Yeast Protein–Protein Interaction Assays and Screens

Methods in Molecular Biology

Volumn 754, Issue , 2011, Pages 145-165

  de Folter, Stefan ^a   Immink, Richard G H ^b  

^a DEPARTAMENTO DE FÍSICA   (Mexico)

^b CENTRE FOR BIOSYSTEMS GENOMICS   (Netherlands)

Author keywords

complexes; GAL4 system; Protein protein interactions; transcription factors; Y2H; yeast two hybrid; YnH

Indexed keywords

EID: 79960746743     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-154-3_8     Document Type: Chapter

References (35)

1. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J. M. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627.
2. 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, 4569–4574.
3. Walhout, A. J. M., Sordella, R., Lu, X., Hartley, J. L., Temple, G. F., Brasch, M. A., Thierry-Mieg, N., and Vidal, M. (2000) Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287, 116–122.
4. Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y. L., Ooi, C. E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M., Voss, E., Furtak, K., Renzulli, R., Aanensen, N., Carrolla, S., Bickelhaupt, E., Lazovatsky, Y., DaSilva, A., Zhong, J., Stanyon, C. A., Finley, R. L., Jr., White, K. P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R. A., McKenna, M. P., Chant, J., and Rothberg, J. M. (2003) A protein interaction map of Drosophila melanogaster. Science 302, 1727–1736.
5. Stelzl, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F. H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., Timm, J., Mintzlaff, S., Abraham, C., Bock, N., Kietzmann, S., Goedde, A., Tok-soz, E., Droege, A., Krobitsch, S., Korn, B., Birchmeier, W., Lehrach, H., and Wanker, E. E. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957–968.
6. Rual, J.-F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D. S., Zhang, L. V., Wong, S. L., Franklin, G., Li, S., Albala, J. S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R. S., Vandenhaute, J., Zoghbi, H. Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M. E., Hill, D. E., Roth, F. P., and Vidal, M. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173–1178.
7. Parrish, J. R., Yu, J., Liu, G., Hines, J. A., Chan, J. E., Mangiola, B. A., Zhang, H., Pacifico, S., Fotouhi, F., DiRita, V. J., Ideker, T., Andrews, P., and Finley, R. L., Jr. (2007) A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol. 8, R130.
8. Rain, J. C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F., Wojcik, J., Schachter, V., Chemama, Y., Labigne, A., and Legrain, P. (2001) The protein-protein interaction map of Heli-cobacter pylori. Nature 409, 211–215.
9. Fields, S., and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature 340, 245–246.
10. Fields, S. (2009) Interactive learning: lessons from two hybrids over two decades. Proteomics 9, 5209–5213.
11. Shoemaker, B. A., and Panchenko, A. R. (2007) Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput. Biol. 3, e42.
12. Causier, B., and Davies, B. (2002) Analysing protein-protein interactions with the yeast two-hybrid system. Plant Mol. Biol. 50, 855–870.
13. Bruckner, A., Polge, C., Lentze, N., Auer-bach, D., and Schlattner, U. (2009) Yeast two-hybrid, a powerful tool for systems biology. Int. J. Mol. Sci. 10, 2763–2788.
14. Suter, B., Kittanakom, S., and Stagljar, I. (2008) Two-hybrid technologies in proteomics research. Curr. Opin. Biotechnol. 19, 316–323.
15. Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M., Scholkopf, B., Weigel, D., and Lohmann, J. U. (2005) A gene expression map of Arabidopsis thaliana development. Nat. Genet. 37, 501–506.
16. Laubinger, S., Zeller, G., Henz, S., Sachsenberg, T., Widmer, C., Naouar, N., Vuylsteke, M., Scholkopf, B., Ratsch, G., and Weigel, D. (2008) At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol. 9, R112.
17. Morsy, M., Gouthu, S., Orchard, S., Thor-neycroft, D., Harper, J. F., Mittler, R., and Cushman, J. C. (2008) Charting plant inter-actomes: possibilities and challenges. Trends Plant Sci. 13, 183–191.
18. Walter, M., Chaban, C., Schutze, K., Batistic, O., Weckermann, K., Nake, C., Blazevic, D., Grefen, C., Schumacher, K., Oecking, C., Harter, K., and Kudla, J. (2004) Visualization of protein interactions in living plant cells using bimolecular fluorescence complementation. Plant J. 40, 428–438.
19. Immink, R. G. H., Gadella, T. W. J., Jr., Ferrario, S., Busscher, M., and Angenent, G. C. (2002) Analysis of MADS box protein-protein interactions in living plant cells. Proc. Natl. Acad. Sci. USA 99, 2416–2421.
20. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504.
21. Iragne, F., Nikolski, M., Mathieu, B., Auber, D., and Sherman, D. (2005) ProViz: protein interaction visualization and exploration. Bioinformatics 21, 272–274.
22. Breitkreutz, B. J., Stark, C., and Tyers, M. (2003) Osprey: a network visualization system. Genome Biol. 4, R22.
23. Mrowka, R. (2001) A Java applet for visualizing protein-protein interaction. Bioinformatics 17, 669–671.
24. Chang, A. N., McDermott, J., and Samudrala, R. (2005) An enhanced Java graph applet interface for visualizing inter-actomes. Bioinformatics 21, 1741–1742.
25. de Folter, S., Immink, R. G. H., Kieffer, M., Parenicová, L., Henz, S. R., Weigel, D., Busscher, M., Kooiker, M., Colombo, L., Kater, M. M., Davies, B., and Angenent, G. C. (2005) Comprehensive interaction map of the Arabidopsis MADS box transcription factors. Plant Cell. 17, 1424–1433.
26. sister MADS-box gene involved in ovule and seed development in petunia and Arabidopsis. Plant J. 47, 934–946.
27. Immink, R. G., Tonaco, I. A., de Folter, S., Shchennikova, A., van Dijk, A. D., Busscher-Lange, J., Borst, J. W., and Angenent, G. C. (2009) SEPALLATA3: the ‘glue’ for MADS box transcription factor complex formation. Genome Biol. 10, R24.
28. Immink, R. G. H., Ferrario, S., Busscher Lange, J., Kooiker, M., Busscher, M., and Angenent, G. C. (2003) Analysis of the petunia MADS-box transcription factor family. Mol. Gen. Genet. 268, 598–606.
29. Ferrario, S., Immink, R. G., Shchennikova, A., Busscher-Lange, J., and Angenent, G. C. (2003) The MADS box gene FBP2 is required for SEPALLATA function in petunia. Plant Cell 15, 914–925.
30. Ciannamea, S., Kaufmann, K., Frau, M., Tonaco, I. A., Petersen, K., Nielsen, K. K., Angenent, G. C., and Immink, R. G. (2006) Protein interactions of MADS box transcription factors involved in flowering in Lolium perenne. J. Exp. Bot. 57, 3419–3431.
31. Koegl, M., and Uetz, P. (2007) Improving yeast two-hybrid screening systems. Brief. Funct. Genomics Proteomics 6, 302–312.
32. Cusick, M. E., Klitgord, N., Vidal, M., and Hill, D. E. (2005) Interactome: gateway into systems biology. Hum. Mol. Genet. 14 Spec. No. 2, R171–R181.
33. Gietz, R. D. (2006) http://home.cc. umanitoba.ca/~gietz/
34. 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.
35. Duttweiler, H. M. (1996) A highly sensitive and non-lethal beta-galactosidase plate assay for yeast. Trends Genet. 12, 340–341.