Localization of organelle proteins by isotope tagging (LOPIT)

Molecular and Cellular Proteomics

Volumn 3, Issue 11, 2004, Pages 1128-1134

  Dunkley, T P J ^a   Watson, R ^b   Griffin, J L ^a   Dupree, P ^a   Lilley, K S ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b Applied Biosystems   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

ARABIDOPSIS; ARTICLE; CELL ORGANELLE; CELLULAR DISTRIBUTION; CENTRIFUGATION; DATA ANALYSIS; DENSITY GRADIENT; ENDOPLASMIC RETICULUM; GOLGI COMPLEX; HIGH THROUGHPUT SCREENING; ISOTOPE LABELING; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN TRANSPORT; PROTEOMICS; QUANTITATIVE ANALYSIS;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; ENDOPLASMIC RETICULUM; GOLGI APPARATUS; ISOTOPE LABELING; MASS SPECTROMETRY; MEMBRANE PROTEINS; ORGANELLES; SUBCELLULAR FRACTIONS;

ARABIDOPSIS;

EID: 10944246119     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.T400009-MCP200     Document Type: Article

References (48)

1. Dreger, M. (2003) Subcellular proteomics. Mass Spectrom. Rev. 22, 27-56
2. Dunkley, T. P., Dupree, P., Watson, R. B., and Lilley, K. S. (2004) The use of isotope-coded affinity tags (ICAT) to study organelle proteomes in Arabidopsis thaliana. Biochem. Soc. Trans. 32, 520-523
3. de Duve, C. (1971) Tissue fractionation. J. Cell Biol. 50, 20D-55D
4. Dunphy, W. G., and Rothman, J. E. (1983) Compartmentation of asparagine-linked oligosaccharide processing in the Golgi-apparatus. J. Cell Biol. 97, 270-275
5. Andersen, J. S., Wilkinson, C. J., Mayor, T., Mortensen, P., Nigg, E. A., and Mann, M. (2003) Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426, 570-574
6. Sherrier, D. J., Prime, T. A., and Dupree, P. (1999) Glycosylphosphatidylinositol-anchored cell-surface proteins from Arabidopsis. Electrophoresis 20, 2027-2035
7. Mogelsvang, S. (1999) A family of Arabidopsis thaliana Golgi glycosyltransferases. Ph.D. thesis, University of Cambridge
8. Wee, E. G. T., Sherrier, D. J., Prime, T. A., and Dupree, P. (1998) Targeting of active sialyltransferase to the plant Golgi apparatus. Plant Cell 10, 1759-1768
9. Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. L. (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305, 567-580
10. Ford, T., Graham, J., and Rickwood, D. (1994) lodixanol - a nonionic isosmotic centrifugation medium for the formation of self-generated gradients. Anal. Biochem. 220, 360-366
11. Graham, J., Ford, T., and Rickwood, D. (1994) The preparation of subcellular organelles from mouse-liver in self-generated gradients of iodixanol. Anal. Biochem. 220, 367-373
12. Gygi, S. P., Rist, B., Gerber, S. A., Turecelk, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999
13. Fujiki, Y., Hubbard, A. L., Fowler, S., and Lazarow, P. B. (1982) Isolation of intracellular membranes by means of sodium-carbonate treatment - Application to endoplasmic-reticulum. J. Cell Biol. 93, 97-102
14. Han, D. K., Eng J., Zhou, H. L., and Aebersold, R. (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol., 19, 946-951
15. Lindon, J. C., Holmes, E., and Nicholson, J. K. (2001) Pattern recognition methods and applications in biomedical magnetic resonance. Progr. Nuclear Magn. Reson. Spectr. 39, 1-40
16. Karp, N. A., Griffin, J. L., and Lilley, K. S. (2004) Application of partial least squares discriminant analysis to two dimensional difference gel studies in expression proteomics. Proteomics, in press.
17. Vitale, A., and Denecke, J. (1999) The endoplasmic reticulum - Gateway of the secretory pathway. Plant Cell 11, 615-628
18. Neumann, U., Brandizzi, F., and Hawes, C. (2003) Protein transport in plant cells: in and out of the Golgi. Ann. Botany 92, 167-180
19. Bell, A. W., Ward, M. A., Blackstock, W. P., Freeman, H. N. M., Choudhary, J. S., Lewis, A. P., Chotai, D., Fazel, A., Gushue, J. N., Paiement, J., Palcy, S., Chevet, E., Lafreniere-Roula, M., Solari, R., Thomas, D. Y., Rowley, A., and Bergeron, J. J. M., (2001) Proteomics characterization of abundant Golgi membrane proteins. J. Biol. Chem. 276, 5152-5165
20. Wu, C. C., MacCoss, M. J., Mardones, G., Finnigan, C., Mogelsvang, S., Yates, J. R. 3rd, and Howell, K. E. (2004) Organellar proteomics reveals Golgi arginine dimethylation. Mol. Biol. Cell, 15, 2907-2919
21. Lisenbee, C. S., Karnik, S. K., and Trelease, R. N. (2003) Overexpression and mislocalization of a tail-anchored GFP redefines the identity of peroxisomal ER. Traffic 4, 491-501
22. Bakker, H., Schijlen, E., de Vries, T., Schiphorst, W., Jordi, W., Lommen, A., Bosch, D., and van Die, I. (2001) Plant members of the alpha 1 -> 3/4-fucosyltransferase gene family encode an alpha 1 -> 4-fucosyltransferase, potentially involved in Lewis(a) biosynthesis, and two core alpha 1 -> 3- fucosyltransferases. FEBS Lett. 507, 307-312
23. Kornfeld, R., and Kornfeld, S. (1985) Assembly of asparagine-linked oligosaccharides. Annu. Rev. Biochem. 54, 631-664
24. Bakker, H., Lommen, A., Jordi, W., Stiekema, W., and Bosch, D. (1999) An Arabidopsis thaliana cDNA complements the N-acetylglucosaminyltransferase I deficiency of CHO Lec1 cells. Biochem. Biophys. Res. Commun. 261, 829-832
25. 2+ -ATPase in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 94, 8579-8584
26. BarPeled, M., and Raikhel, N. V. (1997) Characterization of AtSEC12 and AtSAR1 - Proteins likely involved in endoplasmic reticulum and Golgi transport. Plant Physiol. 114, 315-324
27. 5 reductase from Arabidopsis. Plant Physiol. 119, 353-361
28. Huang, L. Q., Franklin, A. E., and Hoffman, N. E. (1993) Primary structure and characterization of an Arabidopsis thaliana calnexin-like protein. J. Biol. Chem. 268, 6560-6566
29. Haferkamp, I., Hackstein, J. H. P., Voncken, F. G. J., Schmit, G., and Tjaden, J. (2002) Functional integration of mitochondrial and hydrogenosomal ADP/ATP carriers in the Escherichia coli membrane reveals different biochemical characteristics for plants, mammals and anaerobic chytrids. Eur. J. Biochem. 269, 3172-3181
30. Takabatake, R., Hata, S., Taniguchi, M., Kouchi, H., Sugiyama, T., and Izui, K. (1999) Isolation and characterization of cDNAs encoding mitochondrial phosphate transporters in soybean, maize, rice, and Arabidopsis. Plant Mol. Biol. 40, 479-486
31. Hamel, P., Saint-Georges, Y., de Pinto, B., Lachacinski, N., Altamura, N., and Dujardin, G. (2004) Redundancy in the function of mitochondrial phosphate transport in Saccharomyces cerevisiae and Arabidopsis thaliana. Mol. Microbiol. 51, 307-317
32. Picault, N., Palmieri, L., Pisano, I., Hodges, M., and Palmieri, F. (2002) Identification of a novel transporter for dicarboxylates and tricarboxylates in plant mitochondria - Bacterial expression, reconstitution, functional characterization, and tissue distribution. J. Biol. Chem. 277, 24204-24211
33. Schnurr, J. A., Shockey, J. M., de Boer, G. J., and Browse, J. A. (2002) Fatty acid export from the chloroplast. Molecular characterization of a major plastidial acyl-coenzyme A synthetase from Arabidopsis. Plant Physiol. 129, 1700-1709
34. Berkemeyer, M., Scheibe, R., and Ocheretina, O. (1998) A novel, nonredox-regulated NAD-dependent malate dehydrogenase from chloroplasts of Arabidopsis thaliana L. J. Biol. Chem. 273, 27927-27933
35. +-ATPase) of Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 86, 1234-1238
36. Henrissat, B., Coutinho, P. M., and Davies, G. J. (2001) A census of carbohydrate-active enzymes in the genome of Arabidopsis thaliana. Plant Mol. Biol. 47, 55-72
37. Faik, A., Price, N. J., Raikhel, N. V., and Keegstra, K. (2002) An Arabidopsis gene encoding an alpha-xylosyltransferase involved in xyloglucan biosynthesis. Proc. Natl. Acad. Sci. U. S. A. 99, 7797-7802
38. Bouton, S., Leboeuf, E., Mouille, G., Leydecker, M. T., Talbotec, J., Granier, F., Lahaye, M., Hofte, H., and Truong, H. N. (2002) Quasimodo1 encodes a putative membrane-bound glycosyltransferase required for normal pectin synthesis and cell adhesion in Arabidopsis. Plant Cell 14, 2577-2590
39. Abeijon, C., Yanagisawa, K., Mandon, E. C., Hausler, A., Moremen, K., Hirschberg, C. B., and Robbins, P. W. (1993) Guanosine diphosphatase is required for protein and sphingolipid glycosylation in the Golgi lumen of Saccharomyces cerevisiae. J. Cell Biol. 122, 307-323
40. Kushiro, M., Nakano, T., Sato, K., Yamagishi, K., Asami, T., Nakano, A., Takatsuto, S., Fujioka, S., Ebizuka, Y., and Yoshida, S. (2001) Obtusifoliol 14 alpha-demethylase (CYP51) antisense Arabidopsis shows slow growth and long life. Biochem. Biophys. Res. Commun. 285, 98-104
41. Xu, X. J., Dietrich, C. R., Lessire, R., Nikolau, B. J., and Schnable, P. S. (2002) The endoplasmic reticulum-associated maize GL8 protein is a component of the acyl-coenzyme A elongase involved in the production of cuticular waxes. Plant Physiol. 128, 924-934
42. Harnikort, V., Prakash, K., Marcantonio, E., Colman, D. R., Rosenfeld, M. G., Adesnik, M., Sabatini, D. D., and Kreibich, G. (1987) Isolation and characterization of cDNA clones for rat ribophorin-1 - Complete coding sequence and in vitro synthesis and insertion of the encoded product into endoplasmic-reticulum membranes. J. Cell Biol. 104, 855-863
43. Ro, D. K., Mah, N., Ellis, B. E., and Douglas, C. J. (2001) Functional characterization and subcellular localization of poplar (Populus trichocarpa × Populus deltoides) cinnamate 4-hydroxylase. Plant Physiol. 126, 317-329
44. Sevier, C. S., and Kaiser, C. A. (2002) Formation and transfer of disulphide bonds in living cells. Nat. Rev. Mol. Cell. Biol. 3, 836-847
45. Hanada, K. (2003) Serine palmitoyltransferase, a key enzyme of sphingolipid metabolism. Biochim. Biophys. Acta Mol. Cell. Biol. Lipids 1632, 16-30
46. Michalecka, A. M., Svensson, A. S., Johansson, F. I., Agius, S. C., Johanson, U., Brennicke, A., Binder, S., and Rasmusson, A. G. (2003) Arabidopsis genes encoding mitochondrial type II NAD(P)H dehydrogenases have different evolutionary origin and show distinct responses to light. Plant Physiol. 133, 642-652
47. Schnell, D. J., Kessler, F., and Blobel, G. (1994) Isolation of components of the chloroplast protein import machinery. Science 266, 1007-1012
48. Hinnah, S. C., Hill, K., Wagner, R., Schlicher, T., and Soll, J. (1997) Reconstitution of a chloroplast protein import channel. EMBO J. 16, 7351-7360