Aminoacyl-tRNA synthetase and U 54 methyltransferase recognize conformations of the yeast tRNA Phe anticodon and T stem/loop domain

Abstract

The enzyme-catalyzed posttranscriptional modification of tRNA and the contributions of modified nucleosides to tRNA structure and function can be investigated with chemically synthesized domains of the tRNA molecule. Heptadecamer RNAs with and without modified nucleosides and DNAs designed as analogs to the anticodon and T stem/loop domains of yeast tRNA Phe were produced by automated chemical synthesis. The unmodified T stem/loop domain of yeast tRNA Phe was a substrate for the E coli m 5U 54-tRNA methyltransferase activity, RUMT. Suprisingly, the DNA analog of the T stem/loop domain composed of d(A,U,G,C) was also a substrate. In addition, the DNA analog inhibited the methylation of unfractionated, undermodified E coli tRNA lacking the U 54 methylation. RNA anticodon domains and DNA analogs differentially and specifically affected aminoacylation of the wild type yeast tRNA Phe. Three differentially modified tRNA Phe anticodon domains with ψ 39 alone, m 1G 37 and m 5C 40, or ψ 39 with m 1G 37 and m 5C 40, stimulated phenylalanyl-tRNA synthetase (FRS) activity. However, one anticodon domain, with m 5C 40 as the only modified nucleoside and a closed loop conformation, inhibited FRS activity. Modifiedand unmodified DNA analogs of the anticodon, tDNA- Phe AC, inhibited FRS activity. Analysis of the enzyme activity in the presence of the DNA analog characterized the DNA/enzyme interaction as either partial or allosteric inhibition. The disparity of action between the DNA and RNA hairpins provides new insight into the potential allosteric relationship of anticodon binding and open loop conformational requirements for active site function of FRS and other aaRSs. The comparison of the stimulatory and inhibitory properties of variously modified RNA domains and DNA analogs demonstrates that conformation, in addition to primary sequence, is important for tRNA-protein interaction. The enzyme recognition of various DNA analogs as substrate and/or inhibitors of activity demonstrates that conformational determinants are not restricted to ribose and the standard A-form RNA structure.