Skip to main content

Use of Rolling-Circle Amplification for Large-Scale Yeast Two-Hybrid Analyses

  • Protocol
Plant-Pathogen Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 354))

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Fields, S. and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature 340, 245–246.

    Article  PubMed  CAS  Google Scholar 

  2. Brent, R., Jr. and Finley, R. L. (1997) Understanding gene and allele function with two-hybrid methods. Annu. Rev. Genet. 31, 663–704.

    Article  PubMed  CAS  Google Scholar 

  3. 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.

    Google Scholar 

  4. 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.

    Article  PubMed  CAS  Google Scholar 

  5. 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.

    Article  PubMed  CAS  Google Scholar 

  6. Kornberg, A. and Baker, T. A. (1992) DNA Replication. W. H. Freeman and Company, San Francisco.

    Google Scholar 

  7. Fire, A. and Xu, S.-Q. (1995) Rolling replication of short DNA circles. Proc. Natl. Acad. Sci. USA 92, 4641–4645.

    Article  PubMed  CAS  Google Scholar 

  8. 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.

    Article  PubMed  CAS  Google Scholar 

  9. 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.

    PubMed  CAS  Google Scholar 

  10. 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.

    PubMed  CAS  Google Scholar 

  11. 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.

    PubMed  CAS  Google Scholar 

  12. 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.

    PubMed  CAS  Google Scholar 

  13. 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.

    Article  CAS  Google Scholar 

  14. 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.

    PubMed  CAS  Google Scholar 

  15. 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.

    Article  PubMed  CAS  Google Scholar 

  16. Walhout, A. J. and Vidal, M. (2001) High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24, 297–306.

    Article  PubMed  CAS  Google Scholar 

  17. 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.

    Google Scholar 

Download references

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

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints 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

Publish with us

Policies and ethics