Screening of Rice Genes from a cDNA Catalog Based on the Sequence Data-file of Proteins Separated by Two-dimensional Electrophoresis.

Abstract

Rice (Oryza sativa L.) root proteins were separated by two-dimensional electrophoresis and 292 protein spots were detected by Coomassie Blue staining. The N-terminal and internal amino acid sequences of 76 proteins of 292 were determined so as to construct a detailed data-file of rice protein sequences. Sequences for a total of 126 proteins including 50 proteins reported previously have been determined so far. In the Rice Genome Research Project, more than 20, 000 cDNA clones randomly selected from rice cDNA Iibraries have been sequenced to construct a cDNA catalog. The possibility of identifying cDNAS encoding particular proteins from the catalog by homology search based on the protein sequence data-file was investigated. Attempt was made to screen cDNAs encoding 126 proteins from the catalog by homology search. Complementary DNAs encoding 42 proteins were identified in the catalog, indicating that about 30% of the cDNA species could be identified. It was deduced that 20, 000-40, 000 genes are present in the rice genome. Although more than 20, 000 cDNAs were sequenced in the Rice Genome Research Project, only half should have unique sequences when gene redundancy is considered. This corresponds to 25-50 % of genes present in the entire rice genome. This appears consistent with the fact that about 30% of the cDNAs encoding proteins sequenced could be identified in the catalog. If the size of the cDNA catalog is increased enough, all cDNAs encoding proteins separated by two-dimensional electrophoresis can be easily picked up from the catalog by computer search using the sequences determined.