Inter-domain Flexibility of Human Ser/Arg-Rich Splicing Factor 1 Allows Variable Spacer Length in Cognate RNA's Bipartite Motifs

Biochemistry. 2022 Dec 20;61(24):2922-2932. doi: 10.1021/acs.biochem.2c00565. Epub 2022 Dec 1.

Abstract

Ser/Arg-rich splicing factor 1 (SRSF1 or ASF/SF2) is the prototypical member of SR proteins. SRSF1 binds to exonic splicing enhancers, which prompts inclusion of corresponding exons in the mature mRNA. The RNA-binding domain of SRSF1 consists of tandem RNA-recognition motifs (RRM1 and RRM2) separated by a 30 amino acid long linker. In this study, we investigate roles of RRM1, RRM2, and the linker in RNA binding. We find that although both RRMs are crucial to RNA binding, RRM2 plays the dominant role. The linker mildly contributes to RNA binding and remains flexible in the RNA-bound state. Flexibility of the linker allows the RRM1-cognate motif to be either upstream or downstream of the RRM2-cognate motif. In addition, we find that the spacer length between the bipartite motifs varies from 0 to 10 nucleotides. Our binding assays reveal that SRSF1 prefers RNA sequences with shorter spacers and the RRM1-cognate motif being placed upstream. Restrained by nuclear magnetic resonance data, we simulate RNA-bound complexes and demonstrate how tandem RRMs bind to RNA of different spacer lengths and swapped bipartite motifs. We find that when the RRM1-cognate motif is placed downstream, either the RRM1/RRM2 linker needs to be more extended or RNA needs to form a U turn, which may reduce conformational entropy. Our study suggests that the RNA-binding specificity of SRSF1 is broader than traditionally recapitulated by consensus sequences of 7 to 8 nucleotides. Instead, centered on the RRM2-cognate motif, an RNA fragment encompassing 10-nucleotide upstream and downstream should be scrutinized.

Publication types

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

MeSH terms

  • Humans
  • Nucleotides / metabolism
  • Protein Binding
  • RNA / chemistry
  • RNA Splicing Factors / metabolism
  • RNA Splicing*
  • RNA-Binding Proteins* / metabolism
  • Serine-Arginine Splicing Factors / metabolism

Substances

  • RNA-Binding Proteins
  • RNA
  • Nucleotides
  • RNA Splicing Factors
  • Serine-Arginine Splicing Factors
  • SRSF1 protein, human