Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks

Cell

Volumn 127, Issue 3, 2006, Pages 635-648

  Olsen, Jesper V ^a,b   Blagoev, Blagoy ^a   Gnad, Florian ^b   Macek, Boris ^a,b   Kumar, Chanchal ^b   Mortensen, Peter ^a   Mann, Matthias ^a,b  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR; GUANINE NUCLEOTIDE EXCHANGE FACTOR; PHOSPHOPROTEIN; UBIQUITIN PROTEIN LIGASE;

ARTICLE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DYNAMICS; HELA CELL; HUMAN; HUMAN CELL; KINETICS; MASS SPECTROMETRY; PHOSPHORYLATION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PHOSPHORYLATION; SIGNAL TRANSDUCTION; STIMULUS RESPONSE; TECHNOLOGY; TRANSCRIPTION REGULATION;

BINDING SITES; DATABASES, FACTUAL; EPIDERMAL GROWTH FACTOR; HELA CELLS; HUMANS; KINETICS; MASS SPECTROMETRY; NEOPLASM PROTEINS; PEPTIDES; PHOSPHORYLATION; PHOSPHOTYROSINE; PROTEIN BINDING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; SIGNAL TRANSDUCTION;

EID: 33750456519     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2006.09.026     Document Type: Article

References (61)

1. Aebersold R., and Mann M. Mass spectrometry-based proteomics. Nature 422 (2003) 198-207
2. Amanchy R., Kalume D.E., Iwahori A., Zhong J., and Pandey A. Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). J. Proteome Res. 4 (2005) 1661-1671
3. Andersen J.S., Lam Y.W., Leung A.K., Ong S.E., Lyon C.E., Lamond A.I., and Mann M. Nucleolar proteome dynamics. Nature 433 (2005) 77-83
4. Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., and Gygi S.P. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. USA 101 (2004) 12130-12135
5. Blagoev B., Kratchmarova I., Ong S.E., Nielsen M., Foster L.J., and Mann M. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 21 (2003) 315-318
6. Blagoev B., Ong S.E., Kratchmarova I., and Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol. 22 (2004) 1139-1145
7. Bos J.L. Linking Rap to cell adhesion. Curr. Opin. Cell Biol. 17 (2005) 123-128
8. Bromberg J., and Darnell Jr. J.E. The role of STATs in transcriptional control and their impact on cellular function. Oncogene 19 (2000) 2468-2473
9. Chen W.G., and White F.M. Proteomic analysis of cellular signaling. Expert Rev. Proteomics 1 (2004) 343-354
10. Cohen P. The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lecture. Eur. J. Biochem. 268 (2001) 5001-5010
11. Countaway J.L., Northwood I.C., and Davis R.J. Mechanism of phosphorylation of the epidermal growth factor receptor at threonine 669. J. Biol. Chem. 264 (1989) 10828-10835
12. de Godoy L.M., Olsen J.V., de Souza G.A., Li G., Mortensen P., and Mann M. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol. 7 (2006) R50
13. Devoy A., Soane T., Welchman R., and Mayer R.J. The ubiquitin-proteasome system and cancer. Essays Biochem. 41 (2005) 187-203
14. Diella F., Cameron S., Gemund C., Linding R., Via A., Kuster B., Sicheritz-Ponten T., Blom N., and Gibson T.J. Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics 5 (2004) 79
15. Dikic I., and Giordano S. Negative receptor signalling. Curr. Opin. Cell Biol. 15 (2003) 128-135
16. Elias J.E., Haas W., Faherty B.K., and Gygi S.P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2 (2005) 667-675
17. Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., and White F.M. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20 (2002) 301-305
18. Foster L.J., De Hoog C.L., and Mann M. Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc. Natl. Acad. Sci. USA 100 (2003) 5813-5818
19. Futschik M.E., and Carlisle B. Noise-robust soft clustering of gene expression time-course data. J. Bioinform. Comput. Biol. 3 (2005) 965-988
20. Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., and Jensen O.N. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics 4 (2005) 310-327
21. Hunter T. The Croonian Lecture 1997. The phosphorylation of proteins on tyrosine: its role in cell growth and disease. Philos. Trans. R. Soc. Lond. B Biol. Sci. 353 (1998) 583-605
22. Hunter T. Signaling-2000 and beyond. Cell 100 (2000) 113-127
23. Hunter T., and Sefton B.M. Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc. Natl. Acad. Sci. USA 77 (1980) 1311-1315
24. Karin M., and Hunter T. Transcriptional control by protein phosphorylation: signal transmission from the cell surface to the nucleus. Curr. Biol. 5 (1995) 747-757
25. Karin M., Liu Z., and Zandi E. AP-1 function and regulation. Curr. Opin. Cell Biol. 9 (1997) 240-246
26. Kratchmarova I., Blagoev B., Haack-Sorensen M., Kassem M., and Mann M. Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation. Science 308 (2005) 1472-1477
27. Larsen M.R., Thingholm T.E., Jensen O.N., Roepstorff P., and Jorgensen T.J. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell. Proteomics 4 (2005) 873-886
28. Li S., Couvillon A.D., Brasher B.B., and Van Etten R.A. Tyrosine phosphorylation of Grb2 by Bcr/Abl and epidermal growth factor receptor: a novel regulatory mechanism for tyrosine kinase signaling. EMBO J. 20 (2001) 6793-6804
29. Makarov A., Denisov E., Kholomeev A., Balschun W., Lange O., Strupat K., and Horning S. Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem. 78 (2006) 2113-2120
30. Marshall C.J. MAP kinase kinase kinase, MAP kinase kinase and MAP kinase. Curr. Opin. Genet. Dev. 4 (1994) 82-89
31. Mumby M., and Brekken D. Phosphoproteomics: new insights into cellular signaling. Genome Biol. 6 (2005) 230
32. Murphy L.O., Smith S., Chen R.H., Fingar D.C., and Blenis J. Molecular interpretation of ERK signal duration by immediate early gene products. Nat. Cell Biol. 4 (2002) 556-564
33. Olsen J.V., and Mann M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc. Natl. Acad. Sci. USA 101 (2004) 13417-13422
34. Olsen J.V., de Godoy L.M., Li G., Macek B., Mortensen P., Pesch R., Makarov A., Lange O., Horning S., and Mann M. Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 4 (2005) 2010-2021
35. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., and Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1 (2002) 376-386
36. Pagliarini D.J., and Dixon J.E. Mitochondrial modulation: reversible phosphorylation takes center stage?. Trends Biochem. Sci. 31 (2006) 26-34
37. Pawson T., and Nash P. Assembly of cell regulatory systems through protein interaction domains. Science 300 (2003) 445-452
38. Pelicci G., Lanfrancone L., Grignani F., McGlade J., Cavallo F., Forni G., Nicoletti I., Pawson T., and Pelicci P.G. A novel transforming protein (SHC) with an SH2 domain is implicated in mitogenic signal transduction. Cell 70 (1992) 93-104
39. Peri S., Navarro J.D., Kristiansen T.Z., Amanchy R., Surendranath V., Muthusamy B., Gandhi T.K., Chandrika K.N., Deshpande N., Suresh S., et al. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res. 32 (2004) D497-D501
40. Ptacek J., Devgan G., Michaud G., Zhu H., Zhu X., Fasolo J., Guo H., Jona G., Breitkreutz A., Sopko R., et al. Global analysis of protein phosphorylation in yeast. Nature 438 (2005) 679-684
41. Raingeaud J., Whitmarsh A.J., Barrett T., Derijard B., and Davis R.J. MKK3- and MKK6-regulated gene expression is mediated by the p38 mitogen-activated protein kinase signal transduction pathway. Mol. Cell. Biol. 16 (1996) 1247-1255
42. RDC Team (R Development Core Team). R: A Language and Environment for Statistical Computing (2006), R Foundation for Statistical Computing, Vienna
43. Roux P.P., Ballif B.A., Anjum R., Gygi S.P., and Blenis J. Tumor-promoting phorbol esters and activated Ras inactivate the tuberous sclerosis tumor suppressor complex via p90 ribosomal S6 kinase. Proc. Natl. Acad. Sci. USA 101 (2004) 13489-13494
44. Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.M., Polakiewicz R.D., and Comb M.J. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat. Biotechnol. 23 (2005) 94-101
45. Salomon A.R., Ficarro S.B., Brill L.M., Brinker A., Phung Q.T., Ericson C., Sauer K., Brock A., Horn D.M., Schultz P.G., and Peters E.C. Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc. Natl. Acad. Sci. USA 100 (2003) 443-448
46. Schlessinger J. Cell signaling by receptor tyrosine kinases. Cell 103 (2000) 211-225
47. Schroeder M.J., Shabanowitz J., Schwartz J.C., Hunt D.F., and Coon J.J. A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry. Anal. Chem. 76 (2004) 3590-3598
48. Schulze W.X., and Mann M. A novel proteomic screen for peptide-protein interactions. J. Biol. Chem. 279 (2004) 10756-10764
49. Shaulian E., and Karin M. AP-1 as a regulator of cell life and death. Nat. Cell Biol. 4 (2002) E131-E136
50. Soderling S.H., and Scott J.D. WAVE signalling: from biochemistry to biology. Biochem. Soc. Trans. 34 (2006) 73-76
51. Songyang Z., Blechner S., Hoagland N., Hoekstra M.F., Piwnica-Worms H., and Cantley L.C. Use of an oriented peptide library to determine the optimal substrates of protein kinases. Curr. Biol. 4 (1994) 973-982
52. Stephens P., Edkins S., Davies H., Greenman C., Cox C., Hunter C., Bignell G., Teague J., Smith R., Stevens C., et al. A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer. Nat. Genet. 37 (2005) 590-592
53. Stover D.R., Cadwell J., Marto J.A., Root K., Mestan J., Stumm M., Ornatsky O., Orsi C., Radosevic N., Liao L., et al. Differential phosphoprofiles of EGF and EGFR kinase inhibitor-treated human tumor cells and mouse xenografts. Clin. Proteomics 1 (2004) 69
54. Thelemann A., Petti F., Griffin G., Iwata K., Hunt T., Settinari T., Fenyo D., Gibson N., and Haley J.D. Phosphotyrosine signaling networks in epidermal growth factor receptor overexpressing squamous carcinoma cells. Mol. Cell. Proteomics 4 (2005) 356-376
55. van Dam H., and Castellazzi M. Distinct roles of Jun: Fos and Jun: ATF dimers in oncogenesis. Oncogene 20 (2001) 2453-2464
56. Ventura J.J., Kennedy N.J., Lamb J.A., Flavell R.A., and Davis R.J. c-Jun NH(2)-terminal kinase is essential for the regulation of AP-1 by tumor necrosis factor. Mol. Cell. Biol. 23 (2003) 2871-2882
57. Waterman H., and Yarden Y. Molecular mechanisms underlying endocytosis and sorting of ErbB receptor tyrosine kinases. FEBS Lett. 490 (2001) 142-152
58. Winograd-Katz S.E., and Levitzki A. Cisplatin induces PKB/Akt activation and p38(MAPK) phosphorylation of the EGF receptor. Oncogene (2006) 10.1038/sj.onc.1209737 Published online June 19, 2006
59. Yaffe M.B., Leparc G.G., Lai J., Obata T., Volinia S., and Cantley L.C. A motif-based profile scanning approach for genome-wide prediction of signaling pathways. Nat. Biotechnol. 19 (2001) 348-353
60. Zeeberg B.R., Feng W., Wang G., Wang M.D., Fojo A.T., Sunshine M., Narasimhan S., Kane D.W., Reinhold W.C., Lababidi S., et al. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol. 4 (2003) R28
61. Zhang Y., Wolf-Yadlin A., Ross P.L., Pappin D.J., Rush J., Lauffenburger D.A., and White F.M. Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell. Proteomics 4 (2005) 1240-1250