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Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods

Author

Listed:
  • Michiel Waterbeemd

    (Utrecht University
    Netherlands Proteomics Center)

  • Sem Tamara

    (Utrecht University
    Netherlands Proteomics Center)

  • Kyle L. Fort

    (Utrecht University
    Netherlands Proteomics Center
    Thermo Fisher Scientific)

  • Eugen Damoc

    (Thermo Fisher Scientific)

  • Vojtech Franc

    (Utrecht University
    Netherlands Proteomics Center)

  • Philipp Bieri

    (Institute of Molecular Biology and Biophysics, ETH Zurich)

  • Martin Itten

    (Institute of Molecular Biology and Biophysics, ETH Zurich)

  • Alexander Makarov

    (Utrecht University
    Thermo Fisher Scientific)

  • Nenad Ban

    (Institute of Molecular Biology and Biophysics, ETH Zurich)

  • Albert J. R. Heck

    (Utrecht University
    Netherlands Proteomics Center)

Abstract

Biomolecular mass spectrometry has matured strongly over the past decades and has now reached a stage where it can provide deep insights into the structure and composition of large cellular assemblies. Here, we describe a three-tiered hybrid mass spectrometry approach that enables the dissection of macromolecular complexes in order to complement structural studies. To demonstrate the capabilities of the approach, we investigate ribosomes, large ribonucleoprotein particles consisting of a multitude of protein and RNA subunits. We identify sites of sequence processing, protein post-translational modifications, and the assembly and stoichiometry of individual ribosomal proteins in four distinct ribosomal particles of bacterial, plant and human origin. Amongst others, we report extensive cysteine methylation in the zinc finger domain of the human S27 protein, the heptameric stoichiometry of the chloroplastic stalk complex, the heterogeneous composition of human 40S ribosomal subunits and their association to the CrPV, and HCV internal ribosome entry site RNAs.

Suggested Citation

  • Michiel Waterbeemd & Sem Tamara & Kyle L. Fort & Eugen Damoc & Vojtech Franc & Philipp Bieri & Martin Itten & Alexander Makarov & Nenad Ban & Albert J. R. Heck, 2018. "Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-04853-x
    DOI: 10.1038/s41467-018-04853-x
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    Cited by:

    1. Naomi R. Genuth & Zhen Shi & Koshi Kunimoto & Victoria Hung & Adele F. Xu & Craig H. Kerr & Gerald C. Tiu & Juan A. Oses-Prieto & Rachel E. A. Salomon-Shulman & Jeffrey D. Axelrod & Alma L. Burlingame, 2022. "A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    2. Danique M. H. Rijswijck & Albert Bondt & Max Hoek & Karlijn Straten & Tom G. Caniels & Meliawati Poniman & Dirk Eggink & Chantal Reusken & Godelieve J. Bree & Rogier W. Sanders & Marit J. Gils & Alber, 2022. "Discriminating cross-reactivity in polyclonal IgG1 responses against SARS-CoV-2 variants of concern," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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