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Dynamic origins of differential RNA binding function in two dsRBDs from the miRNA "microprocessor" complex.

Christopher Wostenberg1, Kaycee A Quarles, Scott A Showalter

  • 1Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States.

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Investigating the dynamics of Drosha and DGCR8 dsRNA binding domains reveals distinct flexibility patterns. This explains why Drosha-dsRBD alone doesn't bind dsRNA, unlike DGCR8-dsRBD1, impacting microRNA processing.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • MicroRNAs (miRNAs) are crucial regulators of gene expression involved in cellular homeostasis.
  • The microprocessor complex, containing Drosha and DGCR8, initiates miRNA maturation in the nucleus.
  • While structures exist, the solution dynamics of Drosha and DGCR8 dsRNA binding domains (dsRBDs) remain unexplored.

Purpose of the Study:

  • To elucidate the dynamic mechanisms underlying dsRNA binding by Drosha-dsRBD and DGCR8-dsRBD1.
  • To understand the structural basis for differential dsRNA binding observed between Drosha-dsRBD and DGCR8-dsRBD1.
  • To provide insights into the nuclear maturation step of miRNA processing.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spin relaxation experiments on Drosha-dsRBD (1259-1337) and DGCR8-dsRBD1 (505-583).
  • Molecular Dynamics (MD) simulations of the same dsRBDs.
  • Electrophoretic mobility shift assays (EMSAs) to assess dsRNA binding affinity.

Main Results:

  • Loop 2 in both dsRBDs exhibits high dynamics, but with distinct correlation patterns between Drosha and DGCR8.
  • Drosha-dsRBD possesses a more flexible loop 1 compared to DGCR8-dsRBD1.
  • Drosha-dsRBD showed no dsRNA binding, while DGCR8-dsRBD1 bound with a K(d) of 9.4 ± 0.4 μM.

Conclusions:

  • The differential flexibility of loop 1 and its lack of correlation with loop 2 in Drosha-dsRBD likely explains its inability to bind dsRNA independently.
  • DGCR8-dsRBD1's specific dynamic characteristics enable dsRNA binding, crucial for microprocessor complex function.
  • These findings offer critical structural and dynamic insights into dsRBD-dsRNA interactions during miRNA biogenesis.