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José MV, Zamudio GS, Morgado ER. A unified model of the standard genetic code. R Soc Open Sci. 2017;4(3):160908doi: 10.1098/rsos.160908.
José, M. V., Zamudio, G. S., & Morgado, E. R. (2017). A unified model of the standard genetic code. Royal Society open science, 4(3), 160908. https://doi.org/10.1098/rsos.160908
José, Marco V, et al. "A unified model of the standard genetic code." Royal Society open science vol. 4,3 (2017): 160908. doi: https://doi.org/10.1098/rsos.160908
José MV, Zamudio GS, Morgado ER. A unified model of the standard genetic code. R Soc Open Sci. 2017 Mar 01;4(3):160908. doi: 10.1098/rsos.160908. eCollection 2017 Mar. PMID: 28405378; PMCID: PMC5383835.
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R Soc Open Sci. 2017 Mar 01;4(3):160908. doi: 10.1098/rsos.160908. eCollection 2017 Mar.

A unified model of the standard genetic code.

Royal Society open science

Marco V José, Gabriel S Zamudio, Eberto R Morgado

Affiliations

  1. Theoretical Biology Group, Instituto de Investigaciones Biomédicas , Universidad Nacional Autónoma de México , Mexico D.F . 04510 , Mexico.
  2. Facultad de Matemática, Física y Computación , Universidad Central 'Marta Abreu' de Las Villas , Santa Clara , Cuba.

PMID: 28405378 PMCID: PMC5383835 DOI: 10.1098/rsos.160908

Abstract

The Rodin-Ohno (RO) and the Delarue models divide the table of the genetic code into two classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the tRNA acceptor stem, respectively. These models are asymmetric but they are biologically meaningful. On the other hand, the standard genetic code (SGC) can be derived from the primeval RNY code (R stands for purines, Y for pyrimidines and N any of them). In this work, the RO-model is derived by means of group actions, namely, symmetries represented by automorphisms, assuming that the SGC originated from a primeval RNY code. It turns out that the RO-model is symmetric in a six-dimensional (6D) hypercube. Conversely, using the same automorphisms, we show that the RO-model can lead to the SGC. In addition, the asymmetric Delarue model becomes symmetric by means of quotient group operations. We formulate isometric functions that convert the class aaRS I into the class aaRS II and vice versa. We show that the four polar requirement categories display a symmetrical arrangement in our 6D hypercube. Altogether these results cannot be attained, neither in two nor in three dimensions. We discuss the present unified 6D algebraic model, which is compatible with both the SGC (based upon the primeval RNY code) and the RO-model.

Keywords: aminoacyl-tRNA synthetases; automorphisms; group actions; polar requirement; standard genetic code; symmetry groups

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