On the origin of degeneracy in the genetic code

Abstract

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.

Circular Tessera Codes in the Evolution of the Genetic Code

“…In this work we have identified and characterized circular tessera codes and their properties. In Gonzalez et al (2012) and Gonzalez et al (2019) Gonzalez, Giannerini and Rosa had proposed an ancestor code of the universal genetic code that is based on 64 tetranucleotides built from dinucleotides by using the Klein four symmetry group. It was hypothesized that this tessera code existed before LUCA and even before the early genetic code that coded for 20 amino acids using all 64 codons.…”

“…It is hypothesized that during evolution the genetic code had several ancestors that might have consisted not only of trinucleotides but of dinucleotides or tetranucleotides or even combinations of these (see Baranov et al 2009;Gonzalez et al 2012;Seligmann 2014;Patel 2005;Wilhelm and Nikolajewa 2004;Wu et al 2005). In particular, in Gonzalez et al (2012) the tessera code was suggested as an ancestral code that might have been the origin of the mitochondrial code (see also Gonzalez et al 2019). In order to define the tessera code we have to introduce some group theory and how it can be applied in the genetic setting.…”

“…AC GU , the tessera code allows degeneracy 2 and 4 only. Maintaining the degeneracy an algorithm was suggested in Gonzalez et al (2019) for passing from the tessera code back to the (mitochondrial) genetic code in the following way: We assign to each of the transformations from V a letter in the genetic alphabet via I ↔ A, SW ↔ U , K M ↔ C and Y R ↔ G and then perform the following algorithm displayed in Fig. 2.…”

“…One possible machine or rather a model which gives a feasible explanation for an important aspect of the evolutionary processes of the genetic code was found by Gonzalez, Giannerini and Rosa. In their work "On the origin of degeneration in the genetic code" (Gonzalez et al 2019) coding and especially on symmetry as an essential cause and consequence of the natural phenomena of degeneracy (compare also . A famous example, which shows the importance of including symmetry deliberations when considering natural phenomena, can be found in quantum mechanics.…”

“…Taking these general considerations into account, Gonzalez, Giannerini, and Rosa argue that none of the theories regarding the origin of the genetic code pays the necessary attention to the idea of symmetry (Gonzalez et al 2019). As a consequence the concept of tessera codes was developed.…”