Rice Proteomics A Step Toward Functional Analysis of the Rice Genome

Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.
Molecular & Cellular Proteomics (Impact Factor: 6.56). 02/2003; 2(1):2-10. DOI: 10.1074/mcp.R200008-MCP200
Source: PubMed


The technique of proteome analysis with two-dimensional PAGE has the power to monitor global changes that occur in the protein expression of tissues and organisms and/or expression that occurs under stresses. In this study, the catalogues of the rice proteome were constructed, and a functional characterization of some of these proteins was examined. Proteins extracted from tissues of rice and proteins extracted from rice under various kinds of stress were separated by two-dimensional PAGE. An image analyzer was used to reveal a total of 10,589 protein spots on 10 kinds of two-dimensional PAGE gels stained by Coomassie Brilliant Blue. The separated proteins were electroblotted onto a polyvinylidene difluoride membrane, and the N-terminal amino acid sequences of 272 of 905 proteins were determined. The internal amino acid sequences of 633 proteins were determined using a protein sequencer or mass spectrometry after enzyme digestion of the proteins. Finally, a data file of rice proteins that included information on amino acid sequences and sequence homologies was constructed. The major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that turned out to be calreticulin and a gibberellin-binding protein, which is ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice, have functions in the signal transduction pathway. The information thus obtained from the rice proteome will be helpful in predicting the function of the unknown proteins and will aid in their molecular cloning.

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    • "The development of rice protein databases based on 2D-PAGE has enabled the identification of known proteins and facilitated the analysis of new proteins with respect to their physiological significance in rice (Komatsu et al., 1993, 2004). Proteomic analysis of rice has been mainly focused on the changes in protein expressions during rice growth and development under different environmental conditions (Komatsu et al., 2003). Studies on the protein profile of rice in relation to grain quality have been limited and there were no reports yet on the protein expression profile of rice grains with varying functional properties. "
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    ABSTRACT: The proteins from functional rice cultivars (Nogwonchalbyeo, Giant embryonic, Arhyangchalbyeo, and Goamibyeo) and general white rice were extracted and separated using two-dimensional (2D) gel electrophoresis. A wide variation in the molecular weight (MW) and pH range of the expressed proteins in rice samples were observed. The green-kerneled rice (Nogwonchalbyeo) exhibited proteins with MW of 9-57 kDa and appeared at a pH range of 4-7. The Giant embryonic contained proteins with MW of 31-63 kDa and a pH range of 5-6. The aromatic glutinous rice (Arhyangchalbyeo) showed proteins with MW of 24-28 and pH of 5.8-6.8. The high-amylose rice (Goamibyeo) exhibited proteins with MW of 3-63 and pH of 5.2-5.6. The identified proteins uniquely found and highly expressed in each cultivar may have a significant role on rice functionality. The results illustrate that the 2D gel electrophoresis is a valuable method in the determination of the protein expression profiles in functional rice grains and may be useful in the identification of specific marker proteins associated with the functional property of rice.
    Preview · Article · Dec 2013
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    • "With huge available data of genome information and the development of mass spectrometry (MS) technology, proteomics is exerting great influence in analyzing the dynamic and diverse biological processes. A series of comprehensive reviews have summarized the progresses of proteomics and its impacts on rice (Komatsu et al., 2003; Rakwal and Agrawal, 2003; Agrawal and Rakwal, 2006; Agrawal et al., 2006, 2009; Komatsu and Yano, 2006; Agrawal et al., 2011). A literature survey indicates that the number of proteomic studies on rice seed germination was gradually increased during the early period (1991–2001) and sharply risen in the last decade (2002-; Figure 1). "
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    ABSTRACT: Seed is a condensed form of plant. Under suitable environmental conditions, it can resume the metabolic activity from physiological quiescent status, and mobilize the reserves, biosynthesize new proteins, regenerate organelles, and cell membrane, eventually protrude the radicle and enter into seedling establishment. So far, how these activities are regulated in a coordinated and sequential manner is largely unknown. With the availability of more and more genome sequence information and the development of mass spectrometry (MS) technology, proteomics has been widely applied in analyzing the mechanisms of different biological processes, and proved to be very powerful. Regulation of rice seed germination is critical for rice cultivation. In recent years, a lot of proteomic studies have been conducted in exploring the gene expression regulation, reserves mobilization and metabolisms reactivation, which brings us new insights on the mechanisms of metabolism regulation during this process. Nevertheless, it also invokes a lot of questions. In this mini-review, we summarized the progress in the proteomic studies of rice seed germination. The current challenges and future perspectives were also discussed, which might be helpful for the following studies.
    Full-text · Article · Jul 2013 · Frontiers in Plant Science
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    • "One of the most popular methods to study of the plant responses to environmental stresses is proteome analysis since the extraction of proteins is easy and the obtained two-dimensional electrophoresis gels have great reproducibility and also the mass spectrometry (MS) for sequencing of proteins are very sensitive (Komatsu et al., 2003). Proteomics has been used to study of the expression of salt stress related proteins in several crops such as rice (Parker et al., 2006), potato (Aghaei et al., 2008a), soybean (Aghaei et al., 2008b), and foxtail millet (Veeranagamallaiah et al., 2008), which can provide a better indication of cellular activities under salt stress. "
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    ABSTRACT: Increasing of world population marks a serious need to create new crop cultivars and medicinal plants with high growth and production at any environmental situations. Among the environmental unfavorable conditions, salinity is the most widespread in the world. Crop production and growth severely decreases under salt stress; however, some crop cultivars show significant tolerance against the negative effects of salinity. Among salt stress responses of crops, proteomic responses play a pivotal role in their ability to cope with it and have become the main center of notification. Many physiological responses are detectable in terms of protein increase and decrease even before physiological responses take place. Thus proteomic approach makes a short cut in the way of inferring how crops response to salt stress. Nowadays many salt-responsive proteins such as heat shock proteins, pathogen-related proteins, protein kinases, ascorbate peroxidase, osmotin, ornithine decarboxylase, and some transcription factors, have been detected in some major crops which are thought to give them the ability of withstanding against salt stress. Proteomic analysis of medicinal plants also revealed that alkaloid biosynthesis related proteins such as tryptophan synthase, codeinone reductase, strictosidine synthase, and 12-oxophytodienoate reductase might have major role in production of secondary metabolites. In this review we are comparing some different or similar proteomic responses of several crops and medicinal plants to salt stress and discuss about the future prospects.
    Full-text · Article · Jan 2013 · Frontiers in Plant Science
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