arXiv subjects

Jacques H. Daniel

Publications and source records attributed to Jacques H. Daniel.

4 recordsLinked to original sources

arXiv2026

The origin of the genetic code is encrypted in the structure of present-day transfer RNAs

Background/ Objectives: Resolving the origin of the genetic code is fundamental to understanding how life began its journey out of the chemical world. Since its deciphering some 60 years ago, there is still no general theory of the emergence of the genetic code. My objectives are to bring some unique data that might provide some insight into this particular issue. Methods: Because tRNA (transfer RNA) constitutes a crucial piece of the present translational system, having unique structural characteristics, I hypothesized that they might constitute the key elements at the origin of the genetic code and thus decided to compare the primary structure of the tRNAs from a bacterium, Bacillus subtilis. Results: The comparison of the primary structure of the tRNAs from Bacillus subtilis generated a genealogical tree, meaning that the tRNAs were all related and appeared gradually in a precise time sequence. Remarkably, analysis of the various characteristics of this tRNAs tree showed that it very likely reflects the time of entry of amino acids into the Universal Codon Table. Conclusions: These results strongly suggest that the tRNA entity was indeed a major component in the formation of the genetic code and, further, provide a likely scenario for the time sequence of codon colonization of the Universal Codon Table by the various amino acids at the very beginning of life. Also, these data are interpreted in terms of a general theory of the origin of the genetic code I propose, the poly-tRNA theory.

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arXiv2020

On some predictions of the poly-tRNA model for the origin and evolution of genetic coding

The poly-tRNA model was recently presented for the origin and evolution of genetic coding. This model has led to a rather precise description of what might have occurred at the beginning of protein synthesis in the first life form. Here, we further discuss some interesting implications of this model. First, the system of encoded peptide/protein synthesis appears to have started and developed on the breeding ground of a rich RNA world, responsible for the infancy of life existence and complexity. Furthermore, once protein synthesis was fully established and apparently superseding the RNA world, and at a very early stage of life beginnings, we already see what has been a recurrent theme in the likely interpretation of modern comparative molecular studies on species: the full ability of this nascent life entity to develop itself by tinkering, using all kinds of available pieces to improve itself. Lastly, and very instructively, it is deduced from this model that the first peptides to be produced probably had unique properties, not shared by the arsenal of molecules present hitherto, which allowed a functional connection between the then omnipotent RNA world and the lipid membrane vesicles containing it. These specific functions might have initially been at the origin of the Darwinian selection of the full-blown protein-synthesis machinery.

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arXiv2020

On the possible origin and evolution of genetic coding

To synthesize peptides alongside the RNAs making the so-called RNA world, some genetic coding involving RNA had to develop. Herein, it is proposed that the first real-coding setup was a direct one, made up of continuous poly-tRNA-like molecules, with each tRNA-like moiety carrying, beyond and near its 5 prime or 3 prime end, a trinucleotide site for specific amino acid binding: the sequence and continuity of the tRNA moieties of a particular poly-tRNA would ensure the sequence and continuity of the amino acids of the corresponding peptide or small protein. In parallel with these particular entities, and enhancing their peptide-forming function, a proto-ribosome and primitive amino acid-activation system would develop. At some stage, one critical innovation would be the appearance of RNA fragments that could tighten several adjacent tRNA moieties together on a particular poly-tRNA molecule, by pairing with the second trinucleotide sequence (identical to the first one carrying the specific amino acid-binding site) situated at, or close to, the middle of each tRNA moiety (i.e., the present anticodon site). These RNA fragments, acting as authentic co-ribozymes in the peptide-synthesizing apparatus, would constitute the ancestors of the present mRNAs. Later, on these mRNA-like guiding fragments, free tRNA forms would be additionally used, first keeping their amino acid-binding sites, then losing them in favor of a specific amino acid attachment at a CCA arm at their 3 prime end. Finally, these latter mechanisms would progressively prevail, leading to the modern and universal indirect genetic coding system. Experimental and theoretical arguments are presented and discussed in favor of such a scenario for the origin and evolution of genetic coding.

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arXiv2019

On the natural selection of macromolecular network and biological complexity

Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches applied to individual model cell systems have led to the mapping of large networks of macromolecular interactions with similar general properties. Although gene, mechanism and network structure similarities among species tend to suggest the existence of important constraints applied to organisms, it is surprising that the elucidation of the precise general mechanisms by which natural selection could have operated appears to have taken a back seat in most, if not all, studies concerning the evolutionary development of cell macromolecular networks. Herein, a possible explanation is presented for how cells could have evolved into the sophisticated and integrated organisms we know today, using natural selection. Based on the new concept of gene toxicity, essentially applied to unicellular organisms with their rapid multiplication rate, it is proposed that natural selection likely exerts its effects in two opposing and complementary directions to integrate a new gene function into the host system; a simple and basic qualitative model for the buildup of cell macromolecular networks is suggested. Finally, as a radical consequence, it is proposed that complex life evolution has proceeded through a long alternation of unicellular and multicellular states.

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