The naturally trans-acting ribozyme RNase P RNA has leadzyme properties

Abstract

Divalent metal ions promote hydrolysis of RNA backbones generating 5′OH and 2′;3′P as cleavage products. In these reactions, the neighboring 2′OH act as the nucleophile. RNA catalyzed reactions also require divalent metal ions and a number of different metal ions function in RNA mediated cleavage of RNA. In one case, the LZV leadzyme, it was shown that this catalytic RNA requires lead for catalysis. So far, none of the naturally isolated ribozymes have been demonstrated to use lead to activate the nucleophile. Here we provide evidence that RNase P RNA, a naturally transacting ribozyme, has leadzyme properties. But, in contrast to LZV RNA, RNase P RNA mediated cleavage promoted by Pb2+ results in 5′ phosphate and 3′OH as cleavage products. Based on our findings, we infer that Pb 2+ activates H2O to act as the nucleophile and we identified residues both in the substrate and RNase P RNA that most likely influenced the positioning of Pb2+ at the cleavage site. Our data suggest that Pb2+ can promote cleavage of RNA by activating either an inner sphere H2O or a neighboring 2′OH to act as nucleophile. © The Author 2005. Published by Oxford University Press. All rights reserved.