On the evolution of the standard genetic code: vestiges of critical scale invariance from the RNA world in current prokaryote genomes.
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.
José
Marco V
MV
Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México DF, México. marcojose@biomedicas.unam.mx
Govezensky
Tzipe
T
García
José A
JA
Bobadilla
Juan R
JR
D000595:Amino Acid Sequence; D001483:Base Sequence; D019143:Evolution, Molecular; D005815:Genetic Code / Q000235:genetics*; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D011387:Prokaryotic Cells / Q000378:metabolism; D012313:RNA / Q000737:chemistry*
D012313:RNA