Molecular Evolution in the primitive Earth:nonlinear analysis of archaea tRNAs compared to computer-generated random sequences

Nothing is known about the way(s) from which life born, and plausibile pathways of prebiotic evolution remain obscure, however, in that context, RNA may be considered the most oldest known informational genetic polymer (Howland, 200). Billions years ago, according to the exon theory of genes (Di Giulio, 1998), small RNAs translated into peptides of 15–20 aminoacids: minigenes of pre-tRNAs codifying RNA hairpin structures. The dimerization of two equal RNA hairpin structures may have lead to the formation of the cruciform structure of the tRNA molecule: tRNAs may reflect the primordial genes of that era. Nucleotide sequence data of tRNAs in archaea were obtained from the GeneBank library*. Random sequence data (white noise) were obtained from the algorithm by Press and Teukolsky (1992). Nucleotide sequences were analyzed as random walks, where each base represent a different step in a two-dimensional space; vice versa, the uniform and random distributed data points over the unit interval algorithm-generated were divided in 16 intervals to which A,C,G,T (U), letters were attributed. Nonlinear parameters (relative LZ complexity, largest Lyapunov exponent, Hurst exponent, correlation dimension, entropy, BDS statistic, Manhattan and Euclidean fractal dimensions) of nucleotide sequences and computer-generated random sequences were evaluated making use of Chaos Data Analyzer (Sprott & Rowlands (1995) or Gates’ (1986) formulation (fractal dimensions). Our data show that the values of nonlinear parameters obtained from the archaea are lower than the values of randomly generated sequences (p < 0.01). These data are in agreement with the ones by Weiss et al. (2000), showing a significant reduction of the Shannon entropy (−1%) in protein sequences compared to random polypeptides. Our results suggest that in the primitive Earth informational polymers might be originated from slightly edited random strings and that during biologic evolution the distance from pure randomness increased. Deviation from pure randomness should be arisen from some constraints like the secondary structure of the biologic macromolecules. Di Giulio M., Reflections of the Genetic Code: a Hypothesis. J. Theor. Biol., 191, 2, 191–196, 1998. Gates M.A., A simple way to look at DNA, J. Theor. Biol., 119, 319–328, 1986. Howland J.L., The Surprising Archaea, Oxford University Press, 2000. Press W.H. & Teukolsky S.A., Portable Random Number Generators, Computers in Physics, 6, 522–524, 1992. Sprott J.C. & Rowlands G., Chaos data Analyzer, Physics Academic Software, 1995. Weiis O. et al., Information Content of Protein Sequences, J. Theor. Biol., 206, 379–386, 2000. * http://www.ncbi.nlm.nih.gov/ E-mail: gbianciardi@unisi.it