Coordination between nucleotide excision repair and specialized polymerase DnaE2 action enables DNA damage survival in non-replicating bacteria

  1. Asha Mary Joseph
  2. Saheli Daw
  3. Ismath Sadhir
  4. Anjana Badrinarayanan  Is a corresponding author
  1. National Centre for Biological Sciences, India

Abstract

Translesion synthesis (TLS) is a highly conserved mutagenic DNA lesion tolerance pathway, which employs specialized, low-fidelity DNA polymerases to synthesize across lesions. Current models suggest that activity of these polymerases is predominantly associated with ongoing replication, functioning either at or behind the replication fork. Here we provide evidence for DNA damage-dependent function of a specialized polymerase, DnaE2, in replication-independent conditions. We develop an assay to follow lesion repair in non-replicating Caulobacter and observe that components of the replication machinery localize on DNA in response to damage. These localizations persist in the absence of DnaE2 or if catalytic activity of this polymerase is mutated. Single-stranded DNA gaps for SSB binding and low-fidelity polymerase-mediated synthesis are generated by nucleotide excision repair, as replisome components fail to localize in the absence of NER. This mechanism of gap-filling facilitates cell cycle restoration when cells are released into replication-permissive conditions. Thus, such cross-talk (between activity of NER and specialized polymerases in subsequent gap-filling) helps preserve genome integrity and enhances survival in a replication-independent manner.

Data availability

Data analysed during this study are included in the manuscript. Numerical data files (source data files) have been provided for Figure 1_figure supplement1, Figure 2-5 and corresponding figure supplements.

Article and author information

Author details

  1. Asha Mary Joseph

    Biochemistry, microbiology, National Centre for Biological Sciences, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0465-9799
  2. Saheli Daw

    Biochemistry, microbiology, National Centre for Biological Sciences, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
  3. Ismath Sadhir

    Biochemistry, National Centre for Biological Sciences, Bangalore, India
    Competing interests
    The authors declare that no competing interests exist.
  4. Anjana Badrinarayanan

    Biochemistry, microbiology, National Centre for Biological Sciences, Bangalore, India
    For correspondence
    anjana@ncbs.res.in
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5520-2134

Funding

Human Frontier of Sciences Programme (00051/ 2017-C)

  • Anjana Badrinarayanan

Department of Atomic Energy, Government of India (12-R&D-TFR-5.04-0800)

  • Anjana Badrinarayanan

Department of Science and Technology, Ministry of Science and Technology, India (PDF/2018/001164)

  • Asha Mary Joseph

Department of Biotechnology, Ministry of Science and Technology, India (IYBA)

  • Anjana Badrinarayanan

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

Reviewing Editor

  1. Maria Spies, University of Iowa, United States

Version history

  1. Received: February 15, 2021
  2. Accepted: April 14, 2021
  3. Accepted Manuscript published: April 15, 2021 (version 1)
  4. Version of Record published: May 6, 2021 (version 2)

Copyright

© 2021, Joseph 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. Asha Mary Joseph
  2. Saheli Daw
  3. Ismath Sadhir
  4. Anjana Badrinarayanan
(2021)
Coordination between nucleotide excision repair and specialized polymerase DnaE2 action enables DNA damage survival in non-replicating bacteria
eLife 10:e67552.
https://doi.org/10.7554/eLife.67552

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https://doi.org/10.7554/eLife.67552

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