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 th at (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 reg ion occur under a definite functional constraint of maintaining the st able base pairs G:C, C:G, A:U and U:A. In order to obtain a better evo lutionary measure, we derived a theoretical equation for expressing th e changes between the stable base-pairs in the stem region from an ele mentary process, in which the nucleotides in a pair mutate individuall y 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 c omparison of homologous sequences from different species, just like th e estimation of the change rate of individual nucleotides. The applica tion of this method to 5 S rRNAs of eukaryotes reveals a new feature, in which the evolutionary distance of yeasts (Saccharomyces, Pichia an d Hansenula) 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, p rotozoans 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(-10) year(-1), which is less than the mutation rate by o ne 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 th an the mutation rate by about one order of magnitude even for the outs tanding mis-matched pair of G:U and U:G. (C) 1997 Academic Press Limit ed.