The evolutionary significance of the long variable arm in transfer RNA

The charging of amino acids by their cognate transfer RNA (tRNAs) is central to modern translation and links evolution of the genetic code with chronologies that describe the use of amino acids in an emergent protein world. Although it is commonly accepted that only few of the canonical amino acids were initially coded and charged by tRNA, the composition of this early group of amino acids has been controversial. To uncover evolutionary patterns embedded in the structure of these molecules, we conducted phylogenetic analyses of 42 structural characters scored from the cloverleaf secondary structures of 571 tRNAs from organisms belonging to the three domains of life, viruses, and bacteriophages. Results show that class II tRNA molecules containing a long variable arm, including tRNA^Sec, tRNA^Ser, tRNA^Tyr, and tRNA^Leu, were ancestral compared to those lacking this structural feature. This suggests that selenocysteine (Sec), serine (Ser), tyrosine (Tyr), and leucine (Leu) were among the first amino acids to be charged by their cognate tRNAs and that they may represent the first group of amino acids with functional specificities linked to modern biochemistry. Results also suggest that the stop codon UGA, which also codes for Sec, may be the oldest codon to have a modern functional role in the history of the genetic code. Finally, the charging of amino acids by cognate tRNAs appear to have occurred once the canonical cloverleaf structure was fully realized in evolution and before amino acid specificities and organismal domains of life diversified. © 2008 Wiley Periodicals, Inc. Complexity, 2009