Structural and Genetic Determinants of Convergence in theDrosophilatRNA Structure-Function Map

Abstract

The evolution of tRNA multi-gene families remains poorly understood, exhibiting unusual phenomena such as functional conversions of tRNA genes through anticodon shift substitutions. We reannotated tRNA genes from twelve Drosophila species, incorporating previously identified ortholog sets to compare substitution rates across tRNA bodies at single-site resolution. All rapidly evolving sites fell in the same metal-ion-binding pocket at the interface of the two tRNA stacked helical domains. We applied our tRNA Structure-Function Mapper (tSFM) method independently to each Drosophila species and one outgroup species Musca domestica. We found that, although predicted tRNA structure-function maps are generally highly conserved in flies, one tRNA Class-Informative Feature (CIF) within the rapidly-evolving ion-binding pocket — Cytosine 17 (C17), ancestrally informative for lysylation identity — independently gained asparaginylation identity and substituted in parallel across tRNAAsn paralogs at least three times in evolution of the genus. In D. melanogaster, approximately 15 tRNALys and tRNAAsn genes co-occur in heterologous clusters, suggesting that both heterologous gene conversion and structural similarities of the closely related asparaginyl-tRNA synthetase (AsnRS) and lysyl-tRNA synthetase (LysRS) proteins may have played a role in these changes. A previously identified Asn-to-Lys anticodon shift substitution in D. ananassae may have arisen to compensate for the convergent and parallel gains of C17 in tRNAAsn paralogs of the D. ananassae lineage. Our results underscore the functional and evolutionary relevance of our tRNA structure-function map predictions and illuminate multiple genomic and structural factors contributing to rapid, parallel and compensatory evolution of tRNA multi-gene families.