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

Karina Jouravleva; Dmitrij Golovenko; Gabriel Demo; Robert C Dutcher; Traci M Tanaka Hall; Phillip D Zamore; Andrei A Korostelev

doi:10.1016/j.molcel.2022.09.002

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

Mol Cell. 2022 Nov 3;82(21):4049-4063.e6. doi: 10.1016/j.molcel.2022.09.002. Epub 2022 Sep 30.

Authors

Karina Jouravleva¹, Dmitrij Golovenko¹, Gabriel Demo², Robert C Dutcher³, Traci M Tanaka Hall⁴, Phillip D Zamore⁵, Andrei A Korostelev⁶

Affiliations

¹ RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
² RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 62500, Czech Republic.
³ Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
⁴ Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA. Electronic address: hall4@niehs.nih.gov.
⁵ RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Electronic address: phillip.zamore@umassmed.edu.
⁶ RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Electronic address: andrei.korostelev@umassmed.edu.

Abstract

In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 that show how Dicer-1 and its partner Loqs‑PB cooperate (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, and (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicer‑1⋅Loqs‑PB heterodimer. The Dicer-1 dsRBD and three Loqs‑PB dsRBDs form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-miRNA cleavage shifts the dsRBDs and partially closes Dicer-1, which may promote product release. Our data suggest a model for how the Dicer‑1⋅Loqs‑PB complex affects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and product release.

Keywords: Dcr-1; Dicer; Dicer-partner proteins; Loqs-PB; Loquacious; RNase III; cryo-EM; dsRBD; isomiR; miRNA; microRNA.

Publication types

Research Support, N.I.H., Intramural
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Drosophila / genetics
Drosophila Proteins* / genetics
Drosophila Proteins* / metabolism
MicroRNAs* / genetics
MicroRNAs* / metabolism
RNA-Binding Proteins / metabolism
Ribonuclease III / genetics
Ribonuclease III / metabolism

Substances

Ribonuclease III
Drosophila Proteins
RNA-Binding Proteins
MicroRNAs

Abstract

Publication types

MeSH terms

Substances

Grants and funding