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Discovery of the widespread site-specific single-stranded nuclease family Ssn

Author

Listed:
  • Martin Chenal

    (Bacterial Symbionts Evolution)

  • Alex Rivera-Millot

    (Bacterial Symbionts Evolution)

  • Luke B. Harrison

    (Bacterial Symbionts Evolution)

  • Ahmed S. Khairalla

    (Bacterial Symbionts Evolution
    University of Regina)

  • Cecilia Nieves

    (Bacterial Symbionts Evolution)

  • Ève Bernet

    (Bacterial Symbionts Evolution)

  • Mansoore Esmaili

    (Bacterial Symbionts Evolution)

  • Manel Belkhir

    (Bacterial Symbionts Evolution)

  • Jonathan Perreault

    (INRS-Centre Armand-Frappier Santé Biotechnologie)

  • Frédéric J. Veyrier

    (Bacterial Symbionts Evolution)

Abstract

Site-specific endonucleases that exclusively cut single-stranded DNA have hitherto never been described and constitute a barrier to the development of ssDNA-based technologies. We identify and characterize one such family, from the GIY-YIG superfamily, of widely distributed site-specific single-stranded nucleases (Ssn) exhibiting unique ssDNA cleavage properties. By first comprehensively studying the Ssn homolog from Neisseria meningitidis, we demonstrate that it interacts specifically with a sequence (called NTS) present in hundreds of copies and surrounding important genes in pathogenic Neisseria. In this species, NTS/Ssn interactions modulate natural transformation and thus constitute an additional mechanism shaping genome dynamics. We further identify thousands of Ssn homologs and demonstrate, in vitro, a range of Ssn nuclease specificities for their corresponding sequence. We demonstrate proofs of concept for applications including ssDNA detection and digestion of ssDNA from RCA. This discovery and its applications set the stage for the development of innovative ssDNA-based molecular tools and technologies.

Suggested Citation

  • Martin Chenal & Alex Rivera-Millot & Luke B. Harrison & Ahmed S. Khairalla & Cecilia Nieves & Ève Bernet & Mansoore Esmaili & Manel Belkhir & Jonathan Perreault & Frédéric J. Veyrier, 2025. "Discovery of the widespread site-specific single-stranded nuclease family Ssn," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-57514-1
    DOI: 10.1038/s41467-025-57514-1
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    References listed on IDEAS

    as
    1. Martin C Frith & Neil F W Saunders & Bostjan Kobe & Timothy L Bailey, 2008. "Discovering Sequence Motifs with Arbitrary Insertions and Deletions," PLOS Computational Biology, Public Library of Science, vol. 4(5), pages 1-12, May.
    2. J. Parkhill & M. Achtman & K. D. James & S. D. Bentley & C. Churcher & S. R. Klee & G. Morelli & D. Basham & D. Brown & T. Chillingworth & R. M. Davies & P. Davis & K. Devlin & T. Feltwell & N. Hamlin, 2000. "Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491," Nature, Nature, vol. 404(6777), pages 502-506, March.
    Full references (including those not matched with items on IDEAS)

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