Dynamic visualization of expressed gene networks

Journal of Cellular Physiology

Volumn 196, Issue 3, 2003, Pages 419-429

  Remy, Ingrid ^a   Michnick, Stephen W ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; ENZYME INHIBITOR; HORMONE;

ENZYME ACTIVITY; GENE EXPRESSION; GENETIC ORGANIZATION; GENOME; MACROMOLECULE; MOLECULAR INTERACTION; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN FRAGMENT COMPLEMENTATION ASSAY; PROTEIN INTERACTION; REVIEW;

ANIMALS; CLONING, MOLECULAR; GENE EXPRESSION REGULATION; GENETIC COMPLEMENTATION TEST; PROTEIN BINDING; PROTEIN FOLDING; SIGNAL TRANSDUCTION;

EID: 0042268037     PISSN: 00219541     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcp.10328     Document Type: Review

References (67)

1. Alessi DR, Kozlowski MT, Weng QP, Morrice N, Avruch J. 1998. 3-Phosphoinositide-dependent protein kinase 1 (PDK1) phosphorylates and activates the p70 S6 kinase in vivo and in vitro. Curr Biol 8:69-81.
2. Andjelkovic M, Jakubowicz T, Cron P, Ming XF, Han JW, Hemmings BA. 1996. Activation and phosphorylation of a pleckstrin homology domain containing protein kinase (RAC-PK/PKB) promoted by serum and protein phosphatase inhibitors. Proc Natl Acad Sci USA 93:5699-5704.
3. Aruffo A, Seed B. 1987. Molecular cloning of a CD28 cDNA by a high-efficiency COS cell expression system. Proc Natl Acad Sci USA 84:8573-8577.
4. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29.
5. Avruch J. 1998. Insulin signal transduction through protein kinase cascades. Mol Cell Biochem 182:31-48.
6. Belham C, Wu S, Avruch J. 1999. Intracellular signalling: PDK1 - a kinase at the hub of things. Curr Biol 9:R93-R96.
7. Bishop AL, Hall A. 2000. Rho GTPases and their effector proteins. Biochem J 348:241-255.
8. Brown EJ, Albers MW, Shin TB, Ichikawa K, Keith CT, Lane WS, Schreiber SL. 1994. A mammalian protein targeted by G1-arresting rapamycin-receptor complex. Nature 369:756-758.
9. Brunn GJ, Hudson CC, Sekulic A, Williams JM, Hosoi H, Houghton PJ, Lawrence J, Jr., Abraham RT. 1997. Phosphorylation of the translational repressor PHAS-I by the mammalian target of rapamycin. Science 277:99-101.
10. Burnett PE, Barrow RK, Cohen NA, Snyder SH, Sabatini DM. 1998. RAFT1 phosphorylation of the translational regulators p70 S6 kinase and 4E-BP1. Proc Natl Acad Sci USA 95:1432-1437.
11. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 12:323-337.
12. Chen J, Peterson RT, Schreiber SL. 1998. Alpha 4 associates with protein phosphatases 2A, 4, and 6. Biochem Biophys Res Commun 247:827-832.
13. Chou MM, Blenis J. 1996. The 70 kDa S6 kinase complexes with and is activated by the Rho family G proteins Cdc42 and Rac1. Cell 85:573-583.
14. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. 1998. The transcriptional program of sporulation in budding yeast. Science 282:699-705.
15. D'Andrea AD, Lodish HF, Wong GG. 1989. Expression cloning of the murine erythropoietin receptor. Cell 57:277-285.
16. Di Como CJ, Arndt KT. 1996. Nutrients, via the Tor proteins, stimulate the association of Tap42 with type 2A phosphatases. Genes Dev 10:1904-1916.
17. Diggle TA, Moule SK, Avison MB, Flynn A, Foulstone EJ, Proud CG, Denton RM. 1996. Both rapamycin-sensitive and -insensitive pathways are involved in the phosphorylation of the initiation factor-4E-binding protein (4E-BP1) in response to insulin in rat epididymal fat-cells. Biochem J 316:447-453.
18. Drees BL. 1999. Progress and variations in two-hybrid and three-hybrid technologies. Curr Opin Chem Biol 3:64-70.
19. Dufner A, Andjelkovic M, Burgering BM, Hemmings BA, Thomas G. 1999. Protein kinase B localization and activation differentially affect S6 kinase 1 activity and eukaryotic translation initiation factor 4E-binding protein 1 phosphorylation. Mol Cell Biol 19:4525-4534.
20. Fadden P, Haystead TA, Lawrence J, Jr. 1997. Identification of phosphorylation sites in the translational regulator, PHAS-I, that are controlled by insulin and rapamycin in rat adipocytes. J Biol Chem 272:10240-10247.
21. Fambrough D, McClure K, Kazlauskas A, Lander ES. 1999. Diverse signaling pathways activated by growth factor receptors induce broadly overlapping, rather than independent, sets of genes. Cell 97:727-741.
22. Gingras AC, Kennedy SG, O'Leary MA, Sonenberg N, Hay N. 1998. 4E-BP1, a repressor of mRNA translation, is phosphorylated and inactivated by the Akt(PKB) signaling pathway. Genes Dev 12:502-513.
23. Gingras AC, Gygi SP, Raught B, Palakiewicz RD, Abraham RT, Hoekstra MF, Aebersold R, Sonenberg N. 1999. Regulation of 4E-BP1 phosphorylation: A novel two-step mechanism. Genes Dev 13:1422-1437.
24. Halse R, Rochford JJ, McCormack JG, Vandenheede JR, Hemmings BA, Yeaman SJ. 1999. Control of glycogen synthesis in cultured human muscle cells. J Biol Chem 274:776-780.
25. Hardwick JS, Kuruvilla FG, Tong JK, Shamji AF, Schreiber SL. 1999. Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins. Proc Natl Acad Sci USA 96:14866-14870.
26. Heesom KJ, Avison MB, Diggle TA, Denton RM. 1998. Insulin-stimulated kinase from rat fat cells that phosphorylates initiation factor 4E-binding protein 1 on the rapamycin-insensitive site (serine-111). Biochem J 336:39-48.
27. Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95:717-728.
28. Hosoi H, Dilling MB, Shikata T, Liu LN, Shu L, Ashmun RA, Germain GS, Abraham RT, Houghton PJ. 1999. Rapamycin causes poorly reversible inhibition of mTOR and induces p53-independent apoptosis in human rhabdomyosarcoma cells. Cancer Res 59:886-894.
29. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, et al. 2000a. Functional discovery via a compendium of expression profiles. Cell 102:109-126.
30. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, et al. 2000b. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19:342-347.
31. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292:929-934.
32. Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee J, Trent JM, Staudt LM, Hudson J, Jr., Boguski MS, et al. 1999. The transcriptional program in the response of human fibroblasts to serum. Science 283:83-87.
33. Jiang Y, Broach JR. 1999. Tor proteins and protein phosphatase 2A reciprocally regulate Tap42 in controlling cell growth in yeast. EMBO J 18:2782-2792.
34. Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW. 1997. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci USA 94:13057-13062.
35. Li J, DeFea K, Roth RA. 1999. Modulation of insulin receptor substrate-1 tyrosine phosphorylation by an Akt/phosphatidylinositol 3-kinase pathway. J Biol Chem 274:9351-9356.
36. Lin HY, Wang XF, Ng-Eaton E, Weinberg RA, Lodish HF. 1992. Expression cloning of the TGF-beta type II receptor, a functional transmembrane serine/threonine kinase. Cell 68:775-785.
37. Lorenz MC, Heitman J. 1995. TOR mutations confer rapamycin resistance by preventing interaction with FKBP12-rapamycin. J Biol Chem 270:27531-27537.
38. Mamounas M, Gervin D, Englesberg E. 1989. The insulin receptor as a transmitter of a mitogenic signal in Chinese hamster ovary CHO-K1 cells. Proc Natl Acad Sci USA 86:9294-9298.
39. Mamounas M, Ross S, Luong CL, Brown E, Coulter K, Carroll G, Englesberg E. 1991. Analysis of the genes involved in the insulin transmembrane mitogenic signal in Chinese hamster ovary cells, CHO-K1, utilizing insulin-independent mutants. Proc Natl Acad Sci USA 88:3530-3534.
40. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, et al. 1998. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med 4:1293-1301.
41. Murata K, Wu J, Brautigan DL. 1997. B cell receptor-associated protein alpha4 displays rapamycin-sensitive binding directly to the catalytic subunit of protein phosphatase 2A. Proc Natl Acad Sci USA 94:10624-10629.
42. Muthukkumar S, Ramesh TM, Bondada S. 1995. Rapamycin, a potent immunosuppressive drug, causes programmed cell death in B lymphoma cells. Transplantation 60:264-270.
43. Nave BT, Ouwens M, Withers DJ, Alessi DR, Shepherd PR. 1999. Mammalian target of rapamycin is a direct target for protein kinase B: Identification of a convergence point for opposing effects of insulin and amino-acid deficiency on protein translation. Biochem J 2:427-431.
44. Pawson T, Nash P. 2000. Protein-protein interactions define specificity in signal transduction. Genes Dev 14:1027-1047.
45. Pelletier JN, Campbell-Valois F, Michnick SW. 1998. Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments. Proc Natl Acad Sci USA 95:12141-12146.
46. Perham RN. 1975. Self-assembly of biological macromolecules. Philos Trans R Soc Lond B Biol Sci 272:123-136.
47. Peterson RT, Desai BN, Hardwick JS, Schreiber SL. 1999. Protein phosphatase 2A interacts with the 70-kDa S6 kinase and is activated by inhibition of FKBP12-rapamycinassociated protein. Proc Natl Acad Sci USA 96:4438-4442.
48. Peterson RT, Beal PA, Comb MJ, Schreiber SL. 2000. FKBP12-rapamycin-associated protein (FRAP) autophosphorylates at serine 2481 under translationally repressive conditions. J Biol Chem 275:7416-7423.
49. Proud CG, Denton RM. 1997. Molecular mechanisms for the control of translation by insulin. Biochem J 328:329-341.
50. Pullen N, Dennis PB, Andjelkovic M, Dufner A, Kozma SC, Hemmings BA, Thomas G. 1998. Phosphorylation and activation of p70s6k by PDK1. Science 279:707-710.
51. Reed LJ. 1974. Multienzyme complexes. Acc Chem Res 7:40-46.
52. Remy I, Michnick SW. 1999. Clonal selection and in vivo quantitation of protein interactions with protein fragment complementation assays. Proc Natl Acad Sci USA 96:5394-5399.
53. Remy I, Michnick SW. 2001. Visualization of biochemical networks in living cells. Proc Natl Acad Sci USA 98:7678-7683.
54. Remy I, Wilson IA, Michnick SW. 1999. Erythropoietin receptor activation by a ligand-induced conformation change. Science 283:990-993.
55. Remy I, Pelletier JN, Galarneau A, Michnick SW. 2001. Protein interactions and library screening with protein fragment complementation strategies. In: Golemis EA, editor. Protein-protein interactions: A molecular cloning manual. Woodbury, New York, USA: Cold Spring Harbor Laboratory Press. pp 449-475.
56. Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dai H, Walker WL, Hughes TR, et al. 2000. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287:873-880.
57. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, et al. 2000. Comparative genomics of the eukaryotes. Science 287:2204-2215.
58. Ruderman NB, Kapeller R, White MF, Cantley LC. 1990. Activation of phosphatidylinositol 3-kinase by insulin. Proc Natl Acad Sci USA 87:1411-1415.
59. Sabatini DM, Erdjument-Bromage H, Lui M, Tempst P, Snyder SH. 1994. RAFT1: A mammalian protein that binds to FKBP12 in a rapamycin-dependent fashion and is homologous to yeast TORs. Cell 78:35-43.
60. Sako D, Chang XJ, Barone KM, Vachino G, White HM, Shaw G, Veldman GM, Bean KM, Ahern TJ, Furie B, et al. 1993. Expression cloning of a functional glycoprotein ligand for P-selectin. Cell 75:1179-1186.
61. Shi Y, Frankel A, Radvanyi LG, Penn LZ, Miller RG, Mills GB. 1995. Rapamycin enhances apoptosis and increases sensitivity to cisplatin in vitro. Cancer Res 55:1982-1988.
62. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9:3273-3297.
63. Subramaniam R, Desveaux D, Spickler C, Michnick SW, Brisson N. 2001. Direct visualization of protein interactions in plant cells. Nat Biotechnol 19:769-772.
64. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627.
65. Vanhaesebroeck B, Alessi DR. 2000. The PI3K-PDK1 connection: More than just a road to PKB. Biochem J 3:561-576.
66. Vidal M, Legrain P. 1999. Yeast forward and reverse 'n'-hybrid systems. Nucleic Acids Res 27:919-929.
67. Walhout AJ, 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.