A physicochemical perspective of aging from single-cell analysis of pH, macromolecular and organellar crowding in yeast

  1. Sara N Mouton
  2. David J Thaller
  3. Matthew M Crane
  4. Irina L Rempel
  5. Owen T Terpstra
  6. Anton Steen
  7. Matt Kaeberlein
  8. C Patrick Lusk
  9. Arnold J Boersma  Is a corresponding author
  10. Liesbeth M Veenhoff  Is a corresponding author
  1. University of Groningen, Netherlands
  2. Yale School of Medicine, United States
  3. University of Washington, United States
  4. DWI-Leibniz Institute for Interactive Materials, Germany

Abstract

Cellular aging is a multifactorial process that is characterized by a decline in homeostatic capacity, best described at the molecular level. Physicochemical properties such as pH and macromolecular crowding are essential to all molecular processes in cells and require maintenance. Whether a drift in physicochemical properties contributes to the overall decline of homeostasis in aging is not known. Here we show that the cytosol of yeast cells acidifies modestly in early aging and sharply after senescence. Using a macromolecular crowding sensor optimized for long-term FRET measurements, we show that crowding is rather stable and that the stability of crowding is a stronger predictor for lifespan than the absolute crowding levels. Additionally, in aged cells we observe drastic changes in organellar volume, leading to crowding on the µm scale, which we term organellar crowding. Our measurements provide an initial framework of physicochemical parameters of replicatively aged yeast cells.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 1,2,3,4.

The following previously published data sets were used

Article and author information

Author details

  1. Sara N Mouton

    European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9429-3788
  2. David J Thaller

    Department of Cell Biology, Yale School of Medicine, New Haven, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3577-5562
  3. Matthew M Crane

    Department of Pathology, School of Medicine, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6234-0954
  4. Irina L Rempel

    European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
    Competing interests
    No competing interests declared.
  5. Owen T Terpstra

    European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
    Competing interests
    No competing interests declared.
  6. Anton Steen

    European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
    Competing interests
    No competing interests declared.
  7. Matt Kaeberlein

    Department of Pathology, University of Washington, Seattle, United States
    Competing interests
    Matt Kaeberlein, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1311-3421
  8. C Patrick Lusk

    Department of Cell Biology, Yale School of Medicine, New Haven, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4703-0533
  9. Arnold J Boersma

    DWI-Leibniz Institute for Interactive Materials, DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
    For correspondence
    boersma@dwi.rwth-aachen.de
    Competing interests
    No competing interests declared.
  10. Liesbeth M Veenhoff

    European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
    For correspondence
    l.m.veenhoff@rug.nl
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0158-4728

Funding

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (737.016.016)

  • Liesbeth M Veenhoff

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (723.015.002)

  • Arnold J Boersma

National Institutes of Health (RO1 GM105672)

  • C Patrick Lusk

National Institutes of Health (P30 AG013280)

  • Matt Kaeberlein

National Institutes of Health (R01 AG056359)

  • Matt Kaeberlein

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

Copyright

© 2020, Mouton 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.

Metrics

  • 4,296
    views
  • 574
    downloads
  • 34
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Sara N Mouton
  2. David J Thaller
  3. Matthew M Crane
  4. Irina L Rempel
  5. Owen T Terpstra
  6. Anton Steen
  7. Matt Kaeberlein
  8. C Patrick Lusk
  9. Arnold J Boersma
  10. Liesbeth M Veenhoff
(2020)
A physicochemical perspective of aging from single-cell analysis of pH, macromolecular and organellar crowding in yeast
eLife 9:e54707.
https://doi.org/10.7554/eLife.54707

Share this article

https://doi.org/10.7554/eLife.54707

Further reading

    1. Biochemistry and Chemical Biology
    2. Cancer Biology
    Flavie Coquel, Sing-Zong Ho ... Philippe Pasero
    Research Article

    Cancer cells display high levels of oncogene-induced replication stress (RS) and rely on DNA damage checkpoint for viability. This feature is exploited by cancer therapies to either increase RS to unbearable levels or inhibit checkpoint kinases involved in the DNA damage response. Thus far, treatments that combine these two strategies have shown promise but also have severe adverse effects. To identify novel, better-tolerated anticancer combinations, we screened a collection of plant extracts and found two natural compounds from the plant, Psoralea corylifolia, that synergistically inhibit cancer cell proliferation. Bakuchiol inhibited DNA replication and activated the checkpoint kinase CHK1 by targeting DNA polymerases. Isobavachalcone interfered with DNA double-strand break repair by inhibiting the checkpoint kinase CHK2 and DNA end resection. The combination of bakuchiol and isobavachalcone synergistically inhibited cancer cell proliferation in vitro. Importantly, it also prevented tumor development in xenografted NOD/SCID mice. The synergistic effect of inhibiting DNA replication and CHK2 signaling identifies a vulnerability of cancer cells that might be exploited by using clinically approved inhibitors in novel combination therapies.

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Ana Patrícia Graça, Vadim Nikitushkin ... Gerald Lackner
    Research Article

    Mycofactocin is a redox cofactor essential for the alcohol metabolism of mycobacteria. While the biosynthesis of mycofactocin is well established, the gene mftG, which encodes an oxidoreductase of the glucose-methanol-choline superfamily, remained functionally uncharacterized. Here, we show that MftG enzymes are almost exclusively found in genomes containing mycofactocin biosynthetic genes and are present in 75% of organisms harboring these genes. Gene deletion experiments in Mycolicibacterium smegmatis demonstrated a growth defect of the ∆mftG mutant on ethanol as a carbon source, accompanied by an arrest of cell division reminiscent of mild starvation. Investigation of carbon and cofactor metabolism implied a defect in mycofactocin reoxidation. Cell-free enzyme assays and respirometry using isolated cell membranes indicated that MftG acts as a mycofactocin dehydrogenase shuttling electrons toward the respiratory chain. Transcriptomics studies also indicated remodeling of redox metabolism to compensate for a shortage of redox equivalents. In conclusion, this work closes an important knowledge gap concerning the mycofactocin system and adds a new pathway to the intricate web of redox reactions governing the metabolism of mycobacteria.