A Realistic Model under which the Genetic Code is Optimal

H. Buhrman, P.T.S. van der Gulik, G.W. Klau, C. Schaffner, D. Speijer, L. Stougie

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the mean square measure as a function quantifying error robustness, a value can be obtained for a genetic code which reflects the error robustness of that code. By comparing this value with a distribution of values belonging to codes generated by random permutations of amino acid assignments, the level of error robustness of a genetic code can be quantified. We present a calculation in which the standard genetic code is shown to be optimal. We obtain this result by (1) using recently updated values of polar requirement as input; (2) fixing seven assignments (Ile, Trp, His, Phe, Tyr, Arg, and Leu) based on aptamer considerations; and (3) using known biosynthetic relations of the 20 amino acids. This last point is reflected in an approach of subdivision (restricting the random reallocation of assignments to amino acid subgroups, the set of 20 being divided in four such subgroups). The three approaches to explain robustness of the code (specific selection for robustness, amino acid-RNA interactions leading to assignments, or a slow growth process of assignment patterns) are reexamined in light of our findings. We offer a comprehensive hypothesis, stressing the importance of biosynthetic relations, with the code evolving from an early stage with just glycine and alanine, via intermediate stages, towards 64 codons carrying todays meaning. © 2013 Springer Science+Business Media New York.
Original languageEnglish
Pages (from-to)170-184
JournalJournal of Molecular Evolution
Volume77
Issue number4
Early online date1 Jul 2013
DOIs
Publication statusPublished - 2013

Fingerprint

Genetic Code
genetic code
Amino Acids
amino acids
amino acid
Proxy
hydrophobicity
Hydrophobic and Hydrophilic Interactions
glycine (amino acid)
codons
Codon
Alanine
Glycine
alanine
code
RNA
Growth

Cite this

Buhrman, H., van der Gulik, P. T. S., Klau, G. W., Schaffner, C., Speijer, D., & Stougie, L. (2013). A Realistic Model under which the Genetic Code is Optimal. Journal of Molecular Evolution, 77(4), 170-184. https://doi.org/10.1007/s00239-013-9571-2
Buhrman, H. ; van der Gulik, P.T.S. ; Klau, G.W. ; Schaffner, C. ; Speijer, D. ; Stougie, L. / A Realistic Model under which the Genetic Code is Optimal. In: Journal of Molecular Evolution. 2013 ; Vol. 77, No. 4. pp. 170-184.
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Buhrman, H, van der Gulik, PTS, Klau, GW, Schaffner, C, Speijer, D & Stougie, L 2013, 'A Realistic Model under which the Genetic Code is Optimal' Journal of Molecular Evolution, vol. 77, no. 4, pp. 170-184. https://doi.org/10.1007/s00239-013-9571-2

A Realistic Model under which the Genetic Code is Optimal. / Buhrman, H.; van der Gulik, P.T.S.; Klau, G.W.; Schaffner, C.; Speijer, D.; Stougie, L.

In: Journal of Molecular Evolution, Vol. 77, No. 4, 2013, p. 170-184.

Research output: Contribution to JournalArticleAcademicpeer-review

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