Structural and functional basis of mammalian microRNA biogenesis by Dicer

Zapletal, David; Táborská, Eliška; Pasulka, Josef; Malı́k, Radek; Kubíček, Karel; Zanova, Martina; Much, Christian; Šebesta, Marek; Buccheri, Valéria; Horvat, Filip; Jenickova, Irena; Procházková, Michaela; Procházka, Jan; Pinkas, Matyáš; Nováček, Jiří; Joseph, Diego F.; Sedláček, Radislav; Bernecky, Carrie; O’Carroll, Dónal; Štefl, Richard; Svoboda, Petr

doi:10.1016/j.molcel.2022.10.010

Cited by 34 publications

(71 citation statements)

References 101 publications

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“…Again, density for the helicase domain was not well resolved in the EM map and is blurred in the 2D class averages. As mentioned previously, a 6.2 Å cryo-EM structure of mouse Dicer bound to pre-miR-15a in a cleavage-competent conformation also showed a loss in density within the helicase domain and has a similar overall structure compared to DCL3. , This lack of density for the helicase domain in multiple cryo-EM structures from multiple organisms suggests extensive flexibility in this domain and/or that a large conformational change occurs in this region during the cleavage process. More work remains to find ways to stabilize the helicase domain in the cleavage-competent state.…”

Section: Inferring Human Dicer Mechanism Cleavage Activation and Prod...supporting

confidence: 53%

“…These results are surprising when compared to available structures for dmDicer-2 in which there is a large conformational change occurring in the helicase domain moving from an apo- to cleavage-component state (Figure ). Large conformational changes in the helicase domain have also been reported in cleavage-competent cryo-EM structures of a 3.1 Å DCL3–pre-siRNA complex and a recent 6.2 Å mouse Dicer–pre-miR-15a complex . Thus, the dmDicer-1 structure suggests that, at least in Drosophila , Dicer may perform its cleavage reactions through an alternative mechanism that is not as strongly dependent on conformational changes in the helicase domain.…”

Section: Cryo-em Studies Of Drosophila Dicer-1 and Dicer-2 Reveal Ste...mentioning

confidence: 80%

“…By comparing the structures of hsDicer and DCL3, we can start to propose a mechanism for understanding and explaining hsDicer function. We focus on DLC3 rather than the other structures of Dicer due to its overall structurally similarity to the cleavage-competent mouse Dicer cryo-EM structure and since DLC3 contains an ATP-independent helicase . Furthermore, while the mouse Dicer shares far more similarities in size and sequence to hsDicer, , at 3.1 Å, the DCL3-siRNA cleavage-competent structure gives us much more structural information to learn from compared to the 6.2 Å mouse Dicer structure.…”

Section: Inferring Human Dicer Mechanism Cleavage Activation and Prod...mentioning

confidence: 99%

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Structural Insights into the Advances and Mechanistic Understanding of Human Dicer

2022

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Section: Inferring Human Dicer Mechanism Cleavage Activation and Prod...supporting

confidence: 53%

Section: Cryo-em Studies Of Drosophila Dicer-1 and Dicer-2 Reveal Ste...mentioning

confidence: 80%

Section: Inferring Human Dicer Mechanism Cleavage Activation and Prod...mentioning

confidence: 99%

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Structural Insights into the Advances and Mechanistic Understanding of Human Dicer

2022

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“…An ATP-dependent helicase domain is important for Dicer's antiviral role in invertebrates such as dmDcr2 and ceDCR-1, while mammalian Dicer has not been observed to require ATP 29,[54][55][56] . One model is that mammalian Dicer's helicase domain exists to stabilize the interaction of pre-miRNAs with the platform/PAZ domain during processing to mature miRNAs 24,26,57 . Arthropods and nematodes are invertebrate ecdysozoan protostomes, and so far, these are the only two phyla where Dicer's helicase domain is known to be essential for antiviral defense.…”

Section: Discussionmentioning

confidence: 99%

Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function

Aderounmu

Aruscavage

Kolaczkowski

et al. 2022

Preprint

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Antiviral defense in ecdysozoan invertebrates requires Dicer with a helicase domain capable of ATP hydrolysis. But despite well-conserved ATPase motifs, human Dicer is incapable of ATP hydrolysis, consistent with a muted role in antiviral defense. To investigate this enigma, we used ancestral protein reconstruction to resurrect Dicer's helicase in animals and trace the evolutionary trajectory of ATP hydrolysis. Biochemical assays indicated ancient Dicer possessed ATPase function, that like extant invertebrate Dicers, is stimulated by dsRNA. Analyses revealed that dsRNA stimulates ATPase activity by increasing ATP affinity, reflected in Michaelis constants. Deuterostome Dicer-1 ancestor, while exhibiting lower dsRNA affinity, retained ATPase activity; importantly, ATPase activity was undetectable in the vertebrate Dicer-1 ancestor, which had even lower dsRNA affinity. Reverting residues in the ATP hydrolysis pocket was insufficient to rescue hydrolysis, but including additional substitutions distant from the ATPase pocket rescued vertebrate Dicer-1's ATPase function. Our work suggests Dicer lost ATPase function in the vertebrate ancestor due to loss of ATP affinity, involving motifs distant from the active site, important for coupling dsRNA binding to the active conformation. RLRs important for interferon signaling, and their competition with Dicer for viral dsRNAs, possibly provided incentive to jettison an active helicase in vertebrate Dicer.

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“…DICER has two RNase III domains and one dsRBD located at the Cterminal region, the PAZ domain in the middle region, and three tandem RNA helicase domains (DExD/H domain) located at the N-terminal region, which are associated with pre-miRNA binding and cleavage. Among a series of functional and structural studies of DICER [7,[35][36][37][38], a recent study demonstrated that the DExD/H domain has an ATPindependent essential structural role in mice and ensures the high fidelity of miRNA biogenesis in vivo [35]. The PAZ domain is thought to recognize the 5 -and 3 -ends of pre-miRNAs and determine their cleavage sites [39].…”

Section: Structural Basis Of Pre-mirna Processingmentioning

confidence: 99%

Network Regulation of microRNA Biogenesis and Target Interaction

Komatsu

Kitai

Suzuki

2023

Cells

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MicroRNAs (miRNAs) are versatile, post-transcriptional regulators of gene expression. Canonical miRNAs are generated through the two-step DROSHA- and DICER-mediated processing of primary miRNA (pri-miRNA) transcripts with optimal or suboptimal features for DROSHA and DICER cleavage and loading into Argonaute (AGO) proteins, whereas multiple hairpin-structured RNAs are encoded in the genome and could be a source of non-canonical miRNAs. Recent advances in miRNA biogenesis research have revealed details of the structural basis of miRNA processing and cluster assistance mechanisms that facilitate the processing of suboptimal hairpins encoded together with optimal hairpins in polycistronic pri-miRNAs. In addition, a deeper investigation of miRNA–target interaction has provided insights into the complexity of target recognition with distinct outcomes, including target-mediated miRNA degradation (TDMD) and cooperation in target regulation by multiple miRNAs. Therefore, the coordinated or network regulation of both miRNA biogenesis and miRNA–target interaction is prevalent in miRNA biology. Alongside recent advances in the mechanistic investigation of miRNA functions, this review summarizes recent findings regarding the ordered regulation of miRNA biogenesis and miRNA–target interaction.

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Structural and functional basis of mammalian microRNA biogenesis by Dicer

Cited by 34 publications

References 101 publications

Structural Insights into the Advances and Mechanistic Understanding of Human Dicer

Structural Insights into the Advances and Mechanistic Understanding of Human Dicer

Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function

Network Regulation of microRNA Biogenesis and Target Interaction

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