The Drosophila Dicer-1 Partner Loquacious Enhances miRNA Processing from Hairpins with Unstable Structures at the Dicing Site

Lim, Mandy Yu Theng; Ng, Alvin Wei Tian; Chou, Yu-Ting; Lim, Teck Por; Simcox, Amanda; Tucker‐Kellogg, Greg; Okamura, Katsutomo

doi:10.1016/j.celrep.2016.04.059

Cited by 23 publications

(24 citation statements)

References 88 publications

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“…Biochemical and structural studies indicate the third dsRBM of TRBP interacts with Hel2i of Dicer (52,53). A recent study suggests this interaction is conserved in the fly homologs Dcr-1 and Loqs-PB (20). In contrast, our data indicate that Loqs-PD primarily interacts with Hel2 of Dcr-2's helicase (Fig.…”

Section: Discussioncontrasting

confidence: 48%

Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA

Trettin

Sinha

Eckert

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Loquacious-PD (Loqs-PD) is required for biogenesis of many endogenous siRNAs in In vitro, Loqs-PD enhances the rate of dsRNA cleavage by Dicer-2 and also enables processing of substrates normally refractory to cleavage. Using purified components, and Loqs-PD truncations, we provide a mechanistic basis for Loqs-PD functions. Our studies indicate that the 22 amino acids at the C terminus of Loqs-PD, including an FDF-like motif, directly interact with the Hel2 subdomain of Dicer-2's helicase domain. This interaction is RNA-independent, but we find that modulation of Dicer-2 cleavage also requires dsRNA binding by Loqs-PD. Furthermore, while the first dsRNA-binding motif of Loqs-PD is dispensable for enhancing cleavage of optimal substrates, it is essential for enhancing cleavage of suboptimal substrates. Finally, our studies define a previously unrecognized Dicer interaction interface and suggest that Loqs-PD is well positioned to recruit substrates into the helicase domain of Dicer-2.

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Section: Discussioncontrasting

confidence: 48%

Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA

Trettin

Sinha

Eckert

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Furthermore, other previous crystal structures showed that dsRBDs of Dicer partner proteins bind a perfectly base-paired A-form dsRNA substrate in a canonical manner as observed in other dsRBDs ( 25 ), supporting our model that Loqs-PB binding changes the conformation of base-mismatched nucleotides to base-paired one. Previous studies showed that Loqs-PB helps DmDicer-1 process pre-miRNAs containing mismatches at the dicing cleavage site ( 47 ). Such pre-miRNAs are not efficiently processed by DmDicer-1 alone, while pre-miRNAs containing base-pairs at the dicing cleavage site are efficiently processed by DmDcer-1 in the presence or absence of Loqs-PB.…”

Section: Discussionmentioning

confidence: 99%

Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem

Zhu

Kandasamy

Fukunaga

2018

Nucleic Acids Research

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Dicer partner proteins Drosophila Loquacious-PB (Loqs-PB) and human TRBP tune the length of miRNAs produced by Dicer from a subset of pre-miRNAs and thereby alter their target repertoire, by an unknown mechanism. Here, we developed a novel high-throughput method that we named Dram-seq (Dice randomized pre-miRNA pool and seq) to study length distributions of miRNAs produced from thousands of different pre-miRNA variants. Using Dram-seq, we found that a base-mismatch in the pre-miRNA stem can alter the length of miRNAs compared with a base-pair at the same position in both Drosophila and human, and is important for the miRNA length tuning by Loqs-PB. Loqs-PB directly bound base-mismatched nucleotides in the pre-miRNA stem. We speculate that Loqs-PB tunes miRNA length by changing the conformation of base-mismatched nucleotides in the pre-miRNA stem to that of base-paired ones and thereby altering the distance of the pre-miRNA stem.

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“…Reports in other insects suggest such a functionality in processing exogenous dsRNAs for LOQS 39 , 63 , though its role in the siRNA pathway is currently thought to predominate in the processing of endogenous siRNAs 64 , 65 . Characterization of LOQS as a core component of the D. melanogaster miRNA pathway has also been recently questioned; it has been reported as important late in pupation and ovary and ovariole formation, but some individuals survive the absence of this transcript and not all miRNAs require it for maturation 53 , 62 , 66 – 68 . The relevance of loqs expression to the WCR RNAi pathways and eRNAi requires further study.…”

Section: Discussionmentioning

confidence: 99%

Knockdown of RNA interference pathway genes impacts the fitness of western corn rootworm

Davis-Vogel

Ortíz

Procyk

et al. 2018

Sci Rep

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Western corn rootworm (Diabrotica virgifera virgifera) is a serious agricultural pest known for its high adaptability to various management strategies, giving rise to a continual need for new control options. Transgenic maize expressing insecticidal RNAs represents a novel mode of action for rootworm management that is dependent on the RNA interference (RNAi) pathways of the insect for efficacy. Preliminary evidence suggests that western corn rootworm could develop broad resistance to all insecticidal RNAs through changes in RNAi pathway genes; however, the likelihood of field-evolved resistance occurring through this mechanism remains unclear. In the current study, eight key genes involved in facilitating interference in the microRNA and small interfering RNA pathways were targeted for knockdown in order to evaluate impact on fitness of western corn rootworm. These genes include drosha, dicer-1, dicer-2, pasha, loquacious, r2d2, argonaute 1, and argonaute 2. Depletion of targeted transcripts in rootworm larvae led to changes in microRNA expression, decreased ability to pupate, reduced adult beetle emergence, and diminished reproductive capacity. The observed effects do not support evolution of resistance through changes in expression of these eight genes due to reduced insect fitness.

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The Drosophila Dicer-1 Partner Loquacious Enhances miRNA Processing from Hairpins with Unstable Structures at the Dicing Site

Cited by 23 publications

References 88 publications

Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA

Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA

Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem

Knockdown of RNA interference pathway genes impacts the fitness of western corn rootworm

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