A Theoretical Study on the Nucleotide Changes Under a Definite Functional Constraint of Forming Stable Base-Pairs in the Stem Regions of Ribosomal RNAs; Its Application to the Phylogeny of Eukaryotes

Homologous alignment of 5 S rRNAs shows the characteristic features that (i) nucleotide changes are more remarkably seen in the stem region than in the loop region and (ii) most of the changes in the former region occur under a definite functional constraint of maintaining the stable base pairs G:C, C:G, A:U and U:A. In order to obtain a better evolutionary measure, we derived a theoretical equation for expressing the changes between the stable base-pairs in the stem region from an elementary process, in which the nucleotides in a pair mutate individually and the mis-matched pairs thus generated are eliminated by selection or return to the stable pairs by successive mutations. This equation leads us to a simple method of estimating the base-pair change rate by formally enumerating the base-pair changes observed in the pairwise comparison of homologous sequences from different species, just like the estimation of the change rate of individual nucleotides. The application of this method to 5 S rRNAs of eukaryotes reveals a new feature, in which the evolutionary distance of yeasts (Saccharomyces,PichiaandHansenula) from higher plants and animals is much more expanded than that obtained previously by the enumeration of individual nucleotide changes observed in a whole region of 5 S rRNA and many other fungi, protozoans and algae are allocated to the middle positions between the yeasts and higher plants. The base-pair change rate is estimated to be about 2 x 10−10year−1, which is less than the mutation rate by one order of magnitude, and is suitable for resolving the phylogeny of species which diverged a few billion years ago. The selective term for eliminating the mis-matched pairs is also evaluated to be stronger than the mutation rate by about one order of magnitude even for the outstanding mis-matched pair of G:U and U:G.