Skip to main content

Yeast One- and Two-Hybrid High-Throughput Screenings Using Arrayed Libraries

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1629))

Abstract

Since their original description more than 25 years ago, the yeast one- and two-hybrid systems (Y1H/Y2H) have been used by many laboratories to detect DNA–protein (Y1H) and protein–protein interactions (Y2H). These systems use yeast cells (Saccharomyces cerevisiae) as a eukaryotic “test tube” and are amenable for most labs in the world. The development of highly efficient cloning methods has fostered the generation of large collections of open reading frames (ORFs) for several organisms that have been used for yeast screenings. Here, we describe a simple mating based method for high-throughput screenings of arrayed ORF libraries with DNA (Y1H) or protein (Y2H) baits not requiring robotics. One person can easily carry out this protocol in approximately 10 h of labor spread over 5 days. It can also be scaled down to test one-to-one (few) interactions, scaled up (i.e., robotization) and is compatible with several library formats (i.e., 96, 384-well microtiter plates).

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

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   179.99
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

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Brent R, Ptashne M (1985) A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor. Cell 43:729–736

    Article  CAS  PubMed  Google Scholar 

  2. Ma J, Ptashne M (1998) Converting a eukaryotic transcriptional inhibitor into an activator. Cell 55:443–446

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  4. Wilson TE, Fahrner TJ, Johnston M, Milbrandt J (1991) Identification of the DNA binding site for NGFIB by genetic selection in yeast. Science 252:1296–1300

    Article  CAS  PubMed  Google Scholar 

  5. Li JJ, Herskowitz I (1993) Isolation of the ORC6, a component of the yeast origin recognition complex by a one-hybrid system. Science 262:1870–1874

    Article  CAS  PubMed  Google Scholar 

  6. Wang MM, Reed RR (1993) Molecular cloning of the olfactory neuronal transcription factor Olf-1 by genetic selection in yeast. Nature 364:121–126

    Article  CAS  PubMed  Google Scholar 

  7. Dowell SJ, Romanowski P, Diffley JF (1994) Interaction of Dbf4, the Cdc7 protein kinase regulatory subunit, with yeast replication origins in vivo. Science 265:1243–1246

    Article  CAS  PubMed  Google Scholar 

  8. Inouye C, Remondelli P, Karin M, Elledge S (1994) Isolation of a cDNA encoding a metal response element binding protein using a novel expression cloning procedure: the one hybrid system. DNA Cell Biol 13:731–742

    Article  CAS  PubMed  Google Scholar 

  9. Rezwan M, Auerbach D (2012) Yeast “N”-hybrid systems for protein-protein and drug-protein interaction discovery. Methods 57(4):423–429

    Article  CAS  PubMed  Google Scholar 

  10. Ferro E, Trabalzini L (2013) The yeast two-hybrid and related methods as powerful tools to study plant cell signalling. Plant Mol Biol 83(4–5):287–301

    Article  CAS  PubMed  Google Scholar 

  11. Ji X, Wang L, Nie X, He L, Zang D, Liu Y, Zhang B, Wang Y (2014) A novel method to identify the DNA motifs recognized by a defined transcription factor. Plant Mol Biol 86:367–380

    Article  CAS  PubMed  Google Scholar 

  12. Ota K, Feng SY, Ito T (2014) Detecting protein-DNA interactions using a modified yeast one-hybrid system. Methods Mol Biol 1164:39–50

    Article  PubMed  Google Scholar 

  13. Mallick J, Jansen G, Wu C, Whiteway M (2016) SRYTH: a new yeast two-hybrid method. Methods Mol Biol 1356:31–41

    Article  CAS  PubMed  Google Scholar 

  14. Snider J, Stagljar I (2016) Membrane Yeast Two-Hybrid (MYTH) mapping of full-length membrane protein interactions. Cold Spring Harb Protoc. doi:10.1101/pdb.top077560

    Google Scholar 

  15. Reece-Hoyes JS, Walhout AJ (2012) Yeast one-hybrid assays: a historical and technical perspective. Methods 57(4):441–447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Mehla J, Caufield JH, Uetz P (2015) The yeast two-hybrid system: a tool for mapping protein-protein interactions. Cold Spring Harb Protoc 5:425–430

    Google Scholar 

  17. Paz-Ares J (2002) REGIA, an EU project on functional genomics of transcription factors from Arabidopsis thaliana. Comp Funct Genomics 3:102–108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Gong W, Shen YP, Ma LG, Pan Y, Du YL, Wang DH, Yang JY, Hu LD, Liu XF, Dong CX, Ma L, Chen YH, Yang XY, Gao Y, Zhu D, Tan X, Mu JY, Zhang DB, Liu YL, Dinesh-Kumar SP, Li Y, Wang XP, Gu HY, Qu LJ, Bai SN, Lu YT, Li JY, Zhao JD, Zuo J, Huang H, Deng XW, Zhu YX (2004) Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol 135:773–782

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Mitsuda N, Ikeda M, Takada S, Takiguchi Y, Kondou Y, Yoshizumi T, Fujita M, Shinozaki K, Matsui M, Ohme-Takagi M (2010) Efficient yeast one-/two-hybrid screening using a library composed only of transcription factors in Arabidopsis thaliana. Plant Cell Physiol 51:2145–2151

    Article  CAS  PubMed  Google Scholar 

  20. Arabidopsis Interactome Mapping Consortium (2011) Evidence for network evolution in an Arabidopsis interactome map. Science 333(6042):601–607

    Article  PubMed Central  Google Scholar 

  21. Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJ, Benfey PN (2011) A stele-enriched gene regulatory network in the Arabidopsis root. Mol Syst Biol 7:459

    Article  PubMed  PubMed Central  Google Scholar 

  22. Castrillo G, Turck F, Leveugle M, Lecharny A, Carbonero P, Coupland G, Paz-Ares J, Oñate-Sánchez L (2011) Speeding cis-trans regulation discovery by phylogenomic analyses coupled with screenings of an arrayed library of Arabidopsis transcription factors. PLoS One 6:e21524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Gaudinier A, Zhang L, Reece-Hoyes JS, Taylor-Teeples M, Pu L, Liu Z, Breton G, Pruneda-Paz JL, Kim D, Kay SA, Walhout AJ, Ware D, Brady SM (2011) Enhanced Y1H assays for Arabidopsis. Nat Methods 8(12):1053–1055

    Article  CAS  PubMed  Google Scholar 

  24. Ou B, Yin KQ, Liu SN, Yang Y, Gu T, Wing Hui JM, Zhang L, Miao J, Kondou Y, Matsui M, Gu HY, Qu LJ (2011) A high-throughput screening system for Arabidopsis transcription factors and its application to Med25-dependent transcriptional regulation. Mol Plant 4:546–555

    Article  CAS  PubMed  Google Scholar 

  25. Burdo B, Gray J, Goetting-Minesky MP, Wittler B, Hunt M, Li T, Velliquette D, Thomas J, Gentzel I, dos Santos Brito M, Mejía-Guerra MK, Connolly LN, Qaisi D, Li W, Casas MI, Doseff AI, Grotewold E (2014) The Maize TFome—development of a transcription factor open reading frame collection for functional genomics. Plant J 80:356–366

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Pruneda-Paz JL, Breton G, Nagel DH, Kang SE, Bonaldi K, Doherty CJ, Ravelo S, Galli M, Ecker JR, Kay SA (2014) A genome-scale resource for the functional characterization of Arabidopsis transcription factors. Cell Rep 8:622–632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Taylor-Teeples M, Lin L, de Lucas M, Turco G, Toal TW, Gaudinier A, Young NF, Trabucco GM, Veling MT, Lamothe R, Handakumbura PP, Xiong G, Wang C, Corwin J, Tsoukalas A, Zhang L, Ware D, Pauly M, Kliebenstein DJ, Dehesh K, Tagkopoulos I, Breton G, Pruneda-Paz JL, Ahnert SE, Kay SA, Hazen SP, Brady SM (2015) An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature 517(7536):571–575

    Article  CAS  PubMed  Google Scholar 

  28. Rueda-Romero P, Barrero-Sicilia C, Gómez-Cadenas A, Carbonero P, Oñate-Sánchez L (2012) Arabidopsis thaliana DOF6 negatively affects germination in non-after-ripened seeds and interacts with TCP14. J Exp Bot 63:1937–1949

    Article  CAS  PubMed  Google Scholar 

  29. Iglesias-Fernández R, Barrero-Sicilia C, Carrillo-Barral N, Oñate-Sánchez L, Carbonero P (2013) Arabidopsis thaliana bZIP44: a transcription factor affecting seed germination and expression of the mannanase encoding gene AtMAN7. Plant J 74:767–780

    Article  PubMed  Google Scholar 

  30. Iglesias-Fernández R, Wozny D, Iriondo-de Hond M, Oñate-Sánchez L, Carbonero P, Barrero-Sicilia C (2014) The AtCathB3 gene, encoding a cathepsin B-like protease, is expressed during germination of Arabidopsis thaliana and transcriptionally repressed by the basic leucine zipperP protein GBF1. J Exp Bot 65:2009–2021

    Article  PubMed  PubMed Central  Google Scholar 

  31. Marín-de la Rosa N, Sotillo B, Mizckolczi P, Gibbs DJ, Vicente J, Carbonero P, Oñate-Sánchez L, Holdsworth MJ, Bhalerao R, Alabadí D, Blázquez MA (2014) Large-scale identification of gibberellin-related transcription factors defines Group VII ERFs as functional DELLA partners. Plant Physiol 166:1022–1032

    Article  PubMed  Google Scholar 

  32. Ballester P, Navarrete-Gomez M, Carbonero P, Oñate-Sánchez L, Ferrándiz C (2015) Leaf expansion in Arabidopsis is controlled by a TCP-NGA regulatory module likely conserved in distantly related species. Physiol Plant 155:21–32

    Article  CAS  PubMed  Google Scholar 

  33. Harper JW, Adami GR, Wei N, Keyomarsi K, Elledge SJ (1993) The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases. Cell 75:805–816

    Article  CAS  PubMed  Google Scholar 

  34. James P, Halladay J, Craig EA (1996) Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144:1425–1436

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Liu J, Wilson TE, Milbrandt J, Johnston M (1993) Identifying DNA-binding sites and analyzing DNA-binding domains using a yeast selection system. Methods 5:125–137

    Article  CAS  Google Scholar 

  36. Elble R (1992) A simple and efficient procedure for transformation of yeasts. BioTechniques 13(1):18–20

    CAS  PubMed  Google Scholar 

  37. Dobi KC, Winston F (2007) Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae. Mol Cell Biol 27(15):5575–5586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Aronheim A, Zandi E, Hennemann H, Elledge SJ, Karin M (1997) Isolation of an AP-1 repressor by a novel method for detecting protein-protein interactions. Mol Cell Biol 17:3094–3102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Stagljar I, Korostensky C, Johnsson N, te Heesen S (1998) A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. Proc Natl Acad Sci U S A 95:5187–5192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Smirnov MN, Smirnov VN, Budowsky EI, Inge-Vechtomov SG, Serebrjakov NG (1967) Red pigment of adenine-deficient yeast Saccharomyces cerevisiae. Biochem Biophys Res Commun 27(3):299–304

    Article  CAS  PubMed  Google Scholar 

  41. Weisman LS, Bacallao R, Wickner W (1987) Multiple methods of visualizing the yeast vacuole permit evaluation of its morphology and inheritance during the cell cycle. J Cell Biol 105(4):1539–1547

    Article  CAS  PubMed  Google Scholar 

  42. Rajagopala SV, Hughes KT, Uetz P (2009) Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins. Proteomics 9:5296–5302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

The work in L.O.-S. lab is supported by MINECO grants BIO2013-46076-R and BIO2016-77840-R. We thank all people that contributed to the development of the Arabidopsis TF library [22] as well as all the labs that have used this resource helping this way to ascertain its potential. Dr. Begoña Benito is also thanked for critical reading. We apologize to those publications not cited here due to space limitations.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Luis Oñate-Sánchez .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Sánchez-Montesino, R., Oñate-Sánchez, L. (2017). Yeast One- and Two-Hybrid High-Throughput Screenings Using Arrayed Libraries. In: Kaufmann, K., Mueller-Roeber, B. (eds) Plant Gene Regulatory Networks. Methods in Molecular Biology, vol 1629. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7125-1_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7125-1_5

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7124-4

  • Online ISBN: 978-1-4939-7125-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics