Evolution and RNA relics. a systems biology view

Acta Biotheor. 2008 Jun;56(1-2):5-25. doi: 10.1007/s10441-008-9028-y. Epub 2008 Feb 14.

Abstract

The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only one codon by synonymy class as solutions of a combinatory variational problem. We compare these solutions to sequences of present RNAs considered as relics, with a high interspecific invariance, like invariant parts of (t)RNAs and micro-RNAs. We conclude by emphasizing some optimal properties of the genetic code.

MeSH terms

  • Animals
  • Base Sequence
  • Evolution, Molecular*
  • Genetic Code
  • Humans
  • Male
  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA / chemistry
  • RNA / genetics*
  • Species Specificity
  • Systems Biology*

Substances

  • RNA