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Identification of flooding stress responsible cascades in root and hypocotyl of soybean using proteome analysis

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Abstract

Flooding inducible proteins were analyzed using a proteomic technique to understand the mechanism of soybean response to immersion in water. Soybeans were germinated for 2 days, and then subjected to flooding for 2 days. Proteins were extracted from root and hypocotyl, separated by two-dimensional polyacrylamide gel electrophoresis, stained by Coomassie brilliant blue, and analyzed by protein sequencing and mass spectrometry. Out of 803 proteins, 21 proteins were significantly up-regulated, and seven proteins were down-regulated by flooding stress. Of the total, 11 up-regulated proteins were classified as related to protein destination/storage and three proteins to energy, while four down-regulated proteins were related to protein destination/storage and three proteins to disease/defense. The expression of 22 proteins significantly changed within 1 day after flooding stress. The effects of flooding, nitrogen substitution without flooding, or flooding with aeration were analyzed for 1–4 days. The expression of alcohol dehydrogenase increased remarkably by nitrogen substitution compared to flooding. The expression of many proteins that changed due to flooding showed the same tendencies observed for nitrogen substitution; however, the expression of proteins classified into protein destination/storage did not.

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Abbreviations

2-DE:

Two-dimensional polyacrylamide gel electrophoresis

MS:

Mass spectrometry

CBB:

Coomassie brilliant blue

IEF:

Isoelectric focusing

IPG:

Immobilized pH gradient

pI:

Isoelectric point

References

  • Aghaei K, Ehsanpour AA, Shah AH, Komatsu S (2009) Proteome analysis of soybean hypocotyl and root under salt stress. Amino Acids 36:91–98. doi:10.1007/s00726-008-0036-7

    Article  CAS  PubMed  Google Scholar 

  • Armstrong W (1979) Aeration in higher plants. Adv Bot Res 7:225–232. doi:10.1016/S0065-2296(08)60089-0

    Article  CAS  Google Scholar 

  • Bailey-Serres J, Voesenek LACJ (2008) Flooding stress: acclimations and genetic diversity. Annu Rev Plant Biol 16:313–339. doi:10.1146/annurev.arplant.59.032607.092752

    Article  Google Scholar 

  • Baxter-Burrell A, Yang Z, Springer PS, Bailey-Serres J (2002) RopGAP4-dependent Rop GTPase rheostat control of Arabidopsis oxygen deprivation tolerance. Science 296:2026–2028. doi:10.1126/science.1071505

    Article  CAS  PubMed  Google Scholar 

  • Bevan M, Bancroft I, Bent E et al (1998) Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391:485–488. doi:10.1038/35140

    Article  CAS  PubMed  Google Scholar 

  • Cho HT, Kende H (1997) Expansins and intermodal growth of deepwater rice. Plant Physiol 113:1145–1151. doi:10.1104/pp.113.4.1137

    Article  CAS  PubMed  Google Scholar 

  • Cleveland DW, Fisher SG, Kirschner MW, Laemmli UK (1977) Peptide mapping proteolysis in sodium dodecyl sulphate and analysis by gel electrophoresis. J Biol Chem 252:1102–1106

    CAS  PubMed  Google Scholar 

  • Coleman HD, Canam T, Kang K-Y, Ellis DD, Mansfield SD (2007) Over-expression of UDP-glucose pyrophosphorylase in hybrid poplar affects carbon allocation. J Exp Bot 58:4257–4268. doi:10.1093/jxb/erm287

    Article  CAS  PubMed  Google Scholar 

  • Darley CP, Forrester AM, McQueen-Mason SJ (2001) The molecular basis of plant cell wall extension. Plant Mol Biol 47:179–195. doi:10.1023/A:1010687600670

    Article  CAS  PubMed  Google Scholar 

  • Dixon MH, Hill SA, Jackson MB, Ratcliffe RC (2006) Physiological and metabolic adaptations of Patamogetom pectinatus L. tubers support rapid elongation of stem tissue in the absence of oxygen. Plant Cell Physiol 47:128–140. doi:10.1093/pcp/pci229

    Article  CAS  PubMed  Google Scholar 

  • Dordas C, Hasinoff BB, Rivoal J, Hill RD (2004) Class-1 hemoglobins, nitrate and NO levels in anoxic maize cell-suspension cultures. Planta 219:66–72. doi:10.1007/s00425-004-1212-y

    Article  CAS  PubMed  Google Scholar 

  • Gonzali S, Loreti E, Novi G, Poggi A, Alpi A, Perata P (2005) The use of microarrays to study the anaerobic response in Arabidopsis. Ann Bot (Lond) 96:661–668. doi:10.1093/aob/mci218

    Article  CAS  Google Scholar 

  • Hirano H, Kawasaki H, Sassa H (2000) Two-dimensional gel electrophoresis using immobilized pH gradient tube gels. Electrophoresis 21:440–445. doi:10.1002/(SICI)1522-2683(20000101)21:2<440::AID-ELPS440>3.0.CO;2-X

    Article  CAS  PubMed  Google Scholar 

  • Huang S, Greenway H, Colmer TD, Millar AH (2005) Protein synthesis by rice coleoptiles during prolonged anoxia: implications for glycolysis, growth and energy utilization. Ann Bot (Lond) 96:661–668. doi:10.1093/aob/mci218

    Article  Google Scholar 

  • Hunt PW, Klok EJ, Trevaskis B, Watts RA, Ellis MH, Peacock WJ, Dennis ES (2002) Increased level of hemoglobin 1 enhances survival of hypoxic stress and promotes early growth in Arabidopsis thaliana. Proc Natl Acad Sci USA 99:17197–17202. doi:10.1073/pnas.212648799

    Article  CAS  PubMed  Google Scholar 

  • Jackson MB, Colmer TD (2005) Response and adaptation by plants to flooding stress. Ann Bot (Lond) 96:501–505. doi:10.1093/aob/mci205

    Article  CAS  Google Scholar 

  • Kamauchi S, Wadahama K, Iwasaki K, Nakamoto Y, Nishizawa K, Ishimoto M, Kawada T, Urada R (2008) Molecular cloning and characterization of two soybean protein disulfide isomerases as molecular chaperones for seed storage proteins. FEBS J 275:2644–2658. doi:10.1111/j.1742-4658.2008.06412.x

    Article  CAS  PubMed  Google Scholar 

  • Kim TD (2006) Protein phosphatase inhibitor-1 (PPI-1) has protective activities in stress conditions in E. coli. Int J Biol Macromol 38:70–76. doi:10.1016/j.ijbiomac.2006.01.001

    Article  CAS  PubMed  Google Scholar 

  • Komatsu S, Yano H (2006) Update and challenges on proteomics in rice. Proteomics 6:4057–4068. doi:10.1002/pmic.200600012

    Article  CAS  PubMed  Google Scholar 

  • Komatsu S, Konishi H, Shen S, Yang G (2003) Rice proteomics: a step toward functional analysis of the rice genome. Mol Cell Proteomics 2:2–10. doi:10.1074/mcp.R200008-MCP200

    Article  CAS  PubMed  Google Scholar 

  • Liu F, Vantoai T, Moy L, Bock G, Linford LD, Quackenbush J (2005) Global transcription profiling reveals novel insights into hypoxic response in Arabidopsis. Plant Physiol 137:1115–1129. doi:10.1104/pp.104.055475

    Article  CAS  PubMed  Google Scholar 

  • Loreti E, Poggi A, Novi G, Alpi A, Perata P (2005) Genome-wide analysis of gene expression in Arabidopsis seedlings under anoxia. Plant Physiol 137:1130–1138. doi:10.1104/pp.104.057299

    Article  CAS  PubMed  Google Scholar 

  • Matsumoto H (1998) Inhibition of proton transport activity of microsomal membrane vesicle of barley roots by aluminum. Soil Sci Plant Nutr 34:499–526

    Google Scholar 

  • Mattana M, Coraggio I, Bertani A, Reggiani R (1994) Expression of the enzymes of nitrate reduction during the anaerobic germination of rice. Plant Physiol 106:1605–1608

    CAS  PubMed  Google Scholar 

  • Nakayama N, Hashimoto S, Shimada S, Takahashi M, Kim Y, Oya T, Arihara J (2004) The effect of flooding stress at the germination stage on the growth of soybean in relation to initial seed moisture content (Japanese). Jpn J Crop Sci 74:325–329. doi:10.1626/jcs.74.325

    Article  Google Scholar 

  • Navrot N, Collin V, Gualberto J, Gelhaye E, Hirasawa M, Rey P, Knaff DB, Issakidis E, Jacquot JP, Rouhier N (2006) Plant glutathione peroxidase are functional peroxiredixins distributed in several subcellular compartments and regulated during biotic and abiotic stresses. Plant Physiol 142:1364–1379. doi:10.1104/pp.106.089458

    Article  CAS  PubMed  Google Scholar 

  • O’Farrell PH (1975) High resolution two-dimensional electrophoresis of protein. J Biol Chem 250:4007–4021

    PubMed  Google Scholar 

  • Peumans WJ, van Damme EJM (1995) Lectins as plant defense proteins. Plant Physiol 109:347–352

    Article  CAS  PubMed  Google Scholar 

  • Pezeshki SR (2001) Wetland plant responses to soil flooding. Environ Exp Bot 46:299–312

    Article  Google Scholar 

  • Probert ME, Keating BA (2000) What soil constraints should be included in crop and forest model? Agric Ecosyst Environ 82:273–281

    Article  Google Scholar 

  • Pulido P, Cazalis R, Cejudo FJ (2008) An antioxidant redox system in the nucleus of wheat seed cells suffering oxidative stress. Plant J (on line)

  • Reggiani R (2006) A role for ethylene in low-oxygen signaling in rice roots. Amino Acids 30:299–301

    Article  CAS  PubMed  Google Scholar 

  • Saab IN, Sachs MM (1996) A flooding-induced xyloglucan endo-transglycosylase homolog in maize is responsive to ethylene and associated with aerenchyma. Plant Physiol 112:385–391

    Article  CAS  PubMed  Google Scholar 

  • Sato Y, Murakami T, Funatsuki H, Matsuba S, Saruyama H, Tanida M (2001) Heat shock-mediated APX gene expression and protection against chilling injury in rice seedlings. J Exp Bot 52:145–151

    Article  CAS  PubMed  Google Scholar 

  • Shi F, Yamamoto R, Shimamura S, Hiraga S, Nakayama N, Nakamura T, Yukawa K, Hachinohe M, Matsumoto H, Komatsu S (2008) Cytosolic ascorbate peroxidase 2 (cAPX 2) is involved in the soybean response to flooding. Phytochem 69:1295–1303

    Article  CAS  Google Scholar 

  • Tanaka N, Fihjita M, Handa H et al (2004) Proteomics of the rice cell: systematic identification of the protein populations in subcellular compartments. Mol Genet Genom 271:566–576

    Article  CAS  Google Scholar 

  • Voesenek LA, Colmer TD, Pierik R, Millenaar FF, Peeters AJ (2006) How plants cope with complete submergence. New Phytol 170:213–226

    Article  CAS  PubMed  Google Scholar 

  • Wang K, Jiang Y (2007) Antioxidant responses of creeping bent-grass roots to water-logging. Crop Sci 47:232–238

    Article  CAS  Google Scholar 

  • Zhong Z, Karibe H, Komatsu S, Ichimura H, Nagamura Y, Sasaki T, Hirano H (1997) Screening of rice genes from a cDNA catalog based on the sequence data-file of proteins separated by two-dimensional electrophoresis. Breed Sci 47:245–251

    CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by grants from National Agriculture and Food Research Organization, Japan. The authors thank Dr. S. Kuroda for his kind support of our research. We also thank Dr. S. Shimamura, Dr. N. Nakayama, Dr. R. Yamamoto and Dr. T. Nakamura for their valuable discussion.

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Correspondence to Setsuko Komatsu.

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Komatsu, S., Sugimoto, T., Hoshino, T. et al. Identification of flooding stress responsible cascades in root and hypocotyl of soybean using proteome analysis. Amino Acids 38, 729–738 (2010). https://doi.org/10.1007/s00726-009-0277-0

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