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Center for Nonlinear Studies |
Patterns of substitution rates footprint functional constraints and highlight potential adaptive evolutionary change in macromolecules. The publication of twelve Drosophila genomes in 2007 facilitated one of the first highly resolved molecular evolutionary analyses of noncoding RNAs, specifically microRNAs. Yet, even though tRNAs were the first RNAs to be sequenced and structurally solved, detailed analysis of site rate variation of substitution in tRNAs has not yet been undertaken. A potential obstacle in undertaking such work is its requirement of orthology mapping, which is challenging for such short and repetitive genes. A recent publication of carefully curated tRNA orthology sets in Drosophila, in combination with modern computational tools, has enabled us to address detailed aspects of the evolution of tRNA structure and function. We analyzed evolutionary rates of individual sites and structural elements of tRNA in Drosophila. Three sites in the ‘variable pocket‘ of tRNAs show particularly rapid rates of evolution across different species and classes of tRNAs. These sites form part of a structurally important ion-binding pocket, often bound to Mg2+, but also other ions. We present results integrating these fly divergence data with yeast divergence data, fly polymorphism data, and molecular dynamics simulations to interpret this very surprising evolutionary pattern of eukaryotic tRNAs.