Molecular basis of indispensable accuracy of mammalian miRNA biogenesis

Abstract

Mammalian Dicer is the gatekeeper into the essential gene-regulating miRNA pathway. What is committing mammalian Dicer to the miRNA pathway remains unknown. We report that Dicer's highly conserved DExD/H helicase domain is the key structural element supporting accurate miRNA biogenesis. While ATPase activity of the domain is non-essential, its loss is lethal in mice. It is required during canonical miRNA biogenesis for efficient recognition, high-fidelity cleavage, and strand selection. Structure of Dicer-miRNA precursor complexes showed that the DExD/H domain acquired helicase-unrelated function defining Dicer conformations, which affect substrate loading and facilitate pre-selection of miRNA precursors. Dicer lacking the DExD/H domain favors conformations enabling reduced substrate selectivity and supporting RNA interference, a different small RNA pathway. Therefore, Dicer's DExD/H domain ensures indispensable high-fidelity precursor processing of mammalian miRNAs, which constitutes a structural "mold" for adaptive miRNA evolution.

Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB

“…To accommodate the pre-miRNA, the Dicer-specific α-helix (aa 1222-1232) of the PAZ domain is shifted by ~15 Å from its position in the RNA-free structure (Figure 2C). The RNA-bound conformation of Dcr-1•Loqs-PB differs from the structures of dicing-incompetent human Dicer (Liu et al, 2018) and murine-specific, DHel1 DICER O (Zapletal et al, 2022), in which the 5′ terminal phosphate and first nucleobase are disengaged from the PAZ domain. In structures IIa and IIb, the uracil of the 5′ terminal nucleotide U1 is buried in a binding pocket formed by the PAZ and platform domains, with the nucleobase stacked between Arg994 and Arg1027 (Figure 3B).…”

“…The Hel1 region of the Dcr-1 helicase domain does not directly interact with the pre-miRNA loop, but does support the arrangement of Hel2, DUF283, and RNase IIIa domains. This critical role for Hel1 may explain why its deletion in mouse Dicer leads to widespread somatic changes in the abundance and sequence of miRNAs and increased processing of non-canonical pre-miRNAs with long stems or loops (Zapletal et al, 2022). The cryo-EM structure of murine oocyte-specific Dicer O , which lacks Hel1, shows poor density for the helicase and DUF283 domains (Zapletal et al, 2022), perhaps because mouse Hel1 similarly stabilizes the arrangement of the mouse Hel2, DUF283, and RNase IIIa domains.…”

The Role of MicroRNAs in Liver Functioning: from Biogenesis to Therapeutic Approaches (Review)

“…Reviews [8][9][10][11] describe in detail the current understanding of the microRNA biogenesis pathways. We shall briefly consider the main provisions thereof.…”