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Insertion sequence transposition inactivates CRISPR-Cas immunity

Author

Listed:
  • Yong Sheng

    (Shanghai Jiao Tong University)

  • Hengyu Wang

    (Shanghai Jiao Tong University)

  • Yixin Ou

    (Shanghai Jiao Tong University
    Haihe Laboratory of Synthetic Biology)

  • Yingying Wu

    (Shanghai Jiao Tong University
    Shanghai Academy of Agricultural Sciences)

  • Wei Ding

    (Shanghai Jiao Tong University)

  • Meifeng Tao

    (Shanghai Jiao Tong University
    Haihe Laboratory of Synthetic Biology)

  • Shuangjun Lin

    (Shanghai Jiao Tong University
    Haihe Laboratory of Synthetic Biology)

  • Zixin Deng

    (Shanghai Jiao Tong University
    Haihe Laboratory of Synthetic Biology)

  • Linquan Bai

    (Shanghai Jiao Tong University)

  • Qianjin Kang

    (Shanghai Jiao Tong University
    Haihe Laboratory of Synthetic Biology)

Abstract

CRISPR-Cas immunity systems safeguard prokaryotic genomes by inhibiting the invasion of mobile genetic elements. Here, we screened prokaryotic genomic sequences and identified multiple natural transpositions of insertion sequences (ISs) into cas genes, thus inactivating CRISPR-Cas defenses. We then generated an IS-trapping system, using Escherichia coli strains with various ISs and an inducible cas nuclease, to monitor IS insertions into cas genes following the induction of double-strand DNA breakage as a physiological host stress. We identified multiple events mediated by different ISs, especially IS1 and IS10, displaying substantial relaxed target specificity. IS transposition into cas was maintained in the presence of DNA repair machinery, and transposition into other host defense systems was also detected. Our findings highlight the potential of ISs to counter CRISPR activity, thus increasing bacterial susceptibility to foreign DNA invasion.

Suggested Citation

  • Yong Sheng & Hengyu Wang & Yixin Ou & Yingying Wu & Wei Ding & Meifeng Tao & Shuangjun Lin & Zixin Deng & Linquan Bai & Qianjin Kang, 2023. "Insertion sequence transposition inactivates CRISPR-Cas immunity," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39964-7
    DOI: 10.1038/s41467-023-39964-7
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    References listed on IDEAS

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    1. Florian Tesson & Alexandre Hervé & Ernest Mordret & Marie Touchon & Camille d’Humières & Jean Cury & Aude Bernheim, 2022. "Systematic and quantitative view of the antiviral arsenal of prokaryotes," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    2. Jessika Consuegra & Joël Gaffé & Richard E. Lenski & Thomas Hindré & Jeffrey E. Barrick & Olivier Tenaillon & Dominique Schneider, 2021. "Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
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