Evolution of compensatory substitutions through G·U intermediate state in Drosophila rRNA

Abstract

It has often been suggested that the frequently observed Watson-Crick base-pair compensatory substitutions in RNA helical structures occur mainly through a slightly deleterious G-U intermediate state. We have scored base substitutions in a set of 82 related Drosophila species for the Dl and D2 variable domains of the large rRNA subunit. In all locations where a G-C ↔ A-U compensatory base change occurred, a G·U pair has been observed in one or several species. As this dominant process implies two transitions, their rate was far higher in paired regions (92%) than in unpaired regions (47%). The other types of compensation were rarer and no intermediate states were observed. Most of the G·U base pairs observed in a species are not slightly deleterious. The rate of evolution of compensatory substitution is close to that predicted by a simple model of compensatory substitution through slightly deleterious or slightly advantageous G·U pairs, although some exceptions are presented.