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Cited by 398interferon and immune responsesImmune Response and InflammationRNA regulation and disease

5′-triphosphate RNA requires base-paired structures to activate antiviral signaling via RIG-I

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Schmidt, Andreas, Schwerd, Tobias, Hamm, Wolfgang, Hellmuth, Johannes C., Cui, Sheng, Wenzel, Michael, Hoffmann, Franziska S., Michallet, Marie-Cecile +4 more·2009·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.0900971106PMC PMC2705279
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Abstract

The ATPase retinoid acid-inducible gene (RIG)-I senses viral RNA in the cytoplasm of infected cells and subsequently activates cellular antiviral defense mechanisms. RIG-I recognizes molecular structures that discriminate viral from host RNA. Here, we show that RIG-I ligands require base-paired structures in conjunction with a free 5′-triphosphate to trigger antiviral signaling. Hitherto unavailable chemically synthesized 5′-triphosphate RNA ligands do not trigger RIG-I-dependent IFN production in cells, and they are unable to trigger the ATPase activity of RIG-I without a base-paired stretch. Consistently, immunostimulatory RNA from cells infected with a virus recognized by RIG-I is sensitive to double-strand, but not single-strand, specific RNases. In vitro, base-paired stretches and the 5′-triphosphate bind to distinct sites of RIG-I and synergize to trigger the induction of signaling competent RIG-I multimers. Strengthening our model of a bipartite molecular pattern for RIG-I activation, we show that the activity of supposedly “single-stranded” 5′-triphosphate RNAs generated by in vitro transcription depends on extended and base-paired by-products inadvertently, but commonly, produced by this method. Together, our findings accurately define a minimal molecular pattern sufficient to activate RIG-I that can be found in viral genomes or transcripts.

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  1. [1]Akira S, Uematsu S, Takeuchi O. Pathogen recognition and innate immunity. Cell. 2006;124:783–801. doi: 10.1016/j.cell.2006.02.015. [DOI] [PubMed] [Google Scholar] · DOI
  2. [2]Andrejeva J, et al. The V proteins of paramyxoviruses bind the IFN-inducible RNA helicase, mda-5, and inhibit its activation of the IFN-beta promoter. Proc Natl Acad Sci USA. 2004;101:17264–17269. doi: 10.1073/pnas.0407639101. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  3. [3]Rothenfusser S, et al. The RNA helicase Lgp2 inhibits TLR-independent sensing of viral replication by retinoic acid-inducible gene-I. J Immunol. 2005;175:5260–5268. doi: 10.4049/jimmunol.175.8.5260. [DOI] [PubMed] [Google Scholar] · DOI
  4. [4]Yoneyama M, et al. The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat Immunol. 2004;5:730–737. doi: 10.1038/ni1087. [DOI] [PubMed] [Google Scholar] · DOI
  5. [5]Samanta M, Iwakiri D, Kanda T, Imaizumi T, Takada K. EB virus-encoded RNAs are recognized by RIG-I and activate signaling to induce type I IFN. EMBO J. 2006;25:4207–4214. doi: 10.1038/sj.emboj.7601314. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  6. [6]Sumpter R, Jr, et al. Regulating intracellular antiviral defense and permissiveness to hepatitis C virus RNA replication through a cellular RNA helicase, RIG-I. J Virol. 2005;79:2689–2699. doi: 10.1128/JVI.79.5.2689-2699.2005. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  7. [7]Hiscott J, Lin R, Nakhaei P, Paz S. MasterCARD: A priceless link to innate immunity. Trends Mol Med. 2006;12:53–56. doi: 10.1016/j.molmed.2005.12.003. [DOI] [PubMed] [Google Scholar] · DOI
  8. [8]Kim DH, et al. Interferon induction by siRNAs and ssRNAs synthesized by phage polymerase. Nat Biotechnol. 2004;22:321–325. doi: 10.1038/nbt940. [DOI] [PubMed] [Google Scholar] · DOI
  9. [9]Hornung V, et al. 5′-Triphosphate RNA is the ligand for RIG-I. Science. 2006;314:994–997. doi: 10.1126/science.1132505. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  10. [11]Cui S, et al. The C-terminal regulatory domain is the RNA 5′-triphosphate sensor of RIG-I. Mol Cell. 2008;29:169–179. doi: 10.1016/j.molcel.2007.10.032. [DOI] [PubMed] [Google Scholar] · DOI
  11. [12]Takahasi K, et al. Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses. Mol Cell. 2008;29:428–440. doi: 10.1016/j.molcel.2007.11.028. [DOI] [PubMed] [Google Scholar] · DOI
  12. [13]Malathi K, Dong B, Gale M, Jr, Silverman RH. Small self-RNA generated by RNase L amplifies antiviral innate immunity. Nature. 2007;448:816–819. doi: 10.1038/nature06042. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  13. [14]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. 2008;205:1601–1610. doi: 10.1084/jem.20080091. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  14. [15]Saito T, Owen DM, Jiang F, Marcotrigiano J, Gale M. Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA. Nature. 2008;454:523–527. doi: 10.1038/nature07106. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  15. [17]Hornung V, et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med. 2005;11:263–270. doi: 10.1038/nm1191. [DOI] [PubMed] [Google Scholar] · DOI
  16. [18]Cazenave C, Uhlenbeck OC. RNA template-directed RNA synthesis by T7 RNA polymerase. Proc Natl Acad Sci USA. 1994;91:6972–6976. doi: 10.1073/pnas.91.15.6972. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  17. [19]Nacheva GA, Berzal-Herranz A. Preventing nondesired RNA-primed RNA extension catalyzed by T7 RNA polymerase. Eur J Biochem. 2003;270:1458–1465. doi: 10.1046/j.1432-1033.2003.03510.x. [DOI] [PubMed] [Google Scholar] · DOI
  18. [20]Behrens SE, Tomei L, De Francesco R. Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus. EMBO J. 1996;15:12–22. [PMC free article] [PubMed] [Google Scholar]
  19. [23]Weber F, Wagner V, Rasmussen SB, Hartmann R, Paludan SR. 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. 2006;80:5059–5064. doi: 10.1128/JVI.80.10.5059-5064.2006. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  20. [24]Schlee M, et al. Approaching the RNA ligand for RIG-I? Immunol Rev. 2009;227:66–74. doi: 10.1111/j.1600-065X.2008.00724.x. [DOI] [PubMed] [Google Scholar] · DOI
  21. [25]Leppert M, Kort L, Kolakofsky D. Further characterization of Sendai virus DI-RNAs: A model for their generation. Cell. 1977;12:539–552. doi: 10.1016/0092-8674(77)90130-1. [DOI] [PubMed] [Google Scholar] · DOI
  22. [26]Zhong W, et al. Nucleoside triphosphatase and RNA helicase activities associated with GB virus B nonstructural protein 3. Virology. 1999;261:216–226. doi: 10.1006/viro.1999.9871. [DOI] [PubMed] [Google Scholar] · DOI
  23. [27]Gitlin L, et al. Essential role of mda-5 in type I IFN responses to polyriboinosinic:polyribocytidylic acid and encephalomyocarditis picornavirus. Proc Natl Acad Sci USA. 2006;103:8459–8464. doi: 10.1073/pnas.0603082103. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  24. [28]Yoneyama M, et al. Shared and unique functions of the DExD/H-box helicases RIG-I, MDA5, and LGP2 in antiviral innate immunity. J Immunol. 2005;175:2851–2858. doi: 10.4049/jimmunol.175.5.2851. [DOI] [PubMed] [Google Scholar] · DOI
  25. [29]Durr H, Flaus A, Owen-Hughes T, Hopfner KP. Snf2 family ATPases and DExx box helicases: Differences and unifying concepts from high-resolution crystal structures. Nucleic Acids Res. 2006;34:4160–4167. doi: 10.1093/nar/gkl540. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  26. [30]Ranjith-Kumar CT, et al. Agonist and antagonist recognition by RIG-I, a cytoplasmic innate immunity receptor. J Biol Chem. 2008;284:1155–1165. doi: 10.1074/jbc.M806219200. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  27. [31]Plumet S, et al. Cytosolic 5′-triphosphate ended viral leader transcript of measles virus as activator of the RIG I-mediated interferon response. PLoS ONE. 2007;2:e279. doi: 10.1371/journal.pone.0000279. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  28. [32]Myong S, et al. Cytosolic viral sensor RIG-I is a 5′-triphosphate-dependent translocase on double-stranded RNA. Science. 2009;323:1070–1074. doi: 10.1126/science.1168352. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI

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Authors
Schmidt, A., Schwerd, T., Hamm, W., Hellmuth, J. C., Cui, S., Wenzel, M., Hoffmann, F. S., Michallet, M.-C., Besch, R., Hopfner, K.-P., Endres, S., & Rothenfusser, S.
Affiliations
  • Ludwig-Maximilians-Universität München (DE)
  • Center for Integrated Protein Science Munich (DE)
  • Department of Biochemistry, University of Lausanne, CH-1066 Epalinges, Switzerland
Corresponding author
Rothenfusser, Simon
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2009-07-21
Volume
106
Issue
29
Pages
12067-12072
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.0900971106
PMC
PMC2705279
OpenAlex
W1969601023
Cited by
398
References
5
Citations by year
2026: 10 · 2025: 9 · 2024: 10 · 2023: 9 · 2022: 15 · 2021: 28 · 2020: 20 · 2019: 23 · 2018: 19 · 2017: 13 · 2016: 21 · 2015: 20 · 2014: 40 · 2013: 29 · 2012: 24
FWCI
17.91
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
Deutsche Forschungsgemeinschaft (GK 1202, DFG GK 1202)
Topics
  • Life Sciences › Immunology and Microbiology › Immunology › interferon and immune responses
  • Life Sciences › Immunology and Microbiology › Immunology › Immune Response and Inflammation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords
RIG-I, 5'-triphosphate RNA, base pairing, antiviral signaling, innate immunity, interferon induction, double-stranded RNA, viral RNA sensing
MeSH terms
Adenosine Triphosphatases, Animals, Binding Sites, Cell Line, Humans, Ligands, Protein Binding, RNA, DNA-Directed RNA Polymerases, Transcription, Genetic, Viral Proteins, Viruses, Signal Transduction, Receptors, Retinoic Acid, Base Pairing, Receptors, Pattern Recognition, Mice, Protein Multimerization

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