Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET

  1. Johannes M Keegstra
  2. Keita Kamino
  3. François Anquez
  4. Milena D Lazova
  5. Thierry Emonet
  6. Thomas S Shimizu  Is a corresponding author
  1. AMOLF Institute, Netherlands
  2. Yale University, United States

Abstract

We present in vivo single-cell FRET measurements in the Escherichia coli chemotaxis system that reveal pervasive signaling variability, both across cells in isogenic populations and within individual cells over time. We quantify cell-to-cell variability of adaptation, ligand response, as well as steady-state output level, and analyze the role of network design in shaping this diversity from gene expression noise. In the absence of changes in gene expression, we find that single cells demonstrate strong temporal fluctuations. We provide evidence that such signaling noise can arise from at least two sources: (i) stochastic activities of adaptation enzymes, and (ii) receptor-kinase dynamics in the absence of adaptation. We demonstrate that under certain conditions, (ii) can generate giant fluctuations that drive signaling activity of the entire cell into a stochastic two-state switching regime. Our findings underscore the importance of molecular noise, arising not only in gene expression but also in protein networks.

Article and author information

Author details

  1. Johannes M Keegstra

    AMOLF Institute, Amsterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8877-4881
  2. Keita Kamino

    AMOLF Institute, Amsterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  3. François Anquez

    AMOLF Institute, Amsterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  4. Milena D Lazova

    AMOLF Institute, Amsterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  5. Thierry Emonet

    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6746-6564
  6. Thomas S Shimizu

    AMOLF Institute, Amsterdam, Netherlands
    For correspondence
    shimizu@amolf.nl
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0040-7380

Funding

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO Vidi 680-47-515)

  • Thomas S Shimizu

Stichting voor Fundamenteel Onderzoek der Materie (FOM Projectruimte 11PR2958)

  • Thomas S Shimizu

Paul G. Allen Family Foundation (11562)

  • Thierry Emonet
  • Thomas S Shimizu

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

Copyright

© 2017, Keegstra 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

  • 3,944
    views
  • 643
    downloads
  • 65
    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. Johannes M Keegstra
  2. Keita Kamino
  3. François Anquez
  4. Milena D Lazova
  5. Thierry Emonet
  6. Thomas S Shimizu
(2017)
Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET
eLife 6:e27455.
https://doi.org/10.7554/eLife.27455

Share this article

https://doi.org/10.7554/eLife.27455

Further reading

    1. Computational and Systems Biology
    2. Medicine
    Xin Zhou, Zhinuo Jenny Wang ... Blanca Rodriguez
    Research Article

    Sudden death after myocardial infarction (MI) is associated with electrophysiological heterogeneities and ionic current remodelling. Low ejection fraction (EF) is used in risk stratification, but its mechanistic links with pro-arrhythmic heterogeneities are unknown. We aim to provide mechanistic explanations of clinical phenotypes in acute and chronic MI, from ionic current remodelling to ECG and EF, using human electromechanical modelling and simulation to augment experimental and clinical investigations. A human ventricular electromechanical modelling and simulation framework is constructed and validated with rich experimental and clinical datasets, incorporating varying degrees of ionic current remodelling as reported in literature. In acute MI, T-wave inversion and Brugada phenocopy were explained by conduction abnormality and local action potential prolongation in the border zone. In chronic MI, upright tall T-waves highlight large repolarisation dispersion between the border and remote zones, which promoted ectopic propagation at fast pacing. Post-MI EF at resting heart rate was not sensitive to the extent of repolarisation heterogeneity and the risk of repolarisation abnormalities at fast pacing. T-wave and QT abnormalities are better indicators of repolarisation heterogeneities than EF in post-MI.

    1. Computational and Systems Biology
    Dylan C Sarver, Muzna Saqib ... G William Wong
    Research Article

    Organ function declines with age, and large-scale transcriptomic analyses have highlighted differential aging trajectories across tissues. The mechanism underlying shared and organ-selective functional changes across the lifespan, however, still remains poorly understood. Given the central role of mitochondria in powering cellular processes needed to maintain tissue health, we therefore undertook a systematic assessment of respiratory activity across 33 different tissues in young (2.5 months) and old (20 months) mice of both sexes. Our high-resolution mitochondrial respiration atlas reveals: (1) within any group of mice, mitochondrial activity varies widely across tissues, with the highest values consistently seen in heart, brown fat, and kidney; (2) biological sex is a significant but minor contributor to mitochondrial respiration, and its contributions are tissue-specific, with major differences seen in the pancreas, stomach, and white adipose tissue; (3) age is a dominant factor affecting mitochondrial activity, especially across most brain regions, different fat depots, skeletal muscle groups, eyes, and different regions of the gastrointestinal tract; (4) age effects can be sex- and tissue-specific, with some of the largest effects seen in pancreas, heart, adipose tissue, and skeletal muscle; and (5) while aging alters the functional trajectories of mitochondria in a majority of tissues, some are remarkably resilient to age-induced changes. Altogether, our data provide the most comprehensive compendium of mitochondrial respiration and illuminate functional signatures of aging across diverse tissues and organ systems.