A Toll-like receptor–independent antiviral response induced by double-stranded B-form DNA

An Erratum to this article was published on 01 April 2006

This article has been updated

Abstract

The innate immune system recognizes nucleic acids during infection or tissue damage; however, the mechanisms of intracellular recognition of DNA have not been fully elucidated. Here we show that intracellular administration of double-stranded B-form DNA (B-DNA) triggered antiviral responses including production of type I interferons and chemokines independently of Toll-like receptors or the helicase RIG-I. B-DNA activated transcription factor IRF3 and the promoter of the gene encoding interferon-β through a signaling pathway that required the kinases TBK1 and IKKi, whereas there was substantial activation of transcription factor NF-κB independent of both TBK and IKKi. IPS-1, an adaptor molecule linking RIG-I and TBK1, was involved in B-DNA-induced activation of interferon-β and NF-κB. B-DNA signaling by this pathway conferred resistance to viral infection in a way dependent on both TBK1 and IKKi. These results suggest that both TBK1 and IKKi are required for innate immune activation by B-DNA, which might be important in antiviral innate immunity and other DNA-associated immune disorders.

*Note: In the version of this article initially published, the GEO database accession number is missing. This should be the final subsection of Methods, as follows: code. GEO: microarray data, GSE4171. The error has been corrected in the PDF version of the article.

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Figure 1: Activation of MEFs by dsDNA to produce type I interferons and chemokines.
Figure 2: B-DNA activation requires TBK1 and, in part, IKKi, but not TLRs or RIG-I.
Figure 3: B-DNA-induced IFN-β and NF-κB requires IPS-1.
Figure 4: Effects of B-DNA-induced EF activation on viral infection.
Figure 5: B-DNA stimulates DCs via TBK1.

Change history

  • 10 March 2006

    In the version of this article initially published, the GEO database accession number is missing. This should be the final subsection of Methods, as follows: Accession code. GEO: microarray data, GSE4171. The error has been corrected in the PDF version of the article.

References

  1. 1

    Isaacs, A, Cox, R.A. & Rotem, Z. Foreign nucleic acids as the stimulus to make interferon. Lancet 2, 113–116 (1963).

    CAS  Article  Google Scholar 

  2. 2

    Tokunaga, T. et al. Antitumor activity of deoxyribonucleic acid fraction from Mycobacterium bovis BCG. I. Isolation, physicochemical characterization, and antitumor activity. J. Natl. Cancer Inst. 72, 955–962 (1984).

    CAS  PubMed  Google Scholar 

  3. 3

    Akira, S. & Takeda, K. Toll-like receptor signalling. Nat. Rev. Immunol. 4, 499–511 (2004).

    CAS  Article  Google Scholar 

  4. 4

    Iwasaki, A. & Medzhitov, R. Toll-like receptor control of the adaptive immune responses. Nat. Immunol. 5, 987–995 (2004).

    CAS  Article  Google Scholar 

  5. 5

    Theofilopoulos, A.N., Baccala, R., Beutler, B. & Kono, D.H. Type I interferons (α/β) in immunity and autoimmunity. Annu. Rev. Immunol. 23, 307–336 (2005).

    CAS  Article  Google Scholar 

  6. 6

    Bauer, M. et al. Bacterial CpG-DNA triggers activation and maturation of human CD11c, CD123+ dendritic cells. J. Immunol. 166, 5000–5007 (2001).

    CAS  Article  Google Scholar 

  7. 7

    Kawai, T. et al. Interferon-alpha induction through Toll-like receptors involves a direct interaction of IRF7 with MyD88 and TRAF6. Nat. Immunol. 5, 1061–1068 (2004).

    CAS  Article  Google Scholar 

  8. 8

    Uematsu, S. et al. Interleukin-1 receptor-associated kinase-1 plays an essential role for Toll-like receptor (TLR)7 and TLR9-mediated interferon-α induction. J. Exp. Med. 201, 915–923 (2005).

    CAS  Article  Google Scholar 

  9. 9

    Honda, K. et al. Role of a transductional-transcriptional processor complex involving MyD88 and IRF-7 in Toll-like receptor signaling. Proc. Natl. Acad. Sci. USA 101, 15416–15421 (2004).

    CAS  Article  Google Scholar 

  10. 10

    Sharma, S. et al. Triggering the interferon antiviral response through an IKK-related pathway. Science 300, 1148–1151 (2003).

    CAS  Article  Google Scholar 

  11. 11

    Fitzgerald, K.A. et al. IKKε and TBK1 are essential components of the IRF3 signaling pathway. Nat. Immunol. 4, 491–496 (2003).

    CAS  Article  Google Scholar 

  12. 12

    Hemmi, H. et al. The roles of two IκB kinase-related kinases in lipopolysaccharide and double stranded RNA signaling and viral infection. J. Exp. Med. 199, 1641–1650 (2004).

    CAS  Article  Google Scholar 

  13. 13

    Perry, A.K., Chow, E.K., Goodnough, J.B., Yeh, W.C. & Cheng, G. Differential requirement for TANK-binding kinase-1 in type I interferon responses to toll-like receptor activation and viral infection. J. Exp. Med. 199, 1651–1658 (2004).

    CAS  Article  Google Scholar 

  14. 14

    Vallin, H., Perers, A., Alm, G.V. & Ronnblom, L. Anti-double-stranded DNA antibodies and immunostimulatory plasmid DNA in combination mimic the endogenous IFN-α inducer in systemic lupus erythematosus. J. Immunol. 163, 6306–6313 (1999).

    CAS  PubMed  Google Scholar 

  15. 15

    Boule, M.W. et al. Toll-like receptor 9-dependent and -independent dendritic cell activation by chromatin-immunoglobulin G complexes. J. Exp. Med. 199, 1631–1640 (2004).

    CAS  Article  Google Scholar 

  16. 16

    Decker, P., Singh-Jasuja, H., Haager, S., Kotter, I. & Rammensee, H.G. Nucleosome, the main autoantigen in systemic lupus erythematosus, induces direct dendritic cell activation via a MyD88-independent pathway: consequences on inflammation. J. Immunol. 174, 3326–3334 (2005).

    CAS  Article  Google Scholar 

  17. 17

    Kawane, K. et al. Impaired thymic development in mouse embryos deficient in apoptotic DNA degradation. Nat. Immunol. 4, 138–144 (2003).

    CAS  Article  Google Scholar 

  18. 18

    Yoshida, H., Okabe, Y., Kawane, K., Fukuyama, H. & Nagata, S. Lethal anemia caused by interferon-beta produced in mouse embryos carrying undigested DNA. Nat. Immunol. 6, 49–56 (2005).

    CAS  Article  Google Scholar 

  19. 19

    Suzuki, K. et al. Activation of target-tissue immune-recognition molecules by double- stranded polynucleotides. Proc. Natl. Acad. Sci. USA 96, 2285–2290 (1999).

    CAS  Article  Google Scholar 

  20. 20

    Ishii, K.J. et al. Genomic DNA released by dying cells induces the maturation of APCs. J. Immunol. 167, 2602–2607 (2001).

    CAS  Article  Google Scholar 

  21. 21

    Li, S. et al. Induction of IFN-regulated factors and antitumoral surveillance by transfected placebo plasmid DNA. Mol. Ther. 11, 112–119 (2005).

    Article  Google Scholar 

  22. 22

    Yasuda, K. et al. Endosomal translocation of vertebrate DNA activates dendritic cells via TLR9-dependent and -independent pathways. J. Immunol. 174, 6129–6136 (2005).

    CAS  Article  Google Scholar 

  23. 23

    Ishii, K.J. & Akira, S. Innate immune recognition of nucleic acids: Beyond toll-like receptors. Int. J. Cancer 117, 517–523 (2005).

    CAS  Article  Google Scholar 

  24. 24

    Rich, A. & Zhang, S. Timeline: Z-DNA: the long road to biological function. Nat. Rev. Genet. 4, 566–572 (2003).

    CAS  Article  Google Scholar 

  25. 25

    Braun, C.S. et al. The structure of DNA within cationic lipid/DNA complexes. Biophys. J. 84, 1114–1123 (2003).

    CAS  Article  Google Scholar 

  26. 26

    Moller, A., Nordheim, A., Kozlowski, S.A., Patel, D.J. & Rich, A. Bromination stabilizes poly(dG-dC) in the Z-DNA form under low-salt conditions. Biochemistry 23, 54–62 (1984).

    CAS  Article  Google Scholar 

  27. 27

    Kimura, T., Kawai, K., Tojo, S. & Majima, T. One-electron attachment reaction of B- and Z-DNA modified by 8-bromo-2′-deoxyguanosine. J. Org. Chem. 69, 1169–1173 (2004).

    CAS  Article  Google Scholar 

  28. 28

    Kato, H. et al. Cell type-specific involvement of RIG-I in antiviral response. Immunity 23, 19–28 (2005).

    CAS  Article  Google Scholar 

  29. 29

    Yamamoto, M. et al. Role of adaptor TRIF in the MyD88-independent toll-like receptor signaling pathway. Science 301, 640–643 (2003).

    CAS  Article  Google Scholar 

  30. 30

    Yoneyama, M. et al. The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat. Immunol. 5, 730–737 (2004).

    CAS  Article  Google Scholar 

  31. 31

    Kawai, T. et al. IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I interferon induction. Nat. Immunol. 6, 981–988 (2005).

    CAS  Article  Google Scholar 

  32. 32

    Seth, R.B., Sun, L., Ea, C.K. & Chen, Z.J. Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-κB and IRF 3. Cell 122, 669–682 (2005).

    CAS  Article  Google Scholar 

  33. 33

    Xu, L.G. et al. VISA is an adapter protein required for virus-triggered IFN-β signaling. Mol. Cell 19, 727–740 (2005).

    CAS  Article  Google Scholar 

  34. 34

    Meylan, E. et al. Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus. Nature (2005).

  35. 35

    Drexler, I. et al. Identification of vaccinia virus epitope-specific HLA-A*0201-restricted T cells and comparative analysis of smallpox vaccines. Proc. Natl. Acad. Sci. USA 100, 217–222 (2003).

    CAS  Article  Google Scholar 

  36. 36

    Kim, Y.G. et al. A role for Z-DNA binding in vaccinia virus pathogenesis. Proc. Natl. Acad. Sci. USA 100, 6974–6979 (2003).

    CAS  Article  Google Scholar 

  37. 37

    Hornemann, S. et al. Replication of modified vaccinia virus Ankara in primary chicken embryo fibroblasts requires expression of the interferon resistance gene E3L. J. Virol. 77, 8394–8407 (2003).

    CAS  Article  Google Scholar 

  38. 38

    Watson, J.D. & Crick, F.H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953).

    CAS  Article  Google Scholar 

  39. 39

    Smith, E.J., Marie, I., Prakash, A., Garcia-Sastre, A. & Levy, D.E. IRF3 and IRF7 phosphorylation in virus-infected cells does not require double-stranded RNA-dependent protein kinase R or IκB kinase but is blocked by vaccinia virus E3L protein. J. Biol. Chem. 276, 8951–8957 (2001).

    CAS  Article  Google Scholar 

  40. 40

    Kim, Y.G., Lowenhaupt, K., Oh, D.B., Kim, K.K. & Rich, A. Evidence that vaccinia virulence factor E3L binds to Z-DNA in vivo: Implications for development of a therapy for poxvirus infection. Proc. Natl. Acad. Sci. USA 101, 1514–1518 (2004).

    CAS  Article  Google Scholar 

  41. 41

    Kovacsovics, M. et al. Overexpression of Helicard, a CARD-containing helicase cleaved during apoptosis, accelerates DNA degradation. Curr. Biol. 12, 838–843 (2002).

    CAS  Article  Google Scholar 

  42. 42

    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 101, 17264–17269 (2004).

    CAS  Article  Google Scholar 

  43. 43

    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. 175, 2851–2858 (2005).

    CAS  Article  Google Scholar 

  44. 44

    Spies, B. et al. Vaccination with plasmid DNA activates dendritic cells via Toll-like receptor 9 (TLR9) but functions in TLR9-deficient mice. J. Immunol. 171, 5908–5912 (2003).

    CAS  Article  Google Scholar 

  45. 45

    Babiuk, S. et al. TLR9−/− and TLR9+/+ mice display similar immune responses to a DNA vaccine. Immunology 113, 114–120 (2004).

    CAS  Article  Google Scholar 

  46. 46

    Coban, C. et al. Toll-like receptor 9 mediates innate immune activation by the malaria pigment hemozoin. J. Exp. Med. 201, 19–25 (2005).

    CAS  Article  Google Scholar 

  47. 47

    Gursel, M., Verthelyi, D., Gursel, I., Ishii, K.J. & Klinman, D.M. Differential and competitive activation of human immune cells by distinct classes of CpG oligodeoxynucleotide. J. Leukoc. Biol. 71, 813–820 (2002).

    CAS  PubMed  Google Scholar 

  48. 48

    Takeshita, S., Takeshita, F., Haddad, D.E., Ishii, K.J. & Klinman, D.M. CpG oligodeoxynucleotides induce murine macrophages to up-regulate chemokine mRNA expression. Cell. Immunol. 206, 101–106 (2000).

    CAS  Article  Google Scholar 

  49. 49

    Ogasawara, K. et al. Requirement of the IFN-α/β-induced CXCR3 chemokine signalling for CD8+ T cell activation. Genes Cells 7, 309–320 (2002).

    CAS  Article  Google Scholar 

  50. 50

    Sugiyama, T. et al. CpG RNA: identification of novel single-stranded RNA that stimulates human CD14+CD11c+ monocytes. J. Immunol. 174, 2273–2279 (2005).

    CAS  Article  Google Scholar 

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Acknowledgements

We thank Y. Fujita for technical support; K. Matsui, T. Hirotani and H. Kumar for support; K. Sakurai and N. Shimada for circular dichroism measurement of the DNA-lipid complex; T. Abe and Y. Matsuura for providing VSV; H. Shirota for discussions; T. Majima and K. Kawai for providing Z-DNA and for discussions; and other members of Exploratory Research for Advanced Technology, Japan Science and Technology Agency and the Department of Host Defense, Osaka University, for support.

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Correspondence to Shizuo Akira.

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Supplementary Fig. 1

Mda-5 is not involved in B-DNA-induced type-I IFN and chemokine inductions. (PDF 122 kb)

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Ishii, K., Coban, C., Kato, H. et al. A Toll-like receptor–independent antiviral response induced by double-stranded B-form DNA. Nat Immunol 7, 40–48 (2006). https://doi.org/10.1038/ni1282

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