Rice Proteomics

Abstract

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.

Deciphering the proteomic profile of rice (Oryza sativa) bran: A pilot study

“…By using 2-D-PAGE, automated sequencing and MS techniques, proteomics of rice embryo and endosperm [19], root [20], green and ethiolated shoot [21], cultured suspension cells [22], anther [29], leaf sheath [25], Golgi organelles [30] and mitochondria [31] have been systematically investigated. This prompted Komatsu et al [36][37][38] to construct the rice proteome database (see the web site: http://gene 64.dna.affrc.go.jp/RPD) that is an excellent source of information on the progress of rice proteome research. As expected, many of the proteins identified in the above tissues and organelles were common also to rice bran.…”

“…While different analytical procedures, including proteomic studies, have allowed: (i) to differentiate aromatic from nonaromatic rice varieties [16], (ii) to map protein patterns in rice leaf, embryo, endosperm, root, stem, shoot and callus and (iii) to evaluate their quality and fundamental properties [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35], to construct a rice proteome database [36][37][38], identification and characterization of rice bran protein isolate is still partial and confined to a very limited number of publications [14,23,39,40].…”

Screening of a broad range of rice (Oryza sativa L.) germplasm for in vitro rapid plant regeneration and development of an early prediction system

“…Because of these important agronomic and genetic characteristics, rice has emerged as a model crop in monocots for the analysis of the genome, proteome, and metabolome (Katiyar-Agarwal et al 2002;Komatsu et al 2003). Indica rice cultivars are commonly grown in tropical and subtropical regions, although the most widely grown genotypes have proven to be less amenable to in vitro culture (Khanna and Raina 1998).…”

Update and challenges on proteomics in rice

“…The initial objective of proteomics was the large scale identification of all protein species in a cell or tissue. In rice proteomics, considerable research effort has been applied to the analysis of the rice proteome, and remarkable progress has been made in the systematic, functional characterization of proteins in the various tissues and organelles of rice [9][10][11]. This approach is currently being extended to analyze various functional aspects of proteins.…”