The Yeast Two-Hybrid System and Its Several Derived Systems

Abstract

Abstract: The Yeast two-hybrid(Y2H)system is a molecular biology approach to detect protein-protein interactions. A diverse series of technologies derived from it have emerged in the past 20 years, which makes this two-hybrid methodology system more complete and efficient. They have been among the most important and powerful tools to study ptotein-ligand interactions that widely used in functional genomics,proteomics and pathology study. This article provides an overview on the basic principles and application progress of Y2H system and some derived techniques.

Key words: Yeast two-hybrid(Y2H)system, Protein-protein interaction, Two-hybrid methodology system

Huang Xinyuan, Fan Hongbo. The Yeast Two-Hybrid System and Its Several Derived Systems[J]. Biotechnology Bulletin, 2014, 0(1): 75-82.

References

[1] Bruckner A, Polge C, Lentze N, et al. Yeast two-hybrid, a powerful tool for systems biology[J]. Int J Mol Sci, 2009, 10(6): 2763- 2788.
[2] Fields S, Song O. A novel genetic system to detect protein-protein interactions[J]. Nature, 1989, 340(6230): 245-246.
[3] Caufield JH, Sakhawalkar N, Uetz P. A comparison and optimization of yeast two-hybrid systems[J]. Methods, 2012, 58(4): 317- 324.
[4] Huang H, Jedynak BM, Bader JS. Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps[J]. PLoS Comput Biol, 2007, 3(11): e214.
[5] Braun P, Tasan M, Dreze M, et al. An experimentally derived confidence score for binary protein-protein interactions[J]. Nat Methods, 2009, 6(1): 91-97.
[6] Vidal M, Brachmann RK, Fattaey A, et al. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions[J]. Proc Natl Acad Sci USA, 1996, 93 (19): 10315-10320.
[7] Bennett MA, Shern JF, Kahn RA. Reverse two-hybrid techniques in the yeast Saccharomyces cerevisiae[J]. Methods Mol Biol, 2004,261: 313-326.
[8] Li JJ, Herskowitz I. Isolation of ORC6, a component of the yeast origin recognition complex by a one-hybrid system[J]. Science,1993, 262(5141): 1870-1874.
[9] Klein P, Dietz KJ. Identification of DNA-binding proteins and protein-protein interactions by yeast one-hybrid and yeast two-hybrid screen[J]. Methods Mol Biol, 2010, 639: 171-192.
[10] SenGupta DJ, Zhang B, Kraemer B, et al. A three-hybrid system to detect RNA-protein interactions in vivo[J]. Proc Natl Acad Sci USA, 1996, 93(16): 8496-8501.
[11] Serebriiskii I, Khazak V, Golemis EA. A two-hybrid dual bait system to discriminate specificity of protein interactions[J]. J Biol Chem, 1999, 274(24): 17080-17087.
[12] Serebriiskii IG, Kotova E. Analysis of protein-protein interactions utilizing dual bait yeast two-hybrid system[J]. Methods Mol Biol,2004, 261: 263-296.
[13] James P, Halladay J, Craig EA. Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast[J].Genetics, 1996, 144(4): 1425-1436.
[14] Shaffer HA, Rood MK, Kashlan B, et al. BAPJ69-4A: a yeast twohybrid strain for both positive and negative genetic selection[J].J Microbiol Methods, 2012, 91(1): 22-29.
[15] Chen J, Zhou J, Bae W, et al. A yEGFP-based reporter system for high-throughput yeast two-hybrid assay by flow cytometry[J].Cytometry A, 2008, 73(4): 312-320.
[16] Damon C, Boxus M, Twizere JC, et al. An eYFP reporter gene for the yeast two-hybrid system[J]. Protein J, 2013, 32(2): 126- 130.
[17] Chen J, Carter MB, Edwards BS, et al. High throughput flow cytometry based yeast two-hybrid array approach for large-scale analysis of protein-protein interactions[J]. Cytometry A, 2012,81(1): 90-98.
[18] Stellberger T, Hauser R, Baiker A, et al. Improving the yeast twohybrid system with permutated fusions proteins: the Varicella Zoster Virus interactome[J]. Proteome Sci, 2010, 8: 8.
[19] Stellberger T, Hauser R, Uetz P, et al. Yeast two-hybrid screens: improvement of array-based screening results by N- and C-terminally tagged fusion proteins[J]. Methods Mol Biol, 2012, 815: 277-288.
[20] Karimova G, Pidoux J, Ullmann A, et al. A bacterial two-hybrid system based on a reconstituted signal transduction pathway[J].Proc Natl Acad Sci U S A, 1998, 95(10): 5752-5756.
[21] Pellis M, Muyldermans S, Vincke C. Bacterial two hybrid: a versatile one-step intracellular selection method[J]. Methods Mol Biol, 2012, 911: 135-150.
[22] Kim KM, Adyshev DM, Kasa A, et al. Putative protein partners for the human CPI-17 protein revealed by bacterial two-hybrid screening[J]. Microvasc Res, 2013, 88: 19-24.
[23] Battesti A, Bouveret E. Improvement of bacterial two-hybrid vectors for detection of fusion proteins and transfer to pBAD-tandem affinity purification, calmodulin binding peptide, or 6-histidine tag vectors[J]. Proteomics, 2008, 8(22): 4768-4771.
[24] Luo Y, Batalao A, Zhou H, et al. Mammalian two-hybrid system: a complementary approach to the yeast two-hybrid system[J].Biotechniques, 1997, 22(2): 350-352.
[25] Lee JW, Lee SK. Mammalian two-hybrid assay for detecting proteinprotein interactions in vivo[J]. Methods Mol Biol, 2004, 261: 327-336.
[26] Eyckerman S, Verhee A, der Heyden JV, et al. Design and application of a cytokine-receptor-based interaction trap[J]. Nat Cell Biol, 2001, 3(12): 1114-1119.
[27] Thibodeaux GN, Cowmeadow R, Umeda A, et al. A tetracycline repressor-based mammalian two-hybrid system to detect proteinprotein interactions in vivo[J]. Anal Biochem, 2009, 386(1): 129-131.
[28] Moncivais K, Zhang ZJ. Tetracycline repressor-based mammalian two-hybrid systems[J]. Methods Mol Biol, 2012, 812: 259-273.
[29] Lievens S, Caligiuri M, Kley N, et al. The use of mammalian twohybrid technologies for high-throughput drug screening[J].Methods, 2012, 58(4): 335-342.
[30] Guo M, Xia Z, Ma H. Functional phosphosite screening for targeted protein-protein interactions by combining phosphoproteomics strategies and mammalian two-hybrid assays[J]. Mol Biosyst,2011, 7(6): 1838-1841.
[31] Aronheim A. Improved efficiency sos recruitment system: expression of the mammalian GAP reduces isolation of Ras GTPase false positives[J]. Nucleic Acids Res, 1997, 25(16): 3373- 3374.
[32] Johnsson N, Varshavsky A. Split ubiquitin as a sensor of protein interactions in vivo[J]. Proc Natl Acad Sci U S A, 1994, 91(22): 10340-10344.
[33] Wehr MC, Laage R, Bolz U, et al. Monitoring regulated proteinprotein interactions using split TEV. Nat Methods, 2006, 3: [J] (12) 985-993.
[34] Schonhofer-Merl S, Torres-Ruiz RA. The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2[J].Mol Genet Genomics, 2010, 283(5): 439-449.
[35] Moerdyk-Schauwecker M, Destephanis D, Hastie E, et al. Detecting protein-protein interactions in vesicular stomatitis virus using a cytoplasmic yeast two hybrid system[J]. J Virol Methods, 2011,173(2): 203-212.
[36] Petschnigg J, Wong V, Snider J, et al. Investigation of membrane protein interactions using the split-ubiquitin membrane yeast twohybrid system[J]. Methods Mol Biol, 2012, 812: 225-244.
[37] Harty C, Romisch K. Analysis of Sec61p and Ssh1p interactions in the ER membrane using the split-ubiquitin system[J]. BMC Cell Biol, 2013, 14: 14.
[38] Wehr MC, Reinecke L, Botvinnik A, et al. Analysis of transient phosphorylation-dependent protein-protein interactions in living mammalian cells using split-TEV[J]. BMC Biotechnol, 2008, 8: 55.
[39] Capdevila-Nortes X, Lopez-Hernandez T, Ciruela F, et al. A modification of the split-tobacco etch virus method for monitoring interactions between membrane proteins in mammalian cells[J].Anal Biochem, 2012, 423(1): 109-118.
[40] Gray DC, Mahrus S, Wells JA. Activation of specific apoptotic caspases with an engineered small-molecule-activated protease[J].Cell, 2010, 142(4): 637-646.
[41] Mockli N, Auerbach D. Quantitative beta-galactosidase assay suitable for high-throughput applications in the yeast two-hybrid system[J]. Biotechniques, 2004, 36(5): 872-876.
[42] Diaz-Camino C, Risseeuw EP, Liu E, et al. A high-throughput system for two-hybrid screening based on growth curve analysis in microtiter plates[J]. Anal Biochem, 2003, 316(2): 171-174.
[43] Rid R, Herzog J, Maier RH, et al. Real-time monitoring of relative peptide-protein interaction strengths in the yeast two-hybrid system[J]. Assay Drug Dev Technol, 2013, 11(4): 269-275.
[44] Maier RH, Maier CJ, Hintner H, et al. Quantitative real-time PCR as a sensitive protein-protein interaction quantification method and a partial solution for non-accessible autoactivator and false-negative molecule analysis in the yeast two-hybrid system[J]. Methods,2012, 58(4): 376-384.
[45] Lin HY, Lin SE, Chien SF, et al. Electroporation for three commonly used yeast strains for two-hybrid screening experiments[J]. Anal Biochem, 2011, 416(1): 117-119.
[46] Rajagopala SV, Hughes KT, Uetz P. Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins[J].Proteomics, 2009, 9(23): 5296-5302.
[47] Liu Y, Merchant Z, Hsiao HC, et al. Media composition influences yeast one- and two-hybrid results[J]. Biol Proced Online, 2011,13: 6.
[48] Worseck JM, Grossmann A, Weimann M, et al. A stringent yeast two-hybrid matrix screening approach for protein-protein interaction discovery[J]. Methods Mol Biol, 2012, 812: 63-87.
[49] Yoon JM, Nakajima M, Mashiguchi K, et al. Chemical screening of an inhibitor for gibberellin receptors based on a yeast two-hybrid system[J]. Bioorg Med Chem Lett, 2013, 23(4): 1096-1098.
[50] Kim S, Min IM, Ren S, et al. Development of temperature-sensitive mutants of the Drosophila melanogaster P-TEFb(Cyclin T/CDK9) heterodimer using yeast two-hybrid screening[J]. Biochem Biophys Res Commun, 2013, 433(2): 243-248.
[51] Uetz P, Giot L, Cagney G, et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae[J].Nature, 2000, 403(6770): 623-627.
[52] Yu H, Braun P, Yildirim MA, et al. High-quality binary protein interaction map of the yeast interactome network[J]. Science,2008, 322(5898): 104-110.
[53] Giot L, Bader JS, Brouwer C, et al. A protein interaction map of Drosophila melanogaster[J]. Science, 2003, 302(5651): 1727-1736.
[54] Stelzl U, Worm U, Lalowski M, et al. A human protein-protein interaction network: a resource for annotating the proteome[J].Cell, 2005, 122(6): 957-968.
[55] Rual JF, Venkatesan K, Hao T, et al. Towards a proteome-scale map of the human protein-protein interaction network[J]. Nature,2005, 437(7062): 1173-1178.
[56] Simonis N, Rual JF, Carvunis AR, et al. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network[J]. Nat Methods, 2009, 6(1): 47-54.
[57] Bandyopadhyay S, Chiang CY, Srivastava J, et al. A human MAP kinase interactome[J]. Nat Methods, 2010, 7(10): 801-805.
[58] Singh R, Lee MO, Lee JE, et al. Rice mitogen-activated protein kinase interactome analysis using the yeast two-hybrid system[J]. Plant Physiol, 2012, 160(1): 477-487.
[59] Chen JY, Chen WN, Poon KM, et al. Interaction between SARSCoV helicase and a multifunctional cellular protein(Ddx5) revealed by yeast and mammalian cell two-hybrid systems[J].Arch Virol, 2009, 154(3): 507-512.
[60] Silva EM, Conde JN, Allonso D, et al. Mapping the interactions of dengue virus NS1 protein with human liver proteins using a yeast two-hybrid system: identification of C1q as an interacting partner[J]. PLoS One, 2013, 8(3): e57514.
[61] Lopez-Mateo I, Villaronga MA, Llanos S, et al. The transcription factor CREBZF is a novel positive regulator of p53[J]. Cell Cycle, 2012, 11(20): 3887-3895.
[62] Hamdi A, Colas P. Yeast two-hybrid methods and their applications in drug discovery[J]. Trends Pharmacol Sci, 2012, 33(2): 109-118.
[63] Vielemeyer O, Nizak C, Jimenez AJ, et al. Characterization of single chain antibody targets through yeast two hybrid[J]. BMC Biotechnol, 2010, 10: 59.
[64] Ding L, Azam M, Lin YH, et al. Generation of high-affinity fully human anti-interleukin-8 antibodies from its cDNA by two-hybrid screening and affinity maturation in yeast[J]. Protein Sci, 2010,19(10): 1957-1966.
[65] Urano E, Kuramochi N, Ichikawa R, et al. Novel postentry inhibitor of human immunodeficiency virus type 1 replication screened by yeast membrane-associated two-hybrid system[J]. Antimicrob Agents Chemother, 2011, 55(9): 4251-4260.
[66] Fields S. Interactive learning: lessons from two hybrids over two decades[J]. Proteomics, 2009, 9(23): 5209-5213.