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

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.

Genetic Hotels for the Standard Genetic Code: Evolutionary Analysis Based upon Novel Three-Dimensional Algebraic Models

“…The main support of our evolutionary paths comes from a previous work (José et al 2009) in which we have shown that 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 the distance series of codons in current prokaryote genomes. Put it simply, the magnitudes of the scaling exponents of the distance series of the codons of a given prokaryote did not change during the evolution of the SGC.…”

“…Put it simply, the magnitudes of the scaling exponents of the distance series of the codons of a given prokaryote did not change during the evolution of the SGC. We can say that they show critical scale invariance according to the renormalization group theory (José et al 2009). Thus, several scaling and statistical features of the RNA and the Extended RNA type I and II codes are still detectable in current prokaryote chromosomes since they show a critical state, with the interesting exception, to some extent, of some Archeas.…”

“…An Extended RNA code type I derived from the more primitive RNA code was recently proposed as an intermediate stage in the evolution of the Standard Genetic Code (SGC) (José et al 2007). We also proposed a second Extended RNA code type II as a plausible evolutionary path (José et al 2007;José et al 2009). Both evolutionary pathways were shown to be reflected in the current genomes of some prokaryotes making these routes not only biologically plausible but also likely (José et al 2009).…”

“…We also proposed a second Extended RNA code type II as a plausible evolutionary path (José et al 2007;José et al 2009). Both evolutionary pathways were shown to be reflected in the current genomes of some prokaryotes making these routes not only biologically plausible but also likely (José et al 2009). …”

On the Uniqueness of the Standard Genetic Code

“…This concept is not far away from the idea that there was an age of miracles. However, as we show in this article, there are indeed several features that are special about the SGC: first, it can be partitioned into two classes of aminoacyl-tRNA synthetases (aaRSs) [13]; secondly, the SGC can be broken down into a product of simpler groups reflecting the pattern of degeneracy observed [14,15]; third, it has symmetrical properties, and evolution did not erase its own evolutionary footsteps [16]. …”