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.
Highlights
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
In Arabidopsis, the nucleotidyl transferases HESO1 and URT1 are responsible for miRNA uridylation while the exonucleases SDN1 and SDN2 are responsible for miRNA 3′ trimming[11,12,13,14,15]
Only the N-terminal domain (NTD; residues 2–137) and the DEDDh catalytic domain of SDN1 (Fig. 1a), plus nine nucleotides from the 3′ end of the RNA was clearly observed in the structure (Fig. 1b and Supplementary Fig. 2a)
Summary
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. The critical biological functions of miRNAs necessitate tight control of their own abundance in vivo Both biogenesis and degradation contribute to the steady-state levels of miRNAs. The biogenesis of miRNAs is a multi-step process that results in a mature miRNA loaded into its effector ARGONAUTE (AGO) protein to form the RNA-induced silencing complex (RISC)[1]. SDN1 can almost completely degrade free miRNAs, generating products of a very small size[16], but can only trim AGO1-bound miRNAs by a few nucleotides[15] This trimming activity is critical as it removes the last nucleotide that is 2′-O-methylated to allow HESO1 and URT1 to act on the unmethylated, trimmed species[15]
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call