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Structural and biochemical insights into small RNA 3′ end trimming by Arabidopsis SDN1

Author

Listed:
  • Jiayi Chen

    (Fudan University)

  • Li Liu

    (University of California)

  • Chenjiang You

    (University of California)

  • Jiaqi Gu

    (Fudan University)

  • Wenjie Ruan

    (Fudan University)

  • Lu Zhang

    (Fudan University)

  • Jianhua Gan

    (Fudan University)

  • Chunyang Cao

    (Chinese Academy of Sciences)

  • Ying Huang

    (CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences)

  • Xuemei Chen

    (University of California)

  • Jinbiao Ma

    (Fudan University)

Abstract

A family of DEDDh 3′→5′ exonucleases known as Small RNA Degrading Nucleases (SDNs) initiates the turnover of ARGONAUTE1 (AGO1)-bound microRNAs in Arabidopsis by trimming their 3′ ends. Here, we report the crystal structure of Arabidopsis SDN1 (residues 2-300) in complex with a 9 nucleotide single-stranded RNA substrate, revealing that the DEDDh domain forms rigid interactions with the N-terminal domain and binds 4 nucleotides from the 3′ end of the RNA via its catalytic pocket. Structural and biochemical results suggest that the SDN1 C-terminal domain adopts an RNA Recognition Motif (RRM) fold and is critical for substrate binding and enzymatic processivity of SDN1. In addition, SDN1 interacts with the AGO1 PAZ domain in an RNA-independent manner in vitro, enabling it to act on AGO1-bound microRNAs. These extensive structural and biochemical studies may shed light on a common 3′ end trimming mechanism for 3′→5′ exonucleases in the metabolism of small non-coding RNAs.

Suggested Citation

  • Jiayi Chen & Li Liu & Chenjiang You & Jiaqi Gu & Wenjie Ruan & Lu Zhang & Jianhua Gan & Chunyang Cao & Ying Huang & Xuemei Chen & Jinbiao Ma, 2018. "Structural and biochemical insights into small RNA 3′ end trimming by Arabidopsis SDN1," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05942-7
    DOI: 10.1038/s41467-018-05942-7
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