Functional proteomics to identify critical proteins in signal transduction pathways

Amino Acids

Volumn 35, Issue 2, 2008, Pages 267-274

  Yan, G R ^a   He, Q Y ^a  

^a JINAN UNIVERSITY   (China)

Author keywords

Phosphoproteomics; Phosphorylation; Proteomics; Signal transduction

Indexed keywords

LATENT MEMBRANE PROTEIN 1; LIPOCORTIN 2; PDZ PROTEIN; PHOSPHOPROTEIN; PHOSPHORUS 32; PHOSPHORUS 33; POLYPYRIMIDINE TRACT BINDING PROTEIN; PROTEIN 14 3 3; PROTEIN KINASE; PROTEIN SH2; PROTEIN SH3;

CANCER CELL; DERIVATIZATION; EPSTEIN BARR VIRUS; FUNCTIONAL PROTEOMICS; HUMAN; IMMOBILIZED METAL AFFINITY CHROMATOGRAPHY; IMMUNOBLOTTING; IMMUNOPRECIPITATION; ION EXCHANGE CHROMATOGRAPHY; ISOTOPE LABELING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN PURIFICATION; REVIEW; SIGNAL TRANSDUCTION; TISSUE MICROARRAY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ANIMALS; ANNEXIN A2; HUMANS; PHOSPHOPROTEINS; PHOSPHORYLATION; PROTEOMICS; SIGNAL TRANSDUCTION; VIRAL MATRIX PROTEINS;

HUMAN HERPESVIRUS 4;

EID: 49749113582     PISSN: 09394451     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00726-007-0594-0     Document Type: Review

References (63)

1. PG Atkinson HJ Coope M Rowe SC Ley 2003 Latent membrane protein 1 of Epstein-Barr virus stimulates processing of NF-kappa B2 p100 to p52 J Biol Chem 278 51134 51142
2. SA Beausoleil M Jedrychowski D Schwartz JE Elias J Villen J Li MA Cohn LC Cantley SP Gygi 2004 Large-scale characterization of HeLa cell nuclear phosphoproteins Proc Natl Acad Sci USA 101 12130 12135
3. B Blagoev I Kratchmarova SE Ong M Nielsen LJ Foster MA Mann 2003 Proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling Nat Biotechnol 21 315 318
4. LM Brill AR Salomon SB Ficarro M Mukherji M Stettler-Gill EC Peters 2004 Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry Anal Chem 76 2763 2772
5. C Cans R Mangano D Barila G Neubauer G Superti-Furga 2000 Nuclear tyrosine phosphorylation: the beginning of a map Biochem Pharmacol 60 1203 1215
6. P Cao JT Stults 2000 Mapping the phosphorylation sites of proteins using on-line immobilized metal affinity chromatography/capillary electrophoresis/ electrospray ionization multiple stage tandem mass spectrometry Rapid Commun Mass Spectrom 14 1600 1606
7. TP Conrads HJ Issaq TD Veenstra 2002 New tools for quantitative phosphoproteome analysis Biochem Biophys Res Commun 290 885 890
8. M de Graauw P Hensbergen B van de Water 2006 Phospho-proteomic analysis of cellular signaling Electrophoresis 27 2676 2686
9. S Dorion J Berube J Huot J Landry 1999 A short lived protein involved in the heat shock sensing mechanism responsible for stress-activated protein kinase 2 (SAPK2/p38) activation J Biol Chem 274 37591 37597
10. SV Drouva B Poulin V Manceau A Sobel 1998 Luteinizing hormone-releasing hormone-signal transduction and stathmin phosphorylation in the gonadotrope alphaT3-1 cell line Endocrinology 139 2235 2239
11. AG Eliopoulos NJ Gallagher SM Blake CW Dawson LS Young 1999 Activation of the p38 mitogen-activated protein kinase pathway by Epstein-Barr virus-encoded latent membrane protein 1 coregulates interleukin-6 and interleukin-8 production J Biol Chem 274 16085 16096
12. SB Ficarro ML McCleland PT Stukenberg DJ Burke MM Ross J Shabanowitz DF Hunt FM White 2002 Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae Nat Biotechnol 20 301 305
13. O Gires F Kohlhuber E Kilger M Baumann A Kieser C Kaiser R Zeidler B Scheffer M Ueffing W Hammerschmidt 1999 Latent membrane protein 1 of Epstein-Barr virus interacts with JAK3 and activates STAT proteins EMBO J 18 3064 3073
14. KL Gould JR Woodgett CM Isacke T Hunter 1986 The protein-tyrosine kinase substrate p36 is also a substrate for protein kinase C in vitro and in vivo Mol Cell Biol 6 2738 2744
15. S Grein W Pyerin 1999 BTF3 is a potential new substrate of protein kinase CK2 Mol Cell Biochem 191 121 128
16. A Gruhler JV Olsen S Mohammed P Mortensen NJ Faergeman M Mann ON Jensen 2005 Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway Mol Cell Proteomics 4 310 327
17. CM Haystead P Gregory TW Sturgill TA Haystead 1993 Gamma-phosphate-linked ATP-sepharose for the affinity purification of protein kinases. Rapid purification to homogeneity of skeletal muscle mitogen-activated protein kinase kinase Eur J Biochem 214 459 467
18. AM Hinsby JV Olsen KL Bennett M Mann 2003 Signaling initiated by overexpression of the fibroblast growth factor receptor-1 investigated by mass spectrometry Mol Cell Proteomics 2 29 36
19. Hirodshi T (2003) The 42nd Annual Conference of the Japanese Society for Medical and Biological Engineering, June 3
20. VW Hu DS Heikka 2000 Radiolabeling revisited: metabolic labeling with (35)S-methionine inhibits cell cycle progression, proliferation, and survival FASEB J 14 448 454
21. VW Hu DS Heikka PB Dieffenbach L Ha 2001 Metabolic radiolabeling: experimental tool or Trojan horse? (35)S-Methionine induces DNA fragmentation and p53-dependent ROS production FASEB J 15 1562 1568
22. T Hunter 2000 Signaling - 2000 and beyond Cell 100 113 127
23. D Immler D Gremm D Kirsch B Spengler P Presek HE Meyer 1998 Identification of phosphorylated proteins from thrombin-activated human platelets isolated by two-dimensional gel electrophoresis by electrospray ionization-tandem mass spectrometry (ESI-MS/MS) and liquid chromatography- electrospray ionization-mass spectrometry (LC-ESI-MS) Electrophoresis 19 1015 1023
24. JM Irish R Hovland PO Krutzik OD Perez O Bruserud BT Gjertsen GP Nolan 2004 Single cell profiling of potentiated phospho-protein networks in cancer cells Cell 118 217 228
25. N Johnsson P Nguyen Van HD Soling K Weber 1986 Functionally distinct serine phosphorylation sites of p36, the cellular substrate of retroviral protein kinase; differential inhibition of reassociation with p11 EMBO J 5 3455 3460
26. N Katoh 2002 Inhibition by melittin of phosphorylation by protein kinase C of annexin I from cow mammary gland J Vet Med Sci 64 779 783
27. Kenneth A (2002) The 8th International Conference on Malignant Lymphoma, Lugano, Switzerland, June 12
28. HJ Kim EJ Song KJ Lee 2002 Proteomic analysis of protein phosphorylations in heat shock response and thermotolerance J Biol Chem 277 23193 23207
29. PO Krutzik JM Irish GP Nolan OD Perez 2004 Analysis of protein phosphorylation and cellular signaling events by flow cytometry: techniques and clinical applications Clin Immunol 110 206 221
30. MR Larsen GL Sorensen SJ Fey PM Larsen P Roepstorff 2001 Phospho-proteomics: evaluation of the use of enzymatic de-phosphorylation and differential mass spectrometric peptide mass mapping for site specific phosphorylation assignment in proteins separated by gel electrophoresis Proteomics 1 223 238
31. TS Lewis JB Hunt LD Aveline KR Jonscher DF Louie JM Yeh TS Nahreini KA Resing NG Ahn 2000 Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry Mol Cell 6 1343 1354
32. YP Lim CY Wong LL Ooi BJ Druker RJ Epstein 2004 Selective tyrosine hyperphosphorylation of cytoskeletal and stress proteins in primary human breast cancers: implications for adjuvant use of kinase-inhibitory drugs Clin Cancer Res 10 3980 3987
33. M Luftig E Prinarakis T Yasui T Tsichritzis E Cahir-McFarland J Inoue H Nakano TW Mak WC Yeh X Li S Akira N Suzuki S Suzuki G Mosialos E Kieff 2003 Epstein-Barr virus latent membrane protein 1 activation of NF-kappaB through IRAK1 and TRAF6 Proc Natl Acad Sci USA 100 15595 15600
34. JA MacDonald LA Walker RK Nakamoto I Gorenne AV Somlyo AP Somlyo TA Haystead 2000 Phosphorylation of telokin by cyclic nucleotide kinases and the identification of in vivo phosphorylation sites in smooth muscle FEBS Lett 479 83 88
35. JA MacDonald MA Borman A Muranyi AV Somlyo DJ Hartshorne TA Haystead 2001 Identification of the endogenous smooth muscle myosin phosphatase-associated kinase Proc Natl Acad Sci USA 98 2419 2424
36. K Machida BJ Mayer P Nollau 2003 Profiling the global tyrosine phosphorylation state Mol Cell Proteomics 2 215 233
37. M Mann SE Ong M Gronborg H Steen ON Jensen A Pandey 2002 Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome Trends Biotechnol 20 261 268
38. T Mizuno S Mizushima 1990 Signal transduction and gene regulation through the phosphorylation of two regulatory components: the molecular basis for the osmotic regulation of the porin genes Mol Microbiol 4 1077 1082
39. Y Oda T Nagasu BT Chait 2001 Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome Nat Biotechnol 19 379 382
40. E Paine R Palmantier SK Akiyama K Olden JD Roberts 2000 Arachidonic acid activates mitogen-activated protein (MAP) kinase-activated protein kinase 2 and mediates adhesion of a human breast carcinoma cell line to collagen type IV through a p38 MAP kinase-dependent pathway J Biol Chem 275 11284 11290
41. A Pandey AV Podtelejnikov B Blagoev XR Bustelo M Mann HF Lodish 2000 Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors Proc Natl Acad Sci USA 97 179 184
42. KJ Park RB Gaynor YT Kwak 2003 Heat shock protein 27 association with the Ikappa B kinase complex regulates tumor necrosis factor alpha-induced NF-kappa B activation J Biol Chem 278 35272 35278
43. MC Posewitz P Tempst 1999 Immobilized gallium(III) affinity chromatography of phosphopeptides Anal Chem 71 2883 2892
44. S Radke J Austermann F Russo-Marie V Gerke U Rescher 2004 Specific association of annexin 1 with plasma membrane-resident and internalized EGF receptors mediated through the protein core domain FEBS Lett 578 95 98
45. CS Raska CE Parker Z Dominski WF Marzluff GL Glish RM Pope CH Borchers 2002 Direct MALDI-MS/MS of phosphopeptides affinity-bound to immobilized metal ion affinity chromatography beads Anal Chem 74 3429 3433
46. ML Roberts NR Cooper 1998 Activation of a ras-MAPK-dependent pathway by Epstein-Barr virus latent membrane protein 1 is essential for cellular transformation Virology 240 93 99
47. N Saito G Courtois A Chiba N Yamamoto T Nitta N Hironaka M Rowe N Yamamoto S Yamaoka 2003 Two carboxyl-terminal activation regions of Epstein-Barr virus latent membrane protein 1 activate NF-kappaB through distinct signaling pathways in fibroblast cell lines J Biol Chem 278 46565 46575
48. AR Salomon SB Ficarro LM Brill A Brinker QT Phung C Ericson K Sauer A Brock DM Horn PG Schultz EC Peters 2003 Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry Proc Natl Acad Sci USA 100 443 448
49. J Satoh SU Kim 1995 Cytokines and growth factors induce HSP27 phosphorylation in human astrocytes J Neuropathol Exp Neurol 54 504 512
50. A Sobel 1991 Stathmin: a relay phosphoprotein for multiple signal transduction? Trends Biochem Sci 16 301 305
51. V Soskic M Gorlach S Poznanovic FD Boehmer J Godovac-Zimmermann 1999 Functional proteomics analysis of signal transduction pathways of the platelet-derived growth factor beta receptor Biochemistry 38 1757 1764
52. LF Stancato EF Petricoin 2001 Fingerprinting of signal transduction pathways using a combination of anti-phosphotyrosine immunoprecipitations and two-dimensional polyacrylamide gel electrophoresis Electrophoresis 22 2120 2124
53. H Steen B Kuster M Fernandez A Pandey M Mann 2002 Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway J Biol Chem 277 1031 1039
54. TH Steinberg BJ Agnew KR Gee WY Leung T Goodman B Schulenberg J Hendrickson JM Beechem RP Haugland WF Patton 2003 Global quantitative phosphoprotein analysis using multiplexed proteomics technology Proteomics 3 1128 1144
55. A Stensballe S Andersen ON Jensen 2001 Characterization of phosphoproteins from electrophoretic gels by nanoscale Fe(III) affinity chromatography with off-line mass spectrometry analysis Proteomics 1 207 222
56. W Xhou BA Merrick MG Khaledi KB Tomer 2000 Detection and sequencing of phosphopeptides affinity bound to immobilized metal ion beads by matrix-assisted laser desorption/ionization mass spectrometry J Am Soc Mass Spectrom 11 273 282
57. G Yan L Li Y Tao S Liu Y Liu W Luo Wu Y M Tang Z Dong Y Cao 2006a Identification of novel phosphoproteins in signaling pathways triggered by latent membrane protein 1 using functional proteomics technology Proteomics 6 1810 1821
58. Yan G, Luo W, Lu Z, Luo X, Li L, Liu S, Liu Y, Tang M, Dong Z, Cao Y (2006b) Epstein-Barr virus latent membrane protein 1 mediates phosphorylation and nuclear translocation of annexin A2 by activating PKC pathway. Cell Signal [Epub ahead of print]
59. T Yaoi S Chamnongpol X Jiang X Li 2006 Src homology 2 domain-based high throughput assays for profiling downstream molecules in receptor tyrosine kinase pathways Mol Cell Proteomics 5 959 968
60. J Yeargin M Haas 1995 Elevated levels of wild-type p53 induced by radiolabeling of cells leads to apoptosis or sustained growth arrest Curr Biol 5 423 431
61. YG Yeung ER Stanley 2003 Proteomic approaches to the analysis of early events in colony-stimulating factor-1 signal transduction Mol Cell Proteomics 2 1143 1155
62. Y Zhang A Wolf-Yadlin PL Ross DJ Pappin J Rush DA Lauffenburger FM White 2005 Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules Mol Cell Proteomics 4 1240 1250
63. H Zhou JD Watts R Aebersold 2001 A systematic approach to the analysis of protein phosphorylation Nat Biotechnol 19 375 378