Abstract
The allocation of codons in the genetic code makes possible a moderate minimization of the chemical distances between pairs of neighboring amino acids in the code. However, the code is neither a global nor a local optimum with respect to distance minimization. These findings do not support the physicochemical postulate that distance minimization was a major factor shaping the evolution of the genetic code. They agree with the coevolution theory, which proposes that genetic code evolution was predominantly determined by the concession of codons from precursor to product amino acids in an expansion of the code to accommodate new varieties of amino acids, with distance minimization playing a subsidiary role in deciding the choice of codons to be acquired by the product amino acids from the codon domains of the precursor amino acids.
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Selected References
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- Epstein C. J. Non-randomness of amino-acid changes in the evolution of homologous proteins. Nature. 1967 Jul 22;215(5099):355–359. doi: 10.1038/215355a0. [DOI] [PubMed] [Google Scholar]
- Grantham R. Amino acid difference formula to help explain protein evolution. Science. 1974 Sep 6;185(4154):862–864. doi: 10.1126/science.185.4154.862. [DOI] [PubMed] [Google Scholar]
- HINEGARDNER R. T., ENGELBERG J. RATIONALE FOR A UNIVERSAL GENETIC CODE. Science. 1963 Nov 22;142(3595):1083–1085. doi: 10.1126/science.142.3595.1083. [DOI] [PubMed] [Google Scholar]
- Jungck J. R. The genetic code as a periodic table. J Mol Evol. 1978 Aug 2;11(3):211–224. doi: 10.1007/BF01734482. [DOI] [PubMed] [Google Scholar]
- Macino G., Coruzzi G., Nobrega F. G., Li M., Tzagoloff A. Use of the UGA terminator as a tryptophan codon in yeast mitochondria. Proc Natl Acad Sci U S A. 1979 Aug;76(8):3784–3785. doi: 10.1073/pnas.76.8.3784. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Salemme F. R., Miller M. D., Jordan S. R. Structural convergence during protein evolution. Proc Natl Acad Sci U S A. 1977 Jul;74(7):2820–2824. doi: 10.1073/pnas.74.7.2820. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schimmel P. R., Söll D. Aminoacyl-tRNA synthetases: general features and recognition of transfer RNAs. Annu Rev Biochem. 1979;48:601–648. doi: 10.1146/annurev.bi.48.070179.003125. [DOI] [PubMed] [Google Scholar]
- Sneath P. H. Relations between chemical structure and biological activity in peptides. J Theor Biol. 1966 Nov;12(2):157–195. doi: 10.1016/0022-5193(66)90112-3. [DOI] [PubMed] [Google Scholar]
- Weber A. L., Lacey J. C., Jr Genetic code correlations: amino acids and their anticodon nucleotides. J Mol Evol. 1978 Aug 2;11(3):199–210. doi: 10.1007/BF01734481. [DOI] [PubMed] [Google Scholar]
- Wilcox M., Nirenberg M. Transfer RNA as a cofactor coupling amino acid synthesis with that of protein. Proc Natl Acad Sci U S A. 1968 Sep;61(1):229–236. doi: 10.1073/pnas.61.1.229. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Woese C. R., Dugre D. H., Dugre S. A., Kondo M., Saxinger W. C. On the fundamental nature and evolution of the genetic code. Cold Spring Harb Symp Quant Biol. 1966;31:723–736. doi: 10.1101/sqb.1966.031.01.093. [DOI] [PubMed] [Google Scholar]
- Wong J. T. A co-evolution theory of the genetic code. Proc Natl Acad Sci U S A. 1975 May;72(5):1909–1912. doi: 10.1073/pnas.72.5.1909. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wong J. T., Bronskill P. M. Inadequacy of prebiotic synthesis as origin of proteinous amino acids. J Mol Evol. 1979 Jul 18;13(2):115–125. doi: 10.1007/BF01732867. [DOI] [PubMed] [Google Scholar]
- Wong J. T. The evolution of a universal genetic code. Proc Natl Acad Sci U S A. 1976 Jul;73(7):2336–2340. doi: 10.1073/pnas.73.7.2336. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yockey H. P. A prescription which predicts functionally equivalent residues at given sites in protein sequences. J Theor Biol. 1977 Aug 7;67(3):337–343. doi: 10.1016/0022-5193(77)90042-x. [DOI] [PubMed] [Google Scholar]