Deciphering soluble and membrane protein function using yeast systems (Review)

References

• 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. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002; 415: 141–147
   PubMed Web of Science ®Google Scholar
• Wittig I, Braun HP, Schägger H. Blue native PAGE. Nature Protocols 2006; 1: 418–428
   PubMed Web of Science ®Google Scholar
• Akins RE, Levin P, Tuan RS. Cetyltrimethylammonium bromide discontinuous gel electrophoresis: Mr-based separation of proteins with retention of enzymatic activity. Anal Biochem 1992; 202: 172–178
   PubMed Web of Science ®Google Scholar
• Drewes G, Bouwmeester T. Global approaches to protein-protein interactions. Curr Opin Cell Biol 2003; 15: 199–205
   PubMed Web of Science ®Google Scholar
• Vasilescu J, Figeys D. Mapping protein-protein interactions by mass spectrometry. Curr Opin Biotechnol 2006; 17: 394–399
   Google Scholar
• Hultschig C, Kreutzberger J, Seitz H, Konthur Z, Bussow K, Lehrach H. Recent advances of protein microarrays. Curr Opin Chem Biol 2006; 10: 4–10
   PubMed Web of Science ®Google Scholar
• Brachmann RK, Boeke JD. Tag games in yeast: the two-hybrid system and beyond. Curr Opin Biotechnol 1997; 8: 561–568
   PubMedGoogle Scholar
• Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D. DIP: the database of interacting proteins: 2001 update. Nucleic Acids Res 2001; 29: 239–241
   PubMed Web of Science ®Google Scholar
• Fields S, Song OK. A novel genetic system to detect protein-protein interactions. Nature 1989; 340: 245–246
   PubMed Web of Science ®Google Scholar
• Wallach D, Boldin MP, Kovalenko AV, Malinin NL, Mett IL, Camonis JH. The yeast two-hybrid screening technique and its use in the study of protein-protein interactions in apoptosis. Curr Opin Immunol 1998; 10: 131–136
   PubMedGoogle Scholar
• Chien CT, Bartel PL, 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 1991; 88: 9578–9582
   PubMed Web of Science ®Google Scholar
• Wallin E, von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 1998; 7: 1029–1038
   PubMed Web of Science ®Google Scholar
• Muller DJ, Wu N, Palczewski K. Vertebrate membrane proteins: structure, function, and insights from biophysical approaches. Pharmacol Rev 2008; 60: 43–78
   PubMed Web of Science ®Google Scholar
• Reiss T. Drug discovery of the future: the implications of the human genome project. Trends Biotechnol 2001; 19: 496–499
   Google Scholar
• Stagljar I, Fields S. Analysis of membrane protein interactions using yeast-based technologies. Trends Biochem Sci 2002; 27: 559–563
   PubMed Web of Science ®Google Scholar
• Aronheim A, Engelberg D, Li NX, Alalawi N, Schlessinger J, Karin M. Membrane targeting of the nucleotide exchange factor Sos is sufficient for activating the Ras signaling pathway. Cell 1994; 78: 949–961
   PubMed Web of Science ®Google Scholar
• Broder YC, Katz S, Aronheim A. The Ras recruitment system, a novel approach to the study of protein-protein interactions. Curr Biol 1998; 8: 1121–1124
   PubMed Web of Science ®Google Scholar
• Aronheim A. Protein recruitment systems for the analysis of protein +/( protein interactions. Methods 2001; 24: 29–34
   PubMedGoogle Scholar
• Hubsman M, Yudkovsky G, Aronheim A. A novel approach for the identification of protein-protein interaction with integral membrane proteins. Nucl Acids Res 2001; 29: e18
   PubMedGoogle Scholar
• 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 1998; 17: 5374–5387
   PubMed Web of Science ®Google Scholar
• Aronheim A, Zandi E, Hennemann H, Elledge SJ, Karin M. Isolation of an AP-1 repressor by a novel method for detecting protein-protein interactions. Mol Cell Biol 1997; 17: 3094–3102
   PubMed Web of Science ®Google Scholar
• Ehrhard KN, Jacoby JJ, Fu XY, Jahn R, Dohlman HG. Use of G-protein fusions to monitor integral membrane protein-protein interactions in yeast. Nat Biotechnol 2000; 18: 1075–1079
   PubMed Web of Science ®Google Scholar
• Johnsson N, Varshavsky A. Split ubiquitin as a sensor of protein of protein interactions in-vivo. Proc Natl Acad Sci USA 1994; 91: 10340–10344
   PubMed Web of Science ®Google Scholar
• Mockli N, Deplazes A, Hassa PO, Zhang ZL, Peter M, Hottiger MO, Stagljar I, Auerbach D. Yeast split-ubiquitin-based cytosolic screening system to detect interactions between transcriptionally active proteins. Biotechniques 2007; 42: 725–730
   PubMed Web of Science ®Google Scholar
• Stagljar I, Korostensky C, Johnsson N, Heesen S. A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. Proc Natl Acad Sci USA 1998; 95: 5187–5192
   PubMed Web of Science ®Google Scholar
• Reinders A, Schulze W, Thaminy S, Stagljar I, Frommer WB, Ward JM. Intra- and intermolecular interactions in sucrose transporters at the plasma membrane detected by the split-ubiquitin system and functional assays. Structure 2002; 10: 763–772
   PubMed Web of Science ®Google Scholar
• Massaad MJ, Herscovics A. Interaction of the endoplasmic reticulum alpha 1,2-mannosidase Mns1p with Rer1p using the split-ubiquitin system. J Cell Sci 2001; 114: 4629–4635
   PubMedGoogle Scholar
• Paumi CM, Menendez J, Arnoldo A, Engels K, Iyer KR, Thaminy S, Georgiev O, Barral Y, Michaelis S, Stagljar I. Mapping protein-protein interactions for the yeast ABC transporter Ycf1p by integrated split-ubiquitin membrane yeast two-hybrid analysis. Mol Cell 2007; 26: 15–25
   PubMed Web of Science ®Google Scholar
• Thaminy S, Auerbach D, Arnoldo A, Stagljar I. Identification of novel ErbB3-interacting factors using the split-ubiquitin membrane yeast two-hybrid system. Genome Res 2003; 13: 1744–1753
   PubMed Web of Science ®Google Scholar
• Vitale R, Buxbaum JD. Use of the split-ubiquitin two-hybrid system to identify proteins interacting with the Alzheimer proteins APP and LRP. Biol Bull 2004; 207: 167
   Google Scholar
• Matsuda S, Giliberto L, Matsuda Y, Davies P, McGowan E, Pickford F, Ghiso J, Frangione B, D'Adamio L. The familial dementia BRI2 gene binds the Alzheimer gene amyloid-beta precursor protein and inhibits amyloid-beta production. J Biol Chem 2005; 280: 28912–28916
   PubMed Web of Science ®Google Scholar
• Obrdlik P, El-Bakkoury M, Hamacher T, Cappellaro C, Vilarino C, Fleischerf C, Ellerbrok H, Kamuzinzih R, Ledenth V, Blaudezi D, Sandersi D, Revuelta JL, Boles E, André B, Frommer WB. K+ channel interactions detected by a genetic system optimized for systematic studies of membrane protein interactions. Proc Natl Acad Sci USA 2004; 101: 12242–12247
   PubMed Web of Science ®Google Scholar
• Dirnberger D, Messerschmid M, Baumeister R. An optimized split-ubiquitin cDNA-library screening system to identify novel interactors of the human Frizzled 1 receptor. Nucleic Acids Res 2008; 36: e37
   PubMedGoogle Scholar
• Yarden Y, Shilo B. SnapShot: EGFR signaling pathway. Cell 2007; 131: 1018
   PubMed Web of Science ®Google Scholar
• Birge RB, Knudsen BS, Besser D, Hanafusa H. SH2 and SH3-containing adaptor proteins: redundant or independent mediators of intracellular signal transduction. Genes Cells 1996; 1: 595–613
   PubMedGoogle Scholar
• Zhang J, Lautar S. A yeast three-hybrid method to clone ternary protein complex components. Anal Biochem 1996; 242: 68–72
   PubMedGoogle Scholar
• Ozenberger BA, Young KH. Functional interaction of ligands and receptors of the hematopoietic superfamily in yeast. Mol Endocrinol 1995; 9: 1321–1329
   PubMedGoogle Scholar
• Crouin C, Arnaud M, Gesbert F, Camonis J, Bertoglio J. A yeast two-hybrid study of human p97/Gab2 interactions with its SH2 domain-containing binding partners. FEBS Lett 2001; 495: 148–153
   PubMedGoogle Scholar
• Osborne MA, Dalton S, Kochan JP. The yeast tribrid system – genetic detection of trans-phosphorylated ITAM-SH2-interactions. Biotechnology 1995; 13: 1474–1478
   PubMedGoogle Scholar
• Dudkina AS, Lindsley CW. Small molecule protein-protein inhibitors for the p53-MDM2 interaction. Curr Top Med Chem 2007; 7: 952–960
   PubMed Web of Science ®Google Scholar
• Vassilev LT. MDM2 inhibitors for cancer therapy. Trends Mol Med 2007; 13: 23–31
   PubMed Web of Science ®Google Scholar
• Ishi K, Sugawara F. A facile method to screen inhibitors of protein-protein interactions including MDM2-p53 displayed on T7 phage. Biochem Pharmacol 2008; 75: 1743–1750
   Google Scholar
• Vidal M, Brachmann RK, Fattaey A, Harlow E, Boeke JD. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc Natl Acad Sci USA 1996; 93: 10315–10320
   PubMed Web of Science ®Google Scholar
• Huang J, Schreiber SL. A yeast genetic system for selecting small molecule inhibitors of protein-protein interactions in nanodroplets. Proc Natl Acad Sci USA 1997; 94: 13396–13401
   PubMed Web of Science ®Google Scholar
• Henthorn DC, Jaxa-Chamiec AA, Meldrum E. A GAL4-based yeast three-hybrid system for the identification of small molecule-target protein interactions. Biochem Pharmacol 2002; 63: 1619–1628
   PubMed Web of Science ®Google Scholar
• Dirnberger D, Unsin G, Schlenker S, Reichel C. A small-molecule-protein interaction system with split-ubiquitin as sensor. Chembiochem 2006; 7: 936–942
   PubMedGoogle Scholar
• Auerbach D, Thaminy S, Hottiger MO, Stagljar I. The post-genomic era of interactive proteomics: facts and perspectives. Proteomics 2002; 2: 611–623
   PubMed Web of Science ®Google Scholar
• McCraith S, Holtzman T, Moss B, Fields S. Genome-wide analysis of vaccinia virus protein-protein interactions. Proc Natl Acad Sci USA 2000; 97: 4879–4884
   PubMed Web of Science ®Google Scholar
• Rain JC, Selig L, De Reuse H, Battaglia V, Reverdy C, Simon S, Lenzen G, Petel F, Wojcik J, Schachter V, Chemama Y, Labigne A, Legrain P. The protein-protein interaction map of Helicobacter pylori. Nature 2001; 409: 211–215
   PubMed Web of Science ®Google Scholar
• Miller JP, Lo RS, Ben-Hur A, Desmarais C, Stagljar I, Noble WS, Fields S. Large-scale identification of yeast integral membrane protein interactions. Proc Natl Acad Sci USA 2005; 102: 12123–12128
   PubMed Web of Science ®Google Scholar
• Golemis EA, Serebriiskii I, Law SF. The yeast two-hybrid system: criteria for detecting physiologically significant protein-protein interactions. Curr Issues Mol Biol 1999; 1: 31–45
   Google Scholar
• Serebriiskii I, Estojak J, Berman M, Golemis EA. Approaches to detecting false positives in yeast two-hybrid systems. Biotechniques 2000; 28: 328–330
   PubMed Web of Science ®Google Scholar
• Piehler J. New methodologies for measuring protein interactions in vivo and in vitro. Curr Opin Struct Biol 2005; 15: 4–14
   PubMed Web of Science ®Google Scholar
• Villalobos V, Naik S, Piwnica-Worms D. Current state of imaging protein-protein interactions in vivo with genetically encoded reporters. Annu Rev Biomed Eng 2007; 9: 321–349
   PubMed Web of Science ®Google Scholar
• Nyfeler B, Michnick SW, Hauri H-P. Capturing protein interactions in the secretory pathway of living cells. Proc Natl Acad Sci USA 2005; 102: 6350–6355
   PubMed Web of Science ®Google Scholar
• Lim RP, Misra A, Wu Z, Thanabalu T. Analysis of conformational changes in WASP using a split YFP. Biochem Biophys Res Commun 2007; 362: 1085–1089
   PubMed Web of Science ®Google Scholar
• Barnard E, McFerran NV, Trudgett A, Nelson J, Timson DJ. Development and implementation of split-GFP-based bimolecular fluorescence complementation (BiFC) assays in yeast. Biochem Soc Trans 2008; 36: 479–482
   Google Scholar
• Blume-Jensen P, Hunter T. Oncogenic kinase signalling. Nature 2001; 411: 355–365
   PubMed Web of Science ®Google Scholar