Characterization of a tRNA editing activity in Saccharomyces cerevisiae

In mitochondrial genomes of metazoans, some tRNA genes overlap by one to six nucleotides with the neighboring downstream tRNA gene located on the same strand. Examples are the human mitochondrial genes for tRNA^Tyr and tRNA^Cys which overlap by one nucleotide. In the processing pathway of the primary transcript, the downstream located tRNA^Cys is released as a complete molecule, while the upstream tRNA^Tyr carries a corresponding truncation at the 3'-terminus, missing the overlapping nucleotide. Subsequently, an RNA editing reaction restores the missing position and completes this tRNA.

Surprisingly, although S. cerevisiae does not carry overlapping tRNA genes in its genome, it is able to restore such truncated tRNAs. Obviously, S. cerevisiae carries a promiscuous nucleotide incorporating activity that accepts these transcripts and adds the missing terminal nucleotide. These data support the hypothesis of the evolution of RNA editing by recruitment of a pre-existing promiscuous nucleotide inserting activity.

Our rational approach identified Trf4 and Trf5 as two likely candidate activities for this editing reaction in S. cerevisiae, representing members of a family of newly discovered bipartite poly(A) polymerases in yeast. Our analyses identified Trf4 within the TRAMP complex to be responsible for the editing activity in yeast, indicating a surprising multifunctionality of this enzyme.

The presented data show that nucleotidyltransferase activities easily accept additional RNA substrates for NTP incorporation, supporting the idea that RNA editing events evolved on the basis of promiscuous NTP-adding enzymes with a broad substrate range. It is conceivable that the human mitochondrial tRNA editing reaction might also be carried out by a nucleotide incorporating enzyme that was originally identified to catalyze a different reaction.