Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub

  1. Martin Wilkinson
  2. Oliver J Wilkinson
  3. Connie Feyerherm
  4. Emma E Fletcher
  5. Dale B Wigley  Is a corresponding author
  6. Mark Simon Dillingham  Is a corresponding author
  1. Imperial College London, United Kingdom
  2. University of Bristol, United Kingdom

Abstract

Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products.

Data availability

Source data files have been provided for gel-based analyses (Figure 1 - Source data 1).All new cryoEM data/models generated in this work have been deposited at the EMDB and PDB (see Table 1 for accession codes).Validation reports have been provided for structural models with submission.

Article and author information

Author details

  1. Martin Wilkinson

    Department of Infectious Disease, Imperial College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5490-613X
  2. Oliver J Wilkinson

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4107-6434
  3. Connie Feyerherm

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Emma E Fletcher

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Dale B Wigley

    Department of Infectious Disease, Imperial College London, London, United Kingdom
    For correspondence
    d.wigley@imperial.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0786-6726
  6. Mark Simon Dillingham

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    For correspondence
    mark.dillingham@bristol.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4612-7141

Funding

Wellcome Trust (100401/Z/12/Z)

  • Mark Simon Dillingham

Biotechnology and Biological Sciences Research Council (BB/S007261/1)

  • Mark Simon Dillingham

Cancer Research UK (C6913/A2160)

  • Dale B Wigley

Wellcome Trust (209327/Z/17/Z)

  • Dale B Wigley

Medical Research Council (MR/N009258/1)

  • Dale B Wigley

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

Reviewing Editor

  1. Edward H Egelman, University of Virginia, United States

Publication history

  1. Preprint posted: September 12, 2022 (view preprint)
  2. Received: September 12, 2022
  3. Accepted: December 18, 2022
  4. Accepted Manuscript published: December 19, 2022 (version 1)
  5. Version of Record published: January 12, 2023 (version 2)

Copyright

© 2022, Wilkinson 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. Martin Wilkinson
  2. Oliver J Wilkinson
  3. Connie Feyerherm
  4. Emma E Fletcher
  5. Dale B Wigley
  6. Mark Simon Dillingham
(2022)
Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub
eLife 11:e83409.
https://doi.org/10.7554/eLife.83409

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