Quantitative Proteomics Analysis of the Secretory Pathway

Cell

Volumn 127, Issue 6, 2006, Pages 1265-1281

  Gilchrist, Annalyn ^a   Au, Catherine E ^a   Hiding, Johan ^c   Bell, Alexander W ^a   Fernandez Rodriguez, Julia ^c   Lesimple, Souad ^a   Nagaya, Hisao ^a   Roy, Line ^a   Gosline, Sara J C ^b   Hallett, Michael ^b   Paiement, Jacques ^d   Kearney, Robert E ^a   Nilsson, Tommy ^c   Bergeron, John J M ^a  

^a MCGILL UNIVERSITY   (Canada)

^b MCGILL UNIVERSITY   (Canada)

^c UNIVERSITY OF GOTHENBURG   (Sweden)

^d UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALBUMIN; CALNEXIN; COAT PROTEIN COMPLEX I; MANNOSIDASE; RIBOPHORIN I; SIALYLTRANSFERASE;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CELL MATURATION; CELLULAR DISTRIBUTION; CONTROLLED STUDY; ENDOPLASMIC RETICULUM; GOLGI COMPLEX; NONHUMAN; PRIORITY JOURNAL; PROTEIN SECRETION; PROTEOMICS; QUANTITATIVE ANALYSIS; RAT;

EID: 33845500104     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2006.10.036     Document Type: Article

References (45)

1. Alvarez C., Garcia-Mata R., Brandon E., and Sztul E. COPI recruitment is modulated by a Rab1b-dependent mechanism. Mol. Biol. Cell 14 (2003) 2116-2127
2. Anelli T., Alessio M., Mezghrani A., Simmen T., Talamo F., Bachi A., and Sitia R. ERp44, a novel endoplasmic reticulum folding assistant of the thioredoxin family. EMBO J. 21 (2002) 835-844
3. Bard F., Casano L., Mallabiabarrena A., Wallace E., Saito K., Kitayama H., Guizzunti G., Hu Y., Wendler F., Dasgupta R., et al. Functional genomics reveals genes involved in protein secretion and Golgi organization. Nature 439 (2006) 604-607
4. Bell A.W., Ward M.A., Blackstock W.P., Freeman H.N., Choudhary J.S., Lewis A.P., Chotai D., Fazel A., Gushue J.N., Paiement J., et al. Proteomics characterization of abundant Golgi membrane proteins. J. Biol. Chem. 276 (2001) 5152-5165
5. Benetti R., Del Sal G., Monte M., Paroni G., Brancolini C., and Schneider C. The death substrate Gas2 binds m-calpain and increases susceptibility to p53-dependent apoptosis. EMBO J. 20 (2001) 2702-2714
6. Blondeau F., Ritter B., Allaire P.D., Wasiak S., Girard M., Hussain N.K., Angers A., Legendre-Guillemin V., Roy L., Boismenu D., et al. Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling. Proc. Natl. Acad. Sci. USA 101 (2004) 3833-3838
7. Bordier C. Phase separation of integral membrane proteins in Triton X-114 solution. J. Biol. Chem. 256 (1981) 1604-1607
8. Bornhauser B.C., Olsson P.A., and Lindholm D. MSAP is a novel MIR-interacting protein that enhances neurite outgrowth and increases myosin regulatory light chain. J. Biol. Chem. 278 (2003) 35412-35420
9. Chavrier P., Parton R.G., Hauri H.P., Simons K., and Zerial M. Localization of low molecular weight GTP binding proteins to exocytic and endocytic compartments. Cell 62 (1990) 317-329
10. Cox B., Kislinger T., and Emili A. Integrating gene and protein expression data: pattern analysis and profile mining. Methods 35 (2005) 303-314
11. Dahan S., Ahluwalia J.P., Wong L., Posner B.I., and Bergeron J.J. Concentration of intracellular hepatic apolipoprotein E in Golgi apparatus saccular distensions and endosomes. J. Cell Biol. 127 (1994) 1859-1869
12. Dominguez M., Fazel A., Dahan S., Lovell J., Hermo L., Claude A., Melancon P., and Bergeron J.J. Fusogenic domains of golgi membranes are sequestered into specialized regions of the stack that can be released by mechanical fragmentation. J. Cell Biol. 145 (1999) 673-688
13. Foster L.J., de Hoog C.L., Zhang Y., Zhang Y., Xie X., Mootha V.K., and Mann M. A mammalian organelle map by protein correlation profiling. Cell 125 (2006) 187-199
14. Girard M., Allaire P.D., McPherson P.S., and Blondeau F. Non-stoichiometric relationship between clathrin heavy and light chains revealed by quantitative comparative proteomics of clathrin-coated vesicles from brain and liver. Mol. Cell. Proteomics 4 (2005) 1145-1154
15. Girod A., Storrie B., Simpson J.C., Johannes L., Goud B., Roberts L.M., Lord J.M., Nilsson T., and Pepperkok R. Evidence for a COP-I-independent transport route from the Golgi complex to the endoplasmic reticulum. Nat. Cell Biol. 1 (1999) 423-430
16. Goolsby K.M., and Shapiro D.J. RNAi-mediated depletion of the 15 KH domain protein, vigilin, induces death of dividing and non-dividing human cells but does not initially inhibit protein synthesis. Nucleic Acids Res. 31 (2003) 5644-5653
17. Gurkan C., Lapp H., Alory C., Su A.I., Hogenesch J.B., and Balch W.E. Large-scale profiling of Rab GTPase trafficking networks: the membrome. Mol. Biol. Cell 16 (2005) 3847-3864
18. Hay J.C., Hirling H., and Scheller R.H. Mammalian vesicle trafficking proteins of the endoplasmic reticulum and Golgi apparatus. J. Biol. Chem. 271 (1996) 5671-5679
19. Hay J.C., Klumperman J., Oorschot V., Steegmaier M., Kuo C.S., and Scheller R.H. Localization, dynamics, and protein interactions reveal distinct roles for ER and Golgi SNAREs. J. Cell Biol. 141 (1998) 1489-1502
20. Hewett J., Ziefer P., Bergeron D., Naismith T., Boston H., Slater D., Wilbur J., Schuback D., Kamm C., Smith N., et al. TorsinA in PC12 cells: localization in the endoplasmic reticulum and response to stress. J. Neurosci. Res. 72 (2003) 158-168
21. Jermy A.J., Willer M., Davis E., Wilkinson B.M., and Stirling C.J. The Brl domain in Sec63p is required for assembly of functional endoplasmic reticulum translocons. J. Biol. Chem. 281 (2006) 7899-7906
22. Junutula J.R., De Maziere A.M., Peden A.A., Ervin K.E., Advani R.J., van Dijk S.M., Klumperman J., and Scheller R.H. Rab14 is involved in membrane trafficking between the Golgi complex and endosomes. Mol. Biol. Cell 15 (2004) 2218-2229
23. Kartberg F., Hiding J., and Nilsson T. Purification of COPI vesicles. In: Celis J., Carter N., Simons K., Small V., Hunter T., and Shotton D.M. (Eds). Cell Biology: A Laboratory Handbook (2005), Elsevier Academic Press, Burlington, MA, USA 45-50
24. Kislinger T., Cox B., Kannan A., Chung C., Hu P., Ignatchenko A., Scott M.S., Gramolini A.O., Morris Q., Hallett M.T., et al. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125 (2006) 173-186
25. Langbein S., Zerilli M., Zur Hausen A., Staiger W., Rensch-Boschert K., Lukan N., Popa J., Ternullo M.P., Steidler A., Weiss C., et al. Expression of transketolase TKTL1 predicts colon and urothelial cancer patient survival: Warburg effect reinterpreted. Br. J. Cancer 94 (2006) 578-585
26. Lanoix J., Ouwendijk J., Lin C.C., Stark A., Love H.D., Ostermann J., and Nilsson T. GTP hydrolysis by arf-1 mediates sorting and concentration of Golgi resident enzymes into functional COP I vesicles. EMBO J. 18 (1999) 4935-4948
27. Le-Niculescu H., Niesman I., Fischer T., DeVries L., and Farquhar M.G. Identification and characterization of GIV, a novel Galpha i/s-interacting protein found on COPI, endoplasmic reticulum-Golgi transport vesicles. J. Biol. Chem. 280 (2005) 22012-22020
28. Malhotra V., and Mayor S. Cell biology: the Golgi grows up. Nature 441 (2006) 939-940
29. Malsam J., Satoh A., Pelletier L., and Warren G. Golgin tethers define subpopulations of COPI vesicles. Science 307 (2005) 1095-1098
30. Martinez-Menarguez J.A., Prekeris R., Oorschot V.M., Scheller R., Slot J.W., Geuze H.J., and Klumperman J. Peri-Golgi vesicles contain retrograde but not anterograde proteins consistent with the cisternal progression model of intra-Golgi transport. J. Cell Biol. 155 (2001) 1213-1224
31. Murray R.Z., Wylie F.G., Khromykh T., Hume D.A., and Stow J.L. Syntaxin 6 and Vti1b form a novel SNARE complex, which is up-regulated in activated macrophages to facilitate exocytosis of tumor necrosis Factor-alpha. J. Biol. Chem. 280 (2005) 10478-10483
32. Paiement J., Young R., Roy L., and Bergeron J.J. Isolation of rough and smooth membrane domains of the endoplasmic reticulum from rat liver. In: Celis J., Carter N., Simons K., Small V., Hunter T., and Shotton D.M. (Eds). Cell Biology: A Laboratory Handbook (2005), Elsevier Academic Press, Burlington, MA, USA 41-44
33. Peng R.W. Decoding the interactions of SM proteins with SNAREs. ScientificWorldJournal 5 (2005) 471-477
34. Rabouille C., and Klumperman J. Opinion: The maturing role of COPI vesicles in intra-Golgi transport. Nat. Rev. Mol. Cell Biol. 6 (2005) 812-817
35. Rout M.P., Aitchison J.D., Suprapto A., Hjertaas K., Zhao Y., and Chait B.T. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148 (2000) 635-651
36. Scott M., Lu G., Hallett M., and Thomas D.Y. The Hera database and its use in the characterization of endoplasmic reticulum proteins. Bioinformatics 20 (2004) 937-944
37. Scott M.S., Thomas D.Y., and Hallett M.T. Predicting subcellular localization via protein motif co-occurrence. Genome Res. 14 (2004) 1957-1966
38. Short B., Preisinger C., Korner R., Kopajtich R., Byron O., and Barr F.A. A GRASP55-rab2 effector complex linking Golgi structure to membrane traffic. J. Cell Biol. 155 (2001) 877-883
39. Stojanovic M., Germain M., Nguyen M., and Shore G.C. BAP31 and its caspase cleavage product regulate cell surface expression of tetraspanins and integrin-mediated cell survival. J. Biol. Chem. 280 (2005) 30018-30024
40. Valsdottir R., Hashimoto H., Ashman K., Koda T., Storrie B., and Nilsson T. Identification of rabaptin-5, rabex-5, and GM130 as putative effectors of rab33b, a regulator of retrograde traffic between the Golgi apparatus and ER. FEBS Lett. 508 (2001) 201-209
41. Voeltz G.K., Prinz W.A., Shibata Y., Rist J.M., and Rapoport T.A. A class of membrane proteins shaping the tubular endoplasmic reticulum. Cell 124 (2006) 573-586
42. Wegmann D., Hess P., Baier C., Wieland F.T., and Reinhard C. Novel isotypic gamma/zeta subunits reveal three coatomer complexes in mammals. Mol. Cell. Biol. 24 (2004) 1070-1080
43. Wilson B.S., Nuoffer C., Meinkoth J.L., McCaffery M., Feramisco J.R., Balch W.E., and Farquhar M.G. A Rab1 mutant affecting guanine nucleotide exchange promotes disassembly of the Golgi apparatus. J. Cell Biol. 125 (1994) 557-571
44. Wu C.C., MacCoss M.J., Mardones G., Finnigan C., Mogelsvang S., Yates III J.R., and Howell K.E. Organellar proteomics reveals Golgi arginine dimethylation. Mol. Biol. Cell 15 (2004) 2907-2919
45. Yates III J.R., Gilchrist A., Howell K.E., and Bergeron J.J. Proteomics of organelles and large cellular structures. Nat. Rev. Mol. Cell Biol. 6 (2005) 702-714