A mathematical model of he genetic code, the origin of protein coding, and genetic code conservation (Comunicazione a convegno)

  • A mathematical model of he genetic code, the origin of protein coding, and genetic code conservation (Comunicazione a convegno) (literal)
  • 2014-01-01T00:00:00+01:00 (literal)
Alternative label
  • Gonzalez Diego L. (2014)
    A mathematical model of he genetic code, the origin of protein coding, and genetic code conservation
    in First International Conference on Code Biology, Paris, 20-24 may 2014
  • Gonzalez Diego L. (literal)
  • CNR-IMM UOS di Bologna (literal)
  • A mathematical model of he genetic code, the origin of protein coding, and genetic code conservation (literal)
  • We present a mathematical model of the mitochondrial genetic code that explains exactly its degeneracy distribution (1). The same approach, which is based on redundant integer-number numeration-systems (non-power systems), has been previously used for explaining the degeneracy distribution of the Euplotes nuclear genetic code (2). The mitochondrial model suggests a possible origin for protein coding on the basis of the symmetries of primeval adaptors connecting the world of nucleic acids with the world of amino acids. In the optics of code theory we are interested in investigating if some characteristics of primeval genetic codes have been conserved through evolution and, consequently, if such characteristics should be observed in present ones. The results are very surprising: i) we observe a perfect conservation of the degeneracy distribution of the mitochondrial code (note that such property allows to change the meaning of some codons without altering the degeneracy distribution), ii) some primeval degeneracy properties (as for example the Rumer's anti-symmetric transformation) are exactly conserved in present codes, iii) the nuclear codes can be included in the mitochondrial class as a particular case of symmetry breaking. In fact, the main differences between mitochondrial and nuclear codes are due to post-transcriptional modifications, iv) the comparison of all known variants of the genetic code allows to uncover that particular classes of codons are prone to variation. Such unstable codons are described in our model by discrete symmetries involving a lesser number of codons (less constrained codons). Such codons are mutually related by a global symmetry: the palindromic symmetry. Using these properties a hierarchy of codon stabilities can be obtained. The previous results point to two main conclusions: 1) the genetic code emerge as highly conserved, much more that though until now because of the fact that most known variants are compatible with the conservation of the degeneracy distribution; this result enforces one of the main postulates of code biology, 2) the degeneracy distribution seems intimately tied with important, but yet to be determined, biological functions (degeneracy distribution is much more conserved than the assignations codon/amino acid). Some interesting possibilities for such functions include: error correction control (point mutations (1-3) and frame synchronization (2-4)), protein synthesis regulation (5), and control of protein folding (6). (1) On the origin of the mitochondrial genetic code: Towards a unified mathematical framework for the management of genetic information, Gonzalez D. L., Giannerini S., and Rosa, R., Nature Precedings, http://dx.doi.org/10.1038/npre.2012.7136.1, (2012). (2) The Mathematical Structure of the Genetic Code, D.L. Gonzalez, in: The Codes of Life (book chapter 6), Marcello Barbieri Editor, Springer Verlag (2008). (3) Error Detection and Correction Codes, Gonzalez D.L., in: The Codes of Life (book chapter 17), Marcello Barbieri Editor, Springer Verlag (2008). (4) Circular codes revisited: a statistical approach, D.L. Gonzalez, S. Giannerini and R. Rosa, Journal of Theoretical Biology, vol. 275, n.1, pp21-28, (2011). (5) Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria, A.R. Subramaniama, T. Panb, and P. Cluzela, www.pnas.org/cgi/doi/10.1073/pnas.1211077110 (2012). (6) Nucleic Acid Chaperons: A theory of an RNA-assisted Protein Folding, J.C. Biro, Theor. Biol. Med. Model. 1;2:35, (2005). (literal)
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