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An Extensive Study of Mutation and Selection on the Wobble Nucleotide in tRNA Anticodons in Fungal Mitochondrial Genomes

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Abstract

Two alternative hypotheses aim to predict the wobble nucleotide of tRNA anticodons in mitochondrion. The codon-anticodon adaptation hypothesis predicts that the wobble nucleotide of tRNA anticodon should evolve toward maximizing the Watson-Crick base pairing with the most frequently used codon within each synonymous codon family. In contrast, the wobble versatility hypothesis argues that the nucleotide at the wobble site should be occupied by a nucleotide most versatile in wobble pairing, i.e., the wobble site of the tRNA anticodon should be G for NNY codon families and U for NNR and NNN codon families (where Y stands for C or U, R for A or G, and N for any nucleotide). We examined codon usage and anticodon wobble sites in 36 fungal genomes to evaluate these two alternative hypotheses and identify exceptional cases that deserve new explanations. While the wobble versatility hypothesis is generally supported, there are interesting exceptions involving tRNAArg translating the CGN codon family, tRNATrp translating the UGR codon family, and tRNAMet translating the AUR codon family. Our results suggest that the potential to suppress stop codons, the historical inertia, and the conflict between translation initiation and elongation can all contribute to determining the wobble nucleotide of tRNA anticodons.

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Acknowledgments

This study is supported by the CAS/SAFEA International Partnership Program for Creative Research Teams and by NSERC’s Discovery and Strategic Grants to XX. We thank S. Aris-Brosou, E. Rocha, T. Xing, and X. Yao for discussion and comments. Two anonymous reviewers helped clarify ambiguities and correct grammatical errors.

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Authors and Affiliations

  1. Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada, K1N 6N5

    Malisa Carullo & Xuhua Xia

  2. Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada

    Xuhua Xia

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  1. Malisa Carullo
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  2. Xuhua Xia
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Correspondence to Xuhua Xia.

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Carullo, M., Xia, X. An Extensive Study of Mutation and Selection on the Wobble Nucleotide in tRNA Anticodons in Fungal Mitochondrial Genomes. J Mol Evol 66, 484–493 (2008). https://doi.org/10.1007/s00239-008-9102-8

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  • DOI: https://doi.org/10.1007/s00239-008-9102-8

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