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Recognition of the pre-miRNA structure by Drosophila Dicer-1

Nature Structural & Molecular Biology volume 18, pages 1153–1158 (2011)Cite this article

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Abstract

Drosophila melanogaster has two Dicer proteins with specialized functions. Dicer-1 liberates miRNA-miRNA* duplexes from precursor miRNAs (pre-miRNAs), whereas Dicer-2 processes long double-stranded RNAs into small interfering RNA duplexes. It was recently demonstrated that Dicer-2 is rendered highly specific for long double-stranded RNA substrates by inorganic phosphate and a partner protein R2D2. However, it remains unclear how Dicer-1 exclusively recognize pre-miRNAs. Here we show that fly Dicer-1 recognizes the single-stranded terminal loop structure of pre-miRNAs through its N-terminal helicase domain, checks the loop size and measures the distance between the 3′ overhang and the terminal loop. This unique mechanism allows fly Dicer-1 to strictly inspect the authenticity of pre-miRNA structures.

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Figure 1: Dcr-1 recognizes the terminal single-stranded region of pre-miRNAs.
Figure 2: Dcr-1 measures the distance from the 3′ overhang to the terminal single-stranded region of pre-miRNAs.
Figure 3: Dcr-1 recognizes the terminal single-stranded region of pre-miRNAs through its helicase domain.
Figure 4: A proposed model for recognition of authentic pre-miRNA structures by Dcr-1.

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Acknowledgements

We are grateful to Q. Liu (University of Texas Southwestern Medical Center) for the pFastBac-His-Dcr-1 wild type and E1908A E2139A plasmids, to M. Siomi and H. Siomi (Keio University) for the plasmid for expressing Loqs-PB, and to S. Katsuma for his advice on protein expression. We thank P. Bas Kwak for assistance with the amino acid sequence alignment, and we thank K. Förstemann and members of the Tomari laboratory for discussions, suggestions and critical comments on the manuscript. This work was supported in part by a Grant-in-Aid for Scientific Research on Innovative Areas ('Functional machinery for noncoding RNAs') and a a Grant-in-Aid for Young Scientists from the Japan Ministry of Education, Culture, Sports, Science and Technology to Y.T.; and a Carrier Development Award from The International Human Frontier Science Program Organization to Y.T. N.I. is a recipient of a Research Fellowship from the Japan Society for the Promotion of Science.

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Authors and Affiliations

  1. Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan

    Akihisa Tsutsumi, Tomoko Kawamata, Natsuko Izumi & Yukihide Tomari

  2. Department of Medical Genome Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan

    Akihisa Tsutsumi & Yukihide Tomari

  3. Université de Toulouse, Université Paul Sabatier, Laboratoire de Biologie Moléculaire Eucaryote, Toulouse, France

    Hervé Seitz

  4. Centre National de la Recherche Scientifique, Laboratoire de Biologie Moléculaire Eucaryote, Toulouse, France

    Hervé Seitz

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  1. Akihisa Tsutsumi
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A.T. conducted biochemical experiments with the assistance of T.K. and N.I., H.S. conducted bioinformatic analyses, Y.T. supervised the study; A.T. and Y.T. wrote the manuscript, and all authors discussed the results and approved the manuscript.

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Correspondence to Yukihide Tomari.

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Tsutsumi, A., Kawamata, T., Izumi, N. et al. Recognition of the pre-miRNA structure by Drosophila Dicer-1. Nat Struct Mol Biol 18, 1153–1158 (2011). https://doi.org/10.1038/nsmb.2125

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