Gain of C-Ala enables AlaRS to target the L-shaped tRNA(Ala)

Unlike many other aminoacyl-tRNA synthetases, alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout biology. While Caenorhabditis elegans cytoplasmic AlaRS (CeAlaRS(c)) retains the prototype structure, its mitochondrial counterpart (CeAlaRS(m)) contains only a residual C-terminal domain (C-Ala). We demonstrated herein that the C-Ala domain from CeAlaRS(c) robustly binds both tRNA and DNA. It bound different tRNAs but preferred tRNA(Ala). Deletion of this domain from CeAlaRS(c) sharply reduced its aminoacylation activity, while fusion of this domain to CeAlaRS(m) selectively and distinctly enhanced its aminoacylation activity toward the elbow-containing (or L-shaped) tRNA(Ala). Phylogenetic analysis showed that CeAlaRS(m) once possessed the C-Ala domain but later lost most of it during evolution, perhaps in response to the deletion of the T-arm (part of the elbow) from its cognate tRNA. This study underscores the evolutionary gain of C-Ala for docking AlaRS to the L-shaped tRNA(Ala).