Proteomic dissection of the Arabidopsis Golgi and trans-Golgi network

Frontiers in Plant Science

Volumn 3, Issue JAN, 2013, Pages

  Parsons, Harriet T ^a   Drakakaki, Georgia ^b   Heazlewood, Joshua L ^c  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Arabidopsis; Free flow electrophoresis; Golgi; LOPIT; Proteomics; SYP61; Trans Golgi network

Indexed keywords

EID: 84898028540     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2012.00298     Document Type: Article

References (58)

1. Asakura, T., Hirose, S., Katamine, H., Sato, M., Hujiwara, M., Shimamoto, K., et al. (2006). Rice Golgi proteome: analysis of GFP-syp31 labeled cis Golgi membrane. Plant Cell Physiol. 47, S26-S26.
2. Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S. (2002). Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 18, 298-305.
3. Barrowman, J., Bhandari, D., Reinisch, K., and Ferro-Novick, S. (2010). TRAPP complexes in membrane traffic: convergence through a common Rab. Nat. Rev. Mol. Cell Biol. 11, 759-763.
4. Batoko, H., Zheng, H.-Q., Hawes, C., and Moore, I. (2000). A Rab1 GTPase is required for transport between the endoplasmic reticulum and Golgi apparatus and for normal Golgi movement in plants. Plant Cell 12, 2201-2217.
5. Benschop, J. J., Mohammed, S., O'Flaherty, M., Heck, A. J. R., Slijper, M., and Menke, F. L. H. (2007). Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis. Mol. Cell. Proteomics 6, 1198-1214.
6. Bernal, A. J., Jensen, J. K., Harholt, J., Sørensen, S., Moller, I., Blaukopf, C., et al. (2007). Disruption of ATCSLD5 results in reduced growth, reduced xylan and homogalacturonan synthase activity and altered xylan occurrence in Arabidopsis. Plant J. 52, 791-802.
7. Blatt, M. R., Leyman, B., and Geelen, D. (1999). Tansley review no. 108-molecular events of vesicle trafficking and control by SNARE proteins in plants. New Phytol. 144, 389-418.
8. Blum, T., Briesemeister, S., and Kohlbacher, O. (2009). MultiLoc2: integrating phylogeny and gene ontology terms improves subcellular protein localization prediction. BMC Bioinformatics 10:274. doi: 10.1186/1471-2105-10-274
9. Boden, M., and Hawkins, J. (2005). Prediction of subcellular localization using sequence-biased recurrent networks. Bioinformatics 21, 2279-2286.
10. Boevink, P., Oparka, K., Cruz, S. S., Martin, B., Betteridge, A., and Hawes, C. (1998). Stacks on tracks: the plant Golgi apparatus traffics on an actin/ER network. Plant J. 15, 441-447.
11. Brady, S., and Shatkay, H. (2008). EpiLoc: a (working) text-based system for predicting protein subcellular location. Pac. Symp. Biocomput. 13, 604-615.
12. Briesemeister, S., Rahnenfuhrer, J., and Kohlbacher, O. (2010). YLoc-an interpretable web server for predicting subcellular localization. Nucleic Acids Res. 38, W497-W502.
13. Chou, I. T., and Gasser, C. S. (1997). Characterization of the cyclophilin gene family of Arabidopsis thaliana and phylogenetic analysis of known cyclophilin proteins. Plant Mol. Biol. 35, 873-892.
14. Chou, K. C., and Shen, H. B. (2010). Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS ONE 5:e11335. doi: 10.1371/journal.pone.0011335
15. Delgado, I. J., Wang, Z. H., De Rocher, A., Keegstra, K., and Raikhel, N. V. (1998). Cloning and characterization of AtRGP1-a reversibly autoglycosylated Arabidopsis protein implicated in cell wall biosynthesis. Plant Physiol. 116, 1339-1349.
16. Drakakaki, G., Van De Ven, W., Pan, S. Q., Miao, Y. S., Wang, J. Q., Keinath, N. F., et al. (2012). Isolation and proteomic analysis of the SYP61 compartment reveal its role in exocytic trafficking in Arabidopsis. Cell Res. 22, 413-424.
17. Drakakaki, G., Zabotina, O., Delgado, I., Robert, S., Keegstra, K., and Raikhel, N. (2006). Arabidopsis reversibly glycosylated polypeptides 1 and 2 are essential for pollen development. Plant Physiol. 142, 1480-1492.
18. Dunkley, T. P., Watson, R., Griffin, J. L., Dupree, P., and Lilley, K. S. (2004). Localization of organelle proteins by isotope tagging (LOPIT). Mol. Cell. Proteomics 3, 1128-1134.
19. Dunkley, T. P. J., Hester, S., Shadforth, I. P., Runions, J., Weimar, T., Hanton, S. L., et al. (2006). Mapping the Arabidopsis organelle proteome. Proc. Natl. Acad. Sci. U.S.A. 103, 6518-6523.
20. Egelund, J., Petersen, B. L., Motawia, M. S., Damager, I., Faik, A., Olsen, C. E., et al. (2006). Arabidopsis thalianaRGXT1 and RGXT2 encode Golgi-localized (1, 3)-alpha-D-xylosyltransferases involved in the synthesis of pectic rhamnogalacturonan-II. Plant Cell 18, 2593-2607.
21. Emanuelsson, O., Nielsen, H., Brunak, S., and Von Heijne, G. (2000). Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300, 1005-1016.
22. Eubel, H., Meyer, E. H., Taylor, N. L., Bussell, J. D., O'Toole, N., Heazlewood, J. L., et al. (2008). Novel proteins, putative membrane transporters, and an integrated metabolic network are revealed by quantitative proteomic analysis of Arabidopsis cell culture peroxisomes. Plant Physiol. 148, 1809-1829.
23. Feraru, E., Feraru, M. I., Asaoka, R., Paciorek, T., De Rycke, R., Tanaka, H., et al. (2012). BEX5/RabA1b regulates trans-Golgi network-to-plasma membrane protein trafficking in Arabidopsis. Plant Cell 24, 3074-3086.
24. Gao, C., Yu, C. K. Y., Qu, S., San, M. W. Y., Li, K. Y., Lo, S. W., et al. (2012). The Golgi-localized Arabidopsisendomembrane protein12 contains both endoplasmic reticulum export and Golgi retention signals at its C terminus. Plant Cell 24, 2086-2104.
25. Heazlewood, J. L., Verboom, R. E., Tonti-Filippini, J., Small, I., and Millar, A. H. (2007). SUBA: the Arabidopsissubcellular database. Nucleic Acids Res. 35, D213-D218.
26. Horton, P., Park, K. J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J., et al. (2007). WoLF PSORT: protein localization predictor. Nucleic Acids Res. 35, W585-W587.
27. Ingelsson, B., Shapiguzov, A., Kieselbach, T., and Vener, A. V. (2009). Peptidylprolyl isomerase activity in chloroplast thylakoid lumen is a dispensable function of immunophilins in Arabidopsis thaliana. Plant Cell Physiol. 50, 1801-1814.
28. Ito, J., Batth, T. S., Petzold, C. J., Redding-Johanson, A. M., Mukhopadhyay, A., Verboom, R., et al. (2011). Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism. J. Proteome Res. 10, 1571-1582.
29. Kong, Y., Zhou, G., Yin, Y., Xu, Y., Pattathil, S., and Hahn, M. G. (2011). Molecular analysis of a family of Arabidopsis genes related to galacturonosyltransferases. Plant Physiol. 155, 1791-1805.
30. Latijnhouwers, M., Gillespie, T., Boevink, P., Kriechbaumer, V., Hawes, C., and Carvalho, C. M. (2007). Localization and domain characterization of Arabidopsis golgin candidates. J. Exp. Bot. 58, 4373-4386.
31. Lee, C. H., O'Neill, M. A., Tsumuraya, Y., Darvill, A. G., and Ye, Z. H. (2007). The irregular xylem9 mutant is deficient in xylan xylosyltransferase activity. Plant Cell Physiol. 48, 1624-1634.
32. Marmagne, A., Ferro, M., Meinnel, T., Bruley, C., Kuhn, L., Garin, J., et al. (2007). A high content in lipid-modified peripheral proteins and integral receptor kinases features in the Arabidopsis plasma membrane proteome. Mol. Cell. Proteomics 6, 1980-1996.
33. Mast, S., Peng, L. F., Jordan, T. W., Flint, H., Phillips, L., Donaldson, L., et al. (2010). Proteomic analysis of membrane preparations from developing Pinus radiata compression wood. Tree Physiol. 30, 1456-1468.
34. Matsuda, S., Vert, J. P., Saigo, H., Ueda, N., Toh, H., and Akutsu, T. (2005). A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Sci. 14, 2804-2813.
35. Mitra, S. K., Walters, B. T., Clouse, S. D., and Goshe, M. B. (2009). An efficient organic solvent based extraction method for the proteomic analysis of Arabidopsis plasma membranes. J. Proteome Res. 8, 2752-2767.
36. Morre, D. J., and Mollenhauer, H. H. (1964). Isolation of Golgi apparatus from plant cells. J. Cell Biol. 23, 295-305.
37. Morre, D. J., and Mollenhauer, H. H. (2009). The Golgi Apparatus: The First 100 Years. New York: Springer.
38. Mouille, G., Ralet, M. C., Cavelier, C., Eland, C., Effroy, D., Hematy, K., et al. (2007). Homogalacturonan synthesis in Arabidopsis thaliana requires a Golgi-localized protein with a putative methyltransferase domain. Plant J. 50, 605-614.
39. Nikolovski, N., Rubtsov, D., Segura, M. P., Miles, G. P., Stevens, T. J., Dunkley, T. P. J., et al. (2012). Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. Plant Physiol. 160, 1037-1051.
40. Niu, B., Jin, Y. H., Feng, K. Y., Lu, W. C., Cai, Y. D., and Li, G. Z. (2008). Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins. Mol. Divers. 12, 41-45.
41. Ondzighi, C. A., Christopher, D. A., Cho, E. J., Chang, S. C., and Staehelin, L. A. (2008). Arabidopsis protein disulfide isomerase-5 inhibits cysteine proteases during trafficking to vacuoles before programmed cell death of the endothelium in developing seeds. Plant Cell 20, 2205-2220.
42. Osterrieder, A. (2012). Tales of tethers and tentacles: golgins in plants. J. Microsc. 247, 68-77.
43. Paredez, A. R., Somerville, C. R., and Ehrhardt, D. W. (2006). Visualization of cellulose synthase demonstrates functional association with microtubules. Science 312, 1491-1495.
44. Parsons, H. T., Christiansen, K., Knierim, B., Carroll, A., Ito, J., Batth, T. S., et al. (2012a). Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol. 159, 12-26.
45. Parsons, H. T., González Fernández-Niño, S. M., and Heazlewood, J. L. (2012b). "Separation of the plant Golgi apparatus and endoplasmic reticulum by free-flow electrophoresis, " in Plant Proteomics: Methods and Protocols, 2 Edn, eds J. V. Jorrín-Novo, S. Komatsu, W. Weckwerth, and S. Weinkoop (New York: Springer) (in press).
46. Parsons, H. T., Ito, J., Park, E., Carroll, A. W., Joshi, H. J., Petzold, C. J., et al. (2012c). "The current state of the Golgi proteomes, " in Proteomic Applications in Biology, eds J. L. Heazlewood and C. J. Petzold (Rijeka: InTech), 167-188.
47. Pena, M. J., Zhong, R. Q., Zhou, G. K., Richardson, E. A., O'Neill, M. A., Darvill, A. G., et al. (2007). Arabidopsisirregular xylem8 and irregular xylem9: implications for the complexity of glucuronoxylan biosynthesis. Plant Cell 19, 549-563.
48. Pierleoni, A., Martelli, P. L., Fariselli, P., and Casadio, R. (2006). BaCelLo: a balanced subcellular localization predictor. Bioinformatics 22, e408-e416.
49. Rautengarten, C., Ebert, B., Herter, T., Petzold, C. J., Ishii, T., Mukhopadhyay, A., et al. (2011). The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis. Plant Cell 23, 1373-1390.
50. Saint-Jore-Dupas, C., Nebenfuhr, A., Boulaflous, A., Follet-Gueye, M. L., Plasson, C., Hawes, C., et al. (2006). Plant N-glycan processing enzymes employ different targeting mechanisms for their spatial arrangement along the secretory pathway. Plant Cell 18, 3182-3200.
51. Sanderfoot, A. A., and Raikhel, N. V. (1999). The specificity of vesicle trafficking: coat proteins and SNAREs. Plant Cell 11, 629-641.
52. Small, I., Peeters, N., Legeai, F., and Lurin, C. (2004). Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4, 1581-1590.
53. Surpin, M., and Raikhel, N. (2004). Traffic jams affect plant development and signal transduction. Nat. Rev. Mol. Cell Biol. 5, 100-109.
54. Tamura, T., and Akutsu, T. (2007). Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition. BMC Bioinformatics 8:466. doi: 10.1186/1471-2105-8-466
55. Tanaka, N., Fujita, M., Handa, H., Murayama, S., Uemura, M., Kawamura, Y., et al. (2004). Proteomics of the rice cell: systematic identification of the protein populations in subcellular compartments. Mol. Genet. Genomics 271, 566-576.
56. Taylor, R. S., Jones, S. M., Dahl, R. H., Nordeen, M. H., and Howell, K. E. (1997). Characterization of the Golgi complex cleared of proteins in transit and examination of calcium uptake activities. Mol. Biol. Cell 8, 1911-1931.
57. Woollard, A. A., and Moore, I. (2008). The functions of Rab GTPases in plant membrane traffic. Curr. Opin. Plant Biol. 11, 610-619.
58. Zhang, Z. J., and Peck, S. C. (2011). Simplified enrichment of plasma membrane proteins for proteomic analyses in Arabidopsis thaliana. Proteomics 11, 1780-1788.