Type-Specific Features of the Structure of the tRNA Gene Promoters

Abstract

A new method for the recognition of type 2 promoters in the eukaryotic tRNA genes, which takes into consideration not only nucleotide distribution at individual box positions, but also the multiple interactions between the different parts of the A and B boxes, is proposed. The recognition procedure is based on the module organization of the A and B boxes within the intragenic promoters of the tRNA genes. It was shown that each module of a box is represented by a limited number of the sequence variants. Their particular combinations are the characteristic features of every tRNA gene type, and they are conserved within the two kingdoms of multicellular organisms. The same module combinations were identified in the promoters of the tRNA genes of the other types in unicellular organisms. These results suggested that the sequence module variants might have recombined during the evolutionary transition from unicellular to multicellular organisms.