Mirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase

Gene cloning, overproduction and an efficient purification protocol of yeast arginyl-tRNA synthetase (ArgRS) as well as the interaction patterns of this protein with cognate tRNA(Arg) and non-cognate tRNA(Asp) are described, This work was motivated by the fact that the in vitro transcript of tRNA(Asp) is of dual aminoacylation specificity and is not only aspartylated but also efficiently arginylated. The crystal structure of the complex between class II aspartyl-tRNA synthetase (AspRS) and tRNA(Asp), as well as early biochemical data, have shown that tRNA(Asp) is recognized by its variable region side, Here we show by footprinting with enzymatic and chemical probes that transcribed tRNA(Asp) is contacted by class I ArgRS along the opposite D arm side, as is homologous tRNA(Arg), but with idiosyncratic interaction patterns, Besides protection, footprints also show enhanced accessibility of the tRNAs to the structural probes, indicative of conformational changes in the complexed tRNAs, These different patterns are interpreted in relation to the alternative arginine identity sets found in the anticodon loops of tRNA(Arg) and tRNA(Asp), The mirror image alternative interaction patterns of unmodified tRNA(Asp) with either class I ArgRS or class II AspRS, accounting for the dual identity of this tRNA, are discussed in relation to the class defining features of the synthetases, This study indicates that complex formation between unmodified tRNA(Asp) and either ArgRS and AspRS is solely governed by the proteins.