Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities

Abstract

The structure and function of in vitro transcribed tRNA Asp variants with inserted conformational features characteristic of yeast tRNA Phe, such as the length of the variable region or the arrangement of the conserved residues in the D-loop, have been investigated. Although they exhibit significant conformational alterations as revealed by Pb 2+ treatment, these variants are still efficiently aspartylated by yeast aspartyl-tRNA synthetase. Thus, this synthetase can accommodate a variety of tRNA conformers. In a second series of variants, the identity determinants of yeast tRNA Phe were transplanted into the previous structural variants of tRNA Asp. The phenylalanine acceptance of these variants improves with increasing the number of structural characteristics of tRNA Phe, suggesting that phenylalanyl-tRNA synthetase is sensitive to the conformational frame embedding the cognate identity nucleotides. These results contrast with the efficient transplantation of tRNA Asp identity elements into yeast tRNA Phe. This indicates that synthetases respond differently to the detailed conformation of their tRNA substrates. Efficient aminoacylation is not only dependent on the presence of the set of identity nucleotides, but also on a precise conformation of the tRNA.