Paper: On the Evolution of the Standard Genetic Code - Vestiges of Critical Scale Invariance from the RNA World in Current Prokaryote Genomes

On the Evolution of the Standard Genetic Code: Vestiges of Critical Scale
Invariance from the RNA World in Current Prokaryote Genomes
Marco V. José 1, Tzipe Govezensky 1, José A. García 1,2, Juan R. Bobadilla 1

1 Theoretical Biology Group, Instituto de Investigaciones Biomédicas,
Universidad Nacional Autónoma de México, México D.F., México,
2 Department of Preventive and Social Medicine, University of Otago,
Dunedin, New Zealand

Abstract
Herein two genetic codes from which the primeval RNA code could have
originated the standard genetic code (SGC) are derived. One of them, called
extended RNA code type I, consists of all codons of the type RNY (purine-any
base-pyrimidine) plus codons obtained by considering the RNA code but in the
second (NYR type) and third (YRN type) reading frames. The extended RNA code
type II, comprises all codons of the type RNY plus codons that arise from
transversions of the RNA code in the first (YNY type) and third (RNR)
nucleotide bases. In order to test if putative nucleotide sequences in the
RNA World and in both extended RNA codes, share the same scaling and
statistical properties to those encountered in current prokaryotes, we used
the genomes of four Eubacteria and three Archaeas. For each prokaryote, we
obtained their respective genomes obeying the RNA code or the extended RNA
codes types I and II. In each case, we estimated the scaling properties of
triplet sequences via a renormalization group approach, and we calculated
the frequency distributions of distances for each codon. Remarkably, the
scaling properties of the distance series of some codons from the RNA code
and most codons from both extended RNA codes turned out to be identical or
very close to the scaling properties of codons of the SGC. To test for the
robustness of these results, we show, via computer simulation experiments,
that random mutations of current genomes, at the rates of 10^?10 per site
per year during three billions of years, were not enough for destroying the
observed patterns. Therefore, we conclude that most current prokaryotes may
still contain relics of the primeval RNA World and that both extended RNA
codes may well represent two plausible evolutionary paths between the RNA
code and the current SGC.

Source: PLoS One [Open Access]
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004340

Posted by
Robert Karl Stonjek


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