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The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs

Author

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  • Benedikt M. Beckmann

    (European Molecular Biology Laboratory (EMBL)
    Present address: Molecular Infection Biology, IRI for the Life Sciences & Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, Berlin 10115, Germany)

  • Rastislav Horos

    (European Molecular Biology Laboratory (EMBL))

  • Bernd Fischer

    (European Molecular Biology Laboratory (EMBL)
    Present address: Computational Genome Biology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Alfredo Castello

    (European Molecular Biology Laboratory (EMBL)
    Present address: Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK)

  • Katrin Eichelbaum

    (European Molecular Biology Laboratory (EMBL)
    Present address: Cell Signaling and Mass Spectrometry, Max Delbrück Center Berlin, Robert-Rössle-Straße 10, Berlin 13125, Germany)

  • Anne-Marie Alleaume

    (European Molecular Biology Laboratory (EMBL))

  • Thomas Schwarzl

    (European Molecular Biology Laboratory (EMBL))

  • Tomaž Curk

    (European Molecular Biology Laboratory (EMBL)
    Present address: University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, SI-1001 Ljubljana, Slovenia)

  • Sophia Foehr

    (European Molecular Biology Laboratory (EMBL))

  • Wolfgang Huber

    (European Molecular Biology Laboratory (EMBL))

  • Jeroen Krijgsveld

    (European Molecular Biology Laboratory (EMBL))

  • Matthias W. Hentze

    (European Molecular Biology Laboratory (EMBL))

Abstract

RNA-binding proteins (RBPs) exert a broad range of biological functions. To explore the scope of RBPs across eukaryotic evolution, we determined the in vivo RBP repertoire of the yeast Saccharomyces cerevisiae and identified 678 RBPs from yeast and additionally 729 RBPs from human hepatocytic HuH-7 cells. Combined analyses of these and recently published data sets define the core RBP repertoire conserved from yeast to man. Conserved RBPs harbour defined repetitive motifs within disordered regions, which display striking evolutionary expansion. Only 60% of yeast and 73% of the human RBPs have functions assigned to RNA biology or structural motifs known to convey RNA binding, and many intensively studied proteins surprisingly emerge as RBPs (termed ‘enigmRBPs’), including almost all glycolytic enzymes, pointing to emerging connections between gene regulation and metabolism. Analyses of the mitochondrial hydroxysteroid dehydrogenase (HSD17B10) uncover the RNA-binding specificity of an enigmRBP.

Suggested Citation

  • Benedikt M. Beckmann & Rastislav Horos & Bernd Fischer & Alfredo Castello & Katrin Eichelbaum & Anne-Marie Alleaume & Thomas Schwarzl & Tomaž Curk & Sophia Foehr & Wolfgang Huber & Jeroen Krijgsveld &, 2015. "The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs," Nature Communications, Nature, vol. 6(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms10127
    DOI: 10.1038/ncomms10127
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    Cited by:

    1. Ebru Aydin & Silke Schreiner & Jacqueline Böhme & Birte Keil & Jan Weber & Bojan Žunar & Timo Glatter & Cornelia Kilchert, 2024. "DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3’-end of genes and involved in the recycling of cleavage factors," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    2. Andrew J. Heindel & Jeffrey W. Brulet & Xiantao Wang & Michael W. Founds & Adam H. Libby & Dina L. Bai & Michael C. Lemke & David M. Leace & Thurl E. Harris & Markus Hafner & Ku-Lung Hsu, 2023. "Chemoproteomic capture of RNA binding activity in living cells," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Haofan Sun & Bin Fu & Xiaohong Qian & Ping Xu & Weijie Qin, 2024. "Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    4. Lukas Bartonek & Bojan Zagrovic, 2017. "mRNA/protein sequence complementarity and its determinants: The impact of affinity scales," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-16, July.
    5. JohnCarlo Kristofich & Christopher V. Nicchitta, 2023. "Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    6. Meeli Mullari & Nicolas Fossat & Niels H. Skotte & Andrea Asenjo-Martinez & David T. Humphreys & Jens Bukh & Agnete Kirkeby & Troels K. H. Scheel & Michael L. Nielsen, 2023. "Characterising the RNA-binding protein atlas of the mammalian brain uncovers RBM5 misregulation in mouse models of Huntington’s disease," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    7. Joel I. Perez-Perri & Dunja Ferring-Appel & Ina Huppertz & Thomas Schwarzl & Sudeep Sahadevan & Frank Stein & Mandy Rettel & Bruno Galy & Matthias W. Hentze, 2023. "The RNA-binding protein landscapes differ between mammalian organs and cultured cells," Nature Communications, Nature, vol. 14(1), pages 1-20, December.

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