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Influenza virus mRNA trafficking through host nuclear speckles

Nature Microbiology volume 1, Article number: 16069 (2016) Cite this article

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A Corrigendum to this article was published on 09 January 2017

Abstract

Influenza A virus is a human pathogen with a genome composed of eight viral RNA segments that replicate in the nucleus. Two viral mRNAs are alternatively spliced. The unspliced M1 mRNA is translated into the matrix M1 protein, while the ion channel M2 protein is generated after alternative splicing. These proteins are critical mediators of viral trafficking and budding. We show that the influenza virus uses nuclear speckles to promote post-transcriptional splicing of its M1 mRNA. We assign previously unknown roles for the viral NS1 protein and cellular factors to an intranuclear trafficking pathway that targets the viral M1 mRNA to nuclear speckles, mediates splicing at these nuclear bodies and exports the spliced M2 mRNA from the nucleus. Given that nuclear speckles are storage sites for splicing factors, which leave these sites to splice cellular pre-mRNAs at transcribing genes, we reveal a functional subversion of nuclear speckles to promote viral gene expression.

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Figure 1: Influenza M mRNA is localized at nuclear speckles.
Figure 2: M1 mRNA and spliced M2 mRNA accumulate at nuclear speckles after transcription.
Figure 3: Viral NS1 protein promotes M1 mRNA splicing at nuclear speckles and nuclear export.
Figure 4: M mRNA splicing at nuclear speckles is mediated by host factors NS1-BP, hnRNP K and SON.
Figure 5: Aly/REF and UAP56 depletion inhibits M1 and M2 mRNA nuclear export and mediates speckle dependent M1 to M2 splicing enhancement.
Figure 6: Nuclear speckle assembly factor SON interacts with M1 mRNA and mediators of M1 mRNA splicing.

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Acknowledgements

Funding was provided by National Institutes of Health (NIH) grants R01 GM113874-01, AI079110, R01 AI089539 and CPRIT RP121003–RP120718-P2 (to B.F.), NIH T32CA124334 (to A.M.), the Center for Research in Influenza Pathogenesis (CRIP) and the NIAID-funded Center of Excellence for Influenza Research and Surveillance (CEIRS, contract no. HHSN272201400008C to A.-G.S.), and NIH R21 AI119304 (to A.G.-S. and B.M.A.F.). The authors thank R. Cadagan and K. Phelps (Live Cell Imaging Core Facility) for assistance.

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Authors and Affiliations

  1. Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, 75390-9039, Texas, USA

    Amir Mor, Alexander White, Ke Zhang, Matthew Esparza & Beatriz M. A. Fontoura

  2. Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, 19104-6059, Pennsylvania, USA

    Matthew Thompson & Kristen W. Lynch

  3. Department of Microbiology, New York, 10029, New York, USA

    Raquel Muñoz-Moreno & Adolfo García-Sastre

  4. Global Health and Emerging Pathogens Institute, New York, 10029, New York, USA

    Raquel Muñoz-Moreno & Adolfo García-Sastre

  5. Department of Chemistry, University of Pittsburgh, Pittsburgh, 15260, Pennsylvania, USA

    Kazunori Koide

  6. Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, 10029, New York, USA

    Adolfo García-Sastre

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Contributions

A.M., A.W., K.Z. and M.T. designed and conducted experiments. R.M.-M. conducted experiments and generated important reagents. M.E. conducted experiments. K.K. generated important reagent. K.W.L. designed experiments. A.M., A.G.-S. and B.M.A.F. designed experiments and wrote the paper.

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Correspondence to Beatriz M. A. Fontoura.

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Supplementary information

Supplementary information

Supplementary Figures 1–7, Supplementary Video legend, Supplementary Methods and Supplementary References. (PDF 2119 kb)

Supplementary Video 1

M mRNA is localized at nuclear speckles. (AVI 222 kb)

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Mor, A., White, A., Zhang, K. et al. Influenza virus mRNA trafficking through host nuclear speckles. Nat Microbiol 1, 16069 (2016). https://doi.org/10.1038/nmicrobiol.2016.69

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