The determinants of RNA-binding specificity of the heterogeneous nuclear ribonucleoprotein C proteins

J Biol Chem. 1994 Sep 16;269(37):23074-8.

Abstract

The hnRNP C proteins (C1/C2) are tenacious nuclear pre-mRNA-binding proteins that belong to the large RNP motif family of RNA-binding proteins. This motif identifies an RNA-binding domain (RBD) that consists of a four-stranded antiparallel beta-sheet packed against two alpha-helices. Despite considerable information on the structure of the hnRNP C RBD, little is known about its RNA-binding properties. To address this we used in vitro selection/amplification from pools of random sequence RNA to determine the RNA-binding specificity of hnRNP C1. After 8 rounds of selection/amplification nearly all RNAs contained contiguous stretches of at least 5 U residues, and filter-binding assays demonstrated that this sequence constitutes a high-affinity (Kd = 170 nM) binding site for hnRNP C1. The highest affinity we measured for hnRNP C1 was for r(U)14 (Kd = 14 nM). An RBD-containing peptide fragment of hnRNP C1 (amino acids 2-94) bound oligoribonucleotides containing an hnRNP C1 high-affinity binding site with nearly equal affinity to that of hnRNP C1. Unlike hnRNP C1, however, this peptide also bound oligoribonucleotides that do not contain high-affinity hnRNP C1-binding sites. We identified a region of 10 amino acids, immediately COOH-terminal to the RNP motif (amino acids 95-104), that prevents the minimal RBD from binding nonspecific RNA ligands. We propose that the highly conserved beta alpha beta beta alpha beta core structure of the RNP motif RBD confers a general RNA binding activity to RNP motif RBDs and that the determinants of RNA-binding specificity reside in the most variable regions, the loops connecting the beta-strands and/or the contiguous NH2 and COOH termini of the RBD.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Binding Sites
  • Electrophoresis, Polyacrylamide Gel
  • Gene Amplification
  • Heterogeneous-Nuclear Ribonucleoprotein Group C
  • Heterogeneous-Nuclear Ribonucleoproteins
  • Molecular Sequence Data
  • RNA, Heterogeneous Nuclear / metabolism*
  • RNA-Binding Proteins / metabolism*
  • Ribonucleoproteins / metabolism*
  • Sequence Homology, Amino Acid

Substances

  • C1 HNRNP
  • Heterogeneous-Nuclear Ribonucleoprotein Group C
  • Heterogeneous-Nuclear Ribonucleoproteins
  • RNA, Heterogeneous Nuclear
  • RNA-Binding Proteins
  • Ribonucleoproteins