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The Yeast Two-Hybrid System. Anne C. Luebke. What is the yeast two-hybrid system used for?. Identifies novel protein-protein interactions Can identify protein cascades Identifies mutations that affect protein-protein binding

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what is the yeast two hybrid system used for
What is the yeast two-hybrid system used for?
  • Identifies novel protein-protein interactions
  • Can identify protein cascades
  • Identifies mutations that affect protein-protein binding
  • Can identify interfering proteins in known interactions (Reverse Two-Hybrid System)
how does it work
How does it work?
  • Uses yeast as a model for eukaryotic protein interactions
  • A library is screened or a protein is characterized using a bait construct
  • Interactions are identified by the transcription of reporter genes
  • Positives are selected using differential media
the model
The Model




Bait Protein

Prey Protein



Reporter Gene

DNA-Binding Site

steps to screen a library
Steps to Screen a Library
  • Create the Bait Plasmid Construct from the gene of interest and the DNA binding domain of Gal4 or LexA or other suitable domain
  • Transform with the bait construct a yeast strain lacking the promoter for the reporter genes and select for transformed yeast
  • Transform the yeast again with the library plasmids
  • Select for interaction
sequence analysis
Sequence analysis
  • Isolate plasmid from yeast and transform E. coli
  • Purify plasmid from E. coli and sequence
  • Blast sequence against database for known proteins or construct a possible protein sequence from the DNA sequence and compare to other proteins
reporter genes
Reporter Genes
  • LacZ reporter - Blue/White Screening
  • HIS3 reporter - Screen on His+ media (usually need to add 3AT to increase selectivity)
  • LEU2 reporter - Screen on Leu+ media
  • ADE2 reporter - Screen on Ade+ media
  • URA3 reporter - Screen on Ura+ media (can do negative selection by adding FOA)
plasmid constructs
Plasmid Constructs
  • Plasmids are constructed with the Gal4 DNA binding domain (or other suitable domain) in front of a Multiple Cloning Site (MCS)
  • The plasmid contains genes that can be used for selection such as Amp, Leu2, Ura3, or Trp1
sample plasmid
Sample Plasmid

From Golemis Lab Homepage

false positives
False Positives
  • False positives are the largest problem with the yeast two-hybrid system
  • Can be caused by:
  • Non-specific binding of the prey
  • Ability to induce transcription without interaction with the bait (Majority of false positives)
elimination of false positives
Elimination of False Positives
  • Sequence Analysis
  • Plasmid Loss Assays
  • Retransformation of both strain with bait plasmid and strain without bait plasmid
  • Test for interaction with an unrelated protein as bait
  • Two (or more) step selections
  • Immediate availability of the cloned gene of the interacting protein
  • Only a single plasmid construction is required
  • Interactions are detected in vivo
  • Weak, transient interactions can be detected
  • Can accumulate a weak signal over time
examples of uses of the yeast two hybrid system
Examples of Uses of the Yeast Two-Hybrid System
  • Identification of caspase substrates
  • Interaction of Calmodulin and L-Isoaspartyl Methyltransferase
  • Genetic characterization of mutations in E2F1
  • Peptide hormone-receptor interactions
  • Pha-4 interactions in C. elegans
  • Bartel, Paul, C. Chien, R. Sternglanz, S. Fields. “Elimination of False Positives that Arise in Using the Two-Hybrid System.” Biotechniques (1993) Vol. 14, no. 6, p. 920-924.
  • Chien, Cheng-ting, P. Bartel, R. Sternglanz, S. Fields. “The two-hybrid system: A method to identify and clone genes for proteins that interact with a protein of interest.” Proc. Natl. Acad. Sci. USA (1991) Vol. 88, p. 9578-9582.
  • Fields, Stanley, O. Song. "A novel genetic system to detect protein-protein interactions." Nature (1989) Vol. 340, p.245-246.
  • James, Philip, J. Halladay, E. Craig. "Genomic Libraries and a Host Strain Designed for Highly Efficient Two-Hybrid Selection in Yeast." Genetics (1996) Vol. 144, p. 1425-1436.
  • Kamada, S, H. Kusano, H. Fujita, M. Ohtsu, R. Koya, N. Kuzumaki, Y. Tsujimoto. "A cloning method for caspase substrates that uses the yeast two-hybrid system: Cloning of the antiapoptotic gene gelsolin." Proc. Natl. Acad. Sci. USA (1998) Vol 95, p. 8532-8537.
  • O'Connor, Mirriam, C. O'Connor. "Complex Interactions of the Protein L-Isoaspartyl Methyltransferase and Calmodulin Revealed with the Yeast Two-hybrid System." The Journal of Biological Chemistry (1998) Vol. 273, p. 12909-12913.
  • Staudinger, Jeff, J. Zhou, R. Burgess, S. Elledge, E. Olson. "PICK1: A Perinuclear Binding Protein and Substrate for Protein Kinase C Isolated by the Yeast Two-Hybrid System." The Journal of Cell Biology (1995) Vol. 128, p. 263-271.
references continued
References continued
  • Vidal, Marc, P. Braun, E. Chen, J. Boeke, E. Harlow. "Genetic Characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system." Proc. Natl. Acad. Sci. USA (1996) Vol. 93, p. 10321-10326.
  • White, Michael. "The yeast two-hybrid system: Forward and reverse." Proc. Natl. Acad. Sci. USA (1996) Vol 93, p. 10001-10003.
  • Zhu, Jianwei, C. Kahn. "Analysis of a peptide hormone-receptor interaction in the yeast two-hybrid system." Proc. Natl. Acad. Sci. USA (1997) Vol. 94, p. 13063-13068.
  • Lab of Erica Golemis
  • Special thanks to Dr. Susan Mango and the University of Utah