Structural basis of microRNA processing by Dicer-like 1

Wei, Xuesong; Ke, Haiping; Wen, Aijia; Gao, Bo; Shi, Jing; Feng, Yu

doi:10.1038/s41477-021-01000-1

Cited by 70 publications

(49 citation statements)

References 62 publications

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“…Structural studies by NMR combined with surface plasmon resonance were employed to characterize the RNA binding mechanism exhibit by TRBP [60] and to explain the modulatory effect of pre-miRNA maturation when interacting with Dicer (Figure 2b) [60]. The characterization of human Dicer by structural methods supported the previous evidence obtained from the genome mining data regarding the evolutionary conservation of dsRNA processing enzymes [71,73,74]. Plants and simple eukaryotic genomes frequently harbor genes encoding for several Dicer-like proteins (DCL) that could be considered as an evolutionary reminiscence derived from the primitive antiviral defense mechanisms [75,76], whereas complex eukaryotes typically have a single Dicer-encoding gene [77,78].…”

Section: Cytoplasmic Processors: Dicersupporting

confidence: 56%

“…Plants are particularly interesting for miRNA functional studies since they have an increased diversity in the structure and sequence of the miRNA genes, joined to the existence of different DCL protein isoforms [76,79]. Cryo-EM analysis has been recently employed for the characterization of the structure of two plant DCL enzymes (DCL1 and DCL3) in complex with synthetic dsRNAs (Figure 3c,d) [71,72]. Despite the existence of different DCL enzymes, miRNA maturation in plants is ensured only by the action of DCL1, which is able to combine the Drosha and Dicer activities in a single enzyme, recognizing pri-miRNAs and performing two sequential cleavage reactions to generate the mature miRNAs [80].…”

Section: Cytoplasmic Processors: Dicermentioning

confidence: 99%

“…The structure of A. thaliana DCL1 determined by cryo-EM suggested that the PAZ domain together with the helicase domain are responsible for the plasticity of the catalytic activity of the enzyme. The helicase domain serves as a transfer module to perform the two sequential cleavage reactions that convert the pri-miRNA into a mature miRNA, whereas the PAZ domain would stabilize the protein-RNA complex during the enzymatic maturation of the precursors [71]. Interestingly, plants appear to have a different processing system for siRNAs with the involvement of several DCL isoenzymes.…”

Section: Cytoplasmic Processors: Dicermentioning

confidence: 99%

“…[51]. (c) Structure of the Dicerlike protein 1 (DCL1) from A. thaliana in complex with the pre-miR-166f [71]. (d) Structure of the Dicer-like protein 3 (DCL3) from A. thaliana in complex with a synthetic 40 mer dsRNA [72].…”

Section: Cytoplasmic Processors: Dicermentioning

confidence: 99%

“…The post-transcriptional regulation of a miRNA over a cognate target is ensured by of the RISC complex (magenta surface) and the pre-let-7 [51]. (c) Structure of the Dicer-like protein 1 (DCL1) from A. thaliana in complex with the pre-miR-166f [71]. (d) Structure of the Dicer-like protein 3 (DCL3) from A. thaliana in complex with a synthetic 40 mer dsRNA [72].…”

Section: Cytoplasmic Effectors: Argonaute Proteins and Risc Complexmentioning

confidence: 99%

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A Structural View of miRNA Biogenesis and Function

Leitão

Enguita

2022

ncRNA

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Micro-RNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of gene expression. Since their discovery in 1993, they have been the subject of deep study due to their involvement in many important biological processes. Compared with other ncRNAs, miRNAs are generated from devoted transcriptional units which are processed by a specific set of endonucleases. The contribution of structural biology methods for understanding miRNA biogenesis and function has been essential for the dissection of their roles in cell biology and human disease. In this review, we summarize the application of structural biology for the characterization of the molecular players involved in miRNA biogenesis (processors and effectors), starting from the X-ray crystallography methods to the more recent cryo-electron microscopy protocols.

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Section: Cytoplasmic Processors: Dicersupporting

confidence: 56%

Section: Cytoplasmic Processors: Dicermentioning

confidence: 99%

Section: Cytoplasmic Processors: Dicermentioning

confidence: 99%

Section: Cytoplasmic Processors: Dicermentioning

confidence: 99%

Section: Cytoplasmic Effectors: Argonaute Proteins and Risc Complexmentioning

confidence: 99%

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A Structural View of miRNA Biogenesis and Function

Leitão

Enguita

2022

ncRNA

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Electronegative clusters modulate folding status and RNA binding of unstructured RNA‐binding proteins

et al. 2023

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Electronegative clusters (ENCs) made up of acidic residues and/or phosphorylation sites are the most abundant repetitive sequences in RNA‐binding proteins. Previous studies have indicated that ENCs inhibit RNA binding for structured RNA‐binding domains (RBDs). However, this is not the case for the unstructured RBD in histone pre‐mRNA stem‐loop binding protein (SLBP). The SLBP RBD contains 70 amino acids and is followed by a phosphorylatable ENC. ENC phosphorylation increases RNA‐binding affinity of SLBP to the sub‐picomolar range. In this study, we use NMR and molecular dynamics simulations to elucidate the mechanism for this tight binding. Our NMR data demonstrate that the ENC transiently folds apo SLBP into an RNA‐bound resembling state. We find that in the RNA‐bound state, the phosphorylated ENC interacts with the loop region opposite to the RNA‐binding site. This allosteric interaction stabilizes the complex and therefore enhances RNA binding. To evaluate the generality of our findings, we graft an ENC onto endoribonuclease homolog 1's first double‐stranded RNA‐binding motif (DRBM1), an unstructured RBD that shares no homology with SLBP. We find that the engineered ENC increases the folded species of DRBM1 and inhibits RNA binding. On the contrary, introducing basic residues to DRBM1 makes the domain more unfolded, enhances RNA binding, and mitigates the inhibitory effect of the engineered ENC. In summary, our study suggests that ENCs promote folding of unstructured RNA‐binding domains, and their effects on RNA binding depend on the electropositive charges on the RBD surface.

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