Structure, Dynamics, and Interaction of p54(nrb)/NonO RRM1 with 5' Splice Site RNA Sequence

Biochemistry. 2016 May 10;55(18):2553-66. doi: 10.1021/acs.biochem.5b01240. Epub 2016 Apr 26.

Abstract

p54(nrb)/NonO is a nuclear RNA-binding protein involved in many cellular events such as pre-mRNA processing, transcription, and nuclear retention of hyper-edited RNAs. In particular, it participates in the splicing process by directly binding the 5' splice site of pre-mRNAs. The protein also concentrates in a nuclear body called paraspeckle by binding a G-rich segment of the ncRNA NEAT1. The N-terminal section of p54(nrb)/NonO contains tandem RNA recognition motifs (RRMs) preceded by an HQ-rich region including a threonine residue (Thr15) whose phosphorylation inhibits its RNA binding ability, except for G-rich RNAs. In this work, our goal was to understand the rules that characterize the binding of the p54(nrb)/NonO RRMs to their RNA target. We have done in vitro RNA binding experiments which revealed that only the first RRM of p54(nrb)/NonO binds to the 5' splice site RNA. We have then determined the structure of the p54(nrb)/NonO RRM1 by liquid-state NMR which revealed the presence of a canonical fold (β1α1β2β3α2β4) and the conservation of aromatic amino acids at the protein surface. We also investigated the dynamics of this domain by NMR. The p54(nrb)/NonO RRM1 displays some motional properties that are typical of a well-folded protein with some regions exhibiting more flexibility (loops and β-strands). Furthermore, we determined the affinity of p54(nrb)/NonO RRM1 interaction to the 5' splice site RNA by NMR and fluorescence quenching and mapped its binding interface by NMR, concluding in a classical nucleic acid interaction. This study provides an improved understanding of the molecular basis (structure and dynamics) that governs the binding of the p54(nrb)/NonO RRM1 to one of its target RNAs.

MeSH terms

  • Animals
  • Mice
  • Nuclear Matrix-Associated Proteins / chemistry*
  • Nuclear Matrix-Associated Proteins / genetics
  • Nuclear Matrix-Associated Proteins / metabolism
  • Protein Domains
  • Protein Structure, Secondary
  • RNA Precursors / chemistry*
  • RNA Precursors / genetics
  • RNA Precursors / metabolism
  • RNA Splice Sites*
  • RNA Splicing*
  • RNA, Long Noncoding / chemistry*
  • RNA, Long Noncoding / genetics
  • RNA, Long Noncoding / metabolism
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Ribonucleoside Diphosphate Reductase
  • Ribonucleotide Reductases / chemistry*
  • Ribonucleotide Reductases / genetics
  • Ribonucleotide Reductases / metabolism

Substances

  • NEAT1 long non-coding RNA, mouse
  • Nuclear Matrix-Associated Proteins
  • RNA Precursors
  • RNA Splice Sites
  • RNA, Long Noncoding
  • RNA-Binding Proteins
  • p54nrb protein, mouse
  • Ribonucleotide Reductases
  • Ribonucleoside Diphosphate Reductase
  • Rrm1 protein, mouse