Abstract
Combinatorial fusion cascade was proposed as a transition stage between prebiotic chemistry and early forms of life. The combinatorial fusion cascade consists of three stages: eight initial complimentary pairs of amino acids, four protocodes, and the standard genetic code. The initial complimentary pairs and the protocodes are divided into dominant and recessive entities. The transitions between these stages obey the same combinatorial fusion rules for all amino acids. The combinatorial fusion cascade mathematically describes the codon assignments in the standard genetic code. It explains the availability of amino acids with the even and odd numbers of codons, the appearance of stop codons, inclusion of novel canonical amino acids, exceptional high numbers of codons for amino acids arginine, leucine, and serine, and the temporal order of amino acid inclusion into the genetic code. The temporal order of amino acids within the cascade is congruent with the consensus temporal order previously derived from the similarities between the available hypotheses. The control over the combinatorial fusion cascades would open the road for a novel technology to develop artificial microorganisms.
Highlights
If the origin of the genetic code is considered in the scope of protein evolution, this “topdown” approach leads to the consensus about the gradually evolved standard genetic code (SGC) from some initial primordial code
The formation of an even number of codons for canonical amino acids is a direct consequence of the combinatorial fusion cascade
The concept of a gradually evolving genetic code dominates the science about the origin of the SCG
Summary
The fusion rules for the dominant protocodes correspond to the most spontaneously occurring mutation types (A -> G and G -> A as well as C -> U and U -> C) in the third codon (1st anticodon) position noted by Crick shortly after the publication of the code table [33] This wobble position is occupied by a modified base that is part of the universal genetic code and was probably present in the last universal common ancestor [23]. The reconstruction of the combinatorial cascade from the standard genetic code, according to the fusion rules, led to exactly eight initial pairs of amino acids (total of 16 amino acids) This is equal to the number of amino acids in the doublet codon code proposed by Copley et al based on the possible synthesis pathways of amino acids from α-keto acid precursors covalently attached to dinucleotides [34]. Combinatorial fusion rules express this intrinsic fact of the SGC in an explicit and probably the simplest form
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