Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation

In eukaryotes, small RNAs (sRNAs) play critical roles in multiple biological processes. Dicer endonucleases are a central part of sRNA biogenesis. In plants, DICER-LIKE PROTEIN 3 (DCL3) produces 24-nucleotide (nt) small interfering RNAs (siRNAs) that determine the specificity of the RNA-directed DNA...

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Published in:Science (American Association for the Advancement of Science) 2021-11, Vol.374 (6571), p.1152-1157
Main Authors: Wang, Qian, Xue, Yan, Zhang, Laixing, Zhong, Zhenhui, Feng, Suhua, Wang, Changshi, Xiao, Lifan, Yang, Zhenlin, Harris, C Jake, Wu, Zhe, Zhai, Jixian, Yang, Maojun, Li, Sisi, Jacobsen, Steven E, Du, Jiamu
Format: Article
Language:English
Subjects:
Adenosine
Arabidopsis - chemistry
Arabidopsis - genetics
Arabidopsis - metabolism
Arabidopsis Proteins - chemistry
Arabidopsis Proteins - genetics
Arabidopsis Proteins - metabolism
Biological activity
Biosynthesis
Cryoelectron Microscopy
Deoxyribonucleic acid
DNA
DNA methylation
Domains
Eukaryotes
Models, Molecular
Mutagenesis
Nucleic Acid Conformation
Nucleotides
Phosphorylation
Protein Binding
Protein Conformation
Protein Domains
Proteins
Ribonuclease III
Ribonuclease III - chemistry
Ribonuclease III - genetics
Ribonuclease III - metabolism
Ribonucleic acid
RNA
RNA, Plant - chemistry
RNA, Plant - metabolism
RNA, Small Interfering - chemistry
RNA, Small Interfering - metabolism
siRNA
Substrates
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Summary:In eukaryotes, small RNAs (sRNAs) play critical roles in multiple biological processes. Dicer endonucleases are a central part of sRNA biogenesis. In plants, DICER-LIKE PROTEIN 3 (DCL3) produces 24-nucleotide (nt) small interfering RNAs (siRNAs) that determine the specificity of the RNA-directed DNA methylation pathway. Here, we determined the structure of a DCL3–pre-siRNA complex in an active dicing-competent state. The 5′-phosphorylated A1 of the guide strand and the 1-nt 3′ overhang of the complementary strand are specifically recognized by a positively charged pocket and an aromatic cap, respectively. The 24-nt siRNA length dependence relies on the separation between the 5′-phosphorylated end of the guide RNA and dual cleavage sites formed by the paired ribonuclease III domains. These structural studies, complemented by functional data, provide insight into the dicing principle for Dicers in general.
ISSN:0036-8075
1095-9203
DOI:10.1126/science.abl4546