Symmetrical distributions of aminoacyl-tRNA synthetases during the evolution of the genetic code

José, Marco V.; Bobadilla, Juan R.; Zamudio, Gabriel S.; Farías, Sávio Torres de

doi:10.1007/s12064-023-00394-0

Cited by 3 publications

(1 citation statement)

References 53 publications

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“…The relational model of the structure of the standard genetic code analyzed by Konjevoda and Štambuk ( 29) is a valuable attempt to unify these and other evolving studies. Other authors emphasize the role of tRNA in the origin and evolution of the genetic code, highlighting the interactions between aminoacyl-tRNA synthetases and different tRNA domains, an operational code of tRNA aminoacylation and a standard tRNA code composed of 46 anticodons (46)(47)(48)(49)(50)(51)(52).…”

Section: Discussion and Concluding Remarksmentioning

confidence: 99%

Rules governing the genetic code degeneracy/redundancy and spatial organization of the codon informative properties

Rapacioli,

Katz,

Flores

2024

Front. Appl. Math. Stat.

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The present study is devoted to describing the “logic” implicit in the standard genetic code. Bases are considered as physicochemical entities possessing two essential properties: molecular type and number of Hydrogen bonds involved (bases pairing) in the codon-anticodon specific interactions. It is proposed that the codon structure possesses a dual informative function: on the one hand, it determines its discriminating or non-discriminating character, and on the other hand, it determines a specific amino acid. These two aspects constitute the codon global information. Two different sets of rules are introduced to describe these different phenomena. It is established that, depending on the type of base occupying the second position, only two or three of the six codon properties located at defined positions determine the discriminating or non-discriminating behavior. With regard to the amino acid determining function of the codons for different sets of synonymous (singlets, doublets, triplets, quadruplets, or sextets), the number of informative properties integrating the codon and their typical positions characteristically change. Based on the rules presented here, it can be postulated that a codon can be defined as an asymmetric informative entity, whose global informative capacity results from the spatially organized combination of the six properties assigned by the three bases.

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Section: Discussion and Concluding Remarksmentioning

confidence: 99%

Rules governing the genetic code degeneracy/redundancy and spatial organization of the codon informative properties

Rapacioli,

Katz,

Flores

2024

Front. Appl. Math. Stat.

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Major evolutionary transitions before cells: A journey from molecules to organisms

Prosdocimi,

de Farias

2024

Progress in Biophysics and Molecular Biology

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Groups of Symmetries of the Two Classes of Synthetases in the Four-Dimensional Hypercubes of the Extended Code Type II

José,

Morgado,

Bobadilla

2023

Life

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Aminoacyl-tRNA synthetases (aaRSs) originated from an ancestral bidirectional gene (mirror symmetry), and through the evolution of the genetic code, the twenty aaRSs exhibit a symmetrical distribution in a 6-dimensional hypercube of the Standard Genetic Code. In this work, we assume a primeval RNY code and the Extended Genetic RNA code type II, which includes codons of the types YNY, YNR, and RNR. Each of the four subsets of codons can be represented in a 4-dimensional hypercube. Altogether, these 4 subcodes constitute the 6-dimensional representation of the SGC. We identify the aaRSs symmetry groups in each of these hypercubes. We show that each of the four hypercubes contains the following sets of symmetries for the two known Classes of synthetases: RNY: dihedral group of order 4; YNY: binary group; YNR: amplified octahedral group; and RNR: binary group. We demonstrate that for each hypercube, the group of symmetries in Class 1 is the same as the group of symmetries in Class 2. The biological implications of these findings are discussed.

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Symmetrical distributions of aminoacyl-tRNA synthetases during the evolution of the genetic code

Cited by 3 publications

References 53 publications

Rules governing the genetic code degeneracy/redundancy and spatial organization of the codon informative properties

Rules governing the genetic code degeneracy/redundancy and spatial organization of the codon informative properties

Major evolutionary transitions before cells: A journey from molecules to organisms

Groups of Symmetries of the Two Classes of Synthetases in the Four-Dimensional Hypercubes of the Extended Code Type II

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