Aminoacylation of 3′ terminal tRNA-like fragments of turnip yellow mosaic virus RNA: The influence of 5′ nonviral sequences

Abstract

The present model of the L-shaped tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA encompasses 82 nucleotides. A previous kinetic study on 3′ terminal TYMV RNA fragments that contain the tRNA-like structure and a 5′ nonviral GGGAGA sequence, suggested that viral sequences upstream of the tRNA-like domain, i.e., upstream of nucleotide 82, increase the rate of aminoacylation (Dreher et al. (1988) Biochimie 70, 1719–1727). Here we report an increase in the aminoacylation rate when the number of nonviral nucleotides at the 5′ end of TYMV RNA transcripts was reduced. The influence of these 5′ proximal nonviral sequences on the conformation of the RNA molecule was investigated by structure mapping experiments. A structure that deviates from the tRNA-like structure was found in some of the transcripts. The formation of this alternative structure is dependent upon: (1) the nature and number of the nonviral nucleotides; (2) the number and secondary structure of viral nucleotides between the nonviral nucleotides and the tRNA-like domain. Footprinting experiments with valyl-tRNA synthetase from yeast suggest that the enzyme does not recognize the alternative structure.