Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code

Alexander Nesterov-Mueller,Roman Popov,Hervé Seligmann

doi:10.3390/life11010004

Abstract

We propose combinatorial fusion rules that describe the codon assignment in the standard genetic code simply and uniformly for all canonical amino acids. These rules become obvious if the origin of the standard genetic code is considered as a result of a fusion of four protocodes: Two dominant AU and GC protocodes and two recessive AU and GC protocodes. The biochemical meaning of the fusion rules consists of retaining the complementarity between cognate codons of the small hydrophobic amino acids and large charged or polar amino acids within the protocodes. The proto tRNAs were assembled in form of two kissing hairpins with 9-base and 10-base loops in the case of dominant protocodes and two 9-base loops in the case of recessive protocodes. The fusion rules reveal the connection between the stop codons, the non-canonical amino acids, pyrrolysine and selenocysteine, and deviations in the translation of mitochondria. Using fusion rules, we predicted the existence of additional amino acids that are essential for the development of the standard genetic code. The validity of the proposed partition of the genetic code into dominant and recessive protocodes is considered referring to state-of-the-art hypotheses. The formation of two aminoacyl-tRNA synthetase classes is compatible with four-protocode partition.

Highlights

Covering more than 50 years of the literature on the origin of the genetic code, renowned specialists E.V
We doubt that statement 3 from this list is a significant prerequisite for clarifying the codon assignment in the standard genetic code (SGC)
Even though canonical amino acids and RNAs with a specific base content may have appeared on Earth in different ways and at different times, there is no evidence that the non-randomly organized SGC arose as a result of successive expansions with amino acids

Summary

Introduction

Covering more than 50 years of the literature on the origin of the genetic code, renowned specialists E.V. Koonin et al put a shortlist of widespread statements about the code properties and aspects of its evolution [1]: 1. The most commonly used arguments for the sequential entry of amino acids into SGC are differences in the prebiotic abundance of amino acids [2,3], indications of GC-rich content in the most archaic RNAs [4], or branching history of two aminoacyl-tRNA synthetase (aaRS) superfamilies [5]. Even though canonical amino acids and RNAs with a specific base content may have appeared on Earth in different ways and at different times, there is no evidence that the non-randomly organized SGC arose as a result of successive expansions with amino acids. Knight et al critically reviewed hypotheses based on phylogenetic analysis and emphasized the absence of any evidence of code expansion during the evolution of synthetases [6]

Methods

Discussion

Conclusion