    • 18. Stagljar, I., C. Korostensky, N. Johnsson, and S. te Heesen. 1998. A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. Proc. Natl. Acad. Sci. USA 95:5187–5192.
    • 19. Serebriiskii, I., J. Estojak, M. Berman, and E.A. Golemis. 2000. Approaches to detecting false positives in yeast two-hybrid systems. BioTechniques 28:328–330 332-326.
    • 20. Serebriiskii, I., V. Khazak, and E.A. Golemis. 1999. A two-hybrid dual bait system to discriminate specificity of protein interactions. J. Biol. Chem. 274:17080–17087.
    • 21. Serebriiskii, I.G., O.V. Mitina, J. Chernoff, and E.A. Golemis. 2001. Two-hybrid dual bait system to discriminate specificity of protein interactions in small GTPases. Methods Enzymol. 332:277–300.
    • 22. Fields, S. 2005. High-throughput two-hybrid analysis. The promise and the peril. FEBS J. 272:5391–5399.
    • 23. Ito, T., K. Ota, H. Kubota, Y. Yamaguchi, T. Chiba, K. Sakuraba, and M. Yoshida. 2002. Roles for the two-hybrid system in exploration of the yeast protein interactome. Mol. Cell. Proteomics 1:561–566.
    • 24. Ito, T., T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98:4569–4574.
    • 25. Mrowka, R., A. Patzak, and H. Herzel. 2001. Is there a bias in proteome research? Genome Res. 11:1971–1973.
    • 26. von Mering, C., R. Krause, B. Snel, M. Cornell, S.G. Oliver, S. Fields, and P. Bork. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417:399–403.
    • 27. Fashena, S.J., I. Serebriiskii, and E.A. Golemis. 2000. The continued evolution of two-hybrid screening approaches in yeast: how to outwit different preys with different baits. Gene 250:1–14.
    • 28. Osborne, M.A., S. Dalton, and J.P. Kochan. 1995. The yeast tribrid system—genetic detection of trans-phosphorylated ITAM-SH2-interactions. Biotechnology (N. Y.) 13:1474–1478.
    • 29. Osborne, M.A., G. Zenner, M. Lubinus, X. Zhang, Z. Songyang, L.C. Cantley, P. Majerus, P. Burn, and J.P. Kochan. 1996. The inositol 5′-phosphatase SHIP binds to immunoreceptor signaling motifs and responds to high affinity IgE receptor aggregation. J. Biol. Chem. 271:29271–29278.
    • 30. Park, Y.W., J. Wilusz, and M.G. Katze. 1999. Regulation of eukaryotic protein synthesis: selective influenza viral mRNA translation is mediated by the cellular RNA-binding protein GRSF-1. Proc. Natl. Acad. Sci. USA 96:6694–6699.
    • 31. Putz, U., P. Skehel, and D. Kuhl. 1996. A tri-hybrid system for the analysis and detection of RNA--protein interactions. Nucleic Acids Res. 24:4838–4840.
    • 32. SenGupta, D.J., B. Zhang, B. Kraemer, P. Pochart, S. Fields, and M. Wickens. 1996. A three-hybrid system to detect RNA-protein interactions in vivo. Proc. Natl. Acad. Sci. USA 93:8496–8501.
    • 33. Wang, Z.F., M.L. Whitfield, T.C. Ingledue III, Z. Dominski, and W.F. Marzluff. 1996. The protein that binds the 3′ end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing. Genes Dev. 10:3028–3040.
    • 34. Vidal, M., R.K. Brachmann, A. Fattaey, E. Harlow, and J.D. Boeke. 1996. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc. Natl. Acad. Sci. USA 93:10315–10320.
    • 35. Vidal, M., P. Braun, E. Chen, J.D. Boeke, and E. Harlow. 1996. Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system. Proc. Natl. Acad. Sci. USA 93:10321–10326.
    • 36. Huang, J. and S.L. Schreiber. 1997. A yeast genetic system for selecting small molecule inhibitors of protein-protein interactions in nanodroplets. Proc. Natl. Acad. Sci. USA 94:13396–13401.
    • 37. Vidal, M. and H. Endoh. 1999. Prospects for drug screening using the reverse two-hybrid system. Trends Biotechnol. 17:374–381.
    • 38. Young, K., S. Lin, L. Sun, E. Lee, M. Modi, S. Hellings, M. Husbands, B. Ozenberger, and R. Franco. 1998. Identification of a calcium channel modulator using a high throughput yeast two-hybrid screen. Nat. Biotechnol. 16:946–950.
    • 39. International Human Genome Sequencing Consortium. 2004. Finishing the euchromatic sequence of the human genome. Nature 431:931–945.
    • 40. Goffeau, A., B.G. Barrell, H. Bussey, R.W. Davis, B. Dujon, H. Feldmann, F. Galibert, J.D. Hoheisel, et al.. 1996. Life with 6000 genes. Science 274:546, 563–567.
    • 41. McPherson, J.D., M. Marra, L. Hillier, R.H. Waterston, A. Chinwalla, J. Wallis, M. Sekhon, K. Wylie, et al.. 2001. A physical map of the human genome. Nature 409:934–941.
    • 42. C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012–2018.
    • 43. Adams, M.D., S.E. Celniker, R.A. Holt, C.A. Evans, J.D. Gocayne, P.G. Amanatides, S.E. Scherer, P.W. Li, et al.. 2000. The genome sequence of Drosophila melanogaster. Science 287:2185–2195.
    • 44. Bartel, P.L., J.A. Roecklein, D. SenGupta, and S. Fields. 1996. A protein linkage map of Escherichia coli bacteriophage T7. Nat. Genet. 12:72–77.
    • 45. Giot, L., J.S. Bader, C. Brouwer, A. Chaudhuri, B. Kuang, Y. Li, Y.L. Hao, C.E. Ooi, et al.. 2003. A protein interaction map of Drosophila melanogaster. Science 302:1727–1736.
    • 46. LaCount, D.J., M. Vignali, R. Chettier, A. Phansalkar, R. Bell, J.R. Hesselberth, L.W. Schoenfeld, I. Ota, et al.. 2005. A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 438:103–107.
    • 47. Li, S., C.M. Armstrong, N. Bertin, H. Ge, S. Milstein, M. Boxem, P.O. Vidalain, J.D. Han, et al.. 2004. A map of the interactome network of the metazoan C. elegans. Science 303:540–543 .
    • 48. Rain, J.C., L. Selig, H. De Reuse, V. Battaglia, C. Reverdy, S. Simon, G. Lenzen, F. Petel, et al.. 2001. The protein-protein interaction map of Helicobacter pylori. Nature 409:211–215.
    • 49. Rual, J.F., K. Venkatesan, T. Hao, T. Hirozane-Kishikawa, A. Dricot, N. Li, G.F. Berriz, F.D. Gibbons, et al.. 2005. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173–1178.
    • 50. Stelzl, U., U. Worm, M. Lalowski, C. Haenig, F.H. Brembeck, H. Goehler, M. Stroedicke, M. Zenkner, et al.. 2005. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122:957–968.
    • 51. Uetz, P., Y.A. Dong, C. Zeretzke, C. Atzler, A. Baiker, B. Berger, S.V. Rajagopala, M. Roupelieva, et al.. 2006. Herpesviral protein networks and their interaction with the human proteome. Science 311:239–242.
    • 52. Fromont-Racine, M., A.E. Mayes, A. Brunet-Simon, J.C. Rain, A. Colley, I. Dix, L. Decourty, N. Joly, et al.. 2000. Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins. Yeast 17:95–110.
    • 53. Uetz, P., L. Giot, G. Cagney, T.A. Mansfield, R.S. Judson, J.R. Knight, D. Lockshon, V. Narayan, et al.. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623–627.
    • 54. Finley, R.L., Jr. and R. Brent. 1994. Interaction mating reveals binary and ternary connections between Drosophila cell cycle regulators. Proc. Natl. Acad. Sci. USA 91:12980–12984.
    • 55. Ma, H., S. Kunes, P.J. Schatz, and D. Botstein. 1987. Plasmid construction by homologous recombination in yeast. Gene 58:201–216.
    • 56. Sanger, F., S. Nicklen, and A.R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463–5467.
    • 57. Grigoriev, A. 2003. On the number of protein-protein interactions in the yeast proteome. Nucleic Acids Res. 31:4157–4161.
    • 58. Han, J.D., D. Dupuy, N. Bertin, M.E. Cusick, and M. Vidal. 2005. Effect of sampling on topology predictions of protein-protein interaction networks. Nat. Biotechnol. 23:839–844.
    • 59. Walhout, A.J., S.J. Boulton, and M. Vidal. 2000. Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17:88–94.
    • 60. Hart, G.T., A.K. Ramani, and E.M. Marcotte. 2006. How complete are current yeast and human protein-interaction networks? Genome Biol. 7:120.
    • 61. Parrish, J.R., K.D. Gulyas, R.L., and Finley, Jr. 2006. Yeast two-hybrid contributions to interactome mapping. Curr. Opin. Biotechnol. 17:387–393.
    • 62. Stanyon, C.A., G. Liu, B.A. Mangiola, N. Patel, L. Giot, B. Kuang, H. Zhang, J. Zhong, and R.L. Finley Jr. 2004. A Drosophila protein-interaction map centered on cell-cycle regulators. Genome Biol. 5:R96.
    • 63. Gavin, A.C., M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J.M. Rick, et al.. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141–147.
    • 64. Ho, Y., A. Gruhler, A. Heilbut, G.D. Bader, L. Moore, S.L. Adams, A. Millar, P. Taylor, et al.. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180–183.
    • 65. Cho, R.J., M.J. Campbell, E.A. Winzeler, L. Steinmetz, A. Conway, L. Wodicka, T.G. Wolfsberg, A.E. Gabrielian, et al.. 1998. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2:65–73.
    • 66. Hughes, T.R., M.J. Marton, A.R. Jones, C.J. Roberts, R. Stoughton, C.D. Armour, H.A. Bennett, E. Coffey, et al.. 2000. Functional discovery via a compendium of expression profiles. Cell 102:109–126.
    • 67. Mewes, H.W., D. Frishman, U. Guldener, G. Mannhaupt, K. Mayer, M. Mokrejs, B. Morgenstern, M. Munsterkotter, et al.. 2002. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 30:31–34.
    • 68. Tong, A.H., M. Evangelista, A.B. Parsons, H. Xu, G.D. Bader, N. Page, M. Robinson, S. Raghibizadeh, et al.. 2001. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294:2364–2368.
    • 69. Enright, A.J., I. Iliopoulos, N.C. Kyrpides, and C.A. Ouzounis. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86–90.
    • 70. Marcotte, E.M., M. Pellegrini, H.L. Ng, D.W. Rice, T.O. Yeates, and D. Eisenberg. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285:751–753.
    • 71. Overbeek, R., M. Fonstein, M. D'Souza, G.D. Pusch, and N. Maltsev. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96:2896–2901.
    • 72. Pellegrini, M., E.M. Marcotte, M.J. Thompson, D. Eisenberg, and T.O. Yeates. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96:4285–4288.
    • 73. Huynen, M., B. Snel, W. Lathe III, and P. Bork. 2000. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 10:1204–1210.
    • 74. Marcotte, E.M., M. Pellegrini, M.J. Thompson, T.O. Yeates, and D. Eisenberg. 1999. A combined algorithm for genome-wide prediction of protein function. Nature 402:83–86.
    • 75. Friedman, A. and N. Perrimon. 2007. Genetic screening for signal transduction in the era of network biology. Cell 128:225–231.
    • 76. Han, J.D., N. Bertin, T. Hao, D.S. Goldberg, G.F. Berriz, L.V. Zhang, D. Dupuy, A.J. Walhout, et al.. 2004. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430:88–93.
    • 77. Friedman, A. and N. Perrimon. 2006. A functional RNAi screen for regulators of receptor tyrosine kinase and ERK signalling. Nature 444:230–234.
    • 78. Jeong, H., S.P. Mason, A.L. Barabasi, and Z.N. Oltvai. 2001. Lethality and centrality in protein networks. Nature 411:41–42.
    • 79. Strogatz, S.H. 2001. Exploring complex networks. Nature 410:268–276.
    • 80. Winzeler, E.A., D.D. Shoemaker, A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, et al.. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901–906.
    • 81. Gandhi, T.K., J. Zhong, S. Mathivanan, L. Karthick, K.N. Chandrika, S.S. Mohan, S. Sharma, S. Pinkert, et al.. 2006. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat. Genet. 38:285–293.
    • 82. Suter, B., S. Kittanakom, and I. Stagljar. Interactive proteomics: what lies ahead? BioTechniques 44: 681–691.
    • 83. Deane, C.M., L. Salwinski, I. Xenarios, and D. Eisenberg. 2002. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol. Cell. Proteomics 1:349–356.
    • 84. Kelley, B.P., B. Yuan, F. Lewitter, R. Sharan, B.R. Stockwell, and T. Ideker. 2004. PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res. 32:W83–W88.
    • 85. Stuart, J.M., E. Segal, D. Koller, and S.K. Kim. 2003. A gene-coexpression network for global discovery of conserved genetic modules. Science 302:249–255.
    • 86. Yu, H., N.M. Luscombe, H.X. Lu, X. Zhu, Y. Xia, J.D. Han, N. Bertin, S. Chung, et al.. 2004. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 14:1107–1118.
    • 87. Bandyopadhyay, S., R. Sharan, and T. Ideker. 2006. Systematic identification of functional orthologs based on protein network comparison. Genome Res. 16:428–435.
    • 88. Suthram, S., T. Sittler, and T. Ideker. 2005. The Plasmodium protein network diverges from those of other eukaryotes. Nature 438:108–112.
    • 89. Peri, S., J.D. Navarro, T.Z. Kristiansen, R. Amanchy, V. Surendranath, B. Muthusamy, T.K. Gandhi, K.N. Chandrika, et al.. 2004. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res. 32:D497–D501.
    • 90. Collins, S.R., K.M. Miller, N.L. Maas, A. Roguev, J. Fillingham, C.S. Chu, M. Schuldiner, M. Gebbia, et al.. 2007. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446:806–810.
    • 91. Pierce, S.E., E.L. Fung, D.F. Jaramillo, A.M. Chu, R.W. Davis, C. Nislow, and G. Giaever. 2006. A unique and universal molecular barcode array. Nat. Methods 3:601–603.
    • 92. Zhong, W. and P.W. Sternberg. 2006. Genome-wide prediction of C. elegans genetic interactions. Science (New York, N. Y.) 311:1481–1484.
    • 93. Breitkreutz, B.J., C. Stark, T. Reguly, L. Boucher, A. Breitkreutz, M. Livstone, R. Oughtred, D.H. Lackner, et al.. 2008. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res. 36:D637–D640.
    • 94. Alfarano, C., C.E. Andrade, K. Anthony, N. Bahroos, M. Bajec, K. Bantoft, D. Betel, B. Bobechko, et al.. 2005. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res. 33:D418–D424.
    • 95. Orchard, S., L. Montechi-Palazzi, E.W. Deutsch, P.A. Binz, A.R. Jones, N. Paton, A. Pizarro, D.M. Creasy, et al.. 2007. Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative, April 23-25, 2007 Ecole Nationale Superieure (ENS), Lyon, France. Proteomics 7:3436–3440.