Sequence- and structure-based analysis of proteins involved in miRNA biogenesis

Abstract

miRNA biogenesis is a multistage process for the generation of a mature miRNA and involves several different proteins. In this work, we have carried out both sequence- and structure-based analysis for crucial proteins involved in miRNA biogenesis, namely Dicer, Drosha, Argonaute (Ago), and Exportin-5 to understand evolution of these proteins in animal kingdom and also to identify key sequence and structural features that are determinants of their function. Our analysis reveals that in animals the miRNA biogenesis pathway first originated in molluscs. The phylogeny of Dicer and Ago indicated evolution through gene duplication followed by sequence divergence that resulted in functional divergence. Our detailed structural analysis also revealed that RIIIDb domains of Drosha and Dicer, share significant similarity in sequence, structure, and substrate-binding pocket. On the other hand, PAZ domains of Dicer and Ago show only conservation of the substrate-binding pockets in the catalytic sites despite significant divergence in sequence and overall structure. Based on a comparative structural analysis of all four human Ago proteins (hAgo1–4) and their known biochemical activity, we have also attempted to identify key residues in Ago2 which are responsible for the unique slicer activity of hAgo2 among all isoforms. We have identified six key residues in N domain of hAgo2, which are located far away from the catalytic pocket, but might be playing a major role in slicer activity of hAgo2 protein because of their involvement in mRNA binding.