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Error Minimization and Coding Triplet/Binding Site Associations Are Independent Features of the Canonical Genetic Code

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Abstract

The canonical genetic code has been reported both to be error minimizing and to show stereochemical associations between coding triplets and binding sites. In order to test whether these two properties are unexpectedly overlapping, we generated 200,000 randomized genetic codes using each of five randomization schemes, with and without randomization of stop codons. Comparison of the code error (difference in polar requirement for single-nucleotide codon interchanges) with the coding triplet concentrations in RNA binding sites for eight amino acids shows that these properties are independent and uncorrelated. Thus, one is not the result of the other, and error minimization and triplet associations probably arose independently during the history of the genetic code. We explicitly show that prior fixation of a stereochemical core is consistent with an effective later minimization of error.

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Acknowledgments

This work was supported in part by NIH Grant GM 48080 and NASA Center for Astrobiology Grant NCC2-1052 to M. Yarus. We would like to thank members of the Yarus and Knight labs, Eors Szathmary, and an anonymous reviewer for critical discussion of the manuscript.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Mail Stop 8303, P.O. Box 6511, Aurora, CO, 80045, USA

    J. Gregory Caporaso

  2. Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, Campus Box 347, CO, 80309, USA

    Michael Yarus

  3. Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Campus Box 215, CO, 80309, USA

    Rob Knight

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  1. J. Gregory Caporaso
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  2. Michael Yarus
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  3. Rob Knight
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Correspondence to Rob Knight.

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[Reviewing Editor : Dr. Stephen Freeland]

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Caporaso, J.G., Yarus, M. & Knight, R. Error Minimization and Coding Triplet/Binding Site Associations Are Independent Features of the Canonical Genetic Code. J Mol Evol 61, 597–607 (2005). https://doi.org/10.1007/s00239-004-0314-2

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  • DOI: https://doi.org/10.1007/s00239-004-0314-2

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