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Atomic-level insight into mRNA processing bodies by combining solid and solution-state NMR spectroscopy

Author

Listed:
  • Reinier Damman

    (NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8)

  • Stefan Schütz

    (University of Regensburg)

  • Yanzhang Luo

    (NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8)

  • Markus Weingarth

    (NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8)

  • Remco Sprangers

    (University of Regensburg)

  • Marc Baldus

    (NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8)

Abstract

Liquid–liquid phase separation is increasingly recognized as a process involved in cellular organization. Thus far, a detailed structural characterization of this intrinsically heterogeneous process has been challenging. Here we combine solid- and solution-state NMR spectroscopy to obtain atomic-level insights into the assembly and maturation of cytoplasmic processing bodies that contain mRNA as well as enzymes involved in mRNA degradation. In detail, we have studied the enhancer of decapping 3 (Edc3) protein that is a central hub for processing body formation in yeast. Our results reveal that Edc3 domains exhibit diverse levels of structural organization and dynamics after liquid–liquid phase separation. In addition, we find that interactions between the different Edc3 domains and between Edc3 and RNA in solution are largely preserved in the condensed protein state, allowing processing bodies to rapidly form and dissociate upon small alterations in the cellular environment.

Suggested Citation

  • Reinier Damman & Stefan Schütz & Yanzhang Luo & Markus Weingarth & Remco Sprangers & Marc Baldus, 2019. "Atomic-level insight into mRNA processing bodies by combining solid and solution-state NMR spectroscopy," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-12402-3
    DOI: 10.1038/s41467-019-12402-3
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    Cited by:

    1. Agnes Adler & Mamata Bangera & J. Wouter Beugelink & Salima Bahri & Hugo Ingen & Carolyn A. Moores & Marc Baldus, 2024. "A structural and dynamic visualization of the interaction between MAP7 and microtubules," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. Jack E. Bramham & Alexander P. Golovanov, 2022. "Temporal and spatial characterisation of protein liquid-liquid phase separation using NMR spectroscopy," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    3. Changmiao Guo & Raymundo Alfaro-Aco & Chunting Zhang & Ryan W. Russell & Sabine Petry & Tatyana Polenova, 2023. "Structural basis of protein condensation on microtubules underlying branching microtubule nucleation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Raju Roy & Gitartha Das & Ishwarya Achappa Kuttanda & Nupur Bhatter & Purusharth I. Rajyaguru, 2022. "Low complexity RGG-motif sequence is required for Processing body (P-body) disassembly," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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