The mechanism and evolution of the recognition scheme between key components of the translation system, that is, tRNAs, synthetases, and elongation factors, are fundamental issues in understanding the translation of genetic information into proteins. Statistical analysis of bacterial tRNA sequences reveals that for six amino acids, a string of 10 nucleotides preceding the tRNA 3' end carries cognate coding triplets to nearly full extent. The triplets conserved in positions 63–67 are implicated in the recognition by the elongation factor EF‐Tu, and those conserved in positions 68–72, in the identification of cognate tRNAs, and their derived minihelices by class IIa synthetases. These coding triplets are suggested to have primordial origin, being engaged in aminoacylation of prebiotic tRNAs and in the establishment of the canonical codon set.

BackgroundThe evolutionary pathway of tRNA established the linking of the genetic code and protein synthesis, thus, revealing the characteristics of the prebiotic tRNA is crucial for presenting a feasible scenario for the emergence of life. ResultsAnalysis of bacterial tRNA sequences reveals that for nine amino acids, mostly those considered to be the most ancient ones, the acceptor-TC arm carries cognate coding triplets far beyond statistical expectation. The contemporary determinants for the recognition of tRNAs and minihelices by the cognate synthetases and by EF-Tu, are part of these conserved triplets. We also find a strong correlation between the extent of the coding triplet conservation and amino acids whose contemporary synthetases belong to class IIa. ConclusionsIdentification of conserved coding triplets within the tRNA acceptor-TC stem, along with the analysis of their distinctive layout, is suggestive of a continuous evolutionary path that could have led to the appearance of the early translation system. Synthetase 3Background tRNA is a critical component of the translation system due to its role in linking the genetic code with the synthesized protein. The modern tRNA is an L-shaped molecule. One end of the molecule is the universally conserved single stranded NCCA tail which carries the cognate amino acid (aa), while at the other end, about 75Å away, the anticodon (AC) loop that fully characterizes the attached amino acid is located. The mature tRNA interacts with three key components of the translation system -the cognate aminoacyl-tRNA-synthetase (aaRS) that specifically aminoacylates it; the elongation factor (EF-Tu in bacteria) that accommodates the aa-tRNAs and carries them, in a ternary complex, to the ribosome; and the ribosome where the attached amino acid is incorporated into the growing polypeptide. Recognition of aa-tRNA on the ribosome is accomplished via the interactions of the mRNA codon accommodated on the small subunit, with the AC loop. EF-Tu, which carries a variety of different tRNAs, recognizes each of them specifically [1]. The minimal fragment of tRNA that can interact efficiently with EF-Tu, consists of a 10 base-pair helix from the acceptor-TC stem, nucleotides 63-72, linked to the aa-3'end tail [1], from which nucleotides 63-67 form the contact interface [2].Aminoacyl-tRNA-synthetase typically acquires the identity of the cognate amino acid from the anticodon stem-loop [3,4], from the discriminator base (N73) and from specific nucleotides in the acceptor stem of the tRNA, named identity determinants [5,6,7,8]. Minimal RNA substrates comprising 4-12 base-pairs, derived from the acceptor-TC stem of the tRNA, were shown to be specifically aminoacylated by their cognate synthetases [5,6,7,9,10,11], even though the main provider of identity information, i.e. in the AC loop, was absent. This non-AC aminoacylation process was proposed to be controlled by an "operational code" [6] that relates few nucleotides in the acceptor stem to specific amino acids. The major recognition de...

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