The key role of the elongation factors in the origin of the organization of the genetic code

Theories of the origin of the genetic code: Strong corroboration for the coevolution theory

I analyzed all the theories and models of the origin of the genetic code, and over the years, I have considered the main suggestions that could explain this origin. The conclusion of this analysis is that the coevolution theory of the origin of the genetic code is the theory that best captures the majority of observations concerning the organization of the genetic code. In other words, the biosynthetic relationships between amino acids would have heavily influenced the origin of the organization of the genetic code, as supported by the coevolution theory. Instead, the presence in the genetic code of physicochemical properties of amino acids, which have also been linked to the physicochemical properties of anticodons or codons or bases by stereochemical and physicochemical theories, would simply be the result of natural selection. More explicitly, I maintain that these correlations between codons, anticodons or bases and amino acids are in fact the result not of a real correlation between amino acids and codons, for example, but are only the effect of the intervention of natural selection. Specifically, in the genetic code table we expect, for example, that the most similar codons - that is, those that differ by only one base - will have more similar physicochemical properties. Therefore, the 64 codons of the genetic code table ordered in a certain way would also represent an ordering of some of their physicochemical properties. Now, a study aimed at clarifying which physicochemical property of amino acids has influenced the allocation of amino acids in the genetic code has established that the partition energy of amino acids has played a role decisive in this. Indeed, under some conditions, the genetic code was found to be approximately 98% optimized on its columns. In this same work, it was shown that this was most likely the result of the action of natural selection. If natural selection had truly allocated the amino acids in the genetic code in such a way that similar amino acids also have similar codons - this, not through a mechanism of physicochemical interaction between, for example, codons and amino acids - then it might turn out that even different physicochemical properties of codons (or anticodons or bases) show some correlation with the physicochemical properties of amino acids, simply because the partition energy of amino acids is correlated with other physicochemical properties of amino acids. It is very likely that this would inevitably lead to a correlation between codons (or anticodons or bases) and amino acids. In other words, since the codons (anticodons or bases) are ordered in the genetic code, that is to say, some of their physicochemical properties should also be ordered by a similar order, and given that the amino acids would also appear to have been ordered in the genetic code by selection natural, then it should inevitably turn out that there is a correlation between, for example, the hydrophobicity of anticodons and that of amino acids. Instead, the intervention of natural selection in organizing the genetic code would appear to be highly compatible with the main mechanism of structuring the genetic code as supported by the coevolution theory. This would make the coevolution theory the only plausible explanation for the origin of the genetic code.

The time of appearance of the genetic code

I support the hypothesis that the origin of the genetic code occurred simultaneously with the evolution of cellularity. That is to say, I favour the hypothesis that the origin of the genetic code is a very, very late event in the history of life on Earth. I corroborate this hypothesis with observations favouring the progenote's stage for the Last Universal Common Ancestor (LUCA), for the ancestor of bacteria and that of archaea. Indeed, these progenotic stages would imply that - at that time - the origin of the genetic code was still ongoing simply because this origin would fall within the very definition of progenote. Therefore, if the evolution of cellularity had truly been coeval with the origin of the genetic code - at least in its terminal part - then this would favour theories such as the coevolution theory of the origin of the genetic code because this theory would postulate that this origin must have occurred in extremely complex protocellular conditions and not concerning stereochemical or physicochemical interactions having to do with other stages of the origin of life. In this sense, the coevolution theory would be corroborated while the stereochemical and physicochemical theories would be damaged. Therefore, the origin of the genetic code would be linked to the origin of the cell and not to the origin of life as sometimes asserted. Therefore, I will discuss the late hypothesis of the origin of the genetic code in the context of the theories proposed to explain this origin and more generally of its implications for the early evolution of life.

The evolutionary stages of the complexity of biological catalysts mark and clarify the phases of the origin of the genetic code: A model for the origin of the reading frame with codons from proto-mRNAs with different frames

I analyse the origin of the genetic code in the light of the evolution of biological catalysts. I discuss the rudimentary forms that the genetic code assumed in the presence of a catalysis performed by ions or by low molecular weight molecules, such as nucleotide coenzymes. However, it is only with the advent of a mixed polymer made of RNA and peptides - covalently linked - that the genetic code took on a clearer form. Indeed, the first true form of coding appeared. Furthermore, interacting peptidated RNAs promoted an extremely rudimentary form of protein synthesis. This stage evolved into a stage in which proto-mRNAs guided interactions among peptidated RNAs aimed at the synthesis of peptidated RNAs having an active catalytic function. Finally, the invasion of aminoacylated proto-tRNAs with specific amino acids, coming from amino acid metabolism, and recognising only three bases on these proto-mRNAs with reading frames larger than three bases, would have triggered the birth of actual mRNAs, i.e. the origin of codons. All this would have linked the metabolism of amino acids to the origin of mRNAs and therefore to the origin of the organization of the genetic code, as maintained by the coevolution theory of the genetic code.

The origin of the genetic code and origin of ideas

Inouye et al. (2020) use the observation that Ser is coded in the genetic code by two blocks of codons that differ on more than one base to understand some aspects of the origin of the genetic code organization. I argue instead that this observation per se cannot be used to understand any aspect of the origin of the genetic code, unless it is accompanied by other assumptions concerning in the specific case: (i) the ancestrality of some amino acids, (ii) the hypothesis that the first mRNA to be translated was poly-G, which can be translated into poly-Gly, and (iii) an evolutionary mechanism for the genetic code origin based on the duplication of tRNAs. However, both the tRNA duplication mechanism and the existence of poly-G as the first mRNA to be translated are not corroborated as mechanisms through which the genetic code would have been structured. For example, the origin of the actual mRNA should have been preceded by the evolution of a proto-mRNA which evidently already coded for more than one amino acid. Therefore, when it evolved from proto-mRNA, the mRNA should already have coded for more than one amino acid. In other words, poly-G as mRNA would most likely never have existed because the first mRNAs already had to code for more than one amino acid. On the contrary, all these assumptions would have been operational if the observations of Inouye et al. (2020) had been discussed within the coevolution theory of the origin of the genetic code, which they do not.