Abstract
Rice is one of the most important food and cereal crop plants in the world. Rice proteomics began in the 1990s. Since then, considerable progress has been made in establishing protocols from isolation of rice proteins from different tissues, organs, and organelles, to separation of complex proteins and to their identification by mass spectrometry. Since the year 2000, global proteomics studies have been performed during growth and development under numerous biotic and abiotic environmental conditions. Two-dimensional (2-D) gel-based proteomics platform coupled with mass spectrometry has been retained as the workhorse for proteomics of a variety of rice samples. In this chapter, we describe in detail the different protocols used for isolation of rice proteins, their separation, detection, and identification using gel-based proteomics and mass spectrometry approaches.
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Goff SA, Ricke D, Lan TH et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100
Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92
International rice genome sequencing project (2005) The map-based sequence of the rice genome. Nature 436:793–800
Rakwal R, Agrawal GK (2003) Rice proteomics: current status and future perspectives. Electrophoresis 24:3378–3389
Agrawal GK, Rakwal R (2006) Rice proteomics: a cornerstone for cereal food crop proteomes. Mass Spectrom Rev 25:1–53
Agrawal GK, Jwa NS, Iwahashi Y, Yonekura M, Iwahashi H, Rakwal R (2006) Rejuvenating rice proteomics: facts, challenges, and visions. Proteomics 6:5549–5576
Agrawal GK, Rakwal R (2008) Rice proteome at a glance. In: Agrawal GK, Rakwal R (eds) Plant proteomics: technologies, strategies, and applications. Wiley, Hoboken, NJ, pp 165–178
Agrawal GK, Jwa NS, Rakwal R (2009) Rice proteomics: ending phase I and the beginning of phase II. Proteomics 9:935–963
Agrawal GK, Rakwal R (2011) Rice proteomics: a move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology. Proteomics 11:1630–1649
Agrawal GK, Rakwal R (eds) (2008) Plant proteomics: technologies, strategies, and applications. Wiley, Hoboken, NJ
Han X, Aslanian A, Yates JR 3rd (2008) Mass spectrometry for proteomics. Curr Opin Chem Biol 12:483–490
Righetti PG, Antonioli P, Simo C, Citterio A (2008) Gel-based proteomics. In: Agrawal GK, Rakwal R (eds) Plant Proteomics: Technologies, Strategies, and Applications. Wiley, Hoboken, NJ, pp 11–30
Gorg A, Weiss W, Dunn MJ (2004) Current two-dimensional electrophoresis technology for proteomics. Proteomics 4:3665–3685
Miller I, Crawford J, Gianazza E (2006) Protein stains for proteomic applications: which, when, why? Proteomics 6:5385–5408
Görg A, Drews O, Luck C, Weiland F, Weiss W (2009) 2-DE with IPGs. Electrophoresis 30:S122–S132
Thiellement H, Zivy M, Damerval C, Mechin V (eds) (2007) Plant Proteomics: Methods and Protocols. Humana, Totowa, NJ
Kim ST, Cho KS, Jang YS, Kang KY (2001) Two-dimensional electrophoretic analysis of rice proteins by polyethylene glycol fractionation for protein arrays. Electrophoresis 22:2103–2109
Jensen ON, Mortensen P, Vorm O, Mann M (1997) Automation of matrix-assisted laser desorption/ionization mass spectrometry using fuzzy logic feedback control. Anal Chem 69:1706–1714
Agrawal GK, Thelen JJ (2005) Development of a simplified, economical polyacrylamide gel staining protocol for phosphoproteins. Proteomics 5:4684–4688
Acknowledgments
GKA and RR appreciate the kind support of Dr. Akihiro Kubo (NIES, Japan) for providing the space to grow and conduct rice stress experiments. GKA appreciates the Japan Society for the Promotion of Science (JSPS; ID Number S-10182) for his stay and research at Plant Genome Research Unit (NIAS, Tsukuba, Japan). This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean Government (MEST) (No. 2011-0000139, No. R0602536). This work was also supported by a grant from the BioGreen 21 Program (No. PJ007993), Rural Development Administration, Republic of Korea. K.C. was supported at NIES as an Eco-Frontier Fellow (09-Ba086-02). RR acknowledges the great support of Professors Yoshihiro Shiraiwa (Chairperson, Faculty of Life and Environmental Sciences, University of Tsukuba) and Seiji Shioda and Dr. Tetsuo Ogawa (Department of Anatomy I, Showa University School of Medicine) in promoting interdisciplinary research and unselfish encouragement. For all correspondence, contact Ganesh Kumar Agrawal or Randeep Rakwal at plantproteomics@gmail.com.
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Agrawal, G.K. et al. (2013). Rice Proteomic Analysis: Sample Preparation for Protein Identification. In: Yang, Y. (eds) Rice Protocols. Methods in Molecular Biology, vol 956. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-194-3_12
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DOI: https://doi.org/10.1007/978-1-62703-194-3_12
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Publisher Name: Humana Press, Totowa, NJ
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