Abstract
Detection of protein–protein interactions on a large-scale has become a major focus of functional genomics after the completion of genome sequencing. The information generated from these studies not only assembles proteins into signaling networks, but also reveals potential functions of uncharacterized proteins when their interacting partners have known functions. We have developed a rolling circle amplification-based yeast two-hybrid scheme that allows one to test reproducibility and specificity of the interactions on a large scale. Using this scheme, technical false-positives from yeast two-hybrid analyses can be efficiently minimized.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Fields, S. and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature 340, 245–246.
Brent, R., Jr. and Finley, R. L. (1997) Understanding gene and allele function with two-hybrid methods. Annu. Rev. Genet. 31, 663–704.
Nodzon, L. and Song, W.-Y. (2004). Yeast two-hybrid technology, in Encyclopedia of Plant and Crop Science (Goodman, R. M., ed.), Marcel Dekker, Inc.: New York, pp. 1302–1304.
Xenarios, I., Salwinski, L., Duan, X. J., Higney, P., Kim, S. M., and Eisenberg, D. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30, 303–305.
Vidalain, P. O., Boxem, M., Ge, H., Li, S., and Vidal, M. (2004) Increasing specificity in high-throughput yeast two-hybrid experiments. Methods 32, 363–370.
Kornberg, A. and Baker, T. A. (1992) DNA Replication. W. H. Freeman and Company, San Francisco.
Fire, A. and Xu, S.-Q. (1995) Rolling replication of short DNA circles. Proc. Natl. Acad. Sci. USA 92, 4641–4645.
Dean, F. B., Nelson, J. R., Giesler, T. L., and Lasken, R. S. (2001) Rapid amplification of plasmid and phage DNA using phi29 DNA polymerase and multipleprimed rolling circle amplification. Genome Res. 11, 1095–1099.
Blanco, L., Bernad, A., Lazaro, J. M., Martin, G., Garmendia, C., and Salas, M. (1989) Highly efficient DNA synthesis by the phage phi29 DNA polymerase. Symmetrical mode of DNA replication. J. Biol. Chem. 264, 8935–8940.
Garmendia, C., Bernad, A., Esteban, J. A., Blanco, L., and Salas, M. (1992) The bacteriophage phi29 DNA polymerase, a proofreading enzyme. J. Biol. Chem. 267, 2594–2599.
Esteban, J. A., Salas, M., and Blanco, L. (1993) Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization. J. Biol. Chem. 268, 2719–2726.
Ding, X., Cory, G., and Song, W.-Y. (2004) A high-throughput system to verify candidate interactors from yeast two-hybrid screening using rolling circle amplification. Anal. Biochem. 331, 195–197.
Chen, X., Ding, X., and Song, W.-Y. (2003) Isolation of plasmid DNA rescued from single colonies of Agrobacterium tumefaciens by means of rolling circle amplification. Plant Mol. Biol. Rep. 21, 411–415.
Ding, X., Snyder, A. K., Shaw, R., Farmerie, W.G., and Song, W.-Y. (2003) Direct retransformation of yeast with plasmid DNA isolated from single yeast colonies using rolling circle amplification. Biotechniques 35, 774–779.
Toyn, J. H., Gunyuzlu, P. L., White, W. H., Thompson, L. A., and Hollis, G. F. (2000) A counterselection for the tryptophan pathway in yeast: 5-fluoroanthranilic acid resistance. Yeast 16, 553–560.
Walhout, A. J. and Vidal, M. (2001) High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24, 297–306.
Soellick, T. R. and Uhrig, J. F. (2001) Development of an optimized interactionmating protocol for large-scale yeast two-hybrid analyses. Genome Biol. 2, research0052.1–0052.7.
Acknowledgments
We thank Dr. M. Vidal for providing the yeast strain MaV203, Dr. P. C. Ronald for the precursors of the pXDGATcy86 and pXDGATU86 vectors, and Lisa Nodzon for critical reading of the manuscript. This research was supported by the Florida Agricultural Experiment Station and a grant from the National Science Foundation Plant Genome Research to W-Y S. This work was approved for publication as Journal Series No. R-10865.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc.
About this protocol
Cite this protocol
Ding, X., Zhang, Y., Song, WY. (2007). Use of Rolling-Circle Amplification for Large-Scale Yeast Two-Hybrid Analyses. In: Ronald, P.C. (eds) Plant-Pathogen Interactions. Methods in Molecular Biology, vol 354. Humana Press. https://doi.org/10.1385/1-59259-966-4:85
Download citation
DOI: https://doi.org/10.1385/1-59259-966-4:85
Publisher Name: Humana Press
Print ISBN: 978-1-58829-448-7
Online ISBN: 978-1-59259-966-0
eBook Packages: Springer Protocols