Vectorial proteomics

IUBMB Life

Volumn 57, Issue 6, 2005, Pages 433-440

  Vener, Alexander V ^a   Strålfors, Peter ^a  

^a LINKÖPING UNIVERSITY   (Sweden)

Author keywords

Mass spectrometry; Membrane proteins; Post translational modifications; Protein phosphorylation; Protein topology; Proteolysis; Vectorial proteomics

Indexed keywords

MEMBRANE PROTEIN; TRYPSIN;

ADIPOCYTE; CAVEOLA; CHROMATOGRAPHY; EXPERIMENTAL MODEL; HUMAN; HUMAN CELL; HUMAN EXPERIMENT; MASS SPECTROMETRY; MEMBRANE VESICLE; METHODOLOGY; PLANT CELL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; REVIEW;

ANIMALS; CAVEOLAE; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; HUMANS; PHOSPHORYLATION; PLANTS; PROTEIN INTERACTION MAPPING; PROTEOMICS;

EID: 23044476511     PISSN: 15216543     EISSN: None     Source Type: Journal    
DOI: 10.1080/15216540500138360     Document Type: Review

References (39)

1. Langen, H., Takacs, B., Evers, S., Berndt, P., Lahm, H. W., Wipf, B., Gray, C., and Fountoulakis, M. (2000) Two-dimensional map of the proteome of Haemophilus influenzae. Electrophoresis 21, 411-429.
2. Washburn, M. P., Wolters, D., and Yates, J. R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247.
3. Rezaul, K., Wu, L., Mayya, V., Hwang, S. I., and Han, D. K. (2005) A systematic characterization of mitochondrial proteome from a human T leukemia cells. Mol. Cell Proteomics 4, 169-181.
4. Friso, G., Giacomelli, L., Ytterberg, A. J., Peltier, J. B., Rudella, A., Sun, Q., and Wijk, K. J. (2004) In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database. Plant Cell 16, 478-499.
5. Pendle, A. F., Clark, G. P., Boon, R., Lewandowska, D., Lam, Y. W., Andersen, J., Mann, M., Lamond, A. I., Brown, J. W., and Shaw, P. J. (2005) Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Mol. Biol. Cell 16, 260-269.
6. Grunenfelder, B., Rummel, G., Vohradsky, J., Roder, D., Langen, H., and Jenal, U. (2001) Proteomic analysis of the bacterial cell cycle. Proc. Natl. Acad. Sci. USA 98, 4681-4686.
7. Andersen, J. S., Lam, Y. W., Leung, A. K., Ong, S. E., Lyon, C. E., Lamond, A. I., and Mann, M. (2005) Nucleolar proteome dynamics. Nature 433, 77-83.
8. Wu, C. C., and Yates, J. R., 3rd (2003) The application of mass spectrometry to membrane proteomics. Nat. Biotechnol. 21, 262-267.
9. Wu, C. C., MacCoss, M. J., Howell, K. E., and Yates, J. R., 3rd (2003) A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol. 21, 532-538.
10. Durr, E., Yu, J., Krasinska, K. M., Carver, L. A., Yates, J. R., Testa, J. E., Oh, P., and Schnitzer, J. E. (2004) Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat. Biotechnol. 22, 985-992.
11. Aboulaich, N., Vainonen, J. P., Stralfors, P., and Vener, A. V. (2004) Vectorial proteomics reveal targeting, phosphorylation and specific fragmentation of polymerase I and transcript release factor (PTRF) at the surface of caveolae in human adipocytes. Biochem. J. 383, 237-248.
12. Cohen, A. W., Hnasko, R., Schubert, W., and Lisanti, M. P. (2004) Role of caveolae and caveolins in health and disease. Physiol. Rev. 84, 1341-1379.
13. Strålfors, P. (2005) Insulin signalling and caveolae. Adv. Mol. Cell Biol. 36, in press
14. Tandon, N. N., Lipsky, R. H., Burgess, W. H., and Jamieson, G. A. (1989) Isolation and characterization of platelet glycoprotein IV (CD36). J. Biol. Chem. 264, 7570-7575.
15. Souto, R. P., Vallega, G., Wharton, J., Vinten, J., Tranum-Jensen, J., and Pilch, P. F. (2003) Immunopurification and characterization of rat adipocyte caveolae suggest their dissociation from insulin signaling. J. Biol. Chem. 278, 18321-18329.
16. Elortza, F., Nuhse, T. S., Foster, L. J., Stensballe, A., Peck, S. C., and Jensen, O. N. (2003) Proteomic analysis of glycosylphosphatidylinositol- anchored membrane proteins. Mol. Cell Proteomics 2, 1261-1270.
17. Johansson, F., Olbe, M., Sommarin, M., and Larsson, C. (1995) Brij 58, a polyoxyethylene acyl ether, creates membrane vesicles of uniform sidedness. A new tool to obtain inside-out (cytoplasmic side-out) plasma membrane vesicles. Plant J. 7, 165-173.
18. Nuhse, T. S., Stensballe, A., Jensen, O. N., and Peck, S. C. (2003) Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol. Cell Proteomics 2, 1234-1243.
19. Vener, A. V., Harms, A., Sussman, M. R., and Vierstra, R. D. (2001) Mass spectrometric resolution of reversible protein phosphorylation in photosynthetic membranes of Arabidopsis thaliana. J. Biol. Chem. 276, 6959-6966.
20. Hansson, M., and Vener, A. V. (2003) Identification of three previously unknown in vivo protein phosphorylation sites in thylakoid membranes of Arabidopsis thaliana. Mol. Cell Proteomics 2, 550-559.
21. Turkina, M. V., Villarejo, A., and Vener, A. V. (2004) The transit peptide of CP29 thylakoid protein in Chlamydomonas reinhardtii is not removed but undergoes acetylation and phosphorylation. FEBS Lett. 564, 104-108.
22. Vainonen, J. P., Aboulaich, N., Turkina, M. V., Strålfors, P., and Vener, A. V. (2004) N-terminal processing and modifications of caveolin-1 in caveolae from human adipocytes. Biochem. Biophys. Res. Commun. 320, 480-486.
23. Jansa, P., Mason, S. W., Hoffmann-Rohrer, U., and Grummt, I. (1998) Cloning and functional characterization of PTRF, a novel protein which induces dissociation of paused ternary transcription complexes. EMBO J. 17, 2855-2864.
24. Jansa, P., Burek, C., Sander, E. E., and Grummt, I. (2001) The transcript release factor PTRF augments ribosomal gene transcription by facilitating reinitiation of RNA polymerase I. Nucleic Acids Res. 29, 423-429.
25. Rechsteiner, M., and Rogers, S. W. (1996) PEST sequences and regulation by proteolysis. Trends Biochem. Sci. 21, 267-271.
26. Gustavsson, J., Parpal, S., Karlsson, M., Ramsing, C., Thorn, H., Borg, M., Lindroth, M., Peterson, K. H., Magnusson, K. E., and Strålfors, P. (1999) Localization of the insulin receptor in caveolae of adipocyte plasma membrane. FASEB J. 13, 1961-1971.
27. Aro, E.-M., and Ohad, I. (2003) Redox regulation of thylakoid protein phosphorylation. Antioxid. Redox. Signal. 5, 55-67.
28. Aro, E. M., Rokka, A., and Vener, A. V. (2004) Determination of phosphoproteins in higher plant thylakoids. Methods Mol. Biol. 274, 271-286.
29. Carlberg, I., Hansson, M., Kieselbach, T., Schroder, W. P., Andersson, B., and Vener, A. V. (2003) A novel plant protein undergoing light-induced phosphorylation and release from the photosynthetic thylakoid membranes. Proc. Natl. Acad. Sci. USA 100, 757-762.
30. Ficarro, S., Chertihin, O., Westbrook, V. A., White, F., Jayes, F., Kalab, P., Marto, J. A., Shabanowitz, J., Herr, J. C., Hunt, D. F., and Visconti, P. E. (2003) Phosphoproteome analysis of capacitated human sperm. Evidence of tyrosine phosphorylation of a kinase-anchoring protein 3 and valosin-containing protein/p97 during capacitation. J. Biol. Chem. 278, 11579-11589.
31. He, T., Alving, K., Feild, B., Norton, J., Joseloff, E. G., Patterson, S. D., and Domon, B. (2004) Quantitation of phosphopeptides using affinity chromatography and stable isotope labeling. J. Am. Soc. Mass Spectrom. 15, 363-373.
32. Hegeman, A. D., Harms, A. C., Sussman, M. R., Bunner, A. E., and Harper, J. F. (2004) An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins. J. Am. Soc. Mass Spectrom. 15, 647-653.
33. Loyet, K. M., Stults, J. T., and Arnott, D. (2005) Mass spectrometric contributions to the practice of phosphorylation site mapping through 2003: A literature review. Mol. Cell Proteomics 4, 235-245.
34. Nuhse, T. S., Stensballe, A., Jensen, O. N., and Peck, S. C. (2004) Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell 16, 2394-2405.
35. Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J., Ross, M. M., Shabanowitz, J., Hunt, D. F., and White, F. M. (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20, 301-305.
36. Leite, J. F., Amoscato, A. A., and Cascio, M. (2000) Coupled proteolytic and mass spectrometry studies indicate a novel topology for the glycine receptor. J. Biol. Chem. 275, 13683-13689.
37. Jensen, O. N. (2004) Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr. Opin. Chem. Biol. 8, 33-41.
38. Borner, G. H., Lilley, K. S., Stevens, T. J., and Dupree, P. (2003) Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis. Plant Physiol. 132, 568-577.
39. Borner, G. H., Sherrier, D. J., Weimar, T., Michaelson, L. V., Hawkins, N. D., Macaskill, A., Napier, J. A., Beale, M. H., Lilley, K. S., and Dupree, P. (2005) Analysis of detergent-resistant membranes in Arabidopsis. Evidence for plasma membrane lipid rafts. Plant Physiol. 137, 104-116.