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Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure-Function Map
Julie Baker Phillips1,2, David H Ardell3,4
1Quantitative and Systems Biology Program, University of California, Merced, CA, 95343, USA.
Journal of Molecular Evolution
|February 2, 2021
Summary
The evolution of transfer RNA (tRNA) genes involves rapid changes in specific sites, particularly within ion-binding pockets. Cytosine 17 (C17) in tRNA gained asparaginylation identity in parallel across species, influencing tRNA evolution.
Area of Science:
- Genomics
- Molecular Evolution
- Bioinformatics
Background:
- Transfer RNA (tRNA) gene evolution is complex, featuring functional conversions via anticodon shifts.
- Understanding tRNA multigene family evolution requires detailed annotation and comparative analysis.
Purpose of the Study:
- To improve tRNA gene annotations in Drosophila species and analyze substitution rates at single-site resolution.
- To investigate the evolutionary dynamics of tRNA structure-function relationships, focusing on conserved and rapidly evolving sites.
Main Methods:
- Enhanced tRNA gene annotations for twelve Drosophila species and Musca domestica.
- Application of the tRNA Structure-Function Mapper (tSFM) method to predict tRNA structure-function maps.
- Comparative analysis of substitution rates at single-site and base-pair resolution within tRNA genes.
Main Results:
- Rapidly evolving sites were localized to a metal ion-binding pocket at the interface of helical domains.
- Cytosine 17 (C17), crucial for lysylation identity, independently gained asparaginylation identity in parallel across tRNA^Asn paralogs.
- Co-arrayment of tRNA^Lys and tRNA^Asn genes in Drosophila melanogaster suggests gene conversion and similar synthetase binding interfaces influenced evolution.
Conclusions:
- tRNA structure-function maps are largely conserved in flies, with notable exceptions in the ion-binding pocket.
- Convergent and parallel evolution of C17 in tRNA^Asn paralogs may be compensated by anticodon shift substitutions.
- Genomic and structural factors drive rapid, parallel, and compensatory evolution in tRNA multigene families.
Keywords:
Class-informative feature (CIF)Convergent evolutionIon-binding pocketParallel substitutionsStructure–function mapMore Related Videos
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