Evidence for Adaptive Evolutionary Convergence in the Base Composition of Single-Stranded RNA

Like proteins, single-stranded RNAs (ssRNAs) undergo intramolecular folding into complex conformations which determine their metabolic function. We have compiled nucleotide composition data, expressed as G+A and G+U in addition to G+C content, from phylogenetically representative samples of seven functional classes of ssRNA and artificial ribozymes. Unlike G+C content, which is known to vary within and between organisms, G+A and G+U contents are remarkably constrained among ssRNAs unrelated by sequence similarity and function. An analysis of the base composition of secondary structural elements indicates that paired and unpaired nucleotides, known to have different evolutionary rates, also have significantly different compositional biases; stems are G+C- and G+U-rich while loops are G+C-poor and G+A-rich. These universal compositional biases observed among ssRNA sharing little or no sequence similarity suggest, contrary to current understanding, that base composition biases constitute a convergent adaptation among a wide variety of molecular functions.