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Mutuality in Discrete and Compositional Information: Perspectives for Synthetic Genetic Codes

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Abstract

The self-referential model for the formation of the genetic code proposes that protein synthesis was initiated by proto-tRNA dimers. Proto-tRNAs in the dimers recognize each other through anticodon pairing. The proteins produced recognize the producing dimers through binding, forming (proto)ribonucleoprotein (RNP) aggregates. Their functions were stimulated and specificities evolved through cycling. Such cycles would be among the first in the construction of living networks, and examples of processes that might be relevant for modeling cognitive networks. The protein synthesis process is considered a main drive for the living system′s specific attributes of anabolic and evolutionary semi-autonomy. Structures of the anticodon dimer networks are presented. Biological data point to the encoding having been installed on the modules of dimers formed by nonself-complementary triplets. Aminoacyl-tRNA adhesion interactions integrated the dimer networks into RNP networks. Specific questions are proposed for simulation and modeling that should help in designing experimental procedures aiming at testing the model and the development of synthetic genetic codes.

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Abbreviations

 Amino acids :

Are designated by three-letter abbreviations; groups of amino acids may be indicated by one-letter abbreviations

Anticodon:

The code triplet of transfer RNA, the default notation of code triplets

aRS:

Synthetase, aminoacyl-tRNA synthetase

Codon:

The code triplet of messenger RNA

iMet:

Initiator

MaRS:

Multi-aRS complex

mRNA:

Messenger RNA

pDiN:

The principal dinucleotide of code triplets, excluding the wobble position

R:

Purines

RF:

Release factors

RNP:

Ribonucleoprotein

rRNA:

Ribosomal RNA

SRM:

Self-referential model

Transferase:

Peptidyl-transferase

tRNA:

Transfer RNA

-, w, N (any base):

The wobble position of code triplets, anticodon 5′ or codon 3′

X:

Stop or termination

Y:

Pyrimidines

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Acknowledgments

The continued collaboration of the colleagues in the Self-organization Group of the Center for Logics and Epistemology of UNICAMP, especially Alfredo Pereira Júnior, and of Carlos Henrique Costa Moreira and Sávio Torres de Farias are deeply appreciated, as well as the fruitful discussions with Arkadiusz Chworos.

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  1. Laboratório de Biodiversidade e Evolução Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil

    Romeu Cardoso Guimarães

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Guimarães, R.C. Mutuality in Discrete and Compositional Information: Perspectives for Synthetic Genetic Codes. Cogn Comput 4, 115–139 (2012). https://doi.org/10.1007/s12559-011-9116-1

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