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Nucleotide resolution mapping of influenza A virus nucleoprotein-RNA interactions reveals RNA features required for replication

Author

Listed:
  • Graham D. Williams

    (Department of Medicine at Washington University School of Medicine
    Department of Molecular Microbiology at Washington University School of Medicine)

  • Dana Townsend

    (Department of Molecular Microbiology at Washington University School of Medicine)

  • Kristine M. Wylie

    (Department of Pediatrics at Washington University School of Medicine
    The McDonnell Genome Institute at Washington University School of Medicine)

  • Preston J. Kim

    (Department of Pathology and Immunology at Washington University School of Medicine)

  • Gaya K. Amarasinghe

    (Department of Pathology and Immunology at Washington University School of Medicine
    Department of Biochemistry and Biophysics at Washington University School of Medicine)

  • Sebla B. Kutluay

    (Department of Molecular Microbiology at Washington University School of Medicine)

  • Adrianus C. M. Boon

    (Department of Medicine at Washington University School of Medicine
    Department of Molecular Microbiology at Washington University School of Medicine
    Department of Pathology and Immunology at Washington University School of Medicine)

Abstract

Influenza A virus nucleoprotein (NP) association with viral RNA (vRNA) is essential for packaging, but the pattern of NP binding to vRNA is unclear. Here we applied photoactivatable ribonucleoside enhanced cross-linking and immunoprecipitation (PAR-CLIP) to assess the native-state of NP–vRNA interactions in infected human cells. NP binds short fragments of RNA (~12 nucleotides) non-uniformly and without apparent sequence specificity. Moreover, NP binding is reduced at specific locations within the viral genome, including regions previously identified as required for viral genome segment packaging. Synonymous mutations designed to alter the predicted RNA structures in these low-NP-binding regions impact genome packaging and result in virus attenuation, whereas control mutations or mutagenesis of NP-bound regions have no effect. Finally, we demonstrate that the sequence conservation of low-NP-binding regions is required in multiple genome segments for propagation of diverse mammalian and avian IAV in host cells.

Suggested Citation

  • Graham D. Williams & Dana Townsend & Kristine M. Wylie & Preston J. Kim & Gaya K. Amarasinghe & Sebla B. Kutluay & Adrianus C. M. Boon, 2018. "Nucleotide resolution mapping of influenza A virus nucleoprotein-RNA interactions reveals RNA features required for replication," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-02886-w
    DOI: 10.1038/s41467-018-02886-w
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    Cited by:

    1. Lyudmila Shalamova & Patrick Barth & Matthew J. Pickin & Kiriaki Kouti & Benjamin Ott & Katharina Humpert & Stefan Janssen & Gema Lorenzo & Alejandro Brun & Alexander Goesmann & Torsten Hain & Roland , 2024. "Nucleocapsids of the Rift Valley fever virus ambisense S segment contain an exposed RNA element in the center that overlaps with the intergenic region," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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