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Oligomeric transition and dynamics of RNA binding by the HuR RRM1 domain in solution

  • Carolina Lixa
  • Amanda Mujo
  • Mariana T. Q. de Magalhães
  • Fabio C. L. Almeida
  • Luis Mauricio T. R. Lima
  • Anderson S. Pinheiro
Article
  • 18 Downloads

Abstract

Human antigen R (HuR) functions as a major post-transcriptional regulator of gene expression through its RNA-binding activity. HuR is composed by three RNA recognition motifs, namely RRM1, RRM2, and RRM3. The two N-terminal RRM domains are disposed in tandem and contribute mostly to HuR interaction with adenine and uracil-rich elements (ARE) in mRNA. Here, we used a combination of NMR and electrospray ionization–ion mobility spectrometry–mass spectrometry (ESI–IMS–MS) to characterize the structure, dynamics, RNA recognition, and dimerization of HuR RRM1. Our solution structure reveals a canonical RRM fold containing a 19-residue, intrinsically disordered N-terminal extension, which is not involved in RNA binding. NMR titration results confirm the primary RNA-binding site to the two central β-strands, β1 and β3, for a cyclooxygenase 2 (Cox2) ARE I-derived, 7-nucleotide RNA ligand. We show by 15N relaxation that, in addition to the N- and C-termini, the β2–β3 loop undergoes fast backbone dynamics (ps–ns) both in the free and RNA-bound state, indicating that no structural ordering happens upon RNA interaction. ESI–IMS–MS reveals that HuR RRM1 dimerizes, however dimer population represents a minority. Dimerization occurs via the α-helical surface, which is oppositely orientated to the RNA-binding β-sheet. By using a DNA analog of the Cox2 ARE I, we show that DNA binding stabilizes HuR RRM1 monomer and shifts the monomer–dimer equilibrium toward the monomeric species. Altogether, our results deepen the current understanding of the mechanism of RNA recognition employed by HuR.

Keywords

HuR RRM RNA Structure Dynamics Ion-mobility NMR 

Notes

Acknowledgements

We would like to thank the staff of the UEMP-IBqM-UFRJ (Proteomic/Mass Spectrometry Platform) and the CNRMN-UFRJ (NMR Platform) for providing access to their facilities and excellent technical support. This work was supported by grants from Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Conselho Nacional Científico e Tecnológico (CNPq), and by a Brazil Initiative Collaboration Grant from Brown University to ASP. CL is recipient of a Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) “outstanding student” graduate fellowship.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Supplementary material 1 (PDF 1102 KB)

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© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Department of Biochemistry, Institute of ChemistryFederal University of Rio de JaneiroRio de JaneiroBrazil
  2. 2.Department of Biochemistry and ImmunologyFederal University of Minas GeraisBelo HorizonteBrazil
  3. 3.National Center for Nuclear Magnetic Resonance Jiri Jonas, Institute of Medical BiochemistryFederal University of Rio de JaneiroRio de JaneiroBrazil
  4. 4.Faculty of PharmacyFederal University of Rio de JaneiroRio de JaneiroBrazil

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