Clues to tRNA Evolution from the Distribution of Class II tRNAs and Serine Codons in the Genetic Code.

Harold Bernhardt

doi:10.3390/life6010010

Abstract

We have previously proposed that tRNAGly was the first tRNA and glycine was the first amino acid incorporated into the genetic code. The next two amino acids incorporated would have been the other two small hydrophilic amino acids serine and aspartic acid, which occurred through the duplication of the tRNAGly sequence, followed by mutation of its anticodon by single C to U transition mutations, possibly through spontaneous deamination. Interestingly, however, tRNASer has a different structure than most other tRNAs, possessing a long variable arm; because of this tRNASer is classified as a class II tRNA. Also, serine codons are found not only in the bottom right-hand corner of the genetic code table next to those for glycine and aspartic acid, but also in the top row of the table, next to those for two of the most hydrophobic amino acids, leucine and phenylalanine. In the following, I propose that the class II tRNA structure of tRNASer and the arrangement of serine codons in the genetic code provide clues to the early evolution of tRNA and the genetic code. In addition, I address Di Giulio’s recent criticism of our proposal that tRNAGly was the first tRNA, and discuss how early peptides produced from a restricted amino acid alphabet of glycine, serine and aspartic acid might have possessed proteolytic activity, which is possibly important for the early recycling of amino acid monomers.

Highlights

We have previously proposed that tRNAGly was the first tRNA, and glycine was the first amino acid incorporated into the genetic code, with the universally-conserved glycine codons GGN the first codons to be assigned due to their strong base-pairing interaction with the tRNAGly anticodon loop sequence (NCC)A [1,2]
In the contemporary code serine shares the AGN codon box with arginine (Figure 1), the latter was probably incorporated into the genetic code at a later stage, as it is not produced in early earth simulation experiments [7] and has a complex biosynthetic pathway; it is possible that the arginine codons in the AGN codon box are the result of more recent
We have previously proposed that the direction of amino acid incorporation into the codon boxes surrounding those of tRNASer(NGA): tRNALeu, tRNASec, and bacterial tRNATyr genetic code was from the small hydrophilic to the larger hydrophobic amino acids [5]

Summary

Introduction

We have previously proposed that tRNAGly was the first tRNA, and glycine was the first amino acid incorporated into the genetic code, with the universally-conserved glycine codons GGN the first codons to be assigned due to their strong base-pairing interaction with the tRNAGly anticodon loop sequence (NCC)A (anticodon in brackets; N is any of the four bases) [1,2]. Duplication of the tRNAGly sequence followed by mutation of its NCC anticodon by a single C to U transition mutation—possibly through spontaneous deamination—would have produced tRNAs with either NCU or NUC anticodons [5]. While these mutant tRNAs would initially still have coded for glycine, subsequent mutations in the “operational code” contained in their acceptor stems [6] would have altered their aminoacylation specificity to serine (for NCU anticodons) and aspartic acid (for NUC anticodons).

Evolution of tRNA

Evolution of other class

Mutation of the

Discussion