The Diverse Active Sites in Splicing, Debranching, and MicroRNA Processing Around RNA Phosphodiester Bonds

Abstract

The cleavage and ligation reactions at RNA phosphodiester bonds are the central reactions catalyzed by enzymes in critical cellular regulatory pathways. In pre-mRNA splicing, two phospho-transesterifications result in the right mRNA for protein synthesis with the intervening intron removed as a lariat structure. The lariat RNA is then debranched by an enzyme that specifically acts on this 2′-5′-branched RNA. Following debranching, some of these introns that include pre-microRNA sequences can be processed by Dicer that cleaves the RNA to provide microRNAs. Dicer and Drosha, enzymes that act on much bigger primary transcripts, are both RNase III-like enzymes that cleave the RNA phosphodiester linkage. All these reactions are in related pathways, and the RNA phosphodiester bonds are most likely cleaved with the aid of two metal ions, yet the active sites that host these could be composed entirely of RNA or entirely of protein, or possibly a hybrid of the two. Where unknown, it is possible to estimate some of these active site architectures through homology to closely related enzymes. Better insight into these related process and active sites will play a key role in leveraging these important RNA regulatory processes for molecular medicine.