Proteomics of endosomal compartments from plants case study: Isolation of trans-golgi network vesicles

Methods in Molecular Biology

Volumn 1209, Issue , 2014, Pages 179-187

  Park, Eunsook ^a   Drakakaki, Georgia ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Endomembrane trafficking; Immunoisolation; Proteomics; SYP61; Trans Golgi network (TGN); Vesicle isolation

Indexed keywords

ARABIDOPSIS PROTEIN; PROTEIN A;

ARABIDOPSIS; ARTICLE; CELL COMPARTMENTALIZATION; CELL ISOLATION; ENDOPLASMIC RETICULUM; ENDOSOME; LIQUID CHROMATOGRAPHY; NONHUMAN; PLANT DEVELOPMENT; PLANT GROWTH; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEOMICS; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY; TRANS GOLGI NETWORK; TRANSMISSION ELECTRON MICROSCOPY; WESTERN BLOTTING; BIOSYNTHESIS; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR BIOLOGY; PROCEDURES; TRANSPORT AT THE CELLULAR LEVEL;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BIOLOGICAL TRANSPORT; ENDOSOMES; GENE EXPRESSION REGULATION, PLANT; MOLECULAR BIOLOGY; PROTEOMICS; TRANS-GOLGI NETWORK;

EID: 84925883202     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1420-3_14     Document Type: Article

References (25)

1. Surpin M, Raikhel N (2004) Traffic jams affect plant development and signal transduction. Nat Rev Mol Cell Biol 5:100-109
2. Worden N, Park E, Drakakaki G (2012) Trans- Golgi network: an intersection of trafficking cell wall components. J Integr Plant Biol 54: 875-886
3. Hicks GR, Raikhel NV (2010) Advances in dissecting endomembrane trafficking with small molecules. Curr Opin Plant Biol 13: 706-713
4. Brandizzi F, Fricker M, Hawes C (2002) A greener world: the revolution in plant bioimaging. Nat Rev Mol Cell Biol 3:520-530
5. Sparkes I, Brandizzi F (2012) Fluorescent protein- based technologies: shedding new light on the plant endomembrane system. Plant J 70:96-107
6. Geldner N, Denervaud-Tendon V, Hyman DL, Mayer U, Stierhof YD, Chory J (2009) Rapid, combinatorial analysis of membrane compartments in intact plants with a multicolor marker set. Plant J 59:169-178
7. Drakakaki G, Robert S, Szatmari A-M, Brown MQ, Nagawa S, Van Damme D, Leonard M, Yang Z, Girke T, Schmid SL, Russinova E, Friml J, Raikhel NV, Hicks GR (2011) Clusters of bioactive compounds target dynamic endomembrane networks in vivo. Proc Natl Acad Sci U S A 108:17850-17855
8. Kleffmann T, Russenberger D, von Zychlinski A, Christopher W, Sjölander K, Gruissem W, Baginsky S (2004) The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. Curr Biol 14:354-362
9. Mosley AL, Florens L, Wen Z, Washburn MP (2009) A label free quantitative proteomic analysis of the Saccharomyces cerevisiae nucleus. J Proteomics 72:110-120
10. Carter C, Pan S, Zouhar J, Avila EL, Girke T, Raikhel NV (2004) The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins. Plant Cell 16:3285-3303
11. Eubel H, Heazlewood JL, Millar AH (2006) Isolation and subfractionation of plant mitochondria for proteomic analysis. Methods Mol Biol 355:49-62
12. Eubel H, Meyer EH, Taylor NL, Bussell JD, O'Toole N, Heazlewood JL, Castleden I, Small ID, Smith SM, Millar AH (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
13. Asakura T, Hirose S, Katamine H, Kitajima A, Hori H, Sato MH, Fujiwara M, Shimamoto K, Mitsui T (2006) Isolation and proteomic analysis of rice Golgi membranes: cis-Golgi membranes labeled with GFP-SYP31. Plant Biotechnol 23:475-485
14. Dunkley TPJ, Hester S, Shadforth IP, Runions J, Weimar T, Hanton SL, Griffin JL, Bessant C, Brandizzi F, Hawes C, Watson RB, Dupree P, Lilley KS (2006) Mapping the Arabidopsis organelle proteome. Proc Natl Acad Sci 103:6518-6523
15. Nikolovski N, Rubtsov D, Segura MP, Miles GP, Stevens TJ, Dunkley TPJ, Munro S, Lilley KS, Dupree P (2012) Putative glycosyltransferases and other plant golgi apparatus proteins are revealed by LOPIT proteomics. Plant Physiol 160:1037-1051
16. Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Smith-Moritz AM, Morrison S, McInerney P, Hadi MZ, Auer M, Mukhopadhyay A, Petzold CJ, Scheller HV, Loque D, Heazlewood JL (2012) Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol 159:12-26
17. Drakakaki G, van de Ven W, Pan S, Miao Y, Wang J, Keinath NF, Weatherly B, Jiang L, Schumacher K, Hicks G, Raikhel N (2012) Isolation and proteomic analysis of the SYP61 compartment reveal its role in exocytic trafficking in Arabidopsis. Cell Res 22:413-424
18. Parsons HT, Drakakaki G, Heazlewood JL (2012) Proteomic dissection of the Arabidopsis Golgi and trans-Golgi network. Front Plant Sci 3:298
19. Drakakaki G, Zabotina O, Delgado I, Robert S, Keegstra K, Raikhel N (2006) Arabidopsis reversibly glycosylated polypeptides 1 and 2 are essential for pollen development. Plant Physiol 142:1480-1492
20. Morris JA, Dorner AJ, Edwards CA, Hendershot LM, Kaufman RJ (1997) Immunoglobulin binding protein (BiP) function is required to protect cells from endoplasmic reticulum stress but is not required for the secretion of selective proteins. J Biol Chem 272:4327-4334
21. da Silva CA, Marty-Mazars D, Bassham DC, Sanderfoot AA, Marty F, Raikhel NV (1997) The syntaxin homolog AtPEP12p resides on a late post-Golgi compartment in plants. Plant Cell 9:571-582
22. Fonslow BR, Carvalho PC, Academia K, Freeby S, Xu T, Nakorchevsky A, Paulus A, Yates JR (2011) Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT. J Proteome Res 10:3690-3700
23. Silva JC, Denny R, Dorschel CA, Gorenstein M, Kass IJ, Li GZ, McKenna T, Nold MJ, Richardson K, Young P, Geromanos S (2005) Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem 77:2187-2200
24. Weatherly DB, Atwood JA 3rd, Minning TA, Cavola C, Tarleton RL, Orlando R (2005) A Heuristic method for assigning a falsediscovery rate for protein identifications from Mascot database search results. Mol Cell Proteomics 4:762-772
25. Cutillas PR, Vanhaesebroeck B (2007) Quantitative profile of five murine core proteomes using label-free functional proteomics. Mol Cell Proteomics 6:1560-1573