Comparative sequence analysis and patterns of covariation in RNA secondarystructures

A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase Pi RNA, eukaryotic small sub unit rRNA, and the 3' untranslated region (UTR) of the Drosophila bicoid (b cd) mRNA. Furthermore, covariations occurring in the helices of these conse rved RNA structures are analyzed. Two physical parameters are found to be i mportant determinants of the evolution of compensator! mutations: the lengt h of a helix and the distance between base-pairing nucleotides. For the hel ices of bcd 3' UTR mRNA and RNase P RNA, a positive correlation between the rate of compensatory evolution and helix length is found. The analysis of Drosophila bcd 3' UTR mRNA further revealed that the rate of compensatory e volution decreases with the physical distance between base-pairing residues . This result is in qualitative agreement with Kimura's model of compensato ry fitness interactions, which assumes that mutations occurring in RNA heli ces are individually deleterious but become neutral in appropriate combinat ions.