Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction

Abstract

The alarmone (p)ppGpp regulates diverse targets, yet its target specificity and evolution remain poorly understood. Here we elucidate the mechanism by which basal (p)ppGpp inhibits the purine salvage enzyme HPRT by sharing a conserved motif with its substrate PRPP. Intriguingly, HPRT regulation by (p)ppGpp varies across organisms and correlates with HPRT oligomeric forms. (p)ppGpp-sensitive HPRT exists as a PRPP-bound dimer or an apo- and (p)ppGpp-bound tetramer, where a dimer-dimer interface triggers allosteric structural rearrangements to enhance (p)ppGpp inhibition. Loss of this oligomeric interface results in weakened (p)ppGpp regulation. Our results reveal an evolutionary principle whereby protein oligomerization allows evolutionary change to accumulate away from a conserved binding pocket to allosterically alter specificity of ligand interaction. This principle also explains how another (p)ppGpp target GMK is variably regulated across species. Since most ligands bind near protein interfaces, we propose that this principle extends to many other protein-ligand interactions.

Data availability

Diffraction data have been deposited in PDB under the accession codes 6D9Q (https://www.rcsb.org/structure/6d9q), 6D9R (https://www.rcsb.org/structure/6d9r), and 6D9S (https://www.rcsb.org/structure/6D9S). All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Table 2.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Brent W Anderson

    Department of Bacteriology, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Kuanqing Liu

    Department of Bacteriology, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Christine Wolak

    Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Katarzyna Dubiel

    Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Fukang She

    Department of Bacteriology, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Kenneth A Satyshur

    Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9371-2493
  7. James L Keck

    Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Jue D Wang

    Department of Bacteriology, University of Wisconsin-Madison, Madison, United States
    For correspondence
    wang@bact.wisc.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1503-170X

Funding

National Institute of General Medical Sciences (R35 GM127088)

  • Jue D Wang

Howard Hughes Medical Institute (Faculty Scholar)

  • Jue D Wang

National Science Foundation (GRFP DGE-1256259)

  • Brent W Anderson

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

Publication history

  1. Received: April 9, 2019
  2. Accepted: September 24, 2019
  3. Accepted Manuscript published: September 25, 2019 (version 1)
  4. Version of Record published: October 8, 2019 (version 2)

Copyright

© 2019, Anderson 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. Brent W Anderson
  2. Kuanqing Liu
  3. Christine Wolak
  4. Katarzyna Dubiel
  5. Fukang She
  6. Kenneth A Satyshur
  7. James L Keck
  8. Jue D Wang
(2019)
Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction
eLife 8:e47534.
https://doi.org/10.7554/eLife.47534
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