“…In evolutionary terms, the proposed decoding system is placed before the early code, the code that preceded the universal genetic code of LUCA. The early code has been hypothesized to have the same symmetry as the mitochondrial genetic code [17,19,20]. Our theory complements this hypothesis since our tessera code, possessing the same symmetry as the present mitochondrial genetic code, can be seen as a pre-early code, an ancestor of the early code.…”
Section: (B) the Mitochondrial Genetic Codesupporting
In this article, we present a mathematical framework based on redundant (non-power) representations of integer numbers as a paradigm for the interpretation of genomic information. The core of the approach relies on modelling the degeneracy of the genetic code. The model allows one to explain many features and symmetries of the genetic code and to uncover hidden symmetries. Also, it provides us with new tools for the analysis of genomic sequences. We review briefly three main areas: (i) the Euplotid nuclear code, (ii) the vertebrate mitochondrial code, and (iii) the main coding/decoding strategies used in the three domains of life. In every case, we show how the non-power model is a natural unified framework for describing degeneracy and deriving sound biological hypotheses on protein coding. The approach is rooted on number theory and group theory; nevertheless, we have kept the technical level to a minimum by focusing on key concepts and on the biological implications.
“…In evolutionary terms, the proposed decoding system is placed before the early code, the code that preceded the universal genetic code of LUCA. The early code has been hypothesized to have the same symmetry as the mitochondrial genetic code [17,19,20]. Our theory complements this hypothesis since our tessera code, possessing the same symmetry as the present mitochondrial genetic code, can be seen as a pre-early code, an ancestor of the early code.…”
Section: (B) the Mitochondrial Genetic Codesupporting
In this article, we present a mathematical framework based on redundant (non-power) representations of integer numbers as a paradigm for the interpretation of genomic information. The core of the approach relies on modelling the degeneracy of the genetic code. The model allows one to explain many features and symmetries of the genetic code and to uncover hidden symmetries. Also, it provides us with new tools for the analysis of genomic sequences. We review briefly three main areas: (i) the Euplotid nuclear code, (ii) the vertebrate mitochondrial code, and (iii) the main coding/decoding strategies used in the three domains of life. In every case, we show how the non-power model is a natural unified framework for describing degeneracy and deriving sound biological hypotheses on protein coding. The approach is rooted on number theory and group theory; nevertheless, we have kept the technical level to a minimum by focusing on key concepts and on the biological implications.
“…are coded by two codons. Figure 4.Representation of the evolution of the genetic code, adapted from [34]. Each circle or square represents a milestone.…”
Section: Evolutionary Implicationsmentioning
confidence: 99%
“…Remarkably, no extant code exceeds this limit and the maximum number of amino acids that are coded directly by some genomes is exactly 23: the 20 standard amino acids plus 2 non-standard ones (selenocysteine and pyrrolysine) and the alternative initiation amino acid N -formylmethionine sum up to 23. Moreover, the number of adaptors used in the vertebrate mitochondrial genetic code is 22: eight tRNAs that recognize four codons each, 14 tRNAs that recognize two codons each, and two pairs of codons not associated with amino acids [34,51]. Remarkably, 22 is the absolute minimum observed among all known versions of the genetic code.…”
Section: Evolutionary Implicationsmentioning
confidence: 99%
“…In the second part of this article, we analyse the possible evolutionary implications of the tessera code. To this aim, we recall the evolutionary hypothesis presented by Watanabe & Yokobori [34] which is based on the analysis of translation in extant mitochondria (see figure 4 adapted from [34]). Figure 4 presents milestones on which there is some agreement and that represent the evolutionary steps from a primitive genetic code to the present variants.…”
Section: Evolutionary Implicationsmentioning
confidence: 99%
“…To this aim, we develop a model of the putative ancestor of the genetic code of LUCA. In the literature, there is some agreement about the fact that the degeneracy distribution of this ancestor genetic code should coincide with that of the present vertebrate mitochondrial genetic code [7,34]. In our view, a satisfactory model of the early code needs to possess: (i) the exact quantitative description of the degeneracy distribution and (ii) the fundamental Rumer’s symmetry which is inherited by the LUCA’s and subsequent codes.…”
The degeneracy of amino acid coding is one of the most crucial and enigmatic aspects of the genetic code. Different theories about the origin of the genetic code have been developed. However, to date, there is no comprehensive hypothesis on the mechanism that might have generated the degeneracy as we observe it. Here, we provide a new theory that explains the origin of the degeneracy based only on symmetry principles. The approach allows one to describe exactly the degeneracy of the early code (progenitor of the genetic code of LUCA, the last universal common ancestor) which is hypothesized to have the same degeneracy as the present vertebrate mitochondrial genetic code. The theory is based upon the tessera code, that fits as the progenitor of the early code. Moreover, we describe in detail the possible evolutionary transitions implied by our theory. The approach is supported by a unified mathematical framework that accounts for the degeneracy properties of both nuclear and mitochondrial genetic codes. Our work provides a new perspective to the understanding of the origin of the genetic code and the roles of symmetry principles in the organization of genetic information.
“What I cannot create, I do not understand.” Richard Feynman’s bon mot seems almost tailored for experimental systems chemists to realise an important step in the chemical sciences: the creation of living synthetic cells from the entirely inanimate. The underlying idea needs to be simple so the system can develop naturally. This proposal aims at the realisation, viz. finding sets of experimentally feasible initial conditions, exploring varied compositions and analysing their outcomes, of a fully synthetic chemical micro‐compartmented and evolvable macromolecular system being fed with monomers and small molecular weight, high energy compounds, to keep the system permanently out of thermodynamic equilibrium and let it self‐evolve, thus gaining: 1) import‐export control of macromolecules across the compartment membranes; 2) food‐dependent increase in macromolecular size, i.e., polymer length inside the compartments; 3) sustained production of new macromolecules through the establishment of a (or several) de novo genetic code(s); leading to 4) the emergence of replicating macromolecular populations; and 5) the emergence of self‐evolved synthetic living cells.
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