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

Michiel Waterbeemd, Sem Tamara, Kyle L. Fort, Eugen Damoc, Vojtech Franc, Philipp Bieri, Martin Itten, Alexander Makarov, Nenad Ban and Albert J. R. Heck ()
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Michiel Waterbeemd: Utrecht University
Sem Tamara: Utrecht University
Kyle L. Fort: Utrecht University
Eugen Damoc: Thermo Fisher Scientific
Vojtech Franc: Utrecht University
Philipp Bieri: Institute of Molecular Biology and Biophysics, ETH Zurich
Martin Itten: Institute of Molecular Biology and Biophysics, ETH Zurich
Alexander Makarov: Utrecht University
Nenad Ban: Institute of Molecular Biology and Biophysics, ETH Zurich
Albert J. R. Heck: Utrecht University

Nature Communications, 2018, vol. 9, issue 1, 1-12

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-04853-x

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