Analysis of initial changes in the proteins of soybean root tip under flooding stress using gel-free and gel-based proteomic techniques

Journal of Proteomics

Volumn 106, Issue , 2014, Pages 1-16

  Yin, Xiaojian ^a,b   Sakata, Katsumi ^c   Nanjo, Yohei ^a   Komatsu, Setsuko ^a,b  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b NATIONAL INSTITUTE OF CROP SCIENCE   (Japan)

^c MAEBASHI INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Flooding stress; Protein protein interaction; Proteomics; Root tips; Soybean

Indexed keywords

CALRETICULIN; CITRIC ACID; HEAT SHOCK PROTEIN 70; LYASE; MESSENGER RNA; CALCIUM; GEL;

ARTICLE; CITRIC ACID CYCLE; CONTROLLED STUDY; DOWN REGULATION; FLOODING; GENE EXPRESSION; GLYCOLYSIS; HORMONE METABOLISM; NONHUMAN; PLANT ROOT; PLANT STRESS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN SYNTHESIS; PROTEOMICS; SIGNAL TRANSDUCTION; SOYBEAN; TWO DIMENSIONAL GEL ELECTROPHORESIS; UPREGULATION; CALCIUM SIGNALING; CHEMISTRY; ENERGY METABOLISM; GEL; GENE EXPRESSION REGULATION; METABOLISM; PROCEDURES;

CALCIUM; CALCIUM SIGNALING; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ENERGY METABOLISM; FLOODS; GELS; GENE EXPRESSION REGULATION, PLANT; PLANT ROOTS; PROTEIN INTERACTION MAPPING; PROTEOMICS; RNA, MESSENGER; SOYBEANS;

EID: 84899883353     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2014.04.004     Document Type: Article

References (36)

1. Setter T.L., Waters I. Review of prospect for germplasm improvement for water-logging tolerance in wheat, barley and oats. Plant Soil 2003, 253:1-34.
2. Gibbs J., Greenway H. Review: mechanisms of anoxia tolerance in plants. I. Growth, survival and anaerobic catabolism. Funct Plant Biol 2003, 30:353.
3. Buttery B.R. Some effects of waterlogging and supply of combined nitrogen on soybean growth. Can J Plant Sci 1987, 67:69-77.
4. Githiri S.M., Watanabe S., Harada K., Takahashi R. QTL analysis of flooding tolerance in soybean at an early vegetative growth stage. Plant Breed 2006, 125:613-618.
5. Hashiguchi A., Sakata K., Komatsu S. Proteome analysis of early-stage soybean seedlings under flooding stress. J Proteome Res 2009, 8:2058-2069.
6. Mathesius U., Djordjevic M.A., Oakes M., Goffard N., Haerizadeh F., Weiller G.F., et al. Comparative proteomic profiles of the soybean (Glycine max) root apex and differentiated root zone. Proteomics 2011, 11:1707-1719.
7. Sun C.N. Zonation and organization of root apical meristem of Glycine max. Bull Torrey Bot Club 1957, 84:69-78.
8. Komatsu S., Hiraga S., Yanagawa Y. Proteomics techniques for the development of flood tolerant crops. J Proteome Res 2012, 11:68-78.
9. Komatsu S., Sugimoto T., Hoshino T., Nanjo Y., Furukawa K. Identification of flooding stress responsible cascades in root and hypocotyls of soybean using proteome analysis. Amino Acids 2010, 38:729-738.
10. Komatsu S., Thibaut D., Hiraga S., Kato M., Chiba M., Hashiguchi A., et al. Characterization of a novel flooding stress-responsive alcohol dehydrogenase expressed in soybean roots. Plant Mol Biol 2011, 77:309-322.
11. Shi F., Yamamoto R., Shimamura S., Hiraga S., Nakayama N., Nakamura T., et al. Cytosolic ascorbate peroxidase 2 (cAPX2) is involved in the soybean response to flooding. Phytochemistry 2008, 69:1295-1303.
12. Nanjo Y., Skultety L., Uváčková L.U., Klubicová K., Hajduch M., Komatsu S. Mass spectrometry-based analysis of proteomic changes in the root tips of flooded soybean seedlings. J Proteome Res 2011, 11:372-385.
13. Nanjo Y., Nouri M.Z., Komatsu S. Quantitative proteomic analyses of crop seedlings subjected to stress conditions; a commentary. Phytochemistry 2011, 72:1263-1272.
14. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976, 72:248-254.
15. Schmutz J., Cannon S.B., Schlueter J., Ma J., Mitros T., Nelson W., et al. Genome sequence of the palaeopolyploid soybean. Nature 2010, 463:178-183.
16. Olsen J.V., de Godoy L.M.F., Li G., Macek B., Mortensen P., Pesch R., et al. Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics 2005, 4:2010-2021.
17. Zhang Y., Wen Z., Washburn M.P., Florens L. Effect of dynamic exclusion duration on spectral count based quantitative proteomics. Anal Chem 2009, 81:6317-6326.
18. Brosch M., Yu L., Hubbard T., Choudhary J. Accurate and sensitive peptide identification with mascot percolator. J Proteome Res 2009, 8:3176-3181.
19. Usadel B., Nagel A., Thimm O., Redestig H., Blaesing O.E., Palacios-Rofas N., et al. Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol 2005, 138:1195-1204.
20. Voit E.O. Computational analysis of biochemical systems 2000, Cambridge University Press, Cambridge, UK.
21. Tanaka N., Mitsui S., Nobori H., Yanagi K., Komatsu S. Expression and function of proteins during development of the basal region in rice seedlings. Mol Cell Proteomics 2005, 4:796-808.
22. Vizcaíno J.A., Côté R.G., Csordas A., Dianes J.A., Fabregat A., Foster J.M., et al. The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 2013, 41:D1063-D1069.
23. Nanjo Y., Skultety L., Ashraf Y., Komatsu S. Comparative proteomic analysis of early-stage soybean seedlings responses to flooding by using gel and gel-free techniques. J Proteome Res 2010, 9:3989-4002.
24. Voesenek L.A., Colmer T.D., Pierik R., Millenaar F.F., Peeters A.J. How plants cope with complete submergence. New Phytol 2006, 170:213-226.
25. Smith A.M., ap Rees T. Pathways of carbohydrate fermentation in the roots of marsh plants. Planta 1979, 146:327-334.
26. Komatsu S., Yamamoto R., Nanjo Y., Mikami Y., Yunokawa H., Sakata K. A comprehensive analysis of the soybean genes and proteins expressed under flooding stress using transcriptome and proteome techniques. J Proteome Res 2009, 8:4766-4778.
27. Wang W., Vinocur B., Shoseyov O., Altman A. Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends Plant Sci 2004, 9:244-252.
28. Komatsu S., Makino T., Yasue H. Proteomic and biochemical analyses of the cotyledon and root of flooding-stressed soybean plants. PLoS One 2013, 8:e65301.
29. Sunna A., Antranikian G. Xylanolytic enzymes from fungi and bacteria. Crit Rev Biotechnol 1997, 17:39-67.
30. Scarafoni A., Ronchi A., Prinsi B., EspenL Assante G., Venturini G., et al. The proteome of exudates from germinating Lupinus albus seeds is secreted through a selective dual-step process and contains proteins involved in plant defence. FEBS J 2013, 280:1443-1459.
31. Elshourbagy N., Near J., Kmetz P., Sathe G., Southan C., Stickler J., et al. Rat ATP citrate-lyase. Molecular cloning and sequence analysis of a full-length cDNA and mRNA abundance as a function of diet, organ, and age. J Biol Chem 1990, 265:1430-1435.
32. Fatland B.L., Nikolau B.J., Wurtele E.S. Reverse genetic characterization of cytosolic acetyl-CoA generation by ATP-citrate lyase in Arabidopsis. Plant Cell 2005, 17:182-203.
33. Langlade N.B., Messerli G., Weisskopf L., Plaza S., Tomasi N., Smutny J., et al. ATP citrate lyase: cloning, heterologous expression and possible implication in root organic acid metabolism and excretion. Plant Cell Environ 2002, 25:1561-1569.
34. 2+ regulation of interactions between endoplasmic reticulum chaperones. J Biochem 1999, 274:6203-6211.
35. Li Z., Onodera H., Ugaki M., Tanaka H., Komatsu S. Characterization of calreticulin as a phosphoprotein interacting with cold-induced protein kinase in rice. Biol Pharm Bull 2003, 26:256-261.
36. Komatsu S., Yang G., Khan M., Onodera H., Toki S., Yamaguchi M. Over-expression of calcium-dependent protein kinase 13 and calreticulin interacting protein 1 confers cold tolerance on rice plants. Mol Gen Genet 2007, 277:713-723.