6 Cereal Proteomics
Annual Plant Reviews book series, Volume 28: Plant Proteomics
Setsuko Komatsu,
Setsuko Komatsu
Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba, 305-8602 Japan
Search for more papers by this authorSetsuko Komatsu,
Setsuko Komatsu
Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba, 305-8602 Japan
Search for more papers by this authorFirst published: 19 April 2018
This article was originally published in 2006 in Plant Proteomics, Volume 28 (ISBN 9781405144292) of the Annual Plant Reviews book series, this volume edited by Christine Finnie. The article was republished in Annual Plant Reviews online in April 2018.
Abstract
The sections in this article are
- Introduction
- Comprehensive Analysis and Cataloguing of Cereal Proteins
- Functional Analysis of Cereal Using Differential Proteomics
- Future Prospects of Cereal Proteomics
References
- Abbasi, F. and Komatsu, S. (2004) A proteomic approach to analyze salt-responsive proteins in rice leaf sheath. Proteomics, 4, 2072–2081.
- Abubakar, Z., Ali, F., Pinel, A., Traore, O., N'Guessan, P., Notteghem, J.L., Kimmins, F., Konate, G. and Fargette, D. (2003) Phylogeography of rice yellow mottle virus in Africa. J. Gen. Virol., 84, 733–743.
- Agrawal, G.K., Rakwal, R., Yonekura, M., Kubo, A. and Saji, H. (2002) Proteome analysis of differentially displayed proteins as a tool for investigating ozone stress in rice (Oryza sativa L.) seedlings. Proteomics, 2, 947–959.
- Bevan, M., Bancroft, I., Bent, E., Love, K., Goodman, H. et al. (1998) Analysis of 1.9 Mb of contagious sequence from chromosome 4 of Arabidopsis thaliana . Nature, 391, 485–488.
- Brugidou, C., Opalka, N., Yeager, M., Beachy, R.N. and Fauquet, C. (2002) Stability of rice yellow mottle virus and cellular compartmentalization during the infection process in Oryza sativa (L.). Virology, 297, 98–108.
- Casimiro, I., Marchant, A., Bhalerao, R.P., Beeckman, T., Dhooge, S., Swarup, R., Graham, N., Inze, D., Sandberg, G., Casero, P.J. and Bennett, M. (2001) Auxin transport promotes Arabidopsis lateral root initiation. Plant Cell, 13, 843–852.
- Chameides, W.L., Saylor, R.D. and Cowling, E.B. (1997) Ozone pollution in the rural United States and the new NAAQS. Science, 276, 916.
- Cleveland, D.W., Fisher, S.G., Kirschner, M.W. and Laemmli, U.K. (1977) Peptide mapping by limited proteolysis in sodium dodecyl sulphate and analysis by gel electrophoresis. J. Biol. Chem., 252, 1102–1106
- Campo, P., Carrascal, M., Coca, M., Abian, J. and San Segundo, B. (2004) The defense response of germinating maize embryos against fungal infection: a proteomics approach. Proteomics, 4, 383–396.
- Cui, S., Huang, F., Wang, J., Ma, X., Cheng, Y. and Liu, J. (2005) A proteomic analysis of cold stress responses in rice seedlings. Proteomics, 5, 3162–3172.
- Dani, V., Simon, W.J., Duranti, M. and Croy, R.R. (2005) Changes in the tobacco leaf apoplast proteome in response to salt stress. Proteomics, 5, 737–745.
- Devos, M.K. and Gale, D.M. (2000) Genome relationships: the grass model in current research. Plant Cell, 12, 637–646.
- Dhugga, K.S., Tiwari, S.C. and Ray, P.M. (1997) A reversibly glycosylated polypeptide (RGP1) possibly involved in plant cell wall synthesis: purification, gene cloning, and trans-Golgi localization. Proc. Natl Acad. Sci., 94, 7679–7684.
- Feng, Q., Zhang, Y., Hao, P., Wang, S., Fu, G. et al. (2002) Sequence and analysis of rice chromosome 4. Nature, 420, 316–320.
- Fukuda, M., Islam, N., Woo, S.H., Yamagishi, A., Takaoka, M. and Hirano, H. (2003) Assessing matrix assisted laser desorption/ionization-time of flight-mass spectrometry as a means of rapid embryo protein identification in rice. Electrophoresis, 24, 1219–1329.
- Gale, M.D. and Devos, K.M. (1998) Comparative genetics in the grasses. Proc. Natl Acad. Sci. USA, 95, 1971–1974.
- Goff, S.A., Ricke, D., Lan, T.-H., Presting, G., Wang, R. et al. (2002) A draft sequence of rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92–100.
- Gygi, S.P., Rochon, Y., Franza, B.R. and Aebersold, M. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol., 19, 1720–1730.
- Hajheidari, M., Abdollahian-Noghabi, M., Askari, H., Heidari, M., Sadeghian, S.Y., Ober, E.S. and Hosseini Salekdeh, G. (2005) Proteome analysis of sugar beet leaves under drought stress. Proteomics, 5, 950–960.
- Heazlewood, J.L., Howell, K.A., Whelan, J. and Millar, A.H. (2003) Towards an analysis of the rice mitochondrial proteome. Plant Physiol., 132, 230–242.
- Hedrich, R. and Schroeder, J.I. (1989) The physiology of ion channels and electrogenic pumps in higher plants. Annu. Rev. Plant Physiol., 40, 539–569.
-
Hirano, H., Kawasaki, H. and Sassa, H. (2000) Two-dimensional gel electrophoresis using immobilized pH gradient tube gels. Electrophoresis, 21, 440–445.
10.1002/(SICI)1522-2683(20000101)21:2<440::AID-ELPS440>3.0.CO;2-X CAS PubMed Web of Science® Google Scholar
- Hooley, R. (1994) Gibberellins: perception, transduction and responses. Plant Mol. Biol., 26, 1529–1555.
-
Imin, N., Kerim, T., Weinman, J.J. and Rolfe, B.G. (2001) Characterization of rice anther proteins expressed at the young microspore stage. Proteomics, 1, 1149–1161.
10.1002/1615-9861(200109)1:9<1149::AID-PROT1149>3.0.CO;2-R CAS PubMed Web of Science® Google Scholar
- International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436, 793–800.
- Islam, N., Lonsdala, M., Upadhyaya, N.M., Higgins, T.J., Hirano, H. and Akhurst, R. (2004) Protein extraction from mature rice leaves for two-dimensional gel electrophoresis and its application in proteome analysis. Proteomics, 4, 1903–1908.
- Kerim, T., Imin, N., Weinman, J.J. and Rolfe, B.G. (2003) Proteome analysis of male gametophyte development in rice anthers. Proteomics, 3, 738–751.
- Khush, G.S. (2003) Challenges for meeting the global food and nutrient needs in the new millennium. Proc. Nutr. Soc., 60, 15–26.
- Kim, S.T., Cho, K.S., Yu, S., Kim, S.G., Hong, J.C. et al. (2003) Proteomic analysis of differentially expressed proteins induced by rice blast fungus and elicitor in suspension-cultured rice cells. Proteomics, 3, 2368–2378.
- Kim, K.M., Kwon, Y.S., Lee, J.J., Eun, M.Y. and Sohn, J.K. (2004) QTL mapping and molecular marker analysis for the resistance of rice to ozone. Mol. Cells, 17, 151–155.
- Koller, A., Washburn, M.P., Lange, B.M., Andon, N.L., Deciu, C. et al. (2002) Proteomic survey of metabolic pathways in rice. Proc. Natl Acad. Sci. USA, 99, 11969–11974.
- Komatsu, S. (2005) Rice Proteome Database: a step toward functional analysis of the rice genome. Plant Mol. Biol., 59, 179–190.
- Komatsu, S. and Tanaka, N. (2004) Rice proteome analysis: a step toward functional analysis of the rice genome. Proteomics, 4, 938–949.
- Komatsu, S., Kajiwara, H. and Hirano, H. (1993) A rice protein library: a data-file of rice proteins separated by two-dimensional electrophoresis. Theor. Appl. Genet., 86, 935–942.
- Komatsu, S., Masuda, T. and Abe, K. (1996) Phosphorylation of a protein (pp56) is related to the regeneration of rice cultured suspension cells. Plant Cell Physiol., 37, 748–753.
-
Komatsu, S., Muhammad, A. and Rakwal, R. (1999a) Separation and characterization of proteins from green and etiolated shoots of rice (Oryza sativa L.): towards a rice proteome. Electrophoresis, 20, 630–636.
10.1002/(SICI)1522-2683(19990301)20:3<630::AID-ELPS630>3.0.CO;2-Z CAS PubMed Web of Science® Google Scholar
- Komatsu, S., Rakwal, R. and Li, Z. (1999b) Separation and characterization of proteins in rice (Oryza sativa) suspension cultured cells. Plant Cell Tiss. Org. Cult., 55, 183–192.
- Komatsu, S., Konishi, H., Shen, S. and Yang, G. (2003) Rice proteomics: a step functional analysis of the rice genome. Mol. Cell. Proteom., 2, 2–10.
- Komatsu, S., Kojima, K., Suzuki, K., Ozaki, K. and Higo, K. (2004) Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003. Nucleic Acid. Res., 32, 388–392.
- Konishi, H. and Komatsu, S. (2003) A proteomics approach to investigating promotive effects of brassinolide on lamina inclination and root growth in rice seedlings. Biol. Pharm. Bull., 26, 401–408.
-
Konishi, H., Ishiguro, K. and Komatsu, S. (2001) A proteomics approach towards understanding blast fungus infection of rice grown under different levels of nitrogen fertilization. Proteomics, 1, 1162–1171.
10.1002/1615-9861(200109)1:9<1162::AID-PROT1162>3.0.CO;2-S CAS PubMed Web of Science® Google Scholar
- Kruft, V., Eubel, H., Jänsch, L., Whehahn, W. and Braun, H.-P. (2001) Proteomic approach to identify novel mitochondrial proteins in Arabidopsis . Plant Physiol., 127, 1694–1710.
- Lee, S., Lee, J.E., Yang, E.J., Lee, J.E., Park, A.R., Song, W.H. and Park, O.K. (2004) Proteomic identification of annexins, calcium-dependent membrane binding proteins that mediate osmotic stress and abscisic acid signal transduction in Arabidopsis . Plant Cell, 16, 1378–1391.
- Lyons, J.M. (1973). Chilling injury in plants. Annu. Rev. Plant Physiol., 24, 445–446.
- Maurel, C. (1997) Aquaporins and water permeability of plant membranes. Annu. Rev. Plant Physiol. Plant Mol. Biol., 48, 399–429.
- Mikami, S., Hori, H. and Mitsui, T. (2001) Separation of distinct components of rice Golgi complex by sucrose density gradient centrifugation. Plant Sci., 161, 665–675.
- Millar, A.H., Sweetlove, L.J., Giege, P. and Leaver, C.J. (2001) Analysis of the Arabidopsis mitochondrial proteome. Plant Physiol., 127, 1711–1727.
- O'Farrell, P.H. (1975) High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem., 250, 4007–4021.
- Oguchi, K., Tanaka, N., Komatsu, S. and Akao, S. (2004a) Methylmalonate-semialdehyde dehydrogenase is induced in auxin- and zinc-stimulated root formation in rice. Plant Cell Rep., 22, 848–858.
- Oguchi, K., Tanaka, N., Komatsu, S. and Akao, S. (2004b) Characterization of NADPH-dependent oxidoreductase from rice induced by auxin and zinc. Plant. Physiol., 121, 124–131.
- Okamoto, T., Higuchi, K., Shinkawa, T., Isobe, T., Lorz, H., Koshiba, T. and Kranz, E. (2004) Identification of major proteins in maize egg cells. Plant Cell Physiol., 45, 1406–1412.
- Peltier, J.-B., Friso, G., Kalume, D.E., Roepstorff, P., Nilsson, F., Adamska, I. and van Wijk, K.J. (2000) Proteomics of the chloroplast: systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell, 12, 319–341.
- Peltier, J.-B., Emanuelsson, O., Kalume, D.E., Ytterberg, J., Friso, G. et al. (2002) Central function of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction. Plant Cell, 14, 211–236.
- Pinel, A., N'Guessan, P., Bousalem, M. and Fargette, D. (2000) Molecular variability of geographically distinct isolates of rice yellow mottle virus in Africa. Arch. Virol., 145, 1621–1638.
- Rabbani, M.A., Maruyama, K., Abe, H., Khan, M.A., Katsura, K., Ito, Y., Yoshiwara, K., Seki, M., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol., 133, 1755–1767.
- Raison, J.K., Lyons, J.M. and Keith, A.D. (1971) Temperature-induced phase changes in mitochondrial membranes detected by spin labeling. J. Biol. Chem., 246, 4036–4040.
-
Rakwal, R. and Komatsu, S. (2000) Role of jasmonate in the rice (Oryza sativa L.) self-defense mechanism using proteome analysis. Electrophoresis, 21, 2492–2500.
10.1002/1522-2683(20000701)21:12<2492::AID-ELPS2492>3.0.CO;2-2 CAS PubMed Web of Science® Google Scholar
-
Salekdeh, G.H., Siopongco, J., Ghareyazie, B. and Bennett, J. (2002) Proteomic analysis of rice leaves during drought stress and recovery. Proteomics, 2, 1131–1145.
10.1002/1615-9861(200209)2:9<1131::AID-PROT1131>3.0.CO;2-1 CAS PubMed Web of Science® Google Scholar
- Salt, L.J., Robertson, J.A., Jenkins, J.A., Mulholland, F. and Mills, E.N. (2005) The identification of foam-forming soluble proteins from wheat (Triticum aestivum) dough. Proteomics, 5, 1612–1623.
- Santoni, V., Rouquie, D., Doumas, P., Mansion, M., Boutry, M., Degand, H., Dupree, P., Packman, L., Sherrier, J., Prime, T., Bauw, G., Posada, E., Rouze, P., Dehais, P., Sahnoun, I., Barlier, I. and Rossignol, M. (1998) Use of a proteome strategy for tagging proteins present at the plasma membrane. Plant J., 16, 633–641.
- Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K., Baba, T. et al. (2002) The genome sequence and structure of rice chromosome 1. Nature, 420, 312–316.
- Sasse, J.M. (1997) Recent progress in brassinosteroids research. Plant Physiol., 100, 696–701.
- Schubert, M., Petersson, U.A., Haas, P.J., Funk, C., Schröder, W.P. and Kiesebach, T. (2002) Proteome map of the chloroplast lumen of Arabidopsis thaliana . J. Biol. Chem., 277, 8354–8365.
- Shen, S., Matsubae, M., Takao, T., Tanaka, N. and Komatsu, S. (2002) A proteomic analysis of leaf sheath from rice. J. Biochem., 132, 613–620.
- Shen, S., Sharma, A. and Komatsu, S. (2003) Characterization of proteins responsive to gibberellin in the leaf-sheath of rice (Oryza sativa L.) seedling using proteome analysis. Biol. Pharm. Bull., 26, 129–136.
- Staehelin, L.A. and Moore, I. (1995) The plant Golgi apparatus: structure, functional organization and trafficking mechanisms. Annu. Rev. Plant Physiol. Plant Mol. Biol., 46, 261–288.
- Sze, H., Liang, F. and Hwang, I. (2000) Diversity and regulation of plant Ca2+ pumps: insights from expression in yeast. Annu. Rev. Plant Physiol. Plant Mol. Biol., 51, 433–462.
- Tanaka, N., Konishi, H., Khan, M. and Komatsu, S. (2004a) Proteome analysis of rice tissues separated and visualized by two-dimensional electrophoresis: approach to investigating the gibberellin regulated proteins. Mol. Genet. Genome, 270, 485–496.
- Tanaka, N., Fujita, M., Handa, H., Murayama, S., Uemura, M., Kawamura, Y., Mitsui, T., Mikami, S., Tozawa, Y., Yoshinaga, T. and Komatsu, S. (2004b) Proteomics of the rice cell: systematic identification of the protein population in subcellular compartments. Mol. Genet. Genome, 271, 566–576.
- Tsugita, A., Kawakami, T., Uchiyama, Y., Kamo, M., Miyatake, N. and Nozu, Y. (1994) Separation and characterization of rice proteins. Electrophoresis, 15, 708–720.
- Valent, B., Farrall, L. and Chumley, F.G. (1991) Magnaporthe grisea genes for pathogenicity and virulence identified through a series of backcrosses. Genetics, 127, 87–101.
- Vensel, W.H., Tanaka, C.K., Cai, N., Wong, J.H., Buchanan, B.B. and Hurkman, W.J. (2005) Developmental changes in the metabolic protein profiles of wheat endosperm. Proteomics, 5, 1594–1611.
- Ventelon-Debout, M., Delalande, F., Brizard, J.-P., Diemer, H., Van Dorsselaer, A. and Brugidou, C. (2004) Proteome analysis of cultivar-specific deregulations of Oryza sativa indica and O. sativa japonica cellular suspensions undergoing rice yellow mottle virus infection. Proteomics, 4, 216–225.
- Vencent, D., Lapierre, C., Pollet, B., Cornic, G., Negroni, L. and Zivy, M. (2005) Water deficits affect caffeate O-mrthyltransferase, lignification, and related enzymes in maize leaves. A proteomic investigation. Plant Physiol., 137, 949–960.
- Wong, J.H., Cai, N., Balmer, Y., Tanaka, C.K., Vensel, W.H., Hurkman, W.J. and Buchanan, B.B. (2004) Thioredoxin targets of developing wheat seeds identified by complementary proteomics approaches. Phytochemistry, 65, 1629–1640.
- Xu, Y., Buchholz, W.G., DeRose, R.T. and Hall, T.C. (1995) Characterization of a rice gene family encoding root-specific proteins. Plant Mol. Biol., 27, 237–248.
- Yan, S., Tang, Z., Su, W. and Sun, W. (2005) Proteomic analysis of salt stress-responsive proteins in rice root. Proteomics, 5, 235–244.
- Yang, G., Inoue, A., Takasaki, H., Kaku, H., Akao, S. and Komatsu, S. (2005) A proteomic approach to analyze auxin and zinc-responsive protein in rice. J. Proteome Res., 4, 456–463.
- Yu, J., Hu, S., Wang, J., Wong, G.K.-S., Li, S. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79–92.
- Zhong, B., Karibe, H., Komatsu, S., Ichimura, H., Nagamura, Y., Sasaki, T. and Hirano, H. (1997) Screening of rice genes from a cDNA based on the sequence data-file of proteins separated by two-dimensional electrophoresis. Breeding Sci., 47, 245–251.
- Zhao, C., Wang, J., Cao, M., Zhao, K., Sgao, J., Lei, T., Yin, J., Hill, G.G., Xu, N. and Liu, S. (2005) Proteomic changes in rice leaves during development of field-grown rice plants. Proteomics, 5, 961–972.
Browse other articles of this reference work: