A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing

Abstract
Article and author information
Metrics

Abstract

Prp3 is an essential U4/U6 di-snRNP-associated protein whose functions and molecular mechanisms in pre-mRNA splicing are presently poorly understood. We show by structural and biochemical analyses that Prp3 contains a bipartite U4/U6 di-snRNA-binding region comprising an expanded ferredoxin-like fold, which recognizes a 3'-overhang of U6 snRNA, and a preceding peptide, which binds U4/U6 stem II. Phylogenetic analyses revealed that the single-stranded RNA-binding domain is exclusively found in Prp3 orthologs, thus qualifying as a spliceosome-specific RNA interaction module. The composite double-stranded/single-stranded RNA-binding region assembles cooperatively with Snu13 and Prp31 on U4/U6 di-snRNAs and inhibits Brr2-mediated U4/U6 di-snRNA unwinding in vitro. RNP-disrupting mutations in Prp3 lead to U4/U6•U5 tri-snRNP assembly and splicing defects in vivo. Our results reveal how Prp3 acts as an important bridge between U4/U6 and U5 in the tri-snRNP and comparison with a Prp24-U6 snRNA recycling complex suggests how Prp3 may be involved in U4/U6 re-assembly after splicing.

Article and author information

Author details

Sunbin Liu

Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany

Competing interests
The authors declare that no competing interests exist.
Sina Mozaffari-Jovin

Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

Competing interests
The authors declare that no competing interests exist.
Jan Wollenhaupt

Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany

Competing interests
The authors declare that no competing interests exist.
Karine F Santos

Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany

Competing interests
The authors declare that no competing interests exist.
Matthias Theuser

Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany

Competing interests
The authors declare that no competing interests exist.
Stanislaw Dunin-Horkawicz

Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland

Competing interests
The authors declare that no competing interests exist.
Patrizia Fabrizio

Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

Competing interests
The authors declare that no competing interests exist.
Janusz M Bujnicki

Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland

Competing interests
The authors declare that no competing interests exist.
Reinhard Lührmann

Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

Competing interests
The authors declare that no competing interests exist.
Markus C Wahl

Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany

For correspondence
mwahl@zedat.fu-berlin.de

Competing interests
The authors declare that no competing interests exist.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.