Crystal structure of Drosophila Piwi

Sonomi Yamaguchi,Naoshi Dohmae,Seiichi Hirano,Naoki Matsumoto,Asako Kajiya,Ryuichiro Ishitani,Osamu Nureki,Hiroshi Nishimasu,Haruhiko Siomi,Kuniaki Saito,Akira Oe,Mikiko C Siomi,Kazumichi M Nishida,Keitaro Yamashita

doi:10.1038/s41467-020-14687-1

Abstract

PIWI-clade Argonaute proteins associate with PIWI-interacting RNAs (piRNAs), and silence transposons in animal gonads. Here, we report the crystal structure of the Drosophila PIWI-clade Argonaute Piwi in complex with endogenous piRNAs, at 2.9 Å resolution. A structural comparison of Piwi with other Argonautes highlights the PIWI-specific structural features, such as the overall domain arrangement and metal-dependent piRNA recognition. Our structural and biochemical data reveal that, unlike other Argonautes including silkworm Siwi, Piwi has a non-canonical DVDK tetrad and lacks the RNA-guided RNA cleaving slicer activity. Furthermore, we find that the Piwi mutant with the canonical DEDH catalytic tetrad exhibits the slicer activity and readily dissociates from less complementary RNA targets after the slicer-mediated cleavage, suggesting that the slicer activity could compromise the Piwi-mediated co-transcriptional silencing. We thus propose that Piwi lost the slicer activity during evolution to serve as an RNA-guided RNA-binding platform, thereby ensuring faithful co-transcriptional silencing of transposons.

Highlights

PIWI-clade Argonautes (PIWIs)-clade Argonaute proteins associate with PIWI-interacting RNAs, and silence transposons in animal gonads
These results indicated that the purified sample represents the Piwi–PIWI-interacting RNAs (piRNAs) complex core lacking the flexible N-terminal region
A series of studies showed that (1) piwi is involved in transposon silencing[58], (2) Piwi binds piRNAs7,8,50,59, and (3) Piwi cotranscriptionally silences transposons via heterochromatin formation[9,10,11,12]

Summary

Introduction

PIWI-clade Argonaute proteins associate with PIWI-interacting RNAs (piRNAs), and silence transposons in animal gonads. Our structural and biochemical data reveal that, unlike other Argonautes including silkworm Siwi, Piwi has a non-canonical DVDK tetrad and lacks the RNA-guided RNA cleaving slicer activity. We propose that Piwi lost the slicer activity during evolution to serve as an RNA-guided RNA-binding platform, thereby ensuring faithful cotranscriptional silencing of transposons. 1234567890():,; Argonaute proteins bind small non-coding RNA guides to form RNA-induced silencing complexes, which recognize target RNAs complementary to the guide RNAs1, 2. The PIWI-clade Argonautes (PIWIs) bind 24–31-nt PIWI-interacting RNAs (piRNAs) to form piRNA-induced silencing complexes, which silence transposons and maintain genome integrity in animal gonads[3,4,5,6].

Methods

Results

Conclusion