BASE-PAIRING BETWEEN ESCHERICHIA-COLI RNASE-P RNA AND ITS SUBSTRATE

Base pairing between the substrate and the ribozyme has previously bee n shown to be essential for catalytic activity of most ribozymes, but not for RNase P RNA. By using compensatory mutations we have demonstra ted the importance of Watson-Crick complementarity between two well-co nserved residues in Escherichia coli RNase P RNA (M1 RNA), G292 and G2 93, and two residues in the substrate, +74C and +75C (the first and se cond C residues in CCA). We suggest that these nucleotides base pair ( G292/+75C and G293/+74C) in the ribozyme-substrate complex and as a co nsequence the amino acid acceptor stem of the precursor is partly unfo lded. Thus, a function of M1 RNA is to anchor the substrate through th is base pairing, thereby exposing the cleavage site such that cleavage is accomplished at the correct position. Our data also suggest possib le base pairing between U294 in M1 RNA and the discriminator base at p osition +73 of the precursor. Our findings are also discussed in terms of evolution.