Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA.
PIWI-clade Argonaute proteins associate with PIWI-interacting RNAs (piRNAs) and silence transposable elements in animal gonads. Here, we report the crystal structure of a silkworm PIWI-clade Argonaute, Siwi, bound to the endogenous piRNA, at 2.4 Å resolution. Siwi adopts a bilobed architecture consisting of N-PAZ and MID-PIWI lobes, in which the 5' and 3' ends of the bound piRNA are anchored by the MID-PIWI and PAZ domains, respectively. A structural comparison of Siwi with AGO-clade Argonautes reveals notable differences in their nucleic-acid-binding channels, likely reflecting the distinct lengths of their guide RNAs and their mechanistic differences in guide RNA loading and cleavage product release. In addition, the structure reveals that Siwi and prokaryotic, but not eukaryotic, AGO-clade Argonautes share unexpected similarities, such as metal-dependent 5'-phosphate recognition and a potential structural transition during the catalytic-tetrad formation. Overall, this study provides a critical starting point toward a mechanistic understanding of piRNA-mediated transposon silencing.
Graduate School of Science, Department of Biological Sciences, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
Naoki
N
Matsumoto
Graduate School of Science, Department of Biological Sciences, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; JST, PRESTO, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: nisimasu@bs.s.u-tokyo.ac.jp.
Hiroshi
H
Nishimasu
Graduate School of Science, Department of Biological Sciences, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
Kazuhiro
K
Sakakibara
Graduate School of Science, Department of Biological Sciences, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
Kazumichi M
KM
Nishida
Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
Takamasa
T
Hirano
Graduate School of Science, Department of Biological Sciences, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
Ryuichiro
R
Ishitani
Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
Haruhiko
H
Siomi
Graduate School of Science, Department of Biological Sciences, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: siomim@bs.s.u-tokyo.ac.jp.
Mikiko C
MC
Siomi
Graduate School of Science, Department of Biological Sciences, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: nureki@bs.s.u-tokyo.ac.jp.
Osamu
O
Nureki
D000818:Animals; D060565:Argonaute Proteins / Q000737:chemistry* / Q000302:isolation & purification; D012831:Bombyx / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D002460:Cell Line; D018360:Crystallography, X-Ray; D004251:DNA Transposable Elements / Q000235:genetics; D020868:Gene Silencing; D006801:Humans; D019476:Insect Proteins / Q000737:chemistry* / Q000302:isolation & purification; D009690:Nucleic Acid Conformation; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000302:isolation & purification
C466422:AGO2 protein, human; D060565:Argonaute Proteins; D004251:DNA Transposable Elements; D019476:Insect Proteins; D034741:RNA, Small Interfering
1U bias; Argonaute; PIWI; RNA silencing; Siwi; piRNA; small RNA; x-ray crystallography