Analysis of the rice genome's function using proteome analysis technology Structural analysis of the rice genome is being pursued at high speed, but there is a limit to what extent the function of genes can be identified from the bare sequence information. To ensure the effective use of genes, it is therefore essential to find out precisely what is their function. Proteome analysis is being applied to carry out large-scale, comprehensive analysis of protein, the final product of life information etched on the genome. It provides information on infrastructure that unravels the relationship between genome and life. In addition to a comprehensive analysis of proteins in cultured cells, plant tissues and their localization during their growth period, rice proteome research is also intended to make a dynamic analysis of biological functions unique to plants, such as organ formation and differentiation control, or environmental response mechanisms, in cooperation with the rice genome project team. It further aims to analyze functional protein-coding genes that will lead to the solution of environmental issues and food problems. In this research, proteins are extracted or fractionated according to cultured cell and plant organism and growth time. The proteins are separated by two dimensional electrophoretic migration and images are then analyzed. After these processes, a high accuracy amino acid sequence of individual proteins is determined using a gas phase sequencer or mass spectrometer. For example, it is possible to isolate 1,000 classes of protein by electrophoresing one tissue. A total of 16,000 proteins have been isolated so far. Proteins identified using two-dimensional electrophoretic migration are analyzed, a homology search is made on the basis of the amino acid sequence information, and rice proteome data files are produced along with information about their biological functions.
A differential display method using two-dimensional electrophoretic migration is also being used as one of the proteome analysis techniques designed to detect functional proteins. Employing this method, calreticulin, a calcium binding protein that acts as a phosphoprotein during redifferentiation and growth, as well as Rubisco activase, that combines with gibberellin were detected in rice. With regard to calreticulin and Rubisco activase, full-length cDNA was isolated by using information on the partial amino acid sequence, and transgenic rice were produced. As a result, it became clear that these proteins influence the control of rice differentiation and growth processes. Analysis of their biochemical characteristics using antibodies is under way, along with the isolation of an interacting protein-coding gene and the investigation into its communication mechanism. The results of these analyses suggest that proteome analysis technology is a useful means of detecting functional proteins. Systematic proteome research in conjunction with the genome study will make it possible to obtain a huge amount of information about protein. Placing that information on databases, along with information on the biological function of proteins, will accelerate the identification of the rice genome's function.
Glossary Proteome: A word coined by linking 'protein' with 'genome'. It represents the entire protein coded into the genome.
Genome: A concept of the totality of the genetic information held in every organism's DNA. The genome regulates the whole life process of every living thing as a kind of life design drawing.
Differential display method: A method designed to isolate cell proteins under different conditions by electrophoretic migration and analyze isolated proteins that change by comparing migration patterns.
Phosphoprotein: A protein that acts as a main switch that influences the activation and inactivation of a communication system within the cell.
A word from the author Proteome research is playing a key role in the elucidation of biological functions. Its purpose is to analyze the dynamics of proteins that generate every phenomenon of life. (Setsuko KOMATSU, NIAS)