On the flexible interaction of yeast factor r with the bipartite promoter of tRNA genes

Abstract

Yeast transcription factor r (analogous to vertebrate TFIIIC) interacts specifically with the internal split promoter of tRNA genes. Binding to the two promoter elements (A block and B block) occurs within 30 seconds even when they are separated by a long intervening sequence. Dimethylsulfate protection analysis of contact points between r and the noncoding strand of a series of internally deleted tRNALeu3 genes shows that the specificity of the interaction is not affected by changes in the distance or in the relative helical orientation of the promoter elements. This result is consistent with the results of previous footprinting experiments (Baker, R.E., Camier, S., Sentenac, A. and Hall, B.D., 1987, Proc. Nat I. Acad. Sci. USA, 84,8768-8772). To test if any physical constraint is imposed on the DNA molecule upon r binding, we analyzed the effect of introducing random single-strand breaks in the noncoding strand of the tRNA gene. Whereas some nicks located in the A block were found to prevent r binding, no single-strand break in the B block region or in the DNA between the A and B blocks were observed to inhibit or facilitate the binding of r. We therefore propose that the great flexibility of the T-tDNA interaction is mostly due to the T protein itself. © 1990 Oxford University Press.