Acceptor Stem Differences Contribute to Species-Specific Use of Yeast and Human tRNA^Ser

The molecular mechanisms of translation are highly conserved in all organisms indicative of a single evolutionary origin. This includes the molecular interactions of tRNAs with their cognate aminoacyl-tRNA synthetase, which must be precise to ensure the specificity of the process. For many tRNAs, the anticodon is a major component of the specificity. This is not the case for the aminoacylation of alanine and serine to their cognate tRNAs. Rather, aminoacylation relies on other features of the tRNA. For tRNA^Ser, a key specificity feature is the variable arm, which is positioned between the anticodon arm and the T-arm. The variable arm is conserved from yeast to human. This work was initiated to determine if the structure/function of tRNA^Ser has been conserved from Saccharomyces cerevisiae to human. We did this by detecting mistranslation in yeast cells with tRNA^Ser derivatives having the UGA anticodon converted to UGG for proline. Despite being nearly identical in everything except the acceptor stem, human tRNA^Ser is less active than yeast tRNA^Ser. A chimeric tRNA with the human acceptor stem and other sequences from the yeast molecule acts similarly to the human tRNA^Ser. The 3:70 base pair in the acceptor stem (C:G in yeast and A:U in humans) is a prime determinant of the specificity. Consistent with the functional difference of yeast and human tRNA^Ser resulting from subtle changes in the specificity of their respective SerRS enzymes, the functionality of the human and chimeric tRNA^Ser_UGG molecules was enhanced when human SerRS was introduced into yeast. Residues in motif 2 of the aminoacylation domain of SerRS likely participated in the species-specific differences. Trp290 in yeast SerRS (Arg313 in humans) found in motif 2 is proximal to base 70 in models of the tRNA-synthetase interaction. Altering this motif 2 sequence of hSerRS to the yeast sequence decreases the activity of the human enzyme with human tRNA^Ser, supporting the coadaptation of motif 2 loop⁻acceptor stem interactions.