Progress and variations in two-hybrid and three-hybrid technologies

Current Opinion in Chemical Biology

Volumn 3, Issue 1, 1999, Pages 64-70

  Drees, Becky L ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN DNA INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; REVIEW; SACCHAROMYCES CEREVISIAE;

EID: 0032983270     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(99)80012-X     Document Type: Article

References (47)

1. Fields S, Song O A novel genetic system to detect protein-protein interactions. Nature. 340:1989;245-246.
2. Sadowski I, Ma J, Triezenberg S, Ptashne M GAL4-VP16 is an unusually potent transcriptional activator. Nature. 335:1988;245-249.
3. Chien CT, Bartel, 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.
4. Tirode F, Malaguti C, Romero F, Attar R, Camonis J, Egly JM A conditionally expressed third partner stabilizes or prevents the formation of a transcriptional activator in a three-hybrid system. J Biol Chem. 272:1997;22995-22999. This paper presents a variation on the two-hybrid assay in which a third protein is expressed along with the DNA-binding domain and activation domain fusions. The system can be used to detect third partners that promote or inhibit an interaction.
5. Printen JA, Sprague G Protein-protein interactions in the yeast pheromone response pathway: Ste5p interacts with all members of the MAP kinase cascade. Genetic. 138:1994;609-619.
6. Zhang J, Lautar S A yeast three-hybrid method to clone ternary protein complex components. Anal Biochem. 242:1996;68-72.
7. Tomashek JJ, Sonnenburg JL, Artimorich JM, Klionsky DJ Resolution of subunit interactions and cytoplasmic subcomplexes of the yeast vacuolar proton-translocating ATPase. J Biol Chem. 271:1996;10397-10404.
8. Osborne MA, Dalton S, Kochan JP The yeast tribrid system - genetic detection of trans-phosphorylated ITAM-SH2-interactions. Biotechnology. 13:1995;1474-1478.
9. Vidal M, Brachmann RK, Fattaey A, Harlow E, Boeke JD Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and protein-DNA interactions. Proc Natl Acad Sci USA. 93:1996;10315-10326.
10. Shih H, Goldman PS, DeMaggio AJ, Hollenberg SM, Goodman RH, Hoekstra MF 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;13896-13901.
11. Inoyue C, Dhillon N, Durfee T, Zambryski PC, 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. This paper presents an adaptation of the original two-hybrid system for the study of proteins that interact simultaneously with two partners. Two different DNA-binding domain fusions are present which bind to distinct sites controlling the transcription of two different reporter genes. Interaction of an activation domain fusion protein with each of the DNA-binding domain fusions is detected by selecting for expression of the associated reporter.
12. SenGupta DJ, 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. 94:1996;8496-8501.
13. Martin F, Schaller A, Eglite S, Schumperli D, Muller B The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding protein. EMBO J. 16:1997;769-778.
14. Wang ZF, Whitfield ML, Ingledue TC III, Dominski Z, Marzluff WF 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.
15. Harrington L, McPhail T, Mar V, Zhou W, Oulton R, Bass MB, Arruda I, Robinson MO A mammalian telomerase-associated protein. Science. 275:1997;973-977.
16. Zhang B, Gallegos M, Puoti A, Durkin E, Fields S, Kimble J, Wickens MP A conserved RNA-binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line. Nature. 390:1997;477-484.
17. Bacharach E, Goff SP Binding of the human immunodeficiency virus type 1 Gag protein to the viral RNA encapsidation signal in the yeast three-hybrid system. J Virol. 72:1998;6944-6949.
18. Finley RL, Brent R Interaction mating reveals binary and ternary connections between Drosophila cell cycle regulators. Proc Natl Acad Sci USA. 91:1994;12980-12984.
19. Evangelista C, Lockshon D, Fields S The yeast two-hybrid system: prospects for protein linkage maps. Trends Cell Biol. 6:1996;196-199.
20. Bartel PL, Roecklein JA, SenGupta DJ, Fields S A protein linkage map of Escherichia coli bacteriophage T7. Nat Genet. 12:1996;72-77.
21. Fromont-Racine M, Rain J-C, Legrain P Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat Genet. 6:1997;277-281. Legrain's group describes their strategy for mapping all protein-protein interactions in S. cerevisiae. A genomic library was screened with DNA-binding domain fusions of a small set of related proteins involved in RNA processing. Positives from the first screens that encode probable in vivo interactors are then used as baits in a second round of screens.
22. Bendixen C, Gangloff S, Rothstein R A yeast mating-selection scheme for detection for protein-protein interactions. Nucleic Acids Res. 22:1994;1778-1779.
23. Cho RJ, Fromont-Racine M, Wodicka L, Feierbach B, Stearns T, Legrain P, Lockhart DJ, Davis RW Parallel analysis of genetic selections using whole genome oligonuceotide arrays. Proc Natl Acad Sci USA. 95:1998;3752-3757.
24. Hudson JR, Dawson EP, Rusing KL, Jackson CH, Lockshon D, Conover D, Lanciault C, Harris JR, Simmons SJ, Rothstein R, Fields S The complete set of predicted genes from S. cerevisiae in readily usable form. Genome Res. 7:1998;1169-1173.
25. Marsolier M-C Prioleau M-N, Sentenac A An RNA polymerase III-based two-hybrid system to study RNA polymerase II transcriptional regulators. J Mol Biol. 268:1997;243-249.
26. Johnsson N, Varshavsky A Split ubiquitin as a sensor of protein interactions in vivo. Proc Natl Acad Sci USA. 91:1994;10340-10344.
27. Staglar I, Korostensky C, Johnsson N, TeHeesen 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. The authors describe a membrane-associated version of the split-ubiquitin two-hybrid system. Cleavage of the Cub (carboxy terminal fragment of ubiquitin)-reporter fusion releases a transcription factor, which is then able to enter the nucleus and activate transcription of a reporter gene.
28. Rossi F, Charlton CA, Blau HM Monitoring protein-protein interactions in intact eukaryotic cells by β-galactosidase complementation. Proc Natl Acad Sci USA. 94:1997;8405-8410. Rossi et al. developed a novel two-hybrid assay for protein-protein interactions in mammalian cells. Intracistronic complementation between noninteracting deletion mutants of β-galactosidase can be restored if the fragments are brought together by interaction of protein domains to which they are fused. β-galactosidase activity can be used to directly monitor protein-protein interactions in different cellular locations.
29. Aronheim A, Zandi E, Hanneman H, Elledge SJ, Karin M Isolation of an AP-1 repressor by a novel method for detecting protein-protein interactions. Mol Cell Biol. 17:1997;3094-3102. This paper describes a membrane-associated two-hybrid system in yeast. Interacting protein fusions recruit Sos to the membrane where it stimulates guanyl nucleotide exchange on yeast Ras, rescuing a temperature-sensitive (Ras) mutant. The system was advanced as an alternative for study of proteins interacting with transcriptional activators, but should be particularly useful for membrane-associated proteins, which are often problematic for the original two-hybrid system.
30. Aronheim A Improved efficiency Sos recruitment system: expression of the mammalian GAP reduces isolation of Ras GTPase false positives. Nucleic Acids Res. 25:1998;3373-3374. Aronheim describes improvements to the Sos recruitment system. Addition of a mammalian GTPase-activating protein protein to the system reduces the isolation of Ras false positives in two-hybrid screens.
31. Aronheim A, Engelberg D, Li N, ai-Alawi N, Schlessinger J, Karin M Membrane targeting of the nucleotide exchange factor Sos is sufficient for activating the Ras signaling pathway. Cell. 78:1994;949-961.
32. Isakoff SJ, Cardozo T, Andreev J, Li Z, Ferguson KM, Abagyan R, Lemmon MA, Aronheim A, Skolnik EY 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. Phosphatidylinositol 3-kinase (PI3K) controls a variety of cellular responses by generating 3-phosphoinositide second messengers that activate downstream signaling pathways by binding pleckstrin homology (PH) domain proteins. In this paper, the authors describe a membrane-associated hybrid system to identify PH domain proteins that bind PI3K-generated phosphoinositides. Co-expression of PI3K and a hybrid protein of activated Ras fused to a PH domain that binds the 3-phosphoinosides rescues the temperature-sensitive yeast Ras mutant. This specialized assay demonstrates that membrane-localized hybrid systems can be a powerful tool as they are adapted for the study of a number of specific processes that occur at the cell membrane.
33. Frech M, Andjelkovic M, Ingley E, Reddy KK, Falck JR, Hemmings BA High affinity binding of inositol phosphates and phosphoinositides to the pleckstrin homology domain of RAC/protein kinase B and their influence on kinase activity. J Biol Chem. 272:1997;8474-8481.
34. Medici R, Bianchi E, DiSegni G, Tocchini-Valentini GP Efficient signal transduction by a chimeric yeast-mammalian G protein α subunit Gpa1-Gsα covalently fused to the yeast receptor Ste2. EMBO J. 24:1997;7241-7249.
35. Spencer DM, Wandless TJ, Schreiber SL, Crabtree GR Controlling signal transduction with synthetic ligands. Science. 262:1993;1019-1024.
36. Spencer DM, Bekshaw PJ, Chen L, Ho SN, Randazzo F, Crabtree GR, Schreiber SL Functional analysis of Fas signaling in vivo using synthetic inducers of dimerization. Curr Biol. 6:1996;839-847.
37. Holsinger LJ, Spencer DM, Austin DJ, Schreiber SL, Crabtree GR Signal transduction in T lymphocytes using a conditional allele of Sos. Proc Natl Acad Sci USA. 92:1995;9810-9814.
38. Luo Z, Tzivion G, Belshaw PJ, Vavvas D, Marshall M, Avruch J Oligomerization activates c-Raf-1 through a Ras-dependent mechanism. Nature. 383:1996;181-185.
39. Stockwell BR, Schreiber SL Probing the role of homomeric and heteromeric receptor interactions in TGF-β signaling using small molecule dimerizers. Curr Biol. 8:1998;761-770.
40. Belshaw PJ, Ho SN, Crabtree GR, Schreiber SL Controlling protein association and subcellular localization with a synthetic ligand that induces heterodimerization of proteins. Proc Natl Acad Sci USA. 93:1996;4604-4607.
41. Freiberg RA, Spencer DM, Choate KA, Peng PD, Schreiber SL, Crabtree GR, Khavari PA Specific triggering of the Fas signal transduction pathway in normal human keratinocytes. J Biol Chem. 271:1996;31666-31669.
42. Blau CA, Peterson KR, Drachman JG, Spencer DM A proliferation switch for genetically modified cells. Proc Natl Acad Sci USA. 94:1997;3076-3081.
43. Rivera VM, Clackson T, Natesan S, Pollock R, Amara JF, Keenan T, Magari SR, Philips T, Courage NL, Cerasoli Fet al. A humanized system for pharmacologic control of gene expression. Nat Med. 2:1996;1028-1032.
44. Spencer DM Creating conditional mutations in mammals. Trends Genet. 12:1996;181-187.
45. Licitra EJ, Liu JQ A three-hybrid system for detecting small ligand-protein receptor interactions. Proc Natl Acad Sci USA. 93:1996;12817-12821.
46. Liberles SD, Diver ST, Austin DJ, Schreiber SL Inducible gene expression and protein translocation using nontoxic ligands identified by a mammalian three-hybrid screen. Proc Natl Acad Sci USA. 94:1997;7825-7830. Rapamycin is useful for controlling protein dimerization in vivo because it can interact with two proteins (FK506-binding protein 12 [FKBP12] and FKBP12-rapamycin-associated protein [FRAP]) simultaneously. One limitation on its use is that its binding to native FRAP has an inhibitory effect on cell growth. Liberles et al. addressed this problem by synthesizing an altered form of rapamycin and used a small-molecule three-hybrid system to identify mutations in the ligand-binding domain of FRAP that stabilized binding to the modified rapamycin.
47. Huang J, Schreiber SL A yeast genetic system for selecting small molecule inhibitors of protein-protein interactions in nanodroplets. Proc Natl Acad Sci USA. 95:1998;13396-13401. Huang and Schreiber combined a miniaturized high-throughput screening method with a reverse two-hybrid assay to create a system for selection of small-molecule inhibitors of protein-protein interactions. High local concentrations of ligands were obtained for testing by photochemically controlled release from small beads. Their method used inducible activation domain and DNA-binding domain fusions and antibiotic resistance reporter genes.