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Soybean Proteomics

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Plant Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1072))

Abstract

Soybean, the world’s most widely grown seed legume, is an important global source of vegetable oil and protein. Though, complete draft genome sequence of soybean is now available, but functional genomics studies remain in their infancy, as this agricultural legume species exhibits genetic constrains like genome duplications and self-incompatibilities. The techniques of proteomics provide much powerful tool for functional analysis of soybean. In the present review, an attempt has been made to summarize all significant contributions in the field of soybean proteomics. Special emphasis is given to subcellular proteomics in response to abiotic stresses for better understanding molecular basis of acquisition of stress tolerance mechanism. Detailed protocols of protein extraction, solubilization, fractionation of subcellular organelle, and proteins identification are explained for soybean proteomics. All this information would not only enrich us in understanding the plants response to environmental stressors but would also enable us to design genetically engineered stress tolerant soybean.

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References

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

    PubMed  Google Scholar 

  2. Bjellqvist B, Ek K, Righetti PG et al (1982) Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods 6:317–339

    Article  CAS  PubMed  Google Scholar 

  3. Görg A, Postel W, Günther S (1988) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 9:531–546

    Article  PubMed  Google Scholar 

  4. Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183

    Article  CAS  PubMed  Google Scholar 

  5. Carpentier SC, Witters E, Laukens K et al (2005) Preparation of protein extracts from recalcitrant plant tissues: an evaluation of different methods for two-dimensional gel electrophoresis analysis. Proteomics 5:2497–2507

    Article  CAS  PubMed  Google Scholar 

  6. Padgette SR, Taylor NB, Nida DL et al (1996) The composition of glyphosate-tolerant soybean seeds is equivalent to that of conventional soybeans. J Nutr 126:702–716

    CAS  PubMed  Google Scholar 

  7. Buttery BR, Buzzell RI (1973) Soybean flavonol glycosides: identification and biochemical genetics. Can J Bot 53:309–313

    Google Scholar 

  8. Cosio EG, McClure JW (1984) Kaempferol glycosides and enzymes of flavonol biosynthesis in leaves of a soybean strain with low photosynthetic rates. Plant Physiol 74:877–881

    Article  CAS  PubMed  Google Scholar 

  9. Tsugita A, Kamo M (1999) 2-D electrophoresis of plant proteins. Methods Mol Biol 112:95–97

    CAS  PubMed  Google Scholar 

  10. Saravanan RS, Rose JK (2004) A critical evaluation of sample extraction techniques for enhanced proteomic analysis of recalcitrant plant tissues. Proteomics 4:2522–2532

    Article  CAS  PubMed  Google Scholar 

  11. Natarajan S, Xu C, Caperna TJ et al (2005) Comparison of protein solubilization methods suitable for proteomic analysis of soybean seed proteins. Anal Biochem 342:214–220

    Article  CAS  PubMed  Google Scholar 

  12. Ahsan N, Komatsu S (2009) Comparative analyses of the proteomes of leaves and flowers at various stages of development reveal organ-specific functional differentiation of proteins in soybean. Proteomics 9:4889–4907

    Article  CAS  PubMed  Google Scholar 

  13. Toorchi M, Nouri MZ, Tsumura M et al (2008) Acoustic technology for high-performance disruption and extraction of plant proteins. J Proteome Res 7:3035–3041

    Article  CAS  PubMed  Google Scholar 

  14. Hurkman WJ, Tanaka CK (1986) Solubilization of plant membrane proteins for analysis by two-dimensional gel electrophoresis. Plant Physiol 81:802–806

    Article  CAS  PubMed  Google Scholar 

  15. Nanjo Y, Skultety L, Ashraf Y et al (2010) Comparative proteomic analysis of early-stage soybean seedlings responses to flooding by using gel and gel-free techniques. J Proteome Res 9:3989–4002

    Article  CAS  PubMed  Google Scholar 

  16. Salavati A, Khatoon A, Nanjo Y et al (2012) Analysis of proteomic changes in roots of soybean seedlings during recovery after flooding. J Proteomics 75:878–893

    Article  CAS  PubMed  Google Scholar 

  17. Zhen Y, Qi JL, Wang SS et al (2007) Comparative proteome analysis of differentially expressed proteins induced by Al toxicity in soybean. Physiol Plant 131:542–554

    Article  CAS  PubMed  Google Scholar 

  18. Mathesius U, Djordjevic MA, Oakes M et al (2011) Comparative proteomic profiles of the soybean (Glycine max) root apex and differentiated root zone. Proteomics 11:1707–1719

    Article  CAS  PubMed  Google Scholar 

  19. Xu C, Garrett WM, Sullivan JH et al (2006) Separation and identification of soybean leaf proteins by two-dimensional gel electrophoresis and mass spectrometry. Phytochemistry 67:2431–2440

    Article  CAS  PubMed  Google Scholar 

  20. Natarajan S, Xu C, Bae H et al (2006) Characterization of storage proteins in wild (Glycine soja) and cultivated (Glycine max) soybean seeds using proteomic analysis. J Agric Food Chem 54:3114–3120

    Article  CAS  PubMed  Google Scholar 

  21. Barbosa HS, Arruda SC, Azevedo RA et al (2012) New insights on proteomics of transgenic soybean seeds: evaluation of differential expressions of enzymes and proteins. Anal Bioanal Chem 402:299–314

    Article  CAS  PubMed  Google Scholar 

  22. Mooney BP, Thelen JJ (2004) High-throughput peptide mass fingerprinting of soybean seed proteins: automated workflow and utility of UniGene expressed sequence tag databases for protein identification. Phytochemistry 65:1733–1744

    Article  CAS  PubMed  Google Scholar 

  23. Hajduch M, Ganapathy A, Stein JW et al (2005) A systematic proteomic study of seed filling in soybean. Establishment of high-resolution two-dimensional reference maps, expression profiles, and an interactive proteome database. Plant Physiol 137:1397–1419

    Article  CAS  PubMed  Google Scholar 

  24. Ahsan N, Nanjo Y, Sawada H et al (2010) Ozone stress-induced proteomic changes in leaf total soluble and chloroplast proteins of soybean reveal that carbon allocation is involved in adaptation in the early developmental stage. Proteomics 10:2605–2619

    Article  CAS  PubMed  Google Scholar 

  25. Agrawal GK, Thelen JJ (2006) Large scale identification and quantification profiling of phosphoproteins expressed during seed filling in oilseed rape. Mol Cell Proteomics 5:2044–2059

    Article  CAS  PubMed  Google Scholar 

  26. Agrawal GK, Hajduch M, Graham K et al (2008) In-depth investigation of the soybean seed-filling proteome and comparison with aparallel study of rapeseed. Plant Physiol 148:504–518

    Article  CAS  PubMed  Google Scholar 

  27. Alam I, Lee DG, Kim KH et al (2010) Proteome analysis of soybean roots under waterlogging stress at an early vegetative stage. J Biosci 35:49–62

    Article  CAS  PubMed  Google Scholar 

  28. Komatsu S, Yamamoto R, Nanjo Y et al (2009) A comprehensive analysis of the soybean genes and proteins expressed under flooding stress using transcriptome and proteome techniques. J Proteome Res 8:4766–4778

    Article  CAS  PubMed  Google Scholar 

  29. Hashiguchi A, Sakata K, Komatsu S (2009) Proteome analysis of early-stage soybean seedlings under flooding stress. J Proteome Res 8:2058–2069

    Article  CAS  PubMed  Google Scholar 

  30. Shi F, Yamamoto R, Shimamura S et al (2008) Cytosolic ascorbate peroxidase 2 (cAPX 2) is involved in the soybean response to flooding. Phytochemistry 69:1295–1303

    Article  CAS  PubMed  Google Scholar 

  31. Mohammadi PP, Moieni A, Hiraga S et al (2012) Organ-specific proteomic analysis of drought-stressed soybean seedlings. J Proteomics 75:1906–1923

    Article  CAS  PubMed  Google Scholar 

  32. Aghaei K, Ehsanpour AA, Shah AH et al (2009) Proteome analysis of soybean hypocotyl and root under salt stress. Amino Acids 36:91–98

    Article  CAS  PubMed  Google Scholar 

  33. Sobhanian H, Razavizadeh R, Nanjo Y et al (2010) Proteome analysis of soybean leaves, hypocotyls and roots under salt stress. Proteome Sci 29:8–19

    Google Scholar 

  34. Ahsan N, Nakamura T, Komatsu S (2012) Differential responses of microsomal proteins and metabolites in two contrasting cadmium-accumulating soybean cultivars. Amino Acids 42:317–327

    Article  CAS  PubMed  Google Scholar 

  35. Hossain Z, Hajika M, Komatsu S (2012) Comparative proteome analysis of high and low cadmium accumulating soybeans under cadmium stress. Amino Acids. doi:10.1007/s00726-012-1319-6

    Google Scholar 

  36. Sobkowiak R, Deckert J (2006) Proteins induced by cadmium in soybean cells. J Plant Physiol 163:1203–1206

    Article  CAS  PubMed  Google Scholar 

  37. Wan J, Torres M, Ganapathy A et al (2005) Proteomic analysis of soybean root hairs after infection by Bradyrhizobium japonicum. Mol Plant Microbe Interact 18:458–467

    Article  CAS  PubMed  Google Scholar 

  38. Hossain Z, Nouri MZ, Komatsu S (2012) Plant cell organelle proteomics in response to abiotic stress. J Proteome Res 11:37–48

    Article  CAS  PubMed  Google Scholar 

  39. Komatsu S, Kobayashi Y, Nishizawa K et al (2010) Comparative proteomics analysis of differentially expressed proteins in soybean cell wall during flooding stress. Amino Acids 39:1435–1449

    Article  CAS  PubMed  Google Scholar 

  40. Komatsu S, Wada T, Abaléa Y et al (2009) Analysis of plasma membrane proteome in soybean and application to flooding stress response. J Proteome Res 8:4487–4499

    Article  CAS  PubMed  Google Scholar 

  41. Nouri MZ, Komatsu S (2010) Comparative analysis of soybean plasma membrane proteins under osmotic stress using gel-based and LC MS/MS-based proteomics approaches. Proteomics 10:1930–1945

    Article  CAS  PubMed  Google Scholar 

  42. Komatsu S, Yamamoto A, Nakamura T et al (2011) Comprehensive analysis of mitochondria in roots and hypocotyls of soybean under flooding stress using proteomics and metabolomics techniques. J Proteome Res 10:3993–4004

    Article  CAS  PubMed  Google Scholar 

  43. Arai Y, Hayashi M, Nishimura M (2008) Proteomic analysis of highly purified peroxisomes from etiolated soybean cotyledons. Plant Cell Physiol 49:526–539

    Article  CAS  PubMed  Google Scholar 

  44. Komatsu S, Sugimoto T, Hoshino T et al (2010) Identification of flooding stress responsible cascades in root and hypocotyl of soybean using proteome analysis. Amino Acids 38:729–738

    Article  CAS  PubMed  Google Scholar 

  45. Xu C, Sullivan JH, Garrett WM et al (2008) Impact of solar ultraviolet-B on the proteome in soybean lines differing in flavonoid contents. Phytochemistry 69:38–48

    Article  CAS  PubMed  Google Scholar 

  46. Nanjo Y, Skultety L, Uváčková L, Klubicová K, Hajduch M, Komatsu S (2012) Mass spectrometry-based analysis of proteomic changes in the root tips of flooded soybean seedlings. J Proteome Res 11:372–385

    Article  CAS  PubMed  Google Scholar 

  47. Sarma AD, Oehrle NW, Emerich DW (2008) Plant protein isolation and stabilization for enhanced resolution of two-dimensional polyacrylamide gel electrophoresis. Anal Biochem 379:192–195

    Article  CAS  PubMed  Google Scholar 

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Hossain, Z., Komatsu, S. (2014). Soybean Proteomics. In: Jorrin-Novo, J., Komatsu, S., Weckwerth, W., Wienkoop, S. (eds) Plant Proteomics. Methods in Molecular Biology, vol 1072. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-631-3_23

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  • DOI: https://doi.org/10.1007/978-1-62703-631-3_23

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-630-6

  • Online ISBN: 978-1-62703-631-3

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