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Induction and suppression of antiviral RNA interference by influenza A virus in mammalian cells

Nature Microbiology volume 2, Article number: 16250 (2016) | Download Citation

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Abstract

Influenza A virus (IAV) causes annual epidemics and occasional pandemics, and is one of the best-characterized human RNA viral pathogens1. However, a physiologically relevant role for the RNA interference (RNAi) suppressor activity of the IAV non-structural protein 1 (NS1), reported over a decade ago2, remains unknown3. Plant and insect viruses have evolved diverse virulence proteins to suppress RNAi as their hosts produce virus-derived small interfering RNAs (siRNAs) that direct specific antiviral defence4,​5,​6,​7 by an RNAi mechanism dependent on the slicing activity of Argonaute proteins (AGOs)8,9. Recent studies have documented induction and suppression of antiviral RNAi in mouse embryonic stem cells and suckling mice10,11. However, it is still under debate whether infection by IAV or any other RNA virus that infects humans induces and/or suppresses antiviral RNAi in mature mammalian somatic cells12,​13,​14,​15,​16,​17,​18,​19,​20,​21. Here, we demonstrate that mature human somatic cells produce abundant virus-derived siRNAs co-immunoprecipitated with AGOs in response to IAV infection. We show that the biogenesis of viral siRNAs from IAV double-stranded RNA (dsRNA) precursors in infected cells is mediated by wild-type human Dicer and potently suppressed by both NS1 of IAV as well as virion protein 35 (VP35) of Ebola and Marburg filoviruses. We further demonstrate that the slicing catalytic activity of AGO2 inhibits IAV and other RNA viruses in mature mammalian cells, in an interferon-independent fashion. Altogether, our work shows that IAV infection induces and suppresses antiviral RNAi in differentiated mammalian somatic cells.

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  • 14 July 2017

    In the PDF version of this article previously published, the year of publication provided in the footer of each page and in the 'How to cite' section was erroneously given as 2017, it should have been 2016. This error has now been corrected. The HTML version of the article was not affected.

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Acknowledgements

The authors thank L.A. Ball, C. Basler, B.R. Cullen, A. Garcia-Sastre, C. Rice, M. McDonald, K.L. Johnson, Q. Liu and P. Palese for providing materials, A. Tarakhovsky for scientific discussions and support, and F. Uhl and A.E. Handte-Reinecker for technical assistance. G. Hannon provided Ago2D587A MEF lines. This study was supported by NIH grants R01AI107087 (to K.L.J.), MGH Executive Committee on Research (ECOR) funds (to K.L.J.), R01AI52447 (to S.W.D.) and R56AI110579 (to S.W.D.), CNAS of UC Riverside (to S.W.D.), AI113333 and DK068181 (to H.C.R.), a Department of Defense PRCRP fellowship CA120212 (to S.C.) and NHMRC grants 1027020 and 1083596 (to P.H.).

Author information

Author notes

    • Yang Li
    • , Megha Basavappa
    • , Jinfeng Lu
    •  & Shuwei Dong

    These authors contributed equally to this work.

Affiliations

  1. Department of Plant Pathology & Microbiology, and Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA

    • Yang Li
    • , Jinfeng Lu
    • , Shuwei Dong
    • , Yanhong Han
    • , Wan-Xiang Li
    •  & Shou-Wei Ding
  2. State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China

    • Yang Li
  3. Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA

    • Megha Basavappa
    • , D. Alexander Cronkite
    • , John T. Prior
    • , Hans-Christian Reinecker
    •  & Kate L. Jeffrey
  4. Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, California 92521, USA

    • Jinfeng Lu
    •  & Shou-Wei Ding
  5. Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, Victoria 3168, Australia

    • Paul Hertzog
  6. Massachusetts General Hospital, Cancer Center and Center for Regenerative Medicine and Harvard Stem Cell Institute, 185 Cambridge Street, Boston, Massachusetts 02114, USA

    • Sihem Cheloufi
  7. Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521, USA

    • Fedor V. Karginov

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Contributions

Y.L. and S.D. performed all virus infection experiments in 293T, A549 and Vero cells. M.B. performed and analysed all virus infection experiments in Ago2D597A cells. J.L. performed all bioinformatic analyses of small RNA libraries. Y.H., W.-X.L. and F.V.K. assisted with cloning of small RNAs. D.A.C. and J.T.P. assisted with viral infections. H.C.R and P.H. provided reagents and interpreted results. S.C. provided Ago2D597A MEFs. S.W.D. and K.L.J conceived of the study, designed experiments, interpreted results and wrote the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Shou-Wei Ding or Kate L. Jeffrey.

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    Supplementary Information

    Supplementary Tables 1 and 2, Supplementary Figures 1–11.

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DOI

https://doi.org/10.1038/nmicrobiol.2016.250