Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation

Abstract

Many metabolic enzymes self-assemble into micron-scale filaments to organize and regulate metabolism. The appearance of these assemblies often coincides with large metabolic changes as in development, cancer, and stress. Yeast undergo cytoplasmic acidification upon starvation, triggering the assembly of many metabolic enzymes into filaments. However, it is unclear how these filaments assemble at the molecular level and what their role is in the yeast starvation response. CTP Synthase (CTPS) assembles into metabolic filaments across many species. Here, we characterize in vitro polymerization and investigate in vivo consequences of CTPS assembly in yeast. Cryo-EM structures reveal a pH-sensitive assembly mechanism and highly ordered filament bundles that stabilize an inactive state of the enzyme, features unique to yeast CTPS. Disruption of filaments in cells with non-assembly or pH-insensitive mutations decreases growth rate, reflecting the importance of regulated CTPS filament assembly in homeotstasis.

Data availability

models deposited to PDB as: 7RL0,7RNR,7RKH,7RL5,7RNL,7RMF,7RMK,7RMC,7RMO,7RMVmaps deposited to EMDB as: EMD-24512,EMD-24581,EMD-24497,EMD-24516,EMD-24579,EMD-24566,EMD-24575,EMD-24560,EMD-24576,EMD-24578

Article and author information

Author details

  1. Jesse M Hansen

    University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Avital Horowitz

    University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Eric M Lynch

    University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5897-5167
  4. Daniel P Farrell

    University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Joel Quispe

    University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Frank DiMaio

    University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7524-8938
  7. Justin M Kollman

    Department of Biochemistry, University of Washington, seattle, United States
    For correspondence
    jkoll@uw.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0350-5827

Funding

National Institutes of Health (R01 grant,GM118396)

  • Justin M Kollman

National Institutes of Health (Graduate Student Training Grant,T32 GM007270)

  • Jesse M Hansen

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Edward H Egelman, University of Virginia, United States

Version history

  1. Preprint posted: August 26, 2021 (view preprint)
  2. Received: August 26, 2021
  3. Accepted: November 3, 2021
  4. Accepted Manuscript published: November 4, 2021 (version 1)
  5. Version of Record published: December 2, 2021 (version 2)

Copyright

© 2021, Hansen 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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  1. Jesse M Hansen
  2. Avital Horowitz
  3. Eric M Lynch
  4. Daniel P Farrell
  5. Joel Quispe
  6. Frank DiMaio
  7. Justin M Kollman
(2021)
Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation
eLife 10:e73368.
https://doi.org/10.7554/eLife.73368

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https://doi.org/10.7554/eLife.73368

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