Evidence from glycine transfer RNA of a frozen accident at the dawn of the genetic code

Abstract

Background: Transfer RNA (tRNA) is the means by which the cell translates DNA sequence into protein according to the rules of the genetic code. A credible proposition is that tRNA was formed from the duplication of an RNA hairpin half the length of the contemporary tRNA molecule, with the point at which the hairpins were joined marked by the canonical intron insertion position found today within tRNA genes. If these hairpins possessed a 3'-CCA terminus with different combinations of stem nucleotides (the ancestral operational RNA code), specific aminoacylation and perhaps participation in some form of noncoded protein synthesis might have occurred. However, the identity of the first tRNA and the initial steps in the origin of the genetic code remain elusive.

Results: Here we show evidence that glycine tRNA was the first tRNA, as revealed by a vestigial imprint in the anticodon loop sequences of contemporary descendents. This provides a plausible mechanism for the missing first step in the origin of the genetic code. In 448 of 466 glycine tRNA gene sequences from bacteria, archaea and eukaryote cytoplasm analyzed, CCA occurs immediately upstream of the canonical intron insertion position, suggesting the first anticodon (NCC for glycine) has been captured from the 3'-terminal CCA of one of the interacting hairpins as a result of an ancestral ligation.

Conclusion: That this imprint (including the second and third nucleotides of the glycine tRNA anticodon) has been retained through billions of years of evolution suggests Crick's 'frozen accident' hypothesis has validity for at least this very first step at the dawn of the genetic code.

Reviewers: This article was reviewed by Dr Eugene V. Koonin, Dr Rob Knight and Dr David H Ardell.

Figure 1

Proposed hairpin duplication origin of tRNA. Hairpin monomer (top left) is in equilibrium with partial duplex (top middle), both of which are able to be specifically aminoacylated with glycine by the RNA predecessor of contemporary glycyl-tRNA synthetase (bottom left and middle). The defining moment in the origin of tRNA was the ligation of the partial duplex, which created a covalently joined molecule (top right), anticodon loop, and anticodon from the 3'-terminal CCA sequence of the upstream hairpin [1,2,32]. Mutations (principally in the central loops) produced the precursor to contemporary glycine tRNA (bottom right). Subsequent duplication and mutation to re-evolve the amino acid-specific RNA operational code sequences of the other amino acid-accepting hairpins (with accompanying mutation of the anticodon) led to a proliferation of tRNA sequences and, eventually, coded protein synthesis.

Figure 2

Glycine tRNA consensus sequences showing canonical intron insertion position. (A) Anticodon arm consensus sequence from 466 glycine tRNA genes from eubacteria, archaea and eukaryote cytoplasm taken from [13]. Note: T has been changed to U for the purpose of showing RNA sequence. Adapted from an image generated by WebLogo software [40]. (B) Cloverleaf consensus sequence of 136 mammalian mitochondrial glycine tRNA gene sequences taken from [14]. In the anticodon loop: conserved in 100% of sequences designated by green squares (e.g. C₃₅, A₃₇); in > 90% of sequences by blue squares (e.g. C₃₆); in > 50% of sequences by the open square. Note: 3'-CCA terminus is not displayed. T has not been changed to U in this depiction.

Figure 3

Phylogenetic tree of glycine tRNA gene sequences from bacteria, archaea and eukaryote cytoplasm. The phylogenetic relaxed neighbour joining tree was constructed by using 466 glycine tRNA gene sequences from eubacteria, archaea and eukaryote cytoplasm, taken from [13]. Branches including tRNA gene sequences not containing an anticodon loop CCA sequence are shown in colour, and indicated by the particular labels (with number of sequences in brackets).