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Structural basis of microRNA processing by Dicer-like 1.

Wei X, Ke H, Wen A, Gao B, Shi J, Feng Y
Nat Plants 7 1389-1396 (2021)
Cited: 22 times
EuropePMC logo PMID: 34593993

Abstract

MicroRNAs (miRNAs) are short non-coding RNAs that inhibit the expression of target genes by directly binding to their mRNAs. In animals, pri-miRNAs are cleaved by Drosha to generate pre-miRNAs, which are subsequently cleaved by Dicer to generate mature miRNAs. Instead of being cleaved by two different enzymes, both cleavages in plants are performed by Dicer-like 1 (DCL1). With a similar domain architecture as human Dicer, it is mysterious how DCL1 recognizes pri-miRNAs and performs two cleavages sequentially. Here, we report the single-particle cryo-electron microscopy structures of Arabidopsis DCL1 complexed with a pri-miRNA and a pre-miRNA, respectively, in cleavage-competent states. These structures uncover the plasticity of the PAZ domain, which is critical for the recognition of both pri-miRNA and pre-miRNA. These structures suggest that the helicase module serves as an engine that transfers the substrate between two sequential cleavage events. This study lays a foundation for dissecting the regulation mechanism of miRNA biogenesis in plants and provides insights into the dicing state of human Dicer.

Reviews - 7eld mentioned but not cited (1)

  1. Dicer structure and function: conserved and evolving features. Zapletal D, Kubicek K, Svoboda P, Stefl R. EMBO Rep 24 e57215 (2023)

Articles - 7eld mentioned but not cited (2)

  1. Structure of the Dicer-2-R2D2 heterodimer bound to a small RNA duplex. Yamaguchi S, Naganuma M, Nishizawa T, Kusakizako T, Tomari Y, Nishimasu H, Nureki O. Nature 607 393-398 (2022)
  2. Electronegative clusters modulate folding status and RNA binding of unstructured RNA-binding proteins. Zaharias S, Fargason T, Greer R, Song Y, Zhang J. Protein Sci 32 e4643 (2023)


Reviews citing this publication (11)

  1. A Structural View of miRNA Biogenesis and Function. Leitão AL, Enguita FJ. Noncoding RNA 8 10 (2022)
  2. microRNAs in action: biogenesis, function and regulation. Shang R, Lee S, Senavirathne G, Lai EC. Nat Rev Genet 24 816-833 (2023)
  3. Research progress on plant noncoding RNAs in response to low-temperature stress. Huo C, Zhang B, Wang R. Plant Signal Behav 17 2004035 (2022)
  4. Recent Insights into Plant miRNA Biogenesis: Multiple Layers of miRNA Level Regulation. Bajczyk M, Jarmolowski A, Jozwiak M, Pacak A, Pietrykowska H, Sierocka I, Swida-Barteczka A, Szewc L, Szweykowska-Kulinska Z. Plants (Basel) 12 342 (2023)
  5. Biogenesis, conservation, and function of miRNA in liverworts. Pietrykowska H, Sierocka I, Zielezinski A, Alisha A, Carrasco-Sanchez JC, Jarmolowski A, Karlowski WM, Szweykowska-Kulinska Z. J Exp Bot 73 4528-4545 (2022)
  6. Dynamic Protein-RNA recognition in primary MicroRNA processing. Ruiz-Arroyo VM, Nam Y. Curr Opin Struct Biol 76 102442 (2022)
  7. RNAi-Based Antiviral Innate Immunity in Plants. Jin L, Chen M, Xiang M, Guo Z. Viruses 14 432 (2022)
  8. Decoding the secrets of longevity: unraveling nutraceutical and miRNA-Mediated aging pathways and therapeutic strategies. Salama RM, Eissa N, Doghish AS, Abulsoud AI, Abdelmaksoud NM, Mohammed OA, Abdel Mageed SS, Darwish SF. Front Aging 5 1373741 (2024)
  9. From diagnosis to resistance: a symphony of miRNAs in pheochromocytoma progression and treatment response. Elsakka EGE, Elshafei A, Elkady MA, Yehia AM, Abulsoud AI, Shahin RK, Abdelmaksoud NM, Elkhawaga SY, Ismail A, Mokhtar MM, Elrebehy MA, Hegazy M, Elballal MS, Mohammed OA, Abdel-Reheim MA, El-Dakroury WA, Abdel Mageed SS, El-Mahdy HA, Doghish AS. Naunyn Schmiedebergs Arch Pharmacol 397 1957-1969 (2024)
  10. Overview of Repressive miRNA Regulation by Short Tandem Target Mimic (STTM): Applications and Impact on Plant Biology. Othman SMIS, Mustaffa AF, Che-Othman MH, Samad AFA, Goh HH, Zainal Z, Ismail I. Plants (Basel) 12 669 (2023)
  11. Structural studies of protein-nucleic acid complexes: A brief overview of the selected techniques. Szpotkowski K, Wójcik K, Kurzyńska-Kokorniak A. Comput Struct Biotechnol J 21 2858-2872 (2023)

Articles citing this publication (8)

  1. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek J, Joseph DF, Sedlacek R, Bernecky C, O'Carroll D, Stefl R, Svoboda P. Mol Cell 82 4064-4079.e13 (2022)
  2. Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB. Jouravleva K, Golovenko D, Demo G, Dutcher RC, Hall TMT, Zamore PD, Korostelev AA. Mol Cell 82 4049-4063.e6 (2022)
  3. Structural insights into dsRNA processing by Drosophila Dicer-2-Loqs-PD. Su S, Wang J, Deng T, Yuan X, He J, Liu N, Li X, Huang Y, Wang HW, Ma J. Nature 607 399-406 (2022)
  4. Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function. Aderounmu AM, Aruscavage PJ, Kolaczkowski B, Bass BL. Elife 12 e85120 (2023)
  5. Functional specialization of monocot DCL3 and DCL5 proteins through the evolution of the PAZ domain. Chen S, Liu W, Naganuma M, Tomari Y, Iwakawa HO. Nucleic Acids Res 50 4669-4684 (2022)
  6. Cofactor-assisted dicing: insights from structural snapshots. Du J, Patel DJ. Cell Res 32 965-966 (2022)
  7. Integrated omics analysis reveals the epigenetic mechanism of visceral hypersensitivity in IBS-D. Lu Y, Chai Y, Qiu J, Zhang J, Wu M, Fu Z, Wang Y, Qin C. Front Pharmacol 14 1062630 (2023)
  8. Structural mechanism of R2D2 and Loqs-PD synergistic modulation on DmDcr-2 oligomers. Deng T, Su S, Yuan X, He J, Huang Y, Ma J, Wang J. Nat Commun 14 5228 (2023)


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