The continued evolution of two-hybrid screening approaches in yeast: How to outwit different preys with different baits

Gene

Volumn 250, Issue 1-2, 2000, Pages 1-14

  Fashena, Sarah J ^a   Serebriiskii, Ilya ^a   Golemis, Erica A ^a  

^a FOX CHASE CANCER CENTER   (United States)

Author keywords

Gal4p and LexA; Protein interaction; S. cerevisiae

Indexed keywords

PROTEIN; TRANSCRIPTION FACTOR;

ANALYTIC METHOD; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; REACTION ANALYSIS; REVIEW; SACCHAROMYCES CEREVISIAE;

ANIMALS; HUMANS; PROTEIN BINDING; RECOMBINANT FUSION PROTEINS; SACCHAROMYCES CEREVISIAE; TWO-HYBRID SYSTEM TECHNIQUES;

SACCHAROMYCES CEREVISIAE;

EID: 0034732963     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(00)00182-7     Document Type: Review

References (94)

1. Aronheim A. Improved efficiency sos recruitment system: expression of the mammalian GAP reduces isolation of Ras GTPase false positives. Nucleic Acids Res. 25:1997;3373-3374.
2. Aronheim A., Zandi E., Hennemann H., Elledge S.J., Karin M. Isolation of an AP-1 repressor by a novel method for detecting protein-protein interactions. Mol. Cell. Biol. 17:1997;3094-3102.
3. Aronheim A., Broder Y.C., Cohen A., Fritsch A., Belisle B., Abo A. Chp, a homologue of the GTPase Cdc42Hs, activates the JNK pathway and is implicated in reorganizing the actin cytoskeleton. Curr. Biol. 8:1998;1125-1128.
4. Bartel P.L., Fields S. Analyzing protein-protein interactions using two-hybrid system. Methods Enzymol. 254:1995;241-263.
5. Bartel P., Fields S. The Yeast Two-hybrid System: A Practical Approach. 1997;Oxford University Press, New York.
6. Bartel P.L., Roecklein J.A., SenGupta D., Fields S. A protein linkage map of Escherichia coli bacteriophage T7. Nature Genet. 12:1996;72-77.
7. Bendixen C., Gangloff S., Rothstein R. A yeast mating-selection scheme for detection of protein-protein interactions. Nucleic Acids Res. 22:1994;1778-1779.
8. Botstein D., Chervitz S.A., Cherry J.M. Yeast as a model organism. Science. 277:1997;1259-1260.
9. Broder Y.C., Katz S., Aronheim A. The ras recruitment system, a novel approach to the study of protein-protein interactions. Curr. Biol. 8:1998;1121-1124.
10. Buckholz R.G., Simmons C.A., Stuart J.M., Weiner M.P. Automation of yeast two-hybrid screening. J. Mol. Microbiol. Biotechnol. 1:1999;135-140.
11. Chang E.C., Barr M., Wang Y., Jung V., Xu H.P., Wigler M.H. Cooperative interaction of S. pombe proteins required for mating and morphogenesis. Cell. 79:1994;131-141.
12. Chervitz S.A., Aravind L., Sherlock G., Ball C.A., Koonin E.V., Dwight S.S., Harris M.A., Dolinski K., Mohr S., Smith T., Weng S., Cherry J.M., Botstein D. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science. 282:1998;2022-2028.
13. Chevray P.M., Nathans D. Protein interaction cloning in yeast: identification of mammalian proteins that react with the leucine zipper of Jun. Proc. Natl. Acad. Sci. USA. 89:1992;5789-5793.
14. Chien C.T., Bartel P.L., Sternglanz R., Fields S. 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. 88:1991;9578-9582.
15. Chiu M.I., Katz H., Berlin V. RAPT1, a mammalian homolog of yeast Tor, interacts with the FKBP12/rapamycin complex. Proc. Natl. Acad. Sci. USA. 91:1994;12 574-12 578.
16. Cho R.J., Fromont-Racine M., Wodicka L., Feierbach B., Stearns T., Legrain P., Lockhart D.J., Davis R.W. Parallel analysis of genetic selections using whole genome oligonucleotide arrays. Proc. Natl. Acad. Sci. USA. 95:1998;3752-3757.
17. Chong J.A., Tapia-Ramirez J., Kim S., Toledo-Aral J.J., Zheng Y., Boutros M.C., Altshuler Y.M., Frohman M.A., Kraner S.D., Mandel G. REST: a mammalian silencer protein that restricts sodium channel expression to neurons. Cell. 80:1995;949-957.
18. Colas P., Cohen B., Jessen T., Grishina I., McCoy J., Brent R. Genetic selection of peptide aptamers that recognize and inhibit cyclin-dependent kinase 2. Nature. 380:1996;548-550.
19. Dalton S., Treisman R. Characterization of SAP-1, a protein recruited by serum response factor to the c-fos serum response element. Cell. 68:1992;597-612.
20. Dowell S.J., Romanowski P., Diffley J.F. Interaction of Dbf4, the Cdc7 protein kinase regulatory subunit, with yeast replication origins in vivo. Science. 265:1994;1243-1246.
21. Drees B.L. Progress and variations in two-hybrid and three-hybrid technologies. Curr. Opin. Chem. Biol. 3:1999;64-70.
22. Du W., Vidal M., Xie J.E., Dyson N. RBF, a novel RB-related gene that regulates E2F activity and interacts with cyclin E in Drosophila. Genes Dev. 10:1996;1206-1218.
23. Dunnwald M., Varshavsky A., Johnsson N. Detection of transient in vivo interactions between substrate and transporter during protein translocation into the endoplasmic reticulum. Mol. Biol. Cell. 10:1999;329-344.
24. Durfee T., Becherer K., Chen P.L., Yeh S.H., Yang Y., Kilburn A.E., Lee W.H., Elledge S.J. The retinoblastoma protein associates with the protein phosphatase type 1 catalytic subunit. Genes Dev. 7:1993;555-569.
25. Estojak J., Brent R., Golemis E.A. Correlation of two-hybrid affinity data with in vitro measurements. Mol. Cell. Biol. 15:1995;5820-5829.
26. Fields S., Song O. A novel genetic system to detect protein-protein interaction. Nature. 340:1989;245-246.
27. Finley R., Brent R. Interaction mating reveals binary and ternary connections between Drosophila cell cycle regulators. Proc. Natl. Acad. Sci. USA. 91:1994;12 980-12 984.
28. Frederickson R.M. Macromolecular matchmaking: advances in two-hybrid and related technologies. Curr. Opin. Biotechnol. 9:1998;90-96.
29. Fromont-Racine M., Rain J.-C., Legrain P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet. 16:1997;277-282.
30. Geyer C.R., Colman-Lerner A., Brent R. Mutagenesis by peptide aptamers identifies genetic network members and pathway connections. Proc. Natl. Acad. Sci. USA. 96:1999;8567-8572.
31. Grossel M.J., Wang H., Gadea B., Yeung W., Hinds P.W. A yeast two-hybrid system for discerning differential interactions using multiple baits. Nature Biotechnol. 17:1999;1232-1233.
32. Gyuris J., Golemis E.A., Chertkov H., Brent R. Cdi1 a human G1 and S phase protein phosphatase that associates with Cdk2. Cell. 75:1993;791-803.
33. Hansson L.O., Widersten M., Mannervik B. An approach to optimizing the active site in a glutathione transferase by evolution in vitro. Biochem. J. 344:1999;93-100.
34. Hua S.B., Luo Y., Qiu M., Chan E., Zhou H., Zhu L. Construction of a modular yeast two-hybrid cDNA library from human EST clones for the human genome protein linkage map. Gene. 215:1998;143-152.
35. Huang J., Schreiber S.L. A yeast genetic system for selecting small molecule inhibitors of protein-protein interactions in nanodroplets. Proc. Natl. Acad. Sci. USA. 94:1997;13 396-13 401.
36. Hudson J.R. Jr., Dawson E.P., Rushing K.L., Jackson C.H., Lockshon D., Conover D., Lanciault C., Harris J.R., Simmons S.J., Rothstein R., Fields S. The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form. Genome Res. 7:1997;1169-1173.
37. Inouye C., Remondelli P., Karin M., Elledge S. Isolation of a cDNA encoding a metal response element binding protein using a novel expression cloning procedure: the one hybrid system. DNA Cell Biol. 13:1994;731-742.
38. Inouye C., Dhillon N., Durfee T., Zambryski P.C., Thorner J. Mutational analysis of STE5 in the yeast Saccharomyces cerevisiae: application of a differential interaction trap assay for examining protein-protein interactions. Genetics. 147:1997;479-492.
39. Isakoff S.J., Cardozo T., Andreev J., Li Z., Ferguson K.M., Abagyan R., Lemmon M.A., Aronheim A., Skolnik E.Y. Identification and analysis of PH domain-containing targets of phosphatidylinositol 3-kinase using a novel in vivo assay in yeast. EMBO J. 17:1998;5374-5387.
40. Ishioka C., Frebourg T., Yan Y.X., Vidal M., Friend S.H., Schmidt S., Iggo R. Screening patients for heterozygous p53 mutations using a functional assay in yeast. Nature Genet. 5:1993;124-129.
41. Jaeger L., Wright M.C., Joyce G.F. A complex ligase ribozyme evolved in vitro from a group I ribozyme domain. Proc. Natl. Acad. Sci. USA. 96:1999;14 712-14 717.
42. Jiang R., Carlson M. Glucose regulates protein interactions within the yeast SNF1 protein kinase complex. Genes Dev. 10:1996;3105-3115.
43. Johnsson N., Varshavsky A. Split ubiquitin as a sensor of proteins interactions in vivo. Proc. Natl. Acad. Sci. USA. 91:1994;10 340-10 344.
44. Kolaczkowski M., Kolaczowska A., Luczynski J., Witek S., Goffeau A. In vivo characterization of the drug resistance profile of the major ABC transporters and other components of the yeast pleiotropic drug resistance network. Microbiol. Drug Resist. 4:1998;143-158.
45. Kornbluth S., Jove R., Hanafusa H. Characterization of avian and viral p60src proteins expressed in yeast. Proc. Natl. Acad. Sci. USA. 84:1987;4455-4459.
46. Lee J.W., Choi H.S., Gyuris J., Brent R., Moore D.D. Two classes of proteins dependent on either the presence or absence of thyroid hormone for interaction with the thyroid hormone receptor. Mol. Endocrinol. 9:1995;243-254.
47. Li J.J., Herskowitz I. Isolation of ORC6, a component of the yeast origin recognition complex by a one-hybrid system. Science. 262:1993;1870-1874.
48. Licitra E.J., Liu J.O. A three-hybrid system for detecting small ligand-protein receptor interactions. Proc. Natl. Acad. Sci. USA. 93:1996;12 817-12 821.
49. Ma J., Ptashne M. Converting a eukaryotic transcriptional inhibitor into an activator. Cell. 55:1988;443-446.
50. Marsolier M.C., Sentenac A. RNA polymerase III-based two-hybrid system. Methods Enzymol. 303:1999;411-422.
51. Marsolier M.C., Prioleau M.N., Sentenac A. A RNA polymerase III-based two-hybrid system to study RNA polymerase II transcriptional regulators. J. Mol. Biol. 268:1997;243-249.
52. Marykwas D.L., Passmore S.E. Mapping by multifragment cloning in vivo. Proc. Natl. Acad. Sci. USA. 92:1995;11 701-11 705.
53. Mendelsohn A.R., Brent R. Applications of interaction traps/two-hybrid systems to biotechnology research. Curr. Opin. Biotechnol. 5:1994;482-486.
54. Naya F.J., Stellrecht C.M.M., Tsai M.-J. Tissue-specific regulation of the insulin gene by a novel basic helix-loop-helix transcription factor. Genes Dev. 9:1995;1009-1019.
55. Norman T.C., Smith D.L., Sorger P.K., Drees B.L., O'Rourke S.M., Hughes T.R., Roberts C.J., Friend S.H., Fields S., Murray A.W. Genetic selection of peptide inhibitors of biological pathways. Science. 285:1999;591-595.
56. Osborne M., Dalton S., Kochan J.P. The yeast tribrid system: genetic detection of trans-phosphorylated ITAM-SH2 interactions. Bio/Technol. 13:1995;1474-1478.
57. Osborne M.A., Zenner G., Lubinus M., Zhang X., Songyang Z., Cantley L.C., Majerus P., Burn P., Kochan J.P. The inositol 5′-phosphatase SHIP binds to immunoreceptor signaling motifs and responds to high affinity IgE receptor aggregation. J. Biol. Chem. 271:1996;29 271-29 278.
58. Ozenberger B.A., Young K.H. Functional interaction of ligands and receptors of the hematopoietic superfamily in yeast. Mol. Endocrinol. 9:1995;1321-1329.
59. Park Y.W., Tan S.L., Katze M.G. Differential sensitivity to 5-fluoro-orotic acid as a screen for bait RNA-independent false positives in a yeast three-hybrid system. Biotechniques. 26:1999;1102-1106.
60. Park Y.W., Wilusz J., Katze M.G. Regulation of eukaryotic protein synthesis: selective influenza viral mRNA translation is mediated by the cellular RNA-binding protein GRSF-1. Proc. Natl. Acad. Sci. USA. 96:1999;6694-6699.
61. Pause A., Peterson B., Schaffar G., Stearman R., Klausner R.D. Studying interactions of four proteins in the yeast two-hybrid system: structural resemblance of the pVHL/elongin BC/hCUL-2 complex with the ubiquitin ligase complex SKP1/cullin/F-box protein. Proc. Natl. Acad. Sci. USA. 96:1999;9533-9538.
62. Polyak K., Lee M.H., Erdjument-Bromage H., Koff A., Roberts J.M., Tempst P., Massague J. Cloning of p27Kip1, a cyclin-dependent kinase inhibitor and a potential mediator of extracellular antimitogenic signals. Cell. 78:1994;59-66.
63. Putz U., Skehel P., Kuhl D. A tri-hybrid system for the analysis and detection of RNA-protein interactions. Nucleic Acids Res. 24:1996;4838-4840.
64. Schwartz H., Alvares C.P., White M.B., Fields S. Mutation detection by a two-hybrid assay. Human Mol. Genet. 7:1998;1029-1032.
65. SenGupta D.J., Zhang B., Kraemer B., Pochart P., Fields S., Wickens M. A three-hybrid system to detect RNA-protein interactions in vivo. Proc. Natl. Acad. Sci. USA. 93:1996;8496-8501.
66. SenGupta D.J., Wickens M., Fields S. Identification of RNAs that bind to a specific protein using the yeast three-hybrid system. Rna. 5:1999;596-601.
67. Serebriiskii I., Khazak V., Golemis E.A. A two-hybrid dual bait system to discriminate specificity of protein interactions. J. Biol. Chem. 274:1999;17 080-17 087.
68. Serebriiskii I.G., Mitina O.V., Chernoff J., Golemis E.A. Use of a two-hybrid dual bait system to discriminate specificity of protein interactions in small GTPases. Methods Enzymol. 2000;. in press.
69. Shah N., Klausner R.D. Brefeldin A reversibly inhibits secretion in Saccharomyces cerevisiae. J. Biol. Chem. 268:1993;5345-5348.
70. Shih H.M., Goldman P.S., DeMaggio A.J., Hollenberg S.M., Goodman R.H., Hoekstra M.F. A positive genetic selection for disrupting protein-protein interactions: identification of CREB mutations that prevent association with the coactivator CBP. Proc. Natl. Acad. Sci. USA. 93:1996;13 896-13 901.
71. Stagljar I., Bourquin J.-P., Schaffner W. Use of the two-hybrid system and random sonicated DNA to identify the interaction domain of a protein. Biotechnique. 21:1996;430-432.
72. Stagljar I., Korostensky C., Johnsson N., te Heesen S. A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. Proc. Natl. Acad. Sci. USA. 95:1998;5187-5192.
73. Tirode F., Malaguti C., Romero F., Attar R., Camonis J., Egly J.M. A conditionally expressed third partner stabilizes or prevents the formation of a transcriptional activator in a three-hybrid system. J. Biol. Chem. 272:1997;22 995-22 999.
74. Tomashek J.J., Sonnenburg J.L., Artimovich J.M., Klionsky D.J. Resolution of subunit interactions and cytoplasmic subcomplexes of the yeast vacuolar proton-translocating ATPase. J. Biol. Chem. 271:1996;10 397-10 404.
75. Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P., Qureshi-Emili A., Li Y., Godwin B., Conover D., Kalbfleish T., Vijayadamodar G., Yang M., Johnston M., Fields S., Rothberg J.M. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403:2000;623-627.
76. Van Criekinge W., van Gurp M., Decoster E., Schotte P., Van de Craen M., Fiers W., Vandenabeele P., Beyaert R. Use of the yeast three-hybrid system as a tool to study caspases. Anal. Biochem. 263:1998;62-66.
77. Vidal M., Endoh H. Prospects for drug screening using the reverse two-hybrid system. Trends Biotechnol. 17:1999;374-381.
78. Vidal M., Legrain P. Yeast forward and reverse 'n'-hybrid systems. Nucleic Acids Res. 27:1999;919-929.
79. Vidal M., Brachmann R.K., Fattaey A., Harlow E., Boeke J.D. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc. Natl. Acad. Sci. USA. 93:1996;10 315-10 320.
80. Vidal M., Braun P., Chen E., Boeke J.D., Harlow E. Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system. Proc. Natl. Acad. Sci. USA. 93:1996;10 321-10 326.
81. Vojtek A.B., Hollenberg S.M., Cooper J.A. Mammalian Ras interacts directly with the serine/threonine kinase Raf. Cell. 74:1993;205-214.
82. Walhout A.J., Vidal M. A genetic strategy to eliminate self-activator baits prior to high-throughput yeast two-hybrid screens. Genome Res. 9:1999;1128-1134.
83. Walhout A.J., Sordella R., Lu X., Hartley J.L., Temple G.F., Brasch M.A., Thierry-Mieg N., Vidal M. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science. 287:2000;116-122.
84. Wang M.M., Reed R.R. Molecular cloning of the olfactory neuronal transcription factor Olf-1 by genetic selection in yeast. Nature. 364:1993;121-126.
85. Wang Z.F., Whitfield M.L., Ingledue T.C. III, Dominski Z., Marzluff W.F. The protein that binds the 3′ end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing. Genes Dev. 10:1996;3028-3040.
86. Wilson T.E., Fahrner T.J., Johnston M., Milbrandt J. Identification of the DNA binding site for NGFI-B by genetic selection in yeast. Science. 252:1991;1296-1300.
87. Wolf S.S., Roder K., Schweizer M. Construction of a reporter plasmid that allows expression libraries to be exploited for the one-hybrid system. BioTechniques. 20:1996;568-574.
88. Xu C.W., Mendelsohn A.R., Brent R. Cells that register logical relationships among proteins. Proc. Natl. Acad. Sci. USA. 94:1997;12 473-12 478.
89. Yang M., Wu Z., Fields S. Protein-peptide interactions analyzed with the yeast two-hybrid system. Nucleic Acids Res. 23:1995;1152-1156.
90. Yasugi T., Vidal M., Sakai H., Howley P.M., Benson J.D. Two classes of human papillomavirus type 16 E1 mutants suggest pleiotropic conformational constraints affecting E1 multimerization, E2 interaction and interaction with cellular proteins. J. Virol. 71:1997;5942-5951.
91. Young K., Lin S., Sun L., Lee E., Modi M., Hellings S., Husbands M., Ozenberger B., Franco R. Identification of a calcium channel modulator using a high throughput yeast two-hybrid screen. Nature Biotechnol. 16:1998;946-950.
92. Yu X., Wu L.C., Bowcock A.M., Aronheim A., Baer R. The C-terminal (BRCT) domains of BRCA1 interact in vivo with CtIP, a protein implicated in the CtBP pathway of transcriptional repression. J. Biol. Chem. 273:1998;25 388-25 392.
93. Yu Y., Yussa M., Song J., Hirsch J., Pick L. A double interaction screen identifies positive and negative ftz gene regulators and ftz-interacting proteins. Mech. Dev. 83:1999;95-105.
94. Zhang J., Lautar S. A yeast three-hybrid method to clone ternary protein complex components. Anal. Biochem. 242:1996;68-72.