title: A realistic model under which the genetic code is optimal.
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.
authors.affiliation: Centrum Wiskunde & Informatica (CWI), P.O. Box 94079, 1090 GB, Amsterdam, The Netherlands.
authors.forename: Harry
authors.initials: H
authors.lastname: Buhrman
authors.forename: Peter T S
authors.initials: PT
authors.lastname: van der Gulik
authors.forename: Gunnar W
authors.initials: GW
authors.lastname: Klau
authors.forename: Christian
authors.initials: C
authors.lastname: Schaffner
authors.forename: Dave
authors.initials: D
authors.lastname: Speijer
authors.forename: Leen
authors.initials: L
authors.lastname: Stougie
mesh_terms: D000596:Amino Acids / Q000737:chemistry* / Q000235:genetics*; D052158:Aptamers, Peptide / Q000737:chemistry / Q000235:genetics; D003062:Codon; D019143:Evolution, Molecular; D005815:Genetic Code; D008957:Models, Genetic; D014176:Protein Biosynthesis / Q000235:genetics / Q000502:physiology
chemical_list: D000596:Amino Acids; D052158:Aptamers, Peptide; D003062:Codon