Allosteric mechanism of signal transduction in the two-component system histidine kinase PhoQ

  1. Bruk Mensa  Is a corresponding author
  2. Nicholas F Polizzi
  3. Kathleen S Molnar
  4. Andrew M Natale
  5. Thomas Lemmin
  6. William F DeGrado  Is a corresponding author
  1. University of California, San Francisco, United States
  2. Codexis Inc., United States
  3. Università della Svizzera Italiana, Switzerland

Abstract

Transmembrane signaling proteins couple extracytosolic sensors to cytosolic effectors. Here, we examine how binding of Mg2+ to the sensor domain of an E. coli two component histidine kinase (HK), PhoQ, modulates its cytoplasmic kinase domain. We use cysteine-crosslinking and reporter-gene assays to simultaneously and independently probe the signaling state of PhoQ's sensor and autokinase domains in a set of over 30 mutants. Strikingly, conservative single-site mutations distant from the sensor or catalytic site strongly influence PhoQ's ligand-sensitivity as well as the magnitude and direction of the signal. Data from 35 mutants are explained by a semi-empirical three-domain model in which the sensor, intervening HAMP, and catalytic domains can adopt kinase-promoting or inhibiting conformations that are in allosteric communication. The catalytic and sensor domains intrinsically favor a constitutively 'kinase-on' conformation, while the HAMP domain favors the 'off' state; when coupled, they create a bistable system responsive to physiological concentrations of Mg2+. Mutations alter signaling by locally modulating domain intrinsic equilibrium constants and interdomain couplings. Our model suggests signals transmit via interdomain allostery rather than propagation of a single concerted conformational change, explaining the diversity of signaling structural transitions observed in individual HK domains.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting file; Source data files have been provided for Figure 8. All source code for modeling work is provided as source code files 1-5.

Article and author information

Author details

  1. Bruk Mensa

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
    For correspondence
    bruk.mensa@ucsf.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8777-5946
  2. Nicholas F Polizzi

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Kathleen S Molnar

    Codexis Inc., Redwood City, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Andrew M Natale

    Biophysics PhD program, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Thomas Lemmin

    Euler Institute, Università della Svizzera Italiana, Lugano, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  6. William F DeGrado

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
    For correspondence
    Bill.DeGrado@ucsf.edu
    Competing interests
    The authors declare that no competing interests exist.

Funding

National Institutes of Health (K99-GM138753)

  • Bruk Mensa
  • Nicholas F Polizzi
  • Andrew M Natale
  • Thomas Lemmin
  • William F DeGrado

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

Reviewing Editor

  1. Michael T Laub, Massachusetts Institute of Technology, United States

Version history

  1. Received: August 25, 2021
  2. Preprint posted: September 5, 2021 (view preprint)
  3. Accepted: December 13, 2021
  4. Accepted Manuscript published: December 14, 2021 (version 1)
  5. Version of Record published: December 31, 2021 (version 2)

Copyright

© 2021, Mensa 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. Bruk Mensa
  2. Nicholas F Polizzi
  3. Kathleen S Molnar
  4. Andrew M Natale
  5. Thomas Lemmin
  6. William F DeGrado
(2021)
Allosteric mechanism of signal transduction in the two-component system histidine kinase PhoQ
eLife 10:e73336.
https://doi.org/10.7554/eLife.73336

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https://doi.org/10.7554/eLife.73336

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    Funding:

    This work was supported by the Weizmann Krenter Foundation and the Weizmann – Ichilov (Tel Aviv Sourasky Medical Center) Collaborative Grant in Biomedical Research, by the Minerva Foundation, by the ISF KillCorona grant 3777/19.