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IFIT1 is an antiviral protein that recognizes 5′-triphosphate RNA

Nature Immunology volume 12, pages 624–630 (2011)Cite this article

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Abstract

Antiviral innate immunity relies on the recognition of microbial structures. One such structure is viral RNA that carries a triphosphate group on its 5′ terminus (PPP-RNA). By an affinity proteomics approach with PPP-RNA as the 'bait', we found that the antiviral protein IFIT1 (interferon-induced protein with tetratricopeptide repeats 1) mediated binding of a larger protein complex containing other IFIT family members. IFIT1 bound PPP-RNA with nanomolar affinity and required the arginine at position 187 in a highly charged carboxy-terminal groove of the protein. In the absence of IFIT1, the growth and pathogenicity of viruses containing PPP-RNA was much greater. In contrast, IFIT proteins were dispensable for the clearance of pathogens that did not generate PPP-RNA. On the basis of this specificity and the great abundance of IFIT proteins after infection, we propose that the IFIT complex antagonizes viruses by sequestering specific viral nucleic acids.

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Figure 1: Identification of an IFN-α/β-induced IFIT-containing complex as a PPP-RNA-binding entity.
Figure 2: Formation of a complex containing IFIT proteins.
Figure 3: Triphosphate-dependent RNA-binding of IFIT1 requires an arginine at position 187.
Figure 4: IFIT1 sequesters PPP-RNA in vitro.
Figure 5: Influence of RNA-mediated interference of IFIT on virus growth.
Figure 6: IFIT1 is needed to contain virus growth and in vivo pathogenicity.

References

  1. Akira, S., Uematsu, S. & Takeuchi, O. Pathogen recognition and innate immunity. Cell 124, 783–801 (2006).

    Article  CAS  Google Scholar 

  2. Pichlmair, A. & Reis e Sousa, C. Innate recognition of viruses. Immunity 27, 370–383 (2007).

    Article  CAS  Google Scholar 

  3. Pichlmair, A. et al. RIG-I-mediated antiviral responses to single-stranded RNA bearing 5′-phosphates. Science 314, 997–1001 (2006).

    Article  CAS  Google Scholar 

  4. Hornung, V. et al. 5′-Triphosphate RNA is the ligand for RIG-I. Science 314, 994–997 (2006).

    Article  Google Scholar 

  5. Yoneyama, M. & Fujita, T. RNA recognition and signal transduction by RIG-I-like receptors. Immunol. Rev. 227, 54–65 (2009).

    Article  CAS  Google Scholar 

  6. Schlee, M. et al. Approaching the RNA ligand for RIG-I? Immunol. Rev. 227, 66–74 (2009).

    Article  CAS  Google Scholar 

  7. Bowie, A.G. & Unterholzner, L. Viral evasion and subversion of pattern-recognition receptor signalling. Natl. Rev. 8, 911–922 (2008).

    Article  CAS  Google Scholar 

  8. Schmolke, M. & Garcia-Sastre, A. Evasion of innate and adaptive immune responses by influenza A virus. Cell. Microbiol. 12, 873–880 (2010).

    Article  CAS  Google Scholar 

  9. Kato, H. et al. Length-dependent recognition of double-stranded ribonucleic acids by retinoic acid-inducible gene-I and melanoma differentiation-associated gene 5. J. Exp. Med. 205, 1601–1610 (2008).

    Article  CAS  Google Scholar 

  10. Sadler, A.J. & Williams, B.R. Interferon-inducible antiviral effectors. Nat. Rev. Immunol. 8, 559–568 (2008).

    Article  CAS  Google Scholar 

  11. Weber, F., Wagner, V., Rasmussen, S.B., Hartmann, R. & Paludan, S.R. Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses. J. Virol. 80, 5059–5064 (2006).

    Article  CAS  Google Scholar 

  12. Gay, N.J., Gangloff, M. & O'Neill, L.A. What the Myddosome structure tells us about the initiation of innate immunity. Trends Immunol. 32, 104–109 (2011).

    Article  CAS  Google Scholar 

  13. Ronald, P.C. & Beutler, B. Plant and animal sensors of conserved microbial signatures. Science 330, 1061–1064 (2010).

    Article  CAS  Google Scholar 

  14. Daffis, S. et al. 2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members. Nature 468, 452–456 (2010).

    Article  CAS  Google Scholar 

  15. Burckstummer, T. et al. An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome. Nat. Immunol. 10, 266–272 (2009).

    Article  Google Scholar 

  16. Ishihama, Y. et al. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 4, 1265–1272 (2005).

    Article  CAS  Google Scholar 

  17. Guo, J., Hui, D.J., Merrick, W.C. & Sen, G.C. A new pathway of translational regulation mediated by eukaryotic initiation factor 3. EMBO J. 19, 6891–6899 (2000).

    Article  CAS  Google Scholar 

  18. Papin, J.A., Hunter, T., Palsson, B.O. & Subramaniam, S. Reconstruction of cellular signalling networks and analysis of their properties. Nat. Rev. Mol. Cell Biol. 6, 99–111 (2005).

    Article  CAS  Google Scholar 

  19. Kocher, T. & Superti-Furga, G. Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat. Methods 4, 807–815 (2007).

    Article  Google Scholar 

  20. Glatter, T., Wepf, A., Aebersold, R. & Gstaiger, M. An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol. Syst. Biol. 5, 237 (2009).

    Article  Google Scholar 

  21. Aranda, B. et al. The IntAct molecular interaction database in 2010. Nucleic Acids Res. 38, D525–D531 (2010).

    Article  CAS  Google Scholar 

  22. Reichelt, M., Stertz, S., Krijnse-Locker, J., Haller, O. & Kochs, G. Missorting of LaCrosse virus nucleocapsid protein by the interferon-induced MxA GTPase involves smooth ER membranes. Traffic 5, 772–784 (2004).

    Article  CAS  Google Scholar 

  23. Jinek, M. et al. The superhelical TPR-repeat domain of O-linked GlcNAc transferase exhibits structural similarities to importin-α. Nat. Struct. Mol. Biol. 11, 1001–1007 (2004).

    Article  CAS  Google Scholar 

  24. D'Andrea, L.D. & Regan, L. TPR proteins: the versatile helix. Trends Biochem. Sci. 28, 655–662 (2003).

    Article  CAS  Google Scholar 

  25. Fensterl, V., White, C.L., Yamashita, M. & Sen, G.C. Novel characteristics of the function and induction of murine p56 family proteins. J. Virol. 82, 11045–11053 (2008).

    Article  CAS  Google Scholar 

  26. Wang, D.Y., Kumar, S. & Hedges, S.B. Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc. R. Soc. Lond. B 266, 163–171 (1999).

    Article  CAS  Google Scholar 

  27. Fensterl, V. & Sen, G.C. The ISG56/IFIT1 gene family. J. Interferon Cytokine Res. 31, 71–78 (2011).

    Article  CAS  Google Scholar 

  28. Racaniello, V.R. in Fields Virology (eds. Knipe, D. et al.) 685–722 (Lippincott Williams & Wilkins, Philadelphia, 2001).

  29. Takaoka, A. et al. DAI (DLM-1/ZBP1) is a cytosolic DNA sensor and an activator of innate immune response. Nature 448, 501–505 (2007).

    Article  CAS  Google Scholar 

  30. Berchtold, S. et al. Forced IFIT-2 expression represses LPS induced TNF-alpha expression at posttranscriptional levels. BMC Immunol. 9, 75 (2008).

    Article  Google Scholar 

  31. Li, Y. et al. ISG56 is a negative-feedback regulator of virus-triggered signaling and cellular antiviral response. Proc. Natl. Acad. Sci. USA 106, 7945–7950 (2009).

    Article  CAS  Google Scholar 

  32. Sauer, J.D. et al. Listeria monocytogenes triggers AIM2-mediated pyroptosis upon infrequent bacteriolysis in the macrophage cytosol. Cell Host Microbe 7, 412–419 (2010).

    Article  CAS  Google Scholar 

  33. Stetson, D.B. & Medzhitov, R. Recognition of cytosolic DNA activates an IRF3-dependent innate immune response. Immunity 24, 93–103 (2006).

    Article  CAS  Google Scholar 

  34. Kochs, G., Janzen, C., Hohenberg, H. & Haller, O. Antivirally active MxA protein sequesters La Crosse virus nucleocapsid protein into perinuclear complexes. Proc. Natl. Acad. Sci. USA 99, 3153–3158 (2002).

    Article  CAS  Google Scholar 

  35. Umbach, J.L., Yen, H.L., Poon, L.L. & Cullen, B.R. Influenza A virus expresses high levels of an unusual class of small viral leader RNAs in infected cells. MBio 1, e00204-10 (2010).

    Article  Google Scholar 

  36. Stojdl, D.F. et al. VSV strains with defects in their ability to shutdown innate immunity are potent systemic anti-cancer agents. Cancer Cell 4, 263–275 (2003).

    Article  CAS  Google Scholar 

  37. Dittmann, J. et al. Influenza A virus strains differ in sensitivity to the antiviral action of Mx-GTPase. J. Virol. 82, 3624–3631 (2008).

    Article  CAS  Google Scholar 

  38. Pichlmair, A. et al. Activation of MDA5 requires higher-order RNA structures generated during virus infection. J. Virol. 83, 10761–10769 (2009).

    Article  CAS  Google Scholar 

  39. Boritz, E., Gerlach, J., Johnson, J.E. & Rose, J.K. Replication-competent rhabdoviruses with human immunodeficiency virus type 1 coats and green fluorescent protein: entry by a pH-independent pathway. J. Virol. 73, 6937–6945 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Habjan, M. et al. NSs protein of rift valley fever virus induces the specific degradation of the double-stranded RNA-dependent protein kinase. J. Virol. 83, 4365–4375 (2009).

    Article  CAS  Google Scholar 

  41. Reutterer, B. et al. Type I IFN are host modulators of strain-specific Listeria monocytogenes virulence. Cell. Microbiol. 10, 1116–1129 (2008).

    Article  CAS  Google Scholar 

  42. Wu, C.H. et al. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 34, D187–D191 (2006).

    Article  CAS  Google Scholar 

  43. Perkins, D.N., Pappin, D.J., Creasy, D.M. & Cottrell, J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567 (1999).

    Article  CAS  Google Scholar 

  44. Colinge, J., Masselot, A., Giron, M., Dessingy, T. & Magnin, J. OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 3, 1454–1463 (2003).

    Article  CAS  Google Scholar 

  45. Roy, A., Kucukural, A. & Zhang, Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 5, 725–738 (2010).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank the NIH Knockout Mouse Project for embryonic stem cells with a targeted Ifit1 allele; L. Andersen for population expansion of embryonic stem cells; K. Kandasamy for bioinformatics support; G. Kochs (University of Freiburg) for plasmid Pol-I FF-luc; T. Decker (University of Vienna) for IRF3-deficient MEFs. Supported by the Austrian Academy of Sciences, the European Research Council (G.S.-F.), the European Molecular Biology Organization (C.L.B.; and ATLF 463-2008 to A.P.), the European Union (Marie Curie Fellowship to C.L.B.), Deutsche Forschungsgemeinschaft (We 2616/5-2 and SFB 593/B13 to F.W.), the Austrian Federal Ministry for Science and Genome Research in the Research Austria program Austromouse (T.R. and M.M.), the Bioinformatics Integration Network (J.C.) and the Austrian Science Fund (FWF SFB F28 to M.M.).

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Authors and Affiliations

  1. Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria

    Andreas Pichlmair, Carol-Ann Eberle, Maria W Górna, Christoph L Baumann, Thomas R Burkard, Tilmann Bürckstümmer, Adrijana Stefanovic, Keiryn L Bennett, Jacques Colinge & Giulio Superti-Furga

  2. Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria

    Caroline Lassnig & Mathias Müller

  3. Biomodels Austria, University of Veterinary Medicine, Vienna, Austria

    Caroline Lassnig, Thomas Rülicke & Mathias Müller

  4. Department of Clinical Pathology, Medical University of Vienna, Vienna, Austria

    Sigurd Krieger

  5. Institute of Laboratory Animal Science, University of Veterinary Medicine, Vienna, Austria

    Thomas Rülicke

  6. Institute for Virology, Philipps University Marburg, Germany

    Friedemann Weber

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  1. Andreas Pichlmair
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Contributions

A.P., C.-A.E., M.W.G., C.L.B., A.S., S.K. and F.W. did experiments; C.L. and M.M. did in vivo experiments; T.B. provided reagents; T.R.B. and J.C. did bioinformatic analysis; K.L.B. did mass spectrometry; T.R. generated the IFIT1-deficient mouse; and A.P. and G.S.-F. designed the overall strategy and wrote the paper.

Corresponding author

Correspondence to Giulio Superti-Furga.

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Pichlmair, A., Lassnig, C., Eberle, CA. et al. IFIT1 is an antiviral protein that recognizes 5′-triphosphate RNA. Nat Immunol 12, 624–630 (2011). https://doi.org/10.1038/ni.2048

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