A comparison and optimization of yeast two-hybrid systems

Methods. 2012 Dec;58(4):317-24. doi: 10.1016/j.ymeth.2012.12.001. Epub 2012 Dec 8.


Two-hybrid (Y2H) assays are available in a variety of different versions, including bacterial, yeast, and mammalian systems. However, even when done exclusively in yeast, multiple different host strains, vectors, reporter genes, or protocols can be used. Here we systematically compare protein-protein interactions (PPIs) from several previously published Y2H datasets. PPIs of a human gold-standard dataset were generated by Y2H assays as well as other methods such as LUMIER or protein fragment complementation assays (PCAs). Different Y2H methods detect substantially different subsets of these PPIs, even when protocols are standardized. In order to maximize the number of interactions found and to minimize the number of false positive interactions we recommend to combine multiple vectors and protocols. While the combined results of all 18 methods detected about 92% of a gold-standard interaction set, a combination of just three Y2H assays detected up to 78% of these protein pairs, or up to 83% when a fourth assay was included. These findings indicate that three or four separate assays may be sufficient to detect the majority of protein-protein interactions in many systems.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Amitrole / metabolism
  • Cluster Analysis
  • Culture Media
  • Genetic Vectors
  • Humans
  • Plasmids / genetics
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Interaction Mapping / methods
  • Protein Interaction Mapping / standards
  • Recombinant Fusion Proteins / biosynthesis
  • Recombinant Fusion Proteins / genetics
  • Reference Standards
  • Reproducibility of Results
  • Signal-To-Noise Ratio
  • Two-Hybrid System Techniques / standards*
  • Yeasts / genetics
  • Yeasts / metabolism


  • Culture Media
  • Recombinant Fusion Proteins
  • Amitrole