Isolation of the Arabidopsis phosphoproteome using a biotin-tagging approach

Molecules and Cells

Volumn 24, Issue 2, 2007, Pages 268-275

  Kwon, Sun Jae ^a   Choi, Eun Young ^a   Seo, Jong Bok ^b   Park, Ohkmae K ^a  

^a Korea University   (South Korea)

^b Korea Basic Science Institute (KBSI)   (South Korea)

Author keywords

Arabidopsis; Biotin tagging; Mass spectrometry; Phosphoproteome; Protein phosphorylation

Indexed keywords

AVIDIN; BIOTIN; OXYGENASE; PHOSPHOPROTEOME; PROTEOME; RIBULOSEBISPHOSPHATE CARBOXYLASE; SERINE; THREONINE; UNCLASSIFIED DRUG;

AFFINITY CHROMATOGRAPHY; ARABIDOPSIS; ARTICLE; BIOTINYLATION; CHEMICAL REACTION; CONTROLLED STUDY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PROTEIN ANALYSIS; PROTEIN ISOLATION; PROTEIN PHOSPHORYLATION; SEEDLING; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ARABIDOPSIS; BIOTIN; BIOTINYLATION; CHEMICAL FRACTIONATION; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; PHOSPHOPROTEINS; PLANT PROTEINS; POLYETHYLENE GLYCOLS; PROTEOME; PROTEOMICS; RIBULOSE-BISPHOSPHATE CARBOXYLASE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

ARABIDOPSIS;

EID: 36549010017     PISSN: 10168478     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (35)

1. Baudry, A., Caboche, M., and Lepiniec, L. (2006) TT8 controls its own expression in a feedback regulation involving TTG1 and homologous MYB and bHLH factors, allowing a strong and cell-specific accumulation of flavonoids in Arabidopsis thaliana. Plant J. 46, 768-779.
2. Bykova, N. V., Egsgaard, H., and Moller, I. M. (2003) Identification of 14 new phosphoproteins involved in important plant mitochondrial processes. FEBS Lett. 540, 141-146.
3. Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J., Ross, M. M., et al. (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 30, 301-305.
4. Fillingame, R. H. and Dmitriev, O. Y. (2000) The oligomeric subunit C rotor in the fo sector of ATP synthase: unresolved questions in our understanding of function. J. Bioenerg. Biomembr. 32, 433-439.
5. Gaberc-Porekar, V. and Menart, V. (2001) Perspectives of immobilized-metal affinity chromatography. J. Biochem. Biophys. Methods 49, 335-360.
6. Goshe, M. B., Conrads, T. P., Panisko, E. A., Angell, N. H., Veenstra, T. D., et al. (2001) Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. Anal. Chem. 73, 2578-2586.
7. Gronborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. S., Ohara, O., et al. (2002) A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, frigg, as a protein kinase a substrate. Mol. Cell. Proteomics 1, 517-527.
8. Heese, A., Ludwig, A. A., and Jones, J. D. (2005) Rapid phosphorylation of a syntaxin during the Avr9/Cf-9-race-specific signaling pathway. Plant Physiol. 138, 2406-2416.
9. Herrmann, L., Bockau, U., Tiedtke, A., Hartmann, M. W., and Weide, T. (2006) The bifunctional dihydrofolate reductase thymidylate synthase of Tetrahymena thermophila provides a tool for molecular and biotechnology applications. BMC Biotechnol. 20, 6-21.
10. Igamberdiev, A. U., Bykova, N. V., and Hill, R. D. (2006) Nitric oxide scavenging by barley hemoglobin is facilitated by a monodehydroascorbate reductase-mediated ascorbate reduction of methemoglobin. Planta 223, 1033-1040.
11. Jensen, O. N., Wilm, M., Shevchenko, A., and Mann, M. (1999) Sample preparation methods for mass spectrometric peptide mapping directly from 2-DE gels. Meth. Mol. Biol. 112, 513-530.
12. Kalume, D. E., Molina, H., and Pandey, A. (2003) Tackling the phosphoproteome: tools and strategies. Curr. Opin. Chem. Biol. 7, 64-69.
13. Kim, S. T., Cho, K. S., Jang, Y. S., and Kang, K. Y. (2001) Two-dimensional electrophoretic analysis of rice proteins by poly-ethylene glycol fractionation for protein arrays. Electrophoresis 22, 2103-2109.
14. Lad, L., Mewies, M., and Randaven, E. L. (2002) Substrate binding and catalytic mechanism in ascorbate peroxidase: evidence for two ascorbate binding sites. Biochemistry 41, 13774-13781.
15. Landry, F., Lombardo, C. R., and Smith, J. W. (2000) A method for application of samples to matrix-assisted laser desorption ionization time-of-flight targets that enhances peptide detection. Anal. Biochem. 279, 1-8.
16. Laugesen, S., Bergoin, A., and Rossignol, M. (2004) Deciphering the plant phosphoproteome: tools and strategies for a challenging task. Plant Physiol. Biochem. 42, 929-936.
17. Lee, S., Lee, E. J., Yang, E. J., Lee, J. E., Park, A. R., et al. (2004) Proteomic identification of annexins, calcium-dependent membrane binding proteins that mediate osmotic stress and abscisic acid signal transduction in Arabidopsis. Plant Cell 16, 1378-1391.
18. Leitner, A. and Lindner, W. (2004) Current chemical tagging strategies for proteome analysis by mass spectrometry. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 813, 1-26.
19. Nowitzki, U., Gelius-Dietrich, G., Schwieger, M., Henze, K., and Martin, W. (2004) Chloroplast phosphoglycerate kinase from Euglena gracilis: endosymbiotic gene replacement going against the tide. Eur. J. Biochem. 271, 4123-4131.
20. 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.
21. 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.
22. Oda, Y., Nagasu, T., and Chait, B. T. (2001) Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol. 19, 379-382.
23. Osanai, T., Magota, K., Tanaka, M., Shimada, M., Murakami, R., et al. (2005) Intracellular signaling for vasoconstrictor coupling factor 6: novel function of beta-subunit of ATP synthase as receptor. Hypertension 46, 1140-1146.
24. Pandey, A., Podtelejnikov, A. V., Blagoev, B., Bustelo, X. R., Mann, M., et al. (2000) Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. Proc. Natl. Acad. Sci. USA 97, 179-184.
25. Pawson, T. and Scott, J. D. (2005) Protein phosphorylation in signaling-50 years and counting. Trends Biochem. Sci. 30, 286-290.
26. Salomon, A. R., Ficarro, S. B., Brill, L. M., Brinker, A., Phung, Q. T., et al. (2003) Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc. Natl. Acad. Sci. USA 100, 443-448.
27. Shimokawa, H., Fujii, Y., Furuichi, M., Sekiguchi, M., and Nakabeppu, Y. (2000) Functional significance of conserved residues in the phosphohydrolase module of Escherichia coli MutT protein. Nucleic Acids Res. 28, 3240-3249.
28. Sorrell, D. A., Marchbank, A. M., Chrimes, D. A., Dickinson, J. R., Rogers, H. J., et al. (2000) The Arabidopsis 14-3-3 protein, GF14omega, binds to the Schizosaccharomyces pombe Cdc25 phosphatase and rescues checkpoint defects in the rad24-mutant. Planta 218, 50-57.
29. Sramko, M., Markus, J., Kabat, J., Wolff, L., and Bies, J. (2006) Stress-induced inactivation of the c-Myb transcription factor through conjugation of SUMO-2/3 proteins. J. Biol. Chem. 281, 40065-40075.
30. Sugihara, K., Hanagata, N., Dubinsky, Z., Baba, S., and Karube, I. (2000) Molecular characterization of cDNA encoding oxygen evolving enhancer protein 1 increased by salt treatment in the mangrove Bruguiera gymnorrhiza. Plant Cell Physiol. 41, 1279-1285.
31. Tsuchisaka, A. and Theologis, A. (2004) Unique and overlapping expression patterns among the Arabidopsis 1-amino-cyclopropane-l-carboxylate synthase gene family members. Plant Physiol. 136, 2982-3000.
32. 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.
33. You, M. K., Oh, S. I., Ok, S. H., Cho, S. K., Shin, H. Y., et al. (2007) Identification of putative MAPK kinases in Oryza minuta and O. sativa responsive to biotic stresses. Mol. Cells 23, 108-114.
34. Zettl, R., Schell, J., and Palme, K. (1994) Photoaffinity labeling of Arabidopsis thaliana plasma membrane vesicles by 5-azido-[7-3H] indole-3-acetic acid: identification of a glutathione S-transferase. Proc. Natl. Acad Sci. USA 91, 689-693.
35. Zhou, H., Watts, J. D., and Aebersold, R. (2001) A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 19, 375-378.