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The YoaA-χ helicase modulates the dynamics of single-stranded DNA binding protein on DNA

Author

Listed:
  • Savannah J. Weeks-Pollenz

    (University of Florida)

  • Matthew J. Petrides

    (University of Florida)

  • Kaylie A. Padgett-Pagliai

    (University of Florida)

  • Robert Davis

    (University of Florida)

  • Kathryn K. Harris

    (University of Florida)

  • Linda B. Bloom

    (University of Florida)

Abstract

The Escherichia coli helicase, YoaA, and DNA polymerase III subunit, χ, form a complex (YoaA-χ) that promotes tolerance to the DNA chain-terminator 3ˈ-azidothymidine (AZT). Single-stranded DNA binding protein (SSB), which accumulates at stalled replication forks, also contributes to AZT tolerance through interactions with χ. Here we show that in vitro, χ mediates interactions between YoaA and SSB that modulate helicase activity in a substrate-specific manner with little effect on overhang DNA but inhibiting unwinding of forked DNA. SSB similarly affects the activity of the YoaA paralog, DinG. Single-molecule experiments show that SSB translocates with YoaA-χ, increasing both the lifetime and frequency of SSB binding events. Mutational analyses show that χ binds at the back of YoaA relative to the direction of translocation supporting a model in which YoaA-χ pulls SSB along DNA as it translocates. To our knowledge, this is the first demonstration of a mechanoenzyme pulling SSB along ssDNA.

Suggested Citation

  • Savannah J. Weeks-Pollenz & Matthew J. Petrides & Kaylie A. Padgett-Pagliai & Robert Davis & Kathryn K. Harris & Linda B. Bloom, 2025. "The YoaA-χ helicase modulates the dynamics of single-stranded DNA binding protein on DNA," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60215-4
    DOI: 10.1038/s41467-025-60215-4
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    References listed on IDEAS

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    1. Josh Abramson & Jonas Adler & Jack Dunger & Richard Evans & Tim Green & Alexander Pritzel & Olaf Ronneberger & Lindsay Willmore & Andrew J. Ballard & Joshua Bambrick & Sebastian W. Bodenstein & David , 2024. "Addendum: Accurate structure prediction of biomolecular interactions with AlphaFold 3," Nature, Nature, vol. 636(8042), pages 4-4, December.
    2. Rahul Roy & Alexander G. Kozlov & Timothy M. Lohman & Taekjip Ha, 2009. "SSB protein diffusion on single-stranded DNA stimulates RecA filament formation," Nature, Nature, vol. 461(7267), pages 1092-1097, October.
    3. Josh Abramson & Jonas Adler & Jack Dunger & Richard Evans & Tim Green & Alexander Pritzel & Olaf Ronneberger & Lindsay Willmore & Andrew J. Ballard & Joshua Bambrick & Sebastian W. Bodenstein & David , 2024. "Accurate structure prediction of biomolecular interactions with AlphaFold 3," Nature, Nature, vol. 630(8016), pages 493-500, June.
    4. Rahul Roy & Alexander G. Kozlov & Timothy M. Lohman & Taekjip Ha, 2009. "Erratum: SSB protein diffusion on single-stranded DNA stimulates RecA filament formation," Nature, Nature, vol. 462(7275), pages 944-944, December.
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