The possible scenario of the origin and evolution of genetic code is proposed, being primarily implicated by the working hypothesis which states that the chronological order of amino acids evolutionary implementation monotonically correlates with their increasing mass. It fulfills the minimalistic claim of the smallest changes of the evolving system at increasing complexity, hereinafter called "the smooth evolution". The working hypothesis was postulated concerning the results of statistical analysis indicating a strong correlation between amino acid mass and the chosen parameters of contemporary genetic code, which are expected to change in a certain individual direction during the evolution of the initial genetic system. It was additionally supplemented by the most common hypotheses adopted from the literature, as stereochemical, 'frozen accident' and coevolutional. The developed scenario allows a detailed description of the twenty-two consecutive episodes of the history of code definition and the estimation of its dynamics. It reveals the main eras of evolution conditioned by the environmental and structural constraints. It also lets the estimation of the evolutionary frequencies of codon sense expansion, and redefinition. Dominating trends and amino acids were indicated. The underlying assumptions, limits, exceptions, and the future of the code evolution have been discussed.
Universal Genetic Code, Evolution, Theory
- Berg J.M., Tymoczko J.L., Stryer L. (2002). Biochemistry. 5th edition. New York: W. H. Freeman; 2002. Section 5.5. Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point. Available from: http://www.ncbi.nlm.nih.gov/books/NBK22342/
- Chechetkin V.R. (2006). Genetic code from tRNA point of view. J Theor Biol. 2006;242(4):922–934.
- Chen I.A., Schindlinger M. (2010). Quadruplet codons: One small step for a ribosome, one giant leap for proteins. An expanded genetic code could address fundamental questions about algorithmic information, biological function, and the origins of life. Bioessays. 2010 Aug; 32(8): 650–654. doi: 10.1002/bies.201000051
- Crick F.H. (1968). The origin of the genetic code. J Mol Biol. 1968;38(3):367–79.
- Duan C., Huan Q., Chen X., Wu S., Carey L.B., Xionglei, H., Wenfeng, Q. (2018). Reduced intrinsic DNA curvature leads to increased mutation rate. Genome Biology 19, 132. Available from: https://doi.org/10.1186/s13059-018-1525-y
- Dufton M.J. (1997). Genetic code synonym quotas and amino acid complexity: cutting the cost of proteins? J Theor Biol. 1997;187:165–173.
- Demongeot, J., & Seligmann, H. (2019b). Bias for 3'-dominant codon directional asymmetry in theoretical minimal RNA rings. J Comput Biol, in press.
- Freeland S.J., Knight R.D., Landweber L.F., Hurst L.D. (2000). "Early fixation of an optimal genetic code". Molecular Biology and Evolution. 17 (4): 511–18.
- Forster A.C., Church, G.M. (2006). Towards synthesis of a minimal cell. Molecular Systems Biology 2:45.
- Frank A., Froese T. (2018). The Standard Genetic Code can Evolve from a Two-Letter GC Code Without Information Loss or Costly Reassignments. Orig Life Evol Biosph. 48(2):259-272. doi: 10.1007/s11084-018-9559-4
- Guilloux A., Jestin J.L. (2012). The genetic code and its optimization for kinetic energy conservation in polypeptide chains. Biosystems. 2012;109(2):141–144.
- Gamow, G. (1954). Possible relation between deoxyribonucleic acid and protein structures. Nature, 1954. 173:318.
- Gánti Tibor (2003): Chemoton Theory. Vol. I.Theory of Fluid Machineries. Kluwer Academic/Plenum Publishers, New York
- Gánti Tibor (2003): Chemoton Theory. Vol. II. Theory of Living Systems. Kluwer Academic/Plenum Publishers, New York
- Di Giulio M. (2003). The late stage of genetic code structuring took place at high temperature. Gene. 2003;261:189–195.
- Gonzalez-Flores JN, Shetty SP, Dubey A, Copeland PR. (2013). The molecular biology of selenocysteine. Biomol Concepts. 4(4):349–365. doi:10.1515/bmc-2013-0007
- Gotoh, O., (1983). Prediction of melting pro®les and local helix stability for sequenced DNA. Adv. Biophys. 16, 1±52.
- Guimarães RC (2013) Formation of the genetic code – a review and update as of November 2012. http://www. icb.ufmg.br/labs/lbem/pdf/GMRTgeneticodeNov12.pdf Original publications available from: https://www. researchgate.net/profile/Romeu_Guimaraes
- Henderson L.J., The fitness of the environment: an inquiry into the biological significance of the properties of matter The Macmillan Company, 1913.
- Itzkovitz S., Alon U. (2007). The genetic code is nearly optimal for allowing additional information within protein‐coding sequences. Genome Research, 17(4), 405–412.
- Koonin E.V. Novozhilov A.S. (2017). Origin and Evolution of the Universal Genetic Code; Annual Review of Genetics. 2017. Vol. 51:45-62
- Kumar B.,Saini S., (2016) Analysis of the optimality of the standard genetic code. Mol. BioSyst., 2016,12, 2642-2651. doi:10.1039/C6MB00262E
- Mat W.K., Xue H., Wong J.T. (2008). The genomics of LUCA. Front Biosci. 1;13:5605-13.
- Nick L., B. Yoshitaka, Wei. Kenneth J.W. Szostak, S. Hiroaki. (2000). Ribozyme-catalyzed tRNA aminoacylation. Nature Structural Biology. 7, 28. Nature America, https://doi.org/10.1038/71225
- Nirenberg, M. W. and Matthaei, J. H. (1961). The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. PNAS, 47(10), 1588-1602. Available from:
- Pelc S.R., Welton M.G.E. (1966). Stereochemical relationship between coding triplets and amino acids. Nature. 1966;209:868–872.
- Seligmann H. (2010). Do anticodons of misacylated tRNAs preferentially mismatch codons coding for the misloaded amino acid? BMC Mol Biol. 2010;11:41.
- Seligmann H. (2011). Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion. Comput Biol Chem. 2011; 35:81–95.
- Seligmann H. (2019). Localized Context-Dependent Effects of the “Ambush” Hypothesis: More Off-Frame Stop Codons Downstream of Shifty Codons. DNA Cell Biol. 38(8):786-795. doi: 10.1089/dna.2019.4725.
- Sonneborn T.M. (1965). Degeneracy of the genetic code: extent, nature, and genetic implications. Evolving genes and proteins. 1965:377–397.
- Söll, D., Ohtsuka, E., Jones, D. S., Lohrmann, R., Hayatsu, H., Nishimura, S., and Khorana, H. G. (1965). Studies on polynucleotides, XLIX. Stimulation of the binding of aminoacyl-sRNA's to ribosomes by ribotrinucleotides and a survey of codon assignments for 20 amino acids. PNAS, 54 (5), 1378-1385. Available from:
- Trifonov E.N., (1997). T. Bettecken. Sequence fossils, triplet expansion, and reconstruction of earliest codons. Gene. 1997: 205, Issue: 1-2, Page: 1-6.
- Trifonov E.N. (2000). Consensus temporal order of amino acids and evolution of the triplet code. Gene. 2000;261:139–151. doi: 10.1016/S0378-1119(00)00476-5.
- Woese C.R. (1965). On the evolution of the genetic code. Proc Natl Acad Sci USA. 1965;54(6):1546–1552. Available from:
- Wong J.T.F. (1975). A Co-Evolution Theory of the Genetic Code. Proceedings of the National Academy of Sciences. 1975;72(5):1909–1912. Available from:
- Wong, J.T.F. (2005). The coevolution hypothesis at age thirty. Bioessays 27, 416-426.
- Xia, T., SantaLucia, J., Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C., Turner, D.H. (1998). Thermodinamical parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37, 14719±14735.
International Journal of Sciences is Open Access Journal.
This article is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) License.
Author(s) retain the copyrights of this article, though, publication rights are with Alkhaer Publications.