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Systematic and quantitative view of the antiviral arsenal of prokaryotes

Author

Listed:
  • Florian Tesson

    (Université de Paris, IAME, UMR 1137, INSERM
    SEED, U1284, INSERM, Université de Paris)

  • Alexandre Hervé

    (Independent Researcher)

  • Ernest Mordret

    (SEED, U1284, INSERM, Université de Paris)

  • Marie Touchon

    (Institut Pasteur, Université de Paris, CNRS, UMR3525, Microbial Evolutionary Genomics)

  • Camille d’Humières

    (Université de Paris, IAME, UMR 1137, INSERM)

  • Jean Cury

    (SEED, U1284, INSERM, Université de Paris
    Université Paris-Saclay, CNRS, INRIA, Laboratoire Interdisciplinaire des Sciences du Numérique, UMR)

  • Aude Bernheim

    (Université de Paris, IAME, UMR 1137, INSERM
    SEED, U1284, INSERM, Université de Paris)

Abstract

Bacteria and archaea have developed multiple antiviral mechanisms, and genomic evidence indicates that several of these antiviral systems co-occur in the same strain. Here, we introduce DefenseFinder, a tool that automatically detects known antiviral systems in prokaryotic genomes. We use DefenseFinder to analyse 21000 fully sequenced prokaryotic genomes, and find that antiviral strategies vary drastically between phyla, species and strains. Variations in composition of antiviral systems correlate with genome size, viral threat, and lifestyle traits. DefenseFinder will facilitate large-scale genomic analysis of antiviral defense systems and the study of host-virus interactions in prokaryotes.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30269-9
    DOI: 10.1038/s41467-022-30269-9
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    References listed on IDEAS

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    4. Bogna J. Smug & Krzysztof Szczepaniak & Eduardo P. C. Rocha & Stanislaw Dunin-Horkawicz & Rafał J. Mostowy, 2023. "Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    5. 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.
    6. Shao-Ming Gao & Han-Lan Fei & Qi Li & Li-Ying Lan & Li-Nan Huang & Peng-Fei Fan, 2024. "Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Jan D. Brüwer & Chandni Sidhu & Yanlin Zhao & Andreas Eich & Leonard Rößler & Luis H. Orellana & Bernhard M. Fuchs, 2024. "Globally occurring pelagiphage infections create ribosome-deprived cells," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    8. Motaher Hossain & Barbaros Aslan & Asma Hatoum-Aslan, 2024. "Tandem mobilization of anti-phage defenses alongside SCCmec elements in staphylococci," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    9. Dimitri Boeckaerts & Michiel Stock & Celia Ferriol-González & Jesús Oteo-Iglesias & Rafael Sanjuán & Pilar Domingo-Calap & Bernard Baets & Yves Briers, 2024. "Prediction of Klebsiella phage-host specificity at the strain level," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    10. Rubén Barcia-Cruz & David Goudenège & Jorge A. Moura de Sousa & Damien Piel & Martial Marbouty & Eduardo P. C. Rocha & Frédérique Roux, 2024. "Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    11. Lingchen He & Laura Miguel-Romero & Jonasz B. Patkowski & Nasser Alqurainy & Eduardo P. C. Rocha & Tiago R. D. Costa & Alfred Fillol-Salom & José R. Penadés, 2024. "Tail assembly interference is a common strategy in bacterial antiviral defenses," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
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    13. Danielle Miller & Adi Stern & David Burstein, 2022. "Deciphering microbial gene function using natural language processing," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    14. Tom J. Arrowsmith & Xibing Xu & Shangze Xu & Ben Usher & Peter Stokes & Megan Guest & Agnieszka K. Bronowska & Pierre Genevaux & Tim R. Blower, 2024. "Inducible auto-phosphorylation regulates a widespread family of nucleotidyltransferase toxins," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    15. Eugen Pfeifer & Eduardo P. C. Rocha, 2024. "Phage-plasmids promote recombination and emergence of phages and plasmids," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    16. Xiangkai Zhen & Biao Zhou & Zihe Liu & Xurong Wang & Heyu Zhao & Shuxian Wu & Zekai Li & Jiamin liang & Wanyue Zhang & Qingjian Zhu & Jun He & Xiaoli Xiong & Songying Ouyang, 2024. "Mechanistic basis for the allosteric activation of NADase activity in the Sir2-HerA antiphage defense system," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    17. Carolien Bastiaanssen & Pilar Bobadilla Ugarte & Kijun Kim & Giada Finocchio & Yanlei Feng & Todd A. Anzelon & Stephan Köstlbacher & Daniel Tamarit & Thijs J. G. Ettema & Martin Jinek & Ian J. MacRae , 2024. "RNA-guided RNA silencing by an Asgard archaeal Argonaute," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    18. Angelina Beavogui & Auriane Lacroix & Nicolas Wiart & Julie Poulain & Tom O. Delmont & Lucas Paoli & Patrick Wincker & Pedro H. Oliveira, 2024. "The defensome of complex bacterial communities," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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