NMR structure of the three quasi RNA recognition motifs (qRRMs) of human hnRNP F and interaction studies with Bcl-x G-tract RNA: a novel mode of RNA recognition

Nucleic Acids Res. 2006 Aug 2;34(13):3634-45. doi: 10.1093/nar/gkl488. Print 2006.

Abstract

The heterogeneous nuclear ribonucleoprotein (hnRNP) F belongs to the hnRNP H family involved in the regulation of alternative splicing and polyadenylation and specifically recognizes poly(G) sequences (G-tracts). In particular, hnRNP F binds a G-tract of the Bcl-x RNA and regulates its alternative splicing, leading to two isoforms, Bcl-x(S) and Bcl-x(L), with antagonist functions. In order to gain insight into G-tract recognition by hnRNP H members, we initiated an NMR study of human hnRNP F. We present the solution structure of the three quasi RNA recognition motifs (qRRMs) of hnRNP F and identify the residues that are important for the interaction with the Bcl-x RNA by NMR chemical shift perturbation and mutagenesis experiments. The three qRRMs exhibit the canonical betaalphabetabetaalphabeta RRM fold but additional secondary structure elements are present in the two N-terminal qRRMs of hnRNP F. We show that qRRM1 and qRRM2 but not qRRM3 are responsible for G-tract recognition and that the residues of qRRM1 and qRRM2 involved in G-tract interaction are not on the beta-sheet surface as observed for the classical RRM but are part of a short beta-hairpin and two adjacent loops. These regions define a novel interaction surface for RNA recognition by RRMs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Amino Acids, Aromatic / genetics
  • Binding Sites
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H / chemistry*
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H / genetics
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H / metabolism
  • Humans
  • Models, Molecular*
  • Molecular Sequence Data
  • Mutagenesis
  • Nuclear Magnetic Resonance, Biomolecular
  • Poly G / chemistry
  • Protein Binding
  • RNA / chemistry*
  • RNA / metabolism
  • Sequence Alignment
  • bcl-X Protein / genetics*

Substances

  • Amino Acids, Aromatic
  • Heterogeneous-Nuclear Ribonucleoprotein Group F-H
  • bcl-X Protein
  • Poly G
  • RNA