Identification of novel signaling complexes by functional proteomics

Circulation Research

Volumn 93, Issue 7, 2003, Pages 595-603

  Ping, Peipei ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Cardiac cell death; Functional subproteomes; Ischemic injury; Multiprotein complexes; Signal transduction

Indexed keywords

BETA ARRESTIN; MITOGEN ACTIVATED PROTEIN KINASE; N METHYL DEXTRO ASPARTIC ACID RECEPTOR; PLATELET DERIVED GROWTH FACTOR RECEPTOR; PRKCE PROTEIN, HUMAN; PROTEIN KINASE C; PROTEIN KINASE C EPSILON;

CELL DEATH; COMPLEX FORMATION; GENE MAPPING; GENOME; GLYCOLYSIS; HEART MUSCLE CELL; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; OXYGEN TENSION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ISOLATION; PROTEIN PHOSPHORYLATION; PROTEOMICS; REVIEW; RNA PROCESSING; RNA SPLICING; SIGNAL TRANSDUCTION; ANIMAL; CYTOLOGY; HUMAN; METABOLISM; METHODOLOGY; PHYSIOLOGY; PROTEIN BINDING;

ANIMALS; HUMANS; MYOCYTES, CARDIAC; PROTEIN BINDING; PROTEIN KINASE C; PROTEIN KINASE C-EPSILON; PROTEOMICS; SIGNAL TRANSDUCTION;

EID: 0141864397     PISSN: 00097330     EISSN: None     Source Type: Journal    
DOI: 10.1161/01.RES.0000093221.98213.E0     Document Type: Review

References (65)

1. 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. The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD). Nucleic Acids Res. 2000;28:73-76.
2. Dunn MJ. Studying heart disease using the proteomic approach. Drug Discov Today. 2000;5:76-84.
3. Gygi SP, Aebersold R. Mass spectrometry and proteomics. Curr Opin Chem Biol. 2000;4:489-494.
4. Pandey A, Mann M. Proteomics to study genes and genomes. Nature. 2000:405:837-846.
5. Arrell DK, Neverova I, Van Eyk JE. Cardiovascular proteomics. Circ Res. 2001;88:763-773.
6. Vondriska TM, Klein JB, Ping P. Use of functional proteomics to investigate PKCε-mediated cardioprotection: the signaling module hypothesis. Am J Physiol. 2001;280:H1434-H1441.
7. Edmondson RD, Vondriska TM, Biederman KJ, Zhang J, Jones RC, Zheng Y, Allen DL, Xiu JX, Cardwell EM, Pisano MR, Ping P. PKCE signaling complexes include metabolism- and transcription/translation-related proteins: complimentary separation techniques with liquid chromatography and tandem mass spectrometry. Mol Cell Proteomics. 2002; 1:421-433.
8. Ping P, Zhang J, Pierce WM Jr, Bolli R. Functional proteomic analysis of PKCE signaling complexes in the normal heart and during cardioprotection. Circ Res. 2001;88:59-62.
9. Godovac-Zimmermann J, Soskic V, Poznanovic S, Brianza F. Functional proteomics of signal transduction by membrane receptors. Electrophoresis. 1999;20:952-961.
10. Hoang VM, Foulk R, Clauser K, Burlingame A, Gibson BW, Fisher SJ. Functional proteomics: examining the effects of hypoxia on the cytotrophoblast protein repertoire. Biochemistry. 2001;40:4077-4086.
11. Husi H, Ward MA, Choudhary JS, Blackstock WP, Grant SG. Proteomic analysis of NMDA receptor-adhesion protein signaling complexes. Nat Neurosci. 2000;3:661-669.
12. Lewis TS, Hunt JB, Aveline LD, Jonscher KR, Louie DF, Yeh JM, Nahreini TS, Resing KA, Ahn NG. Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry. Mol Cell. 2000;6:1343-1354.
13. McDonough JL, Labugger R, Pickett W, Tse MY, MacKenzie S, Pang SC, Atar D, Ropchan G, Van Eyk JE. Cardiac troponin I is modified in the myocardium of bypass patients. Circulation. 2001;103:58-64.
14. Soskic V, Gorlach M, Poznanovic S, Boehmer FD, Godovac-Zimmermann J. Functional proteomics analysis of signal transduction pathways of the platelet-derived growth factor β receptor. Biochemistry. 1999;38:1757-1764.
15. Ohi MD, Link AJ, Ren L, Jennings JL, McDonald WH, Could KL. Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeast containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Mol Cell Biol. 2002;22: 2011-2024.
16. Hunter T. Signaling-2000 and beyond. Cell. 2000;100:113-127.
17. Jordan JD, Landau EM, Iyengar R. Signaling networks. Cell. 2000;103: 193-2000.
18. Heidkamp MC, Bayer AL, Martin JL, Samarel AM. Differential activation of mitogen-activated protein kinase cascades and apoptosis by protein kinase Cε and δ in neonatal rat ventricular myocytes. Circ Res. 2001;89:882-890.
19. Bueno OF, De Windt LJ, Tymitz KM, Witt SA, Kimball TR, Klevitsky R, Hewett TE, Jones SP, Lefer DJ, Peng CF, Kitsis RN, Molkentin JD. The MEK1-ERK1/ 2 signaling pathway promotes compensated cardiac hypertrophy in transgenic mice. EMBO J. 2000;19:6341-6350.
20. Clerk A, Pham FH, Fuller SJ, Sahai E, Aktories K, Marais R, Marshall C, Sugden PH. Regulation of mitogen-activated protein kinases in cardiac myocytes through the small G protein Rac 1. Mol Cell Biol. 2001;21: 1173-1184.
21. Baines PC, Zhang J, Wang GW, Zheng YT, Xiu JX, Cardwell EM, Bolli R, Ping P. Mitochondrial PKCε and MAPK form signaling modules in the murine heart. Circ Res. 2002;90:390-397.
22. 2-adrenergic receptor complex facilitates receptor phosphorylation and signaling. Curr Biol. 2000;10:409-412.
23. MacCoss MJ, McDonald WH, Saraf A, Sadygov R, Clark JM, Tasto JJ, Gould KL, Wolters D, Washburn M, Weiss A, Clark JI, Yates JR III. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci U S A. 2002;99:7900-7905.
24. Nedelkov D, Nelson RW. Delineation of in vivo assembled multiprotein complexes via biomolecular interaction analysis mass spectrometry. Proteomics. 2001;1:1441-1446.
25. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002;415:180-183.
26. Gavin AC, Bosche M, Krause R, Grandi P, Marioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002;415:141-147.
27. Ping P, Song C, Zhang J, Guo Y, Cao X, Li RC, Wu W, Vondriska TM, Pass JM, Tang XL, Pierce WM Jr, Bolli R. Formation of PKCε-Lck signaling modules confers cardioprotection. J Clin Invest. 2002;109: 499-507.
28. Vondriska TM, Zhang J, Song C, Tang XL, Cao X, Baines CP, Pass JM, Wang S, Bolli R, Ping P. PKCε-Src modules direct signal transduction in NO-induced cardioprotection. Circ Res. 2001;88:1306-1313.
29. Baines CP, Song CX, Zheng YT, Wang GW, Zhang J, Wang OL, Guo Y, Bolli R, Cardwell EM, Ping P. PKCε interacts with and inhibits the permeability transition pore in cardiac mitochondria. Circ Res. 2003;92: 873-880.
30. Song C, Vondriska TM, Wang GW, Klein JB, Cao X. Zhang J, Kang Y, D'Souza S, Ping P. Conformation dictates module formation: example of PKCε and Src tyrosine kinase. Am J Physiol. 2002;282:H1166-H1171.
31. Vondriska TM, Ping P. Multiprotein signaling complexes and regulation of cardiac phenotype. J Mol Cell Cardiol. 2003;35:1027-1033.
32. Luttrel LM, Roudabush FL, Choy EW, Miller WE, Field ME, Pierce KL, Lefkowitz RJ. Activation and targeting of extracellular signal-regulated kinases by β-arrestin scaffolds. Proc Natl Acad Sci USA. 2001;98: 2449-2454.
33. Fink MA, Zakhary DR, Mackey JA, Desnoyer RW, Appereson-Hansen C, Damron DS, Bond M. AKAP-mediated targeting of protein kinase A regulates contractility in cardiac myocytes. Circ Res. 2001;88:291-297.
34. Mochly-Rosen D. Localization of protein kinases by anchoring proteins: a theme in signal transduction. Science. 1995;268:247-251.
35. Huber LA, Pfaller K, Vietor I. Organelle proteomics: implications for subcellular fractionation in proteomics. Circ Res. 2003;92:962-968.
36. Bell AW, Ward MA, Blackstock WP, Freeman HN, Choudhary JS, Lewis AP, Chotai D, Fazel A, Gushue JN, Paiement J, Paley S, Chevet E, Lafreniere-Roula M, Solari R, Thomas DY, Rowley A, Bergeron J. Proteomics characterization of abundant Golgi membrane proteins. J Biol Chem. 2001;276:5152-5165.
37. Taylor SW, Fahy E, Zhang B, Glenn GM, Warnock DE, Wiley S, Murphy AN, Gaucher SP, Capaldi RA, Gibson BW, Ghosh SS. Characterization of the human heart mitochondrial proteome. Nat Biotechnol. 2003;21: 281-286.
38. Zhang J, Bolli R, Zheng Y, Xiu JX, Wang G, Pierce WM, Ping P. Subcellular location is a major determinant of PKCE complex assembly: a view gained via functional proteomic analyses in cardioprotection. Circulation. 2001;104(suppl II):II-209. Abstract.
39. Nijtmans LG, Henderson NS, Holt IJ. Blue native electrophoresis to study mitochondrial and other protein complexes. Methods. 2002;26:327-334.
40. Brookes PS, Pinner A, Ramachandran A, Coward L, Barnes S, Kim H, Darley-Usmar VM. High throughput two-dimensional blue-native electrophoresis: a tool for functional proteomics of mitochondria and signaling complexes. Proteomics. 2002;2:969-977.
41. Huang CC, Hall DH, Hedgecock EM, Kao G, Karantza V, Vogel BE, Hutter H, Chisholm AD, Yurchenoco PD, Wadsworth WG. Laminin a subunits and their role in C. elegans development. Development. 2003; 130:3343-3358.
42. Perez-Terzic C, Behfar A, Mery A, van Deursen JM, Terzic A, Puceat M. Structural adaptation of the nuclear pore complex in stem cell-derived cardiomyocytes. Circ Res. 2003;92:444-452.
43. Neubauer G, King A, Rappsilber J, Calvio C, Watson M, Ajuh P, Sleeman J, Lamond A, Mann M. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nat Genet. 1998;20:46-50.
44. Wedaman KP, Reinke A, Anderson S, Yates J III, McCaffery JM, Powers T. Tor kinases are in distinct membrane-associated protein complexes in Saccharomyces cerevisiae. Mol Biol Cell. 2003:14:1204-1220.
45. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003;422:198-207.
46. Hazbun TR, Fields S. Networking proteins in yeast. Proc Natl Acad Sci U S A. 2001;98:4277-4278.
47. Jaken S, Parker PJ. Protein kinase C binding partners. Bioessays. 2000; 22:245-254.
48. Legrain P, Jestin JL, Schachter V. From the analysis of protein complexes to proteome-wide linkage maps. Curr Opin Biotechnol. 2000;11: 402-407.
49. 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.
50. Yanagida M, Shimamoto A, Nishikawa K, Furuichi Y, Isobe T, Takahashi N. Isolation and proteomic characterization of the major proteins of the nucleolin-binding ribonucleoprotein complexes. Proteomics. 2001;1:1390-1404.
51. Kanamoto T, Hellman U, Heldin CH, Souchelnytskyi S. Functional proteomics of transforming growth factor-β1-stimulated Mv1Lu epithelial cells: Rad51 as a target of TGF-β1-dependent regulation of DNA repair. EMBO J. 2002;21:1219-1230.
52. Lin TK, Hughes G, Muratovska A, Blaikie FH, Brookes PS, Darley-Usmar V, Smith RAJ, Murphy MP. Specific modification of mitochondrial protein thiols in response to oxidative stress. J Biol Chem. 2002;277:17048-17056.
53. Ytrehus K, Liu GS, Downey JM. Preconditioning protects ischemic rabbit heart by protein kinase C activation. Am J Physiol. 1994;266: H1145-H1152.
54. Bolli R. The late phase of preconditioning. Circ Res. 2000;87:972-983.
55. Cohen MV, Baines CP, Downey JM. Ischemic preconditioning. Annu Rev Physiol. 2000;62:79-109.
56. Dorn GW II, Souroujon MC, Liron T, Chen CH, Gray MO, Zhou HZ, Csukai M, Wu G, Lorenz JN, Mochly-Rosen D. Sustained in vivo cardiac protection by a rationally designed peptide that causes ε protein kinase C translocation. Proc Natl Acad Sci USA. 1999;96:12798-12803.
57. Gray MO, Karliner JS, Mochly-Rosen D. A selective ε protein kinase C antagonist inhibits protection of cardiac myocytes from hypoxia-induced cell death. J Biol Chem. 1997;272:30945-30951.
58. + channels by protein kinase C. Circ Res. 1998;83:110-114.
59. Pyle WG, Chen Y, Hofmann PA. Cardioprotection through a PKC-dependent decrease in myofilament ATPase. Am J Physiol. 2003;285: H1220-H1228.
60. Aley KO, Messing RO, Mochly-Rosen D, Levine JD. Chronic hypersensitivity for inflammatory nociceptor sensitization mediated by the ε isozyme of protein kinase C. J Neurosci. 2000;20:4680-4685.
61. Chow JY, Uribe JM, Barrett KE. A role for protein kinase Cε in the inhibitory effect of epidermal growth factor on calcium-stimulated chloride secretion in human colonic epithetial cells. J Biol Chem. 2000; 275:21169-21176.
62. Knauf JA, Elisei R, Mochly-Rosen D, Liron T, Chen XN, Gonsky R, Korenberg JR, Fagin JA. Involvement of PKCε in thyroid cell death. J Biol Chem. 1999;274:23414-23425.
63. Tang XL, Kodani E, Takano H, Hill M, Shinmura K, Vondriska TM, Ping P, Bolli R. Protein tyrosine kinase signaling is necessary for NO donor-induced late preconditioning against myocardial stunning. Am J Physiol. 2003;284:H1441-H1448.
64. Vondriska TM, Tang XL, Zhang J, Bolli R, Ping P. Bmx, a member of the Tec family of non-receptor tyrosine kinases, is a novel participant in the signaling system of NO-induced cardioprotection. Circulation. 2001; 104(suppl II):II-61. Abstract.
65. Vondriska TM, Chen J, Wang GW, Lu M, Qiao X, Zong NC, Zhang J, Pantaleon D, Roos K, Ping P. The scaffolding protein Oracle is a necessary mediator of nitric oxide-induced cardioprotection. Circulation. In press. Abstract.