Evolution of transfer RNA.

Abstract Evolution by gene duplication and subsequent divergence is indicated by similarities common to 43 different transfer RNAs. Pairwise comparisons of these tRNAs reveal additional similarity, greatest for certain pairs of tRNAs for the same amino acid in the same organism, and also occurring in certain pairs of tRNAs for different amino acids in the same organism. Although tRNAs functionally interact with several other molecules, there have been surprisingly few restrictions on the divergence of their primary structures. This divergence has proceeded so far that clear phylogenetic separations are absent in most cases: it it impossible to construct a coherent phylogeny for most of the 43. Selection and stochastic processes have both been active in the evolution of tRNA. Selection has favored moderate change more than expected and has reduced radical change below that expected from stochastic processes alone. Two obvious effects of selection are nine invariant loci, another five that are always purines and five others that are always pyrimidines, in the tRNAs involved in protein synthesis. In addition to these constraints in the primary nucleotide sequence, the method of “identical site equivalents”, introduced here, demonstrates that further constraints exist equivalent to about 12 additional invariant loci. These “invisible” restraints reflect disperse chemical forces maintaining the tertiary structure and reducing evolutionary divergence to an extent quantitatively comparable to that of the nine observable invariant loci. The average divergence (49·4%) for pairs of tRNAs for different amino acids involved in protein synthesis represents an equilibrium between natural selection and stochastic processes. These tRNAs have had time to diverge nearly to the 75% maximum expected from stochastic process alone; this is shown by comparing the two glycine tRNAs involved in peptidoglycan synthesis with tRNAs for different amino acids participating in polypeptide synthesis. The rates of nucleotide replacements in genes coding for the tRNAs and the cytochromes c are about the same: 2 × 10 −10 replacements per nucleotide site per year.