Membrane‐Based Yeast Two‐Hybrid System to Detect Protein Interactions

Nicolas Lentze1, Daniel Auerbach1

1 Dualsystems Biotech, Schlieren, Switzerland
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 19.17
DOI:  10.1002/0471140864.ps1917s52
Online Posting Date:  May, 2008
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Abstract

The classical yeast two‐hybrid system and its modifications have been successfully used over the past decade to investigate interactions between most classes of proteins expressed in a given cell or tissue. However, some proteins (e.g., integral membrane proteins or nuclear proteins) are relatively difficult to investigate by standard yeast two‐hybrid methods either because they are retained at cellular membranes or they activate the system in the absence of a true protein interaction. The membrane‐based yeast two‐hybrid (MbY2H) system presented in this unit overcomes some of these limitations. It is based on the split‐ubiquitin protein complementation assay and detects protein interactions directly at the membrane, thereby allowing the use of full‐length integral membrane proteins and membrane‐associated proteins as baits to hunt for novel interaction partners. A simple modification also allows the use of proteins that are self‐activating in a classical yeast two‐hybrid system (e.g., acidic proteins and many transcription factors). Like the yeast two‐hybrid system, the MbY2H system can also be used for interaction discovery by screening complex cDNA libraries for novel interaction partners. Curr. Protoc. Protein Sci. 52:19.7.1‐19.7.28. © 2008 by John Wiley & Sons, Inc.

Keywords: membrane proteins; membrane‐based yeast two‐hybrid system; protein interactions

     
 
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Table of Contents

  • Introduction
  • Strategic Planning
  • Basic Protocol 1: Bait Construction, Transformation into Yeast Reporter Strain, and Detection by Immunoblotting
  • Basic Protocol 2: Functional Assay to Determine Bait Suitability for Screening
  • Basic Protocol 3: Pilot Screen to Optimize the Stringency of Selection
  • Basic Protocol 4: Screening of a cDNA Library to Identify Novel Interactors
  • Basic Protocol 5: Plasmid Recovery from Yeast
  • Basic Protocol 6: Confirmation of Positive Bait‐Prey Interactors
  • Support Protocol 1: Production of Single‐Stranded Carrier DNA from Salmon Sperm
  • Support Protocol 2: Preparation of Membrane Extracts from Yeast
  • Support Protocol 3: Determination of Bait‐Prey Protein Interaction Specificity
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: Bait Construction, Transformation into Yeast Reporter Strain, and Detection by Immunoblotting

  Materials
  • cDNA encoding the bait protein
  • Primers for subcloning bait cDNA into vector:
    • Forward primer: 5′‐TACTCTTATggccattacggcc‐NNN NNN NNN NNN NNN NNN NNN‐3′ (where NNN denotes the gene‐specific sequence)
    • Reverse primer: 5′‐TACTCTTATggccgaggcggcc‐GC NNN NNN NNN NNN NNN NNN NNN‐3′ (where NNN denotes the gene‐specific sequence)
  • DNA gel extraction kit (e.g., NucleoSpin Extract II kit, Macherey‐Nagel; Wizard SV Gel and PCR Clean‐up System, Promega)
  • Appropriate MbY2H bait vector: pBT3‐C, pBT3‐SUC, or pBT3‐STE (Dualsystems Biotech, see and Internet Resources)
  • SfiI restriction enzyme
  • PCR DNA purification kit (e.g. MinElute PCR Purification kit, Qiagen)
  • Competent E. coli cells (XL1‐Blue, DH10B, TOP10, or similar cloning strains)
  • LB plates supplemented with kanamycin (see appendix 4A)
  • Sequencing primers appropriate to the vector:
    • pBT3‐C, pBT3‐SUC, and pBT3‐STE
      • Forward primer: 5′‐TGGCATGCATGTGCTCTG‐3′
      • Reverse primer: 5′‐GTAAGGTGGACTCCTTCT‐3′
    • pBT3‐N
      • Forward primer: 5′‐CAGAAGGAGTCCACCTTAC‐3′
      • Reverse primer: 5′‐AAGCGTGACATAACTAATTAC‐3′
    • pDHB1
      • Forward primer: 5′‐TTTCTGCACAATATTTCAAGC‐3′
      • Reverse primer: 5′‐GTAAGGTGGACTCCTTCT‐3′
  • 1×YPAD liquid medium (see recipe)
  • NMY51 yeast strain: MATa his3Δ200 trp1‐901 leu2‐3,112 ade2 LYS2::(lexAop) 4‐HIS3 ura3::(lexAop) 8‐lacZ ade2::(lexAop) 8‐ADE2 GAL4 (Dualsystems Biotech, see Internet Resources)
  • 50% (w/v) PEG 4000 (see recipe)
  • 1 M LiOAC (see recipe)
  • Single‐stranded carrier DNA ( protocol 7)
  • Control plasmids: pCCW‐Alg5 (positive control) and pPR3‐N (negative control), Dualsystems Biotech (see Internet Resources)
  • 0.9% (w/v) NaCl
  • 10‐cm plates containing SD solid medium lacking leucine (SD−Leu; see recipe)
  • 10‐cm plates containing SD solid medium lacking tryptophan (SD−Trp; see recipe)
  • Bait‐specific antibody or mouse monoclonal antibody against LexA (Dualsystems Biotech, see Internet Resources)
  • Shaking incubator, 30°C
  • Parafilm
  • Additional reagents and equipment for performing PCR amplification ( appendix 4J), restriction enzyme digestion of DNA ( appendix 4I), agarose gel electrophoresis ( appendix 4F), and immunoblotting and immunodetection (unit 10.10), and for preparing minipreps of plasmid DNA ( appendix 4C)

Basic Protocol 2: Functional Assay to Determine Bait Suitability for Screening

  Materials
  • 1×YPAD liquid medium (see recipe)
  • Yeast strain NMY51 (Dualsystems Biotech, see Internet Resources), growing on plates
  • 50% (w/v) PEG 4000 (see recipe)
  • 1 M lithium acetate (LiOAC; see recipe)
  • Single‐stranded carrier DNA ( protocol 7)
  • Bait construct ( protocol 1)
  • Control plasmids: pAI‐Alg5, pDL2‐Alg5, and pPR3‐N (Dualsystems Biotech, see Internet Resources)
  • 10‐cm diameter plates containing SD solid medium lacking tryptophan, leucine, histidine, or adenine (SD−Trp−Leu, SD−Trp−Leu−His, and SD−Trp−Leu−His−Ade; see recipe)
  • 0.9% (w/v) NaCl
  • Shaking incubator, 30°C
  • 42°C water bath
  • Parafilm

Basic Protocol 3: Pilot Screen to Optimize the Stringency of Selection

  Materials
  • Bait‐transformed yeast strain NMY51 ( protocol 2), growing on plate <2 weeks old
  • SD liquid medium lacking leucine (SD−Leu; see recipe)
  • 2×YPAD liquid medium (see recipe)
  • Single‐stranded carrier DNA ( protocol 7)
  • 1 M lithium acetate (LiOAC; see recipe)
  • 10× TE buffer, pH 7.5: 100 mM Tris·Cl, pH 7.5, 10 mM EDTA (see appendix 2E); store up to 1 year at room temperature
  • 50% (w/v) PEG 4000 (see recipe)
  • Library vector pPR3‐N (Dualsystems Biotech, see Internet Resources)
  • Dimethyl sulfoxide (DMSO)
  • 0.9% (w/v) NaCl
  • 10‐cm plates containing SD medium lacking tryptophan and leucine (SD−Trp−Leu; see recipe)
  • 15‐cm selective plates (six total) containing SD medium lacking tryptophan, leucine and histidine (SD−Trp−Leu−His) and (six total) containing SD−Trp−Leu−His−Ade (adenine; see recipe), both supplemented with 0, 1, 2.5, 5, 7.5 and 10 mM 3‐amino‐1,2,4‐triazole (3‐AT; see recipe)
  • Shaking incubator, 30°C
  • 50‐ml conical tube
  • 1‐liter shaker flask
  • 99°C heating block
  • 42°C water bath
  • Plastic bags with tape or Parafilm

Basic Protocol 4: Screening of a cDNA Library to Identify Novel Interactors

  Materials
  • Bait‐transformed yeast strain NMY51 ( protocol 1), growing on plate for no longer than 2 weeks
  • SD liquid medium lacking leucine (SD−Leu; see recipe)
  • 2× YPAD liquid medium (see recipe)
  • Single‐stranded carrier DNA ( protocol 7)
  • 1 M lithium acetate (LiOAc; see recipe)
  • 10× TE buffer: 100 mM Tris·Cl, pH 7.5, 10 mM EDTA (see appendix 2E); store up to 1 year at room temperature
  • 50% (w/v) PEG 4000 (see recipe)
  • Appropriate cDNA library (see Internet Resources)
  • Dimethyl sulfoxide (DMSO)
  • 0.9% (w/v) NaCl
  • Sixteen 15‐cm diameter selective plates with appropriate selection medium (determined in protocol 3)
  • 10‐cm plates containing solid SD medium lacking tryptophan and leucine (SD−Trp−Leu; see recipe)
  • Shaking incubator, 30°C
  • 50‐ml conical tube
  • 1‐liter shaker flask
  • 42°C water bath
  • Plastic bags with tape or Parafilm

Basic Protocol 5: Plasmid Recovery from Yeast

  Materials
  • Yeast colonies positive for bait/prey interaction ( protocol 4)
  • Selection plates (same stringency as protocol 4)
  • SD liquid medium lacking tryptophan and leucine (SD−Trp−Leu; see recipe)
  • Plasmid miniprep kit (e.g., Wizard Plasmid Purification System, Promega), including resuspension buffer, nuclease removal buffer, wash buffer, elution buffer, and spin columns
  • 425 to 600‐µm (30 to 40 U.S. sieve) acid‐washed glass beads (Sigma)
  • E. coli XL‐1 Blue chemically competent cells (Stratagene)
  • SOC medium (see appendix 2E), 37°C
  • SfiI restriction enzyme
  • LB plates supplemented with 100 µg/ml ampicillin (see appendix 2E)
  • Plastic bags or Parafilm
  • 96‐well deep‐well master block (e.g., Greiner Bio‐One GmbH)
  • Breathable plate seal (e.g., EasySeal film, Hampton Research)
  • Shaking incubator, 30°C
  • Centrifuge with rotor adapted for 96‐well plates
  • 42°C water bath
  • Additional reagents and equipment for performing restriction enzyme digestion of DNA ( appendix 4I) and agarose gel electrophoresis ( appendix 4F)

Basic Protocol 6: Confirmation of Positive Bait‐Prey Interactors

  Materials
  • Bait‐transformed yeast strain NMY51 ( protocol 1), growing on plate
  • SD liquid medium lacking leucine (SD−Leu; see recipe)
  • Prey plasmids derived from the library screen (see protocol 5)
  • 50% (w/v) PEG 4000 (see recipe)
  • 1 M lithium acetate (LiOAc; see recipe)
  • Single‐stranded carrier DNA ( protocol 7)
  • 0.9% (w/v) NaCl
  • 10‐cm plates containing SD solid medium lacking tryptophan and leucine (SD−Trp−Leu plates; see recipe)
  • 10‐cm selective plates of the same stringency as used in the original screen ( protocol 4)
  • Appropriate sequencing primers:
    • Forward primer for pPR3‐N, pDSL‐Nx, and pNubG‐X library plasmids: 5′‐GTCGAAAATTCAAGACAAGG‐3′
    • Reverse primer for pPR3‐N and pDSL‐Nx library plasmids: 5′‐AAGCGTGACATAACTAATTAC‐3′
    • Reverse primer for pNubG‐X library plasmids: 5′‐GTTACTCAAGAACAAGAATTTTCG‐3′
    • Forward primer for pPR3‐C, pDL2xN, and pX‐NubG library plasmids: 5′‐TTTCTGCACAATATTTCAAGC‐3′
    • Reverse primer for pPR3‐C, pDL2xN and pX‐NubG library plasmids: 5′‐CTTGACGAAAATCTGCATGG‐3′
  • Shaking incubator, 30°C
  • 96‐well master block (e.g., Greiner Bio‐One GmbH) and plate sealers
  • 42°C water bath
  • Centrifuge with rotor adapted for 96‐well plates
  • Parafilm

Support Protocol 1: Production of Single‐Stranded Carrier DNA from Salmon Sperm

  Materials
  • Salmon sperm DNA, sodium salt (e.g., deoxyribonucleic acid sodium salt from salmon testes, Sigma)
  • Sterile H 2O
  • 250‐ml glass beaker, sterile
  • Magnetic stirring bar, sterile
  • Magnetic stirrer
  • Sterile microcentrifuge tubes
  • Boiling water bath or 99°C heating block
  • Ice/water bath

Support Protocol 2: Preparation of Membrane Extracts from Yeast

  Materials
  • Bait or control construct‐bearing NMY51 yeast strain ( protocol 1)
  • SD liquid medium lacking leucine (SD−Leu; see recipe) or SD liquid medium lacking tryptophan (SD−Trp; see recipe)
  • SDS‐PAGE sample buffer (see unit 10.1 or )
  • 425 to 600‐µm (30 to 40 U.S. sieve) acid‐washed glass beads (Sigma)
  • Triton X‐100
  • Shaking incubator, 30°C
  • 50‐ml conical tube
  • Ultracentrifuge microtubes
  • Ultracentrifuge
  • Liquid nitrogen tank, optional

Support Protocol 3: Determination of Bait‐Prey Protein Interaction Specificity

  Materials
  • Bait‐transformed and control yeast strains NMY51 (see protocol 1)
  • SD liquid medium lacking leucine (SD−Leu; see recipe)
  • Prey plasmids derived from library screen (see protocol 5)
  • 50% (w/v) PEG 4000 (see recipe)
  • 1 M lithium acetate (LiOAc; see recipe)
  • Single‐stranded carrier DNA ( protocol 7)
  • 0.9% (w/v) NaCl
  • 10‐cm plates containing SD solid medium lacking tryptophan and leucine (SD−Trp−Leu; see recipe)
  • 10‐cm selective plates of the same stringency as used in the screen (see protocol 4)
  • Shaking incubator, 30°C
  • 96‐well deep‐well master block (e.g., Greiner Bio‐One GmbH) and sealer
  • 42°C water bath
  • Centrifuge with rotor adapted for 96‐well plates
  • Parafilm
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Figures

Videos

Literature Cited

   Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. (eds.) 2008. Current Protocols in Molecular Biology, Chapters 1 and 2. John Wiley & Sons, Hoboken, N.J.
   Fashena, S.J., Serebriiskii, I., and Golemis, E.A. 2000. The continued evolution of two‐hybrid screening approaches in yeast: How to outwit different preys with different baits. Gene 250: 1‐14.
   Fields, S. and Song, O. 1989. A novel genetic system to detect protein‐protein interactions. Nature 340: 245‐246.
   Johnsson, N. and Varshavsky, A. 1994. Split ubiquitin as a sensor of protein interactions in vivo. Proc. Natl. Acad. Sci. U.S.A. 91: 10340‐10344.
   Mockli, N., Deplazes, A., Hassa, P.O., Zhang, Z., Peter, M., Hottiger, M.O., Stagljar, I., and Auerbach, D. 2007. Yeast split‐ubiquitin‐based cytosolic screening system to detect interactions between transcriptionally active proteins. Biotechniques 42: 725‐730.
   Stagljar, I., Korostensky, C., Johnsson, N., and 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.
   Thaminy, S., Auerbach, D., Arnoldo, A., and Stagljar, I. 2003. Identification of novel ErbB3‐interacting factors using the split‐ubiquitin membrane yeast two‐hybrid system. Genome Res. 13: 1744‐1753.
Internet Resources
   http://psort.ims.u‐tokyo.ac.jp/form2.html
  PSORT, a program used to predict sorting signals in integral membrane proteins.
   http://www.cbs.dtu.dk/services/SignalP
  SignalIP, a program used to predict the N‐terminal cleavable signal sequences found in many type I integral membrane proteins.
   http://www.dualsystems.com
  Additional information on the MbY2H system, including vector maps and sequences, reagents, and available cDNA libraries.
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