The Shu complex prevents mutagenesis and cytotoxicity of single-strand specific alkylation lesions

  1. Braulio Bonilla
  2. Alexander I Brown
  3. Sarah R Hengel
  4. Kyle S Rapchak
  5. Debra Mitchell
  6. Catherine A Pressimone
  7. Adeola A Fagunloye
  8. Thong T Luong
  9. Reagan A Russell
  10. Rudri K Vyas
  11. Tony M Mertz
  12. Hani S Zaher
  13. Nima Mosammaparast
  14. Ewa P Malc
  15. Piotr A Mieczkowski
  16. Steven Roberts  Is a corresponding author
  17. Kara A Bernstein  Is a corresponding author
  1. University of Pittsburgh School of Medicine, United States
  2. Washington State University, United States
  3. Washington University in St Louis, United States
  4. University of North Carolina Chapel Hill, United States

Abstract

Three-methyl cytosine (3meC) are toxic DNA lesions, blocking base pairing. Bacteria and humans, express members of the AlkB enzymes family, which directly remove 3meC. However, other organisms, including budding yeast, lack this class of enzymes. It remains an unanswered evolutionary question as to how yeast repairs 3meC, particularly in single-stranded DNA. The yeast Shu complex, a conserved homologous recombination factor, aids in preventing replication-associated mutagenesis from DNA base damaging agents such as methyl methanesulfonate (MMS). We found that MMS-treated Shu complex-deficient cells, exhibit a genome-wide increase in A:T and G:C substitutions mutations. The G:C substitutions displayed transcriptional and replicational asymmetries consistent with mutations resulting from 3meC. Ectopic expression of a human AlkB homolog in Shu-deficient yeast rescues MMS-induced growth defects and increased mutagenesis. Thus, our work identifies a novel homologous recombination-based mechanism mediated by the Shu complex for coping with alkylation adducts.

Data availability

All unique mutations identified by DNA sequencing are reported in Supplemental Table 3 and all sequencing reads are reported in Supplemental Table 5. Raw sequencing reads in fastq format have been submitted to the NCBI short read archive under BioProject accession number PRJNA694993.

The following data sets were generated

Article and author information

Author details

  1. Braulio Bonilla

    Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Alexander I Brown

    Molecular Biosciences, Washington State University, Pullman, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Sarah R Hengel

    Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Kyle S Rapchak

    Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Debra Mitchell

    Molecular Biosciences, Washington State University, Pullman, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Catherine A Pressimone

    Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Adeola A Fagunloye

    Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2383-9469
  8. Thong T Luong

    Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Reagan A Russell

    Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Rudri K Vyas

    Molecular Biosciences, Washington State University, Pullman, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Tony M Mertz

    Molecular Biosciences, Washington State University, Pullman, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Hani S Zaher

    Biology, Washington University in St Louis, St. Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7424-3617
  13. Nima Mosammaparast

    Washington University in St Louis, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Ewa P Malc

    Genetics, University of North Carolina Chapel Hill, Chapel Hill, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Piotr A Mieczkowski

    Genetics, University of North Carolina Chapel Hill, Chapel Hill, United States
    Competing interests
    The authors declare that no competing interests exist.
  16. Steven Roberts

    Molecular Biosciences, Washington State University, Pullman, United States
    For correspondence
    steven.roberts2@wsu.edu
    Competing interests
    The authors declare that no competing interests exist.
  17. Kara A Bernstein

    Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
    For correspondence
    karab@pitt.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2247-6459

Funding

National Institutes of Health (ES030335)

  • Kara A Bernstein

National Institutes of Health (CA218112)

  • Steven Roberts

American Cancer Society (129182-RSG-16-043-01-DMC)

  • Kara A Bernstein

American Cancer Society (133947-PF-19-132-01-DMC)

  • Sarah R Hengel

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

Reviewing Editor

  1. Andrés Aguilera, CABIMER, Universidad de Sevilla, Spain

Publication history

  1. Received: March 4, 2021
  2. Preprint posted: April 11, 2021 (view preprint)
  3. Accepted: October 29, 2021
  4. Accepted Manuscript published: November 1, 2021 (version 1)
  5. Version of Record published: November 23, 2021 (version 2)

Copyright

© 2021, Bonilla 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. Braulio Bonilla
  2. Alexander I Brown
  3. Sarah R Hengel
  4. Kyle S Rapchak
  5. Debra Mitchell
  6. Catherine A Pressimone
  7. Adeola A Fagunloye
  8. Thong T Luong
  9. Reagan A Russell
  10. Rudri K Vyas
  11. Tony M Mertz
  12. Hani S Zaher
  13. Nima Mosammaparast
  14. Ewa P Malc
  15. Piotr A Mieczkowski
  16. Steven Roberts
  17. Kara A Bernstein
(2021)
The Shu complex prevents mutagenesis and cytotoxicity of single-strand specific alkylation lesions
eLife 10:e68080.
https://doi.org/10.7554/eLife.68080

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