1. Computational and Systems Biology
  2. Microbiology and Infectious Disease
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Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions

  1. Luis V Nobre
  2. Katie Nightingale
  3. Benjamin J Ravenhill
  4. Robin Antrobus
  5. Lior Soday
  6. Jenna Nichols
  7. James A Davies
  8. Sepehr Seirafian
  9. Eddie CY Wang
  10. Andrew J Davison
  11. Gavin WG Wilkinson
  12. Richard J Stanton
  13. Edward L Huttlin
  14. Michael P Weekes  Is a corresponding author
  1. University of Cambridge, United Kingdom
  2. MRC-University of Glasgow Centre for Virus Research, United Kingdom
  3. Cardiff University School of Medicine, United Kingdom
  4. Harvard Medical School, United States
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Cite this article as: eLife 2019;8:e49894 doi: 10.7554/eLife.49894

Abstract

Human cytomegalovirus (HCMV) extensively modulates host cells, downregulating >900 human proteins during viral replication and degrading ≥133 proteins shortly after infection. The mechanism of degradation of most host proteins remains unresolved, and the functions of many viral proteins are incompletely characterised. We performed a mass spectrometry-based interactome analysis of 169 tagged, stably-expressed canonical strain Merlin HCMV proteins, and two non-canonical HCMV proteins, in infected cells. This identified a network of >3,400 virus-host and >150 virus-virus protein interactions, providing insights into functions for multiple viral genes. Domain analysis predicted binding of the viral UL25 protein to SH3 domains of NCK Adaptor Protein-1. Viral interacting proteins were identified for 31/133 degraded host targets. Finally, the uncharacterised, non-canonical ORFL147C protein was found to interact with elements of the mRNA splicing machinery, and a mutational study suggested its importance in viral replication. The interactome data will be important for future studies of herpesvirus infection.

Article and author information

Author details

  1. Luis V Nobre

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Katie Nightingale

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Benjamin J Ravenhill

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Robin Antrobus

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Lior Soday

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Jenna Nichols

    MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. James A Davies

    Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3569-4500
  8. Sepehr Seirafian

    Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  9. Eddie CY Wang

    Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  10. Andrew J Davison

    MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  11. Gavin WG Wilkinson

    Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5623-0126
  12. Richard J Stanton

    Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6799-1182
  13. Edward L Huttlin

    Department of Cell Biology, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Michael P Weekes

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    For correspondence
    mpw1001@cam.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3196-5545

Funding

Wellcome (108070/Z/15/Z)

  • Michael P Weekes

Medical Research Council (MR/L018373/1)

  • Eddie CY Wang
  • Gavin WG Wilkinson
  • Richard J Stanton

Medical Research Council (MR/P001602/1)

  • Eddie CY Wang
  • Gavin WG Wilkinson
  • Richard J Stanton

Wellcome (WT090323MA)

  • Eddie CY Wang
  • Gavin WG Wilkinson
  • Richard J Stanton

Medical Research Council (MC_UU_12014/3)

  • Andrew J Davison

National Institutes of Health (U24 HG006673)

  • Edward L Huttlin

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

Reviewing Editor

  1. Piet Maes, KU Leuven, Rega Institute for Medical Research, Belgium

Publication history

  1. Received: July 3, 2019
  2. Accepted: December 24, 2019
  3. Accepted Manuscript published: December 24, 2019 (version 1)
  4. Version of Record published: January 14, 2020 (version 2)

Copyright

© 2019, Nobre 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

    1. Computational and Systems Biology
    Zhimin Liu et al.
    Research Article Updated

    To characterize how protein-protein interaction (PPI) networks change, we quantified the relative PPI abundance of 1.6 million protein pairs in the yeast Saccharomyces cerevisiae across nine growth conditions, with replication, for a total of 44 million measurements. Our multi-condition screen identified 13,764 pairwise PPIs, a threefold increase over PPIs identified in one condition. A few ‘immutable’ PPIs are present across all conditions, while most ‘mutable’ PPIs are rarely observed. Immutable PPIs aggregate into highly connected ‘core’ network modules, with most network remodeling occurring within a loosely connected ‘accessory’ module. Mutable PPIs are less likely to co-express, co-localize, and be explained by simple mass action kinetics, and more likely to contain proteins with intrinsically disordered regions, implying that environment-dependent association and binding is critical to cellular adaptation. Our results show that protein interactomes are larger than previously thought and contain highly dynamic regions that reorganize to drive or respond to cellular changes.

    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics
    Xiakun Chu et al.
    Research Article

    The way in which multidomain proteins fold has been a puzzling question for decades. Until now, the mechanisms and functions of domain interactions involved in multidomain protein folding have been obscure. Here, we develop structure-based models to investigate the folding and DNA-binding processes of the multidomain Y-family DNA polymerase IV (DPO4). We uncover shifts in folding mechanism among ordered domain-wise folding, backtracking folding, and cooperative folding, modulated by interdomain interactions. These lead to "U-shaped' folding kinetics. We characterize the effects of interdomain flexibility on the promotion of DPO4-DNA (un)binding, which probably contributes to the ability of DPO4 to bypass DNA lesions, a known biological role of Y-family polymerases. We suggest that the native topology of DPO4 leads to a trade-off between fast, stable folding and tight functional DNA binding. Our approach provides an effective way to quantitatively correlate the roles of protein interactions in conformational dynamics at the multidomain level.