Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates

Abstract

Glutamyl-tRNA synthetases (GluRSs) occur in two types, the discriminating and the nondiscriminating enzymes. They differ in their choice of substrates and use either tRNA^Glu or both tRNA^Glu and tRNA^Gln. Although most organisms encode only one GluRS, a number of bacteria encode two different GluRS proteins; yet, the tRNA specificity of these enzymes and the reason for such gene duplications are unknown. A database search revealed duplicated GluRS genes in >20 bacterial species, suggesting that this phenomenon is not unusual in the bacterial domain. To determine the tRNA preferences of GluRS, we chose the duplicated enzyme sets from Helicobacter pylori and Acidithiobacillus ferrooxidans. H. pylori contains one tRNA^Glu and one tRNA^Gln species, whereas A. ferrooxidans possesses two of each. We show that the duplicated GluRS proteins are enzyme pairs with complementary tRNA specificities. The H. pylori GluRS1 acylated only tRNA^Glu, whereas GluRS2 was specific solely for tRNA^Gln. The A. ferrooxidans GluRS2 preferentially charged \begin{equation*}{\mathrm{tRNA}}_{{\mathrm{UUG}}}^{{\mathrm{Gln}}}\end{equation*}. Conversely, A. ferrooxidans GluRS1 glutamylated both tRNA^Glu isoacceptors and the \begin{equation*}{\mathrm{tRNA}}_{{\mathrm{CUG}}}^{{\mathrm{Gln}}}\end{equation*} species. These three tRNA species have two structural elements in common, the augmented D-helix and a deletion of nucleotide 47. It appears that the discriminating or nondiscriminating natures of different GluRS enzymes have been derived by the coevolution of protein and tRNA structure. The coexistence of the two GluRS enzymes in one organism may lay the groundwork for the acquisition of the canonical glutaminyl-tRNA synthetase by lateral gene transfer from eukaryotes.