Roots of Complexity in the Self-referential Genetic Code
The genetic code is the correspondence between ‘letter’ units that cells utilize for translation: triplets of bases in the producers (genes) and amino acids in the products (proteins). The self-referential model indicates that the codes resulted from proto-tRNA dimer-directed protein synthesis. The dimerized proto-tRNAs became codes when the peptides they produced bound back to them and stabilized the correspondence between the units and the protein production system. Anticodons are representative sites of the initial binding oligomers that guided the complementariness at dimerization. The process of producing stabilized associations is a ‘dynamic, epigenetic kind of memory’. The associated system is a module for the construction of polymers—genes, in the realm of ‘memories in strings.’ Memories guarantee stability while plasticity refers to the dynamics, which are the two main and interdependent characters of the living. Further stabilization and partial autonomy come from diversity in proteins at construction of structures and functions for the metabolic flow network. The metabolic system remains dependent on the environment, in a tense relationship with the degradation it provokes. A necessary component of biological complexity is the plasticity in behaviors, which mediates the diversity, adaptations and open-ended evolution. It is constitutive to protein structures and functions. Plastic behaviors are enhanced through the network organization of the system. Interactions that build networks are dependent on the wide range adhesiveness and binding sites of proteins. The model indicates that networks of nucleoprotein interactions are superposed on those of anticodon dimers, while all components are polymers with variable sequences. The complex behaviors of the resulting multi-synthetase complexes are now minimally rationalized.
KeywordsGenetic code Self-reference Coherence-decoherence Memory Metabolic flow Plasticity Networks tRNA dimers Multi-aminoacyl-tRNA synthetase complex Cohesiveness
The friendly collaboration and support of Gustavo Maia Souza and Alfredo Pereira Junior, personally and along our journey in the self-organization group of UNICAMP.
Conflicts of interest
No conflicts of interest are involved with the present communication.
- Balatti V, Nigita G, Veneziano D, Drusco A, Stein GS, Messier TL, Farina NH, Lian JB, Tomasello L, Liu CG, Palamarchuk A, Hart JR, Bell C, Carosi M, Pescarmona E, Perracchio L, Diodoro M, Russo A, Antenucci A, Visca P, Ciardi A, Harris CC, Vogt PK, Pekarsky Y, Croce CM (2017) tsRNA signatures in cancer. PNAS 114(30):8071–8076. www.pnas.org/cgi/doi/10.1073/pnas.1706908114CrossRefGoogle Scholar
- Cho HY, Maeng SJ, Cho HJ, Choi YS, Chung JM, Lee S, Kim HK, Kim JH, Eom CY, Kim YG, Guo M, Jung HS, Kang BS, Kim S (2015) Assembly of multi-tRNA synthetase complex via heterotetrameric glutathione transferase-homology domains. J Biol Chem 290:29313–29328. https://doi.org/10.1074/jbc.M115.690867CrossRefPubMedPubMedCentralGoogle Scholar
- Grosjean H, Houssier C (1990) Codon recognition: evaluation of the effects of modified bases in the anticodon loop of tRNA using the temperature-jump relaxation method. In: Gehrke CW, Kuo KCT (eds) Chromatography and modification of nucleotides. Elsevier, Amsterdam, pp A255–A295Google Scholar
- Guimarães RC (1996) Anti-complementary order in the genetic coding system. Int Conf Orig Life 26:435–436Google Scholar
- Guimarães RC (2013) Formation of the genetic dode—review and update as of November 2012. http://www.icb.ufmg.br/labs/lbem/pdf/GMRTgeneticodeNov12.pdf. All original publications. https://www.researchgate.net/profile/Romeu_Guimaraes (both sites accessed on August 2017)
- Guimarães RC (2015) Emergence of information patterns: in the quantum and biochemical realms. Quantum Biosyst 6:148–159Google Scholar
- Schlosshauer M (2014) The quantum-to-classical transition and decoherence. In: Aspelmeyer M, Calarco T, Eisert J, Schmidt-Kaler F (eds) Handbook of quantum information. Springer, Berlin/HeidelbergGoogle Scholar
- Seligmann H, Ganesh W (2017) Genetic code optimization for cotranslational protein folding: codon directional asymmetry correlates with antiparallel beta-sheets, tRNA synthetase classes. Comput Struct Biotechnol J 15:412–424. https://doi.org/10.1016/j.csbj.2017.08.001CrossRefPubMedPubMedCentralGoogle Scholar
- Zurek WH (2002) Decoherence and the transition from quantum to classical—revisited. Los Alamos Sci 27:2–25Google Scholar