Studying the interactome with the yeast two-hybrid system and mass spectrometry

Mass Spectrometry Reviews

Volumn 23, Issue 5, 2004, Pages 350-367

  Causier, Barry ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

Interactome; Mass spectrometry; Protein protein interaction; Proteomics; Yeast two hybrid

Indexed keywords

CELLS; DATA REDUCTION; GENES; ISOTOPES; MASS SPECTROMETRY; PHYSIOLOGY; YEAST;

INTERACTOMES; PROTEIN-PROTEIN INTERACTION; PROTEOMICS; YEAST TWO-HYBRID;

PROTEINS;

PROTEIN;

ARTICLE; CHEMISTRY; FUNGAL GENE; GENETICS; GENOME; INSTRUMENTATION; MASS SPECTROMETRY; METHODOLOGY; PHYSIOLOGY; PROTEOMICS; YEAST;

GENES, FUNGAL; GENOME; MASS SPECTROMETRY; PROTEINS; PROTEOMICS; YEASTS;

EID: 4444282070     PISSN: 02777037     EISSN: None     Source Type: Journal    
DOI: 10.1002/mas.10080     Document Type: Article

References (80)

1. Aebersold R, Mann M. 2003. Mass spectrometry-based proteomics. Nature 422:198-207.
2. Aronheim A, Zandi E, Hennemann H, Elledge SJ, Karin M. 1997. Isolation of an AP-1 repressor by a novel method for detecting Badeprotein-protein interactions. Mol Cell Biol 17: 3094-3102.
3. Auerbach D, Thaminy S, Hottiger MO, Stagljar I. 2002. The post-genomic era of interactive proteomics: Facts and perspectives. Proteomics 2:611-623.
4. Bader GD, Betel D, Hogue CWV. 2003. BIND: The biomolecular interaction network database. Nucleic Acids Res 31:248-250.
5. Bader GD, Hogue CWV. 2002. Analysing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 20:991-997.
6. Bartel PL, Roecklein JA, SenGupta D, Fields S. 1996. A protein linkage map of Escherichia coli bacteriophage T7. Nat Genet 12:72-77.
7. Bauer A, Kuster B. 2003. Affinity purification-mass spectrometry. Eur J Biochem 270:570-578.
8. Blagoev B, Kratchmarova I, Ong S-E, Nielsen M, Foster LJ, Mann M. 2003. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol 21:315-318.
9. Brent R, Finley RL. 1997. Understanding gene and allele function with two-hybrid methods. Annu Rev Genet 31:663-704.
10. Brent R, Ptashne M. 1984. A bacterial repressor protein or a yeast transcriptional terminator can block upstream activation of a yeast gene. Nature 312:612-615.
11. Brent R, Ptashne M. 1985. A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor. Cell 43:729-736.
12. Broder YC, Katz S, Aronheim A. 1998. The Ras recruitment system, a novel approach to the study of protein-protein interactions. Curr Biol 8:1121-1124.
13. Causier B, Davies B. 2002. Analysing protein-protein interactions with the yeast two-hybrid system. Plant Mol Biol 50:855-870.
14. Colas P, Brent R. 1998. The impact of two-hybrid and related methods on biotechnology. Trends Biotechnol 16:355-363.
15. Costanzo MC, Hogan JD, Cusick ME, Davis BP, Fancher AM, Hodges PE, Kondu P, Lengieza C, Lew-Smith JE, Lingner C, Roberg-Perez KJ, Tillberg M, Brooks JE, Garrels JI. 2000. The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): Comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res 28:73-76.
16. Davy A, Bello P, Thierry-Mieg N, Vaglio P, Hitti J, Doucette-Stamm L, Thierry-Mieg D, Reboul J, Boulton S, Walhout AJ, Coux O, Vidal M. 2001. A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome. EMBO Rep 29:821-828.
17. Deng M, Sun F, Chen T. 2003. Assessment of the reliability of protein-protein interactions and protein function prediction. Pac Symp Biocomput 8:140-151.
18. Deshaies RJ, Seol JH, McDonald WH, Cope G, Lyapina S, Shevchenko A, Shevchenko A, Verma R, Yates JR. 2002. Charting the protein complexome in yeast by mass spectrometry. Mol Cell Proteomics 1:3-10.
19. Diaz-Camino C, Risseeuw EP, Liu E, Crosby WL. 2003. A high-throughput system for two-hybrid screening based on growth curve analysis in microtiter plates. Anal Biochem 316:171-174.
20. Ehrhard KN, Jacoby JJ, Fu X-Y, Jahn R, Dohlman HG. 2000. Use of G-protein fusions to monitor integral membrane protein-protein interactions in yeast. Nat Biotechnol 18:1075-1079.
21. Fang Y, Macool DJ, Xue Z, Heppard EP, Hainey CF, Tingey SV, Miao G-H. 2002. Development of a high-throughput yeast two-hybrid screening system to study protein-protein interactions in plants. Mol Genet Genomics 267:142-153.
22. Fashena SJ, Serebriiskii I, Golemis EA. 2000. The continued evolution of two-hybrid screening approaches in yeast: How to outwit different preys with different baits. Gene 250:1-14.
23. Fields S, Song O-K. 1989. A novel genetic system to detect protein-protein interactions. Nature 340:245-246.
24. Fields S, Sternglanz R. 1994. The yeast two-hybrid system: An assay for protein-protein interactions. Trends Genet 10:286-292.
25. Finley RL, Brent R. 1994. Interaction mating reveals binary and ternary connections between Drosophila cell cycle regulators. Proc Natl Acad Sci USA 91:12980-12984.
26. Flajolet M, Rotondo G, Daviet L, Bergametti F, Inchauspe G, Tiollais P, Transy C, Legrain P. 2000. A genomic approach of the hepatitis C virus generates a protein interaction map. Gene 242:369-379.
27. Flores A, Briand JF, Gadal O, Andrau JC, Rubbi L, Van Mullem V, Boschiero C, Goussot M, Marck C, Carles C, Thuriaux P, Sentenac A, Werner M. 1999. A protein-protein interaction map of yeast RNA polymerase III. Proc Natl Acad Sci USA 96:7815-7820.
28. Fromont-Racine M, Rain JC, Legrain P. 1997. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat Genet 16:277-282.
29. Fromont-Racine M, Mayes AE, Brunet-Simon A, Rain JC, Colley A, Dix I, Decourty L, Joly N, Ricard F, Beggs JD, Legrain P. 2000. Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins. Yeast 17:95-110.
30. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147.
31. Ge H, Liu Z, Church G, Vidal M. 2001. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 29:482-486.
32. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG. 1996. Life with 6000 genes. Science 274:546-567.
33. Grigoriev A. 2001. A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res 29:3513-3519.
34. Gyuris J, Golemis E, Chertov H, Brent R. 1993. Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2. Cell 75:791-803.
35. Hink MA, Bisseling T, Visser AJWG. 2002. Imaging protein-protein interactions in living cells. Plant Mol Biol 50:871-883.
36. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183.
37. Hope IA, Struhl K. 1986. Functional dissection of a eukaryotic transcriptional activator protein, GCN4 of yeast. Cell 46:885-894.
38. Huang W, Wang SL, Lozano G, de Crombrugghe B. 2001. cDNA library screening using the SOS recruitment system. Biotechniques 30:94-98.
39. Hubsman M, Yudkovsky G, Aronheim A. 2001. A novel approach for the identification of protein-protein interaction with integral membrane proteins. Nucleic Acids Res 29:e18.
40. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y. 2000. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci USA 97:1143-1147.
41. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98:4569-4574.
42. Ito T, Ota K, Kubota H, Yamaguchi Y, Chiba T, Sakuraba K, Yoshida M. 2002. Roles for the two-hybrid system in exploration of the yeast interactome. Mol Cell Proteomics 1:561-566.
43. Johnsson N, Varshavsky A. 1994. Split ubiquitin as a sensor of protein interactions in vivo. Proc Natl Acad Sci USA 91:10340-10344.
44. Joung JK, Ramm EI, Pabo CO. 2000. A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc Natl Acad Sci USA 97:7382-7387.
45. Keegan L, Gill G, Ptashne M. 1986. Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein. Science 231:699-704.
46. Kumar A, Snyder M. 2002. Protein complexes take the bait. Nature 415:123-124.
47. Leanna CA, Hannink M. 1996. The reverse two-hybrid system: A genetic scheme for selection against specific protein/protein interactions. Nucleic Acids Res 24:3341-3347.
48. Legrain P, Wojcik J, Gauthier J-M. 2001. Protein-protein interaction maps: A lead towards cellular functions. Trends Genet 17:346-352.
49. Lin D, Tabb DL, Yates JR. 2003. Large-scale protein identification using mass spectrometry. Biochim Biophys Acta 1646:1-10.
50. Luo Y, Batalao A, Zhou H, Zhu L. 1997. Mammalian two-hybrid system. A complementary approach to the yeast two-hybrid system. Biotechniques 22:350-352.
51. Ma J, Ptashne M. 1988. Converting a eukaryotic transcriptional inhibitor into an activator. Cell 55:443-446.
52. Maroun M, Aronheim A. 1999. A novel in vivo assay for the analysis of protein-protein interaction. Nucleic Acids Res 27:e4.
53. Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M. 2001. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res 11:2120-2126.
54. McCraith S, Hotzam T, Moss B, Fields S. 2000. Genome-wide analysis of vaccinia virus protein-protein interactions. Proc Natl Acad Sci USA 97:4879-4884.
55. Mewes HW, Frishman D, Gruber C, Geier B, Haase D, Kaps A, Lemcke K, Mannhaupt G, Pfeiffer F, Schuller C, Stocker S, Weil B. 2000. MIPS: A database for genomes and protein sequences. Nucleic Acids Res 28:37-40.
56. Mohler WA, Blau HM. 1996. Gene expression and cell fusion analysed by lacZ complementation in mammalian cells. Proc Natl Acad Sci USA 93:12423-12427.
57. Phizicky E, Bastiaens PIH, Zhu H, Snyder M, Fields S. 2003. Protein analysis on a proteomic scale. Nature 422:208-215.
58. Rain J-C, Selig L, De Reuse H, Battaglia V, Reverdy C, Simon S, Lenzen G, Petel F, Wojcik J, Schächter V, Chemama VY, Labigne A, Legrain P. 2001. The protein-protein interaction map of Helicobacter pylori. Nature 409:211-215.
59. Reboul J, Vaglio P, Ruai JF, Lamesch P, Martinez M, Armstrong CM, Li S, Jacotot L, Bertin N, Janky R, Moore T, Hudson JR, Jr., Hartley JL, Brasch MA, Vandenhaute J, Boulton S, Endress GA, Jenna S, Chevet E, Papasotiropoulos V, Tolias PP, Ptacek J, Snyder M, Huang R, Chance MR, Lee H, Doucette-Stamm L, Hill DE, Vidal M. 2003. C. elegans ORFeome version 1.1: Experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet 34:35-41.
60. Rigaut G, Schevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17:1030-1032.
61. SenGupta DJ, Zhang B, Kraemer B, Pochart P, Fields S, Wickens M. 1996. A three-hybrid system to detect RNA-protein interactions in vivo. Proc Natl Acad Sci USA 93:8496-8501.
62. Serebriiskii I, Khazak V, Gomelis EA. 1999. A two-hybrid dual bait system to discriminate specificity of protein interactions. J Biol Chem 274:17080-17087.
63. Serebriiskii IG, Toby GG, Golemis EA. 2000. Two-hybrid system for the characterization of protein-protein interactions in E. coli. Biotechniques 29:288-296.
64. Sprinzak E, Sattath S, Margalit H. 2003. How reliable are experimental protein-protein interaction data? J Mol Biol 327:919-923.
65. Stagljar I, Korostensky C, Johnsson N, 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 USA 95:5187-5192.
66. Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G. 2002. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295:321-324.
67. Uetz P, Hughes RE. 2000. Systematic and large-scale two-hybrid screens. Curr Opin Microbiol 3:303-308.
68. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627.
69. Van Criekinge W, Beyaert R. 1999. Yeast two-hybrid: State of the art. Biol Proced Online 2:1-38.
70. Varshavsky A. 1997. The ubiquitin system. Trends Biochem Sci 22:383-387.
71. Vidal M, Legrain P. 1999. Yeast forward and reverse 'n'-hybrid systems. Nucleic Acids Res 27:919-929.
72. Vidal M, Brachmann RK, Fattaey A, Harlow E, Boeke JD. 1996. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc Natl Acad Sci USA 93:10315-10320.
73. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. 2002. Comparative assessment of large-scale data sets from protein-protein interactions. Nature 417:399-403.
74. Walhout AJ, Vidal M. 2001. High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24:297-306.
75. Walhout AJM, Sordella R, Lu X, Hartley JL, Temple GF, Brasch MA, Thierry-Mieg N, Vidal M. 2000. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287:116-122.
76. Walhout AJ, Reboul J, Shtanko O, Bertin N, Vaglio P, Ge H, Lee H, Doucette-Stamm L, Gunsalus KC, Schetter AJ, Morton DG, Kemphues KJ, Reinke V, Kim SK, Piano F, Vidal M. 2002. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr Biol 12:1952-1958.
77. Wang MM, Reed RR. 1993. Molecular cloning of the olfactory neuronal transcription factor Olf-1 by genetic selection in yeast. Nature 364:121-126.
78. Wittke S, Lewke N, Muller S, Johnsson N. 1999. Probing the molecular environment of membrane proteins in vivo. Mol Biol Cell 108:2519-2530.
79. Zhang J, Lautar S. 1996. A yeast three-hybrid method to clone ternary protein complex components. Anal Biochem 242:68-72.
80. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M. 2001. Global analysis of protein activities using proteome chips. Science 293:2101-2105.