1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics
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A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing

  1. Sunbin Liu
  2. Sina Mozaffari-Jovin
  3. Jan Wollenhaupt
  4. Karine F Santos
  5. Matthias Theuser
  6. Stanislaw Dunin-Horkawicz
  7. Patrizia Fabrizio
  8. Janusz M Bujnicki
  9. Reinhard Lührmann
  10. Markus C Wahl  Is a corresponding author
  1. Freie Universität Berlin, Germany
  2. Max Planck Institute for Biophysical Chemistry, Germany
  3. International Institute of Molecular and Cell Biology, Poland
Research Article
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Cite this article as: eLife 2015;4:e07320 doi: 10.7554/eLife.07320

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

  1. Sunbin Liu

    Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. 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.
  3. Jan Wollenhaupt

    Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Karine F Santos

    Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Matthias Theuser

    Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. 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.
  7. Patrizia Fabrizio

    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. 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.
  9. Reinhard Lührmann

    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. 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.

Reviewing Editor

  1. Timothy W Nilsen, Case Western Reserve University, United States

Publication history

  1. Received: March 5, 2015
  2. Accepted: July 9, 2015
  3. Accepted Manuscript published: July 10, 2015 (version 1)
  4. Version of Record published: July 30, 2015 (version 2)

Copyright

© 2015, Liu et al.

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.

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    Proteasome catalyzed peptide splicing (PCPS) of cancer-driving antigens could generate attractive neoepitopes to be targeted by TCR-based adoptive T cell therapy. Based on a spliced peptide prediction algorithm TCRs were generated against putative KRASG12V and RAC2P29L derived neo-splicetopes with high HLA-A*02:01 binding affinity. TCRs generated in mice with a diverse human TCR repertoire specifically recognized the respective target peptides with high efficacy. However, we failed to detect any neo-splicetope specific T cell response when testing the in vivo neo-splicetope generation and obtained no experimental evidence that the putative KRASG12V- and RAC2P29L-derived neo-splicetopes were naturally processed and presented. Furthermore, only the putative RAC2P29L-derived neo-splicetopes was generated by in vitro PCPS. The experiments pose severe questions on the notion that available algorithms or the in vitro PCPS reaction reliably simulate in vivo splicing and argue against the general applicability of an algorithm-driven 'reverse immunology' pipeline for the identification of cancer-specific neo-splicetopes.

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