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

Jiayi Chen, Li Liu, Chenjiang You, Jiaqi Gu, Wenjie Ruan, Lu Zhang, Jianhua Gan, Chunyang Cao, Ying Huang (), Xuemei Chen () and Jinbiao Ma ()
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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

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-05942-7

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