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Methods for protein identification using expressed sequence tags and peptide mass fingerprinting for seed crops without complete genome sequences

Published online by Cambridge University Press:  22 September 2010

Liming Yang
Affiliation:
School of Life Sciences, Huaiyin Normal University, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huai'an223300, Jiangsu, China
Yuming Luo
Affiliation:
School of Life Sciences, Huaiyin Normal University, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huai'an223300, Jiangsu, China
Jifu Wei*
Affiliation:
School of Life Sciences, Huaiyin Normal University, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huai'an223300, Jiangsu, China Clinical Research Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing210029, Jiangsu, China
Chongmiao Ren
Affiliation:
School of Life Sciences, Huaiyin Normal University, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huai'an223300, Jiangsu, China
Xin Zhou
Affiliation:
School of Life Sciences, Huaiyin Normal University, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huai'an223300, Jiangsu, China
Shaoheng He*
Affiliation:
Clinical Research Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing210029, Jiangsu, China
*
*Correspondence Email: weijifu@hotmail.com and shaohenghe@hotmail.com
*Correspondence Email: weijifu@hotmail.com and shaohenghe@hotmail.com

Abstract

Proteomic approaches based on two-dimensional gel electrophoresis, mass spectrometry and database search are widely used to address questions about the development, physiology and quality of seeds. Identification of proteins is of great importance in proteomic analyses. For seed crops without full genome information, cross-species protein identification by mass spectrometry-driven sequence similarity search can be used. However, this approach is risky due to protein polymorphism between different species. Species-specific expressed sequence tag (EST) databases are an invaluable resource, which complements mass spectrometry data analysis for protein identification. Here, we illustrate a modified method of protein identification and characterization using species-specific EST databases and peptide mass fingerprinting with an example of protein identification. This method is reliable, supplements the existing methods, and improves the efficiency and accuracy of protein identification for seed crops for which complete genome information is not available.

Type
Short Communication
Copyright
Copyright © Cambridge University Press 2010

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References

Bradford, M.M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anaytical Biochemistry 72, 248254.CrossRefGoogle ScholarPubMed
Damerval, C., Devienne, D., Zivy, M. and Thiellement, A. (1986) Technical improvements in two-dimensional electrophoresis increase the level of genetic variation detected in wheat-seedling proteins. Electrophoresis 7, 5254.CrossRefGoogle Scholar
Dong, G.J., Pan, W.D. and Liu, G.S. (2006) The analysis of proteome changes in sunflower seeds induced by N+ implantation. Journal of Biosciences 31, 247253.Google Scholar
Gallardo, K., Job, C., Groot, S.P., Puype, M., Demol, H., Vandekerckhove, J. and Job, D. (2001) Proteomic analysis of Arabidopsis seed germination and priming. Plant Physiology 126, 835848.CrossRefGoogle ScholarPubMed
Gallardo, K., Job, C., Groot, S.P., Puype, M., Demol, H., Vandekerckhove, J. and Job, D. (2002) Proteomics of Arabidopsis seed germination. A comparative study of wild-type and gibberellin-deficient seeds. Plant Physiology 129, 823837.CrossRefGoogle ScholarPubMed
Higashi, Y., Hirai, M.Y., Fujiwara, T., Naito, S., Noji, M. and Saito, K. (2006) Proteomic and transcriptomic analysis of Arabidopsis seeds: molecular evidence for successive processing of seed proteins and its implication in the stress response to sulfur nutrition. The Plant Journal 48, 557571.CrossRefGoogle ScholarPubMed
Irar, S., Brini, F., Goday, A., Masmoudi, K. and Pagès, M. (2010) Proteomic analysis of wheat embryos with 2-DE and liquid-phase chromatography (ProteomeLab PF-2D) – A wider perspective of the proteome. Journal of Proteomics 73, 17071721.CrossRefGoogle ScholarPubMed
Kim, S.I., Kim, J.Y., Kim, E.A., Kwon, K.H., Kim, K.W., Cho, K., Lee, J.H., Nam, M.H., Yang, D.C., Yoo, J.S. and Park, Y.M. (2003) Proteome analysis of hairy root from Panax ginseng C.A. Meyer using peptide fingerprinting, internal sequencing and expressed sequence tag data. Proteomics 3, 23792392.CrossRefGoogle Scholar
Komatsu, S., Konishi, H., Shen, S. and Yang, G. (2003) Rice proteomics: a step toward functional analysis of the rice genome. Molecular and Cellular Proteomics 2, 210.CrossRefGoogle ScholarPubMed
Kottapalli, K.R., Payton, P., Rakwal, R., Agrawal, G.K., Shibato, J., Burow, M. and Puppala, N. (2008) Proteomic analysis of mature seed of four peanut cultivars using two-dimensional gel electrophoresis reveals distinct differential expression of storage, anti-nutritional, and allergenic proteins. Plant Science 175, 321329.CrossRefGoogle Scholar
Kwon, K.H., Kim, M., Kim, J.Y., Kim, K.W., Kim, S.I., Park, Y.M. and Yoo, J.S. (2003) Efficiency improvement of peptide identification for an organism without complete sequence, using expressed sequence tag database and tandem mass spectral data. Proteomics 3, 23052309.CrossRefGoogle ScholarPubMed
Laino, P., Shelton, D., Finnie, C., De Leonardis, A.M., Mastrangelo, A.M., Svensson, B., Lafiandra, D. and Masci, S. (2010) Comparative proteome analysis of metabolic proteins from seeds of durum wheat (cv. Svevo) subjected to heat stress. Proteomics 10, 23592368.CrossRefGoogle ScholarPubMed
Lisacek, F.C., Traini, M.D., Sexton, D., Harry, J.L. and Wilkins, M.R. (2001) Strategy for protein isoform identification from expressed sequence tags and its application to peptide mass fingerprinting. Proteomics 1, 186193.3.0.CO;2-G>CrossRefGoogle ScholarPubMed
Mathesius, U., Imin, N., Chen, H.C., Djordjevic, M.A., Weinman, J.J., Natera, S.H.A., Morris, A.C., Kerim, T., Paul, S., Menzel, C., Weiler, G.F. and Rolfe, B.G. (2002) Evaluation of proteome reference maps for cross-species identification of proteins by peptide mass fingerprinting. Proteomics 2, 12881303.3.0.CO;2-H>CrossRefGoogle ScholarPubMed
Merlino, M., Leroy, P., Chambon, C. and Branlard, G. (2009) Mapping and proteomic analysis of albumin and globulin proteins in hexaploid wheat kernels (Triticum aestivum L.). Theoretical and Applied Genetics 118, 13211337.CrossRefGoogle ScholarPubMed
Østergaard, O., Melchior, S., Roepstorff, P. and Svensson, B. (2002) Initial proteome analysis of mature barley seeds and malt. Proteomics 2, 733739.3.0.CO;2-E>CrossRefGoogle ScholarPubMed
Østergaard, O., Finnie, C., Laugesen, S., Roepstorff, P. and Svennson, B. (2004) Proteome analysis of barley seeds: identification of major proteins from two-dimensional gels (pI 4–7). Proteomics 4, 24372447.CrossRefGoogle ScholarPubMed
Rajjou, L., Gallardo, K., Debeaujon, I., Vandekerckhove, J., Job, C. and Job, D. (2004) The effect of alpha-amanitin on the Arabidopsis seed proteome highlights the distinct roles of stored and neosynthesized mRNAs during germination. Plant Physiology 134, 15981613.CrossRefGoogle ScholarPubMed
Rajjou, L., Belghazi, M., Huguet, R., Robin, C., Moreau, A., Job, C. and Job, D. (2006) Proteomic investigation of the effect of salicylic acid on Arabidopsis seed germination and establishment of early defense mechanisms. Plant Physiology 141, 910923.CrossRefGoogle ScholarPubMed
Scippa, G.S., Rocco, M., Ialicicco, M., Trupiano, D., Viscosi, V., Di Michele, M., Arena, S., Chiatante, D. and Scaloni, A. (2010) The proteome of lentil (Lens culinaris Medik.) seeds: discriminating between landraces. Electrophoresis 31, 497506.CrossRefGoogle ScholarPubMed
Shevchenko, A., Wilm, M., Vorm, O. and Mann, M. (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Analytical Chemistry 68, 850858.CrossRefGoogle ScholarPubMed
Skylas, D.J. and Wrigley, C.W. (2004) Proteomics of grains. pp. 480488in Wrigley, C.; Walker, C.; Corke, H. (Eds) Encyclopedia of grain science, Vol. 2, Oxford, UK, Oxford University Press.CrossRefGoogle Scholar
Wasinger, V.C., Cordwell, S.J., Cerpa-Poljak, A., Yan, J.X., Gooley, A.A., Wilkins, M.R., Duncan, M.W., Harris, R., Williams, K.L. and Humphery-Smith, I. (1995) Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16, 10901094.CrossRefGoogle ScholarPubMed
Watson, B.S., Asirvatham, V.S., Wang, L. and Sumner, L.W. (2003) Mapping the proteome of barrel medic (Medicago truncatula). Plant Physiology 131, 11041123.CrossRefGoogle ScholarPubMed
Yahata, E., Maruyama-Funatsuki, W., Nishio, Z., Tabiki, T., Takata, K., Yamamoto, Y., Tanida, M. and Saruyama, H. (2005) Wheat cultivar-specific proteins in grain revealed by 2-DE and their application to cultivar identification of flour. Proteomics 5, 39423953.CrossRefGoogle ScholarPubMed
Yang, P., Li, X., Wang, X., Chen, H., Chen, F. and Shen, S. (2007) Proteomic analysis of rice (Oryza sativa) seeds during germination. Proteomics 7, 33583368.CrossRefGoogle ScholarPubMed