Analysis of Protein–Protein Interactions Using Array-Based Yeast Two-Hybrid Screens (original) (raw)

References

  1. Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., et al (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627.
    Article PubMed CAS Google Scholar
  2. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., et al (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183.
    Article PubMed CAS Google Scholar
  3. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., et al (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147.
    Article PubMed CAS Google Scholar
  4. Fu, H. (2004). Protein-Protein Interactions. Methods and Applications., Volume 261 (Totowa, NJ: Humana Press).
    Google Scholar
  5. Fields, S., and Song, O. (1989). A novel genetic system to detect protein-protein interactions. Nature 340, 245–246.
    Article PubMed CAS Google Scholar
  6. Schwartz, H., Alvares, C.P., White, M.B., and Fields, S. (1998). Mutation detection by a two-hybrid assay. Hum Mol Genet 7, 1029–1032.
    Article PubMed CAS Google Scholar
  7. Vidal, M., and Endoh, H. (1999). Prospects for drug screening using the reverse two-hybrid system. Trends Biotechnol 17, 374–381.
    Article PubMed CAS Google Scholar
  8. Vidal, M., and Legrain, P. (1999). Yeast forward and reverse ‘n’-hybrid systems. Nucleic Acids Res 27, 919–929.
    Article PubMed CAS Google Scholar
  9. SenGupta, D.J., Zhang, B., Kraemer, B., Pochart, P., Fields, S., and Wickens, M. (1996). A three-hybrid system to detect RNA-protein interactions in vivo. Proc Natl Acad Sci U S A 93, 8496–8501.
    Article PubMed CAS Google Scholar
  10. Estojak, J., Brent, R., and Golemis, E.A. (1995). Correlation of two-hybrid affinity data with in vitro measurements. Mol Cell Biol 15, 5820–5829.
    PubMed CAS Google Scholar
  11. Rain, J.C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., et al (2001). The protein-protein interaction map of Helicobacter pylori. Nature 409, 211–215.
    Article PubMed CAS Google Scholar
  12. Raquet, X., Eckert, J.H., Muller, S., and Johnsson, N. (2001). Detection of altered protein conformations in living cells. J Mol Biol 305, 927–938.
    Article PubMed CAS Google Scholar
  13. Cagney, G., Uetz, P., and Fields, S. (2001). Two-hybrid analysis of the Saccharomyces cerevisiae 26S proteasome. Physiol Genomics 7, 27–34.
    PubMed CAS Google Scholar
  14. Rajagopala, S.V., Titz, B., Goll, J., Parrish, J.R., Wohlbold, K., McKevitt, M.T., et al (2007). The protein network of bacterial motility. Mol Syst Biol 3, 128.
    Article PubMed Google Scholar
  15. 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 U S A 98, 4569–4574.
    Article PubMed CAS Google Scholar
  16. Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., et al (2004). A map of the interactome network of the metazoan C. elegans. Science 303, 540–543.
    Article PubMed CAS Google Scholar
  17. Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., et al (2003). A protein interaction map of Drosophila melanogaster. Science 302, 1727–1736.
    Article PubMed CAS Google Scholar
  18. Rual, J.F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., et al (2005). Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173–1178.
    Article PubMed CAS Google Scholar
  19. Stelzl, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F.H., Goehler, H., et al (2005). A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957–968.
    Article PubMed CAS Google Scholar
  20. Schwikowski, B., Uetz, P., and Fields, S. (2000). A network of protein-protein interactions in yeast. Nat Biotechnol 18, 1257–1261.
    Article PubMed CAS Google Scholar
  21. Serebriiskii, I., Estojak, J., Berman, M., and Golemis, E.A. (2000). Approaches to detecting false positives in yeast two-hybrid systems. Biotechniques 28, 328–336.
    PubMed CAS Google Scholar
  22. Serebriiskii, I.G., and Golemis, E.A. (2001). Two-hybrid system and false positives. Approaches to detection and elimination. Methods Mol Biol 177, 123–134.
    PubMed CAS Google Scholar
  23. Koegl, M., and Uetz, P. (2007). Improving yeast two-hybrid screening systems. Brief Funct Genomic Proteomic 6, 302–312.
    Article PubMed CAS Google Scholar
  24. Uetz, P., Dong, Y.A., Zeretzke, C., Atzler, C., Baiker, A., Berger, B., et al (2006). Herpesviral protein networks and their interaction with the human proteome. Science 311, 239–242.
    Article PubMed CAS Google Scholar
  25. Parrish, J.R., Yu, J., Liu, G., Hines, J.A., Chan, J.E., Mangiola, B.A., et al (2007). A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol 8, R130.
    Article PubMed Google Scholar
  26. Zhong, J., Zhang, H., Stanyon, C.A., Tromp, G., and Finley, R.L., Jr. (2003). A strategy for constructing large protein interaction maps using the yeast two-hybrid system: regulated expression arrays and two-phase mating. Genome Res 13, 2691–2699.
    Article PubMed CAS Google Scholar
  27. Jin, F., Avramova, L., Huang, J., and Hazbun, T. (2007). A yeast two-hybrid smart-pool-array system for protein-interaction mapping. Nat Methods 4, 405–407.
    PubMed CAS Google Scholar
  28. Cormack, R.S., Hahlbrock, K., and Somssich, I.E. (1998). Isolation of putative plant transcriptional coactivators using a modified two-hybrid system incorporating a GFP reporter gene. Plant J 14, 685–692.
    Article PubMed CAS Google Scholar
  29. Rossi, F., Charlton, C.A., and Blau, H.M. (1997). Monitoring protein-protein interactions in intact eukaryotic cells by beta-galactosidase complementation. Proc Natl Acad Sci U S A 94, 8405–8410.
    Article PubMed CAS Google Scholar
  30. Drees, B.L. (1999). Progress and variations in two-hybrid and three-hybrid technologies. Curr Opin Chem Biol 3, 64–70.
    Article PubMed CAS Google Scholar
  31. Frederickson, R.M. (1998). Macromolecular matchmaking: advances in two-hybrid and related technologies. Curr Opin Biotechnol 9, 90–96.
    Article PubMed CAS Google Scholar
  32. Walhout, A.J., Temple, G.F., Brasch, M.A., Hartley, J.L., Lorson, M.A., van den Heuvel, S., et al (2000). GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol 328, 575–592.
    Article PubMed CAS Google Scholar
  33. Cagney, G., Uetz, P., and Fields, S. (2000). High-throughput screening for protein-protein interactions using two-hybrid assay. Methods Enzymol 328, 3–14.
    Article PubMed CAS Google Scholar
  34. Landy, A. (1989). Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu Rev Biochem 58, 913–949.
    Article PubMed CAS Google Scholar
  35. Lamesch, P., Milstein, S., Hao, T., Rosenberg, J., Li, N., Sequerra, R., et al (2004). C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. Genome Res 14, 2064–2069.
    Article PubMed CAS Google Scholar
  36. Rual, J.F., Hirozane-Kishikawa, T., Hao, T., Bertin, N., Li, S., Dricot, A., et al (2004). Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res 14, 2128–2135.
    Article PubMed CAS Google Scholar
  37. Gong, W., Shen, Y.P., Ma, L.G., Pan, Y., Du, Y.L., Wang, D.H., et al (2004). Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol 135, 773–782.
    Article PubMed CAS Google Scholar
  38. Uetz, P. (2002). Two-hybrid arrays. Curr Opin Chem Biol 6, 57–62.
    Article PubMed CAS Google Scholar
  39. Harper, J.W., Adami, G.R., Wei, N., Keyomarsi, K., and Elledge, S.J. (1993). The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases. Cell 75, 805–816.
    Article PubMed CAS Google Scholar
  40. James, P., Halladay, J., and Craig, E.A. (1996). Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144, 1425–1436.
    PubMed CAS Google Scholar

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