1. Immunology and Inflammation
  2. Structural Biology and Molecular Biophysics
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An electrostatic selection mechanism controls sequential kinase signaling downstream of the T cell receptor

  1. Neel H Shah
  2. Qi Wang
  3. Qingrong Yan
  4. Deepti Karandur
  5. Theresa A Kadlecek
  6. Ian R Fallahee
  7. William P Russ
  8. Rama Ranganathan
  9. Arthur Weiss
  10. John Kuriyan  Is a corresponding author
  1. Howard Hughes Medical Institute, University of California, Berkeley, United States
  2. D. E. Shaw Research, United States
  3. Janssen Pharmaceutical Companies of Johnson and Johnson, United States
  4. Howard Hughes Medical Institute, University of California, San Francisco, United States
  5. University of Texas Southwestern Medical Center, United States
Research Article
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Cite this article as: eLife 2016;5:e20105 doi: 10.7554/eLife.20105

Abstract

The sequence of events that initiates T cell signaling is dictated by the specificities and order of activation of the tyrosine kinases that signal downstream of the T cell receptor. Using a platform that combines exhaustive point-mutagenesis of peptide substrates, bacterial surface-display, cell sorting, and deep sequencing, we have defined the specificities of the first two kinases in this pathway, Lck and ZAP-70, for the T cell receptor ζ chain and the scaffold proteins LAT and SLP-76. We find that ZAP-70 selects its substrates by utilizing an electrostatic mechanism that excludes substrates with positively-charged residues and favors LAT and SLP-76 phosphosites that are surrounded by negatively-charged residues. This mechanism prevents ZAP-70 from phosphorylating its own activation loop, thereby enforcing its strict dependence on Lck for activation. The sequence features in ZAP-70, LAT, and SLP-76 that underlie electrostatic selectivity likely contribute to the specific response of T cells to foreign antigens.

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Author details

  1. Neel H Shah

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.

  2. Qi Wang

    D. E. Shaw Research, New York, United States
    Competing interests
    No competing interests declared.

  3. Qingrong Yan

    Janssen Pharmaceutical Companies of Johnson and Johnson, Malvern, United States
    Competing interests
    No competing interests declared.

  4. Deepti Karandur

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.

  5. Theresa A Kadlecek

    Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  6. Ian R Fallahee

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.

  7. William P Russ

    Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    No competing interests declared.

  8. Rama Ranganathan

    Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    No competing interests declared.

  9. Arthur Weiss

    Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2414-9024

  10. John Kuriyan

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
    For correspondence
    jkuriyan@mac.com
    Competing interests
    John Kuriyan, Senior editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4414-5477

Funding

National Institutes of Health (PO1 AI091580)

  • Arthur Weiss
  • John Kuriyan

Damon Runyon Cancer Research Foundation

  • Neel H Shah

Cancer Research Institute

  • Qi Wang
  • Qingrong Yan

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

Reviewing Editor

  1. Philip A Cole, Johns Hopkins University, United States

Publication history

  1. Received: July 27, 2016
  2. Accepted: October 3, 2016
  3. Accepted Manuscript published: October 4, 2016 (version 1)
  4. Accepted Manuscript updated: October 5, 2016 (version 2)
  5. Accepted Manuscript updated: October 11, 2016 (version 3)
  6. Version of Record published: November 1, 2016 (version 4)

Copyright

© 2016, Shah 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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Further reading

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    Fine-tuning of substrate preferences of the Src-family kinase Lck revealed through a high-throughput specificity screen

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    The specificity of tyrosine kinases is attributed predominantly to localization effects dictated by non-catalytic domains. We developed a method to profile the specificities of tyrosine kinases by combining bacterial surface-display of peptide libraries with next-generation sequencing. Using this, we showed that the tyrosine kinase ZAP-70, which is critical for T cell signaling, discriminates substrates through an electrostatic selection mechanism encoded within its catalytic domain (Shah et al., 2016). Here, we expand this high-throughput platform to analyze the intrinsic specificity of any tyrosine kinase domain against thousands of peptides derived from human tyrosine phosphorylation sites. Using this approach, we find a difference in the electrostatic recognition of substrates between the closely related Src-family kinases Lck and c-Src. This divergence likely reflects the specialization of Lck to act in concert with ZAP-70 in T cell signaling. These results point to the importance of direct recognition at the kinase active site in fine-tuning specificity.

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