Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA

Huang, Kun; Wu, Xiaoxian; Fang, Chengli; Xu, Zhou-Geng; Zhang, Hongwei; Gao, Jian; Zhou, Chuan‐Miao; You, Linlin; Gu, Zhan-Xi; Mu, Wenhui; Feng, Yu; Wang, Jia-Wei; Zhang, Yu

doi:10.1126/science.abj9184

Cited by 38 publications

(69 citation statements)

References 68 publications

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“…Starting from Pol IV, RDR2 and ssDNA, the team successfully generated dsRNA products in an in vitro reaction system. Recent studies also demonstrated that Pol IV interacts directly with RDR2, forming the Pol IV–RDR2 heterodimer ( 66 , 67 ). No Pol IV homologous proteins exist in N. crassa , and the QDE-1 homodimer may mimic the Pol IV/RDR2 heterodimer in action.…”

Section: Discussionmentioning

confidence: 99%

Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1

Cui

Zhao

et al. 2022

Nucleic Acids Research

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Neurospora crassa protein QDE-1, a member of the two-barrel polymerase superfamily, possesses both DNA- and RNA-dependent RNA polymerase (DdRP and RdRP) activities. The dual activities are essential for the production of double-stranded RNAs (dsRNAs), the precursors of small interfering RNAs (siRNAs) in N. crassa. Here, we report five complex structures of N-terminal truncated QDE-1 (QDE-1ΔN), representing four different reaction states: DNA/RNA-templated elongation, the de novo initiation of RNA synthesis, the first step of nucleotide condensation during de novo initiation and initial NTP loading. The template strand is aligned by a bridge-helix and double-psi beta-barrels 2 (DPBB2), the RNA product is held by DPBB1 and the slab domain. The DNA template unpairs with the RNA product at position –7, but the RNA template remains paired. The NTP analog coordinates with cations and is precisely positioned at the addition site by a rigid trigger loop and a proline-containing loop in the active center. The unique C-terminal tail from the QDE-1 dimer partner inserts into the substrate-binding cleft and plays regulatory roles in RNA synthesis. Collectively, this work elucidates the conserved mechanisms for DNA/RNA-dependent dual activities by QDE-1 and other two-barrel polymerase superfamily members.

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Section: Discussionmentioning

confidence: 99%

Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1

Cui

Zhao

et al. 2022

Nucleic Acids Research

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“…First of all our results demonstrated unanimously that RdRP knockdown could significantly reduce the tissue contents of short derivatives, not the full‐length derivatives, of exogenous dsRNA in A. thaliana and C. elegans . Studies have shown that RdRP is the enzyme capable of catalyzing the synthesis of RNA, siRNA and dsRNA 25,69,70 . However, no function involving dsRNA absorption and cleavage has been reported.…”

Section: Discussionmentioning

confidence: 99%

“…It was first isolated from tomato, 19 and early studies found that it functions in developmental regulation, maintenance of genome integrity and defense against foreign nucleic acids 20 . Subsequent studies found it participated in post‐transcriptional gene silence and amplified RNAi signal, secondary small interfereing (si)RNAs 21–24 and dsRNA 25 . Thus, RdRP may contribute to the long‐lasting validity period of exogenous dsRNA in plants.…”

Section: Introductionmentioning

confidence: 99%

RNA‐dependent RNA polymerase could extend the lasting validity period of exogenous dsRNA

Zhang

Gao

Chen

et al. 2022

Pest Management Science

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BACKGROUND Previous studies have found that pesticide double‐stranded (ds)RNA usually has a long‐lasting validity period in plants. However, it is uncertain if any factors in plants could extend dsRNA duration. It has been reported that RNA‐dependent RNA polymerases (RdRP) in plants and some other eukaryotes could catalyze RNA amplification and be involved in RNAi (interference). Thus, this study evaluated the effect of RdRP on the tissue content, activity, and duration of exogenous dsRNA. RESULTS We found that RdRP knockdown in Arabidopsis thaliana had no significant effect on tissue contents of reporter dsRNA parent molecules (8.91% reduction), but it caused significant decrease in the tissue contents of derived short fragments of 200, 120 and 59 bp tested (51.22%, 52.83% and 59.35%, respectively). Aphid inoculation tests showed that the same dose of insecticidal dsAgZFP exhibited a significantly lower lethal effect (mortality 58.8%) in the plants with RdRP knockdown than in the control plants with normal RdRP (86.0%). For Caenorhabditis elegans, the worms treated simultaneously with dsRdRP and reporter dsRNA had similar body contents to reporter dsRNA parent molecules and its long‐fragment derivative (200 bp) as the control (1.28‐ and 1.07‐fold greater, respectively). However, 120‐ and 59‐bp short‐fragment derivatives were significantly reduced by 28.78% and 59.84%, respectively, which also diminished faster in the descendants. CONCLUSIONS We conclude that RdRP could significantly enhance the tissue content of dsRNA derivatives by catalyzing amplification, thus improving dsRNA activity and extending its lasting validity period. Otherwise, RNAi by exogenous dsRNA was proven to be noninheritable in A. thaliana. This work confirmed the merit of dsRNA as a plant protectant. © 2022 Society of Chemical Industry.

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“…RDR2 mainly associates with Pol IV to form a complex for transcribing short dsRNA precursors, which are cleaved by DCL3 to produce 24 nt siRNAs for directing DNA methylation [86][87][88][89], although RDR2 might also be able to generate 23 to 27 nt small RNAs from MIR genes to mediate DNA methylation [90]. It was reported that RDR2, Pol IV, and DCL3, core components in the RdDM pathway, mediated 24 nt vsiRNA production and played major roles against the infection of DNA viruses, such as geminiviruses [44,45].…”

Section: Production and Amplification Of Vsirnamentioning

confidence: 99%

RNAi-Based Antiviral Innate Immunity in Plants

Jin

Chen

Xiang

et al. 2022

Viruses

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Multiple antiviral immunities were developed to defend against viral infection in hosts. RNA interference (RNAi)-based antiviral innate immunity is evolutionarily conserved in eukaryotes and plays a vital role against all types of viruses. During the arms race between the host and virus, many viruses evolve viral suppressors of RNA silencing (VSRs) to inhibit antiviral innate immunity. Here, we reviewed the mechanism at different stages in RNAi-based antiviral innate immunity in plants and the counteractions of various VSRs, mainly upon infection of RNA viruses in model plant Arabidopsis. Some critical challenges in the field were also proposed, and we think that further elucidating conserved antiviral innate immunity may convey a broad spectrum of antiviral strategies to prevent viral diseases in the future.

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Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA

Cited by 38 publications

References 68 publications

Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1

Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1

RNA‐dependent RNA polymerase could extend the lasting validity period of exogenous dsRNA

RNAi-Based Antiviral Innate Immunity in Plants

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