Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

NLRP4 negatively regulates type I interferon signaling by targeting the kinase TBK1 for degradation via the ubiquitin ligase DTX4

Nature Immunology volume 13, pages 387–395 (2012)Cite this article

Subjects

Abstract

Stringent control of the type I interferon signaling pathway is important for maintaining host immune responses and homeostasis, yet the molecular mechanisms responsible for its tight regulation are still poorly understood. Here we report that the pattern-recognition receptor NLRP4 regulated the activation of type I interferon mediated by double-stranded RNA or DNA by targeting the kinase TBK1 for degradation. NLRP4 recruited the E3 ubiquitin ligase DTX4 to TBK1 for Lys48 (K48)-linked polyubiquitination at Lys670, which led to degradation of TBK1. Knockdown of either DTX4 or NLRP4 abrogated K48-linked ubiquitination and degradation of TBK1 and enhanced the phosphorylation of TBK1 and the transcription factor IRF3. Our results identify a previously unrecognized role for NLRP4 in the regulation of type I interferon signaling and provide molecular insight into the mechanisms by which NLRP4-DTX4 targets TBK1 for degradation.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: NLRP4 negatively regulates the type I interferon signaling pathway.
Figure 2: Knockdown of NLRP4 enhances IFN-β expression as well as antiviral responses.
Figure 3: NLRP4 associates with TBK1 to inhibit IRF3 activation.
Figure 4: NLRP4 mediates the degradation of TBK1.
Figure 5: NLRP4 induces TBK1 degradation by K48-linked ubiquitination.
Figure 6: Nod is required for NLRP4-mediated inhibition of type I interferon signaling.
Figure 7: NLRP4 recruits DTX4 to degrade TBK1.
Figure 8: Ubiquitination of TBK1 at Lys670 is essential for NLRP4-DTX4–mediated inhibition of type I interferon signaling.

Similar content being viewed by others

References

  1. Takeuchi, O. & Akira, S. Pattern recognition receptors and inflammation. Cell 140, 805–820 (2010).

    Article  CAS  PubMed  Google Scholar 

  2. Schroder, K. & Tschopp, J. The inflammasomes. Cell 140, 821–832 (2010).

    Article  CAS  PubMed  Google Scholar 

  3. Chiu, Y.H., Macmillan, J.B. & Chen, Z.J. RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway. Cell 138, 576–591 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Ablasser, A. et al. RIG-I-dependent sensing of poly(dA:dT) through the induction of an RNA polymerase III-transcribed RNA intermediate. Nat. Immunol. 10, 1065–1072 (2009).

    Article  CAS  PubMed  Google Scholar 

  5. Zhang, Z. et al. The helicase DDX41 senses intracellular DNA mediated by the adaptor STING in dendritic cells. Nat. Immunol. 12, 959–965 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Unterholzner, L. et al. IFI16 is an innate immune sensor for intracellular DNA. Nat. Immunol. 11, 997–1004 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Moore, C.B. et al. NLRX1 is a regulator of mitochondrial antiviral immunity. Nature 451, 573–577 (2008).

    Article  CAS  PubMed  Google Scholar 

  8. Tattoli, I. et al. NLRX1 is a mitochondrial NOD-like receptor that amplifies NF-κB and JNK pathways by inducing reactive oxygen species production. EMBO Rep. 9, 293–300 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Benko, S., Magalhaes, J.G., Philpott, D.J. & Girardin, S.E. NLRC5 limits the activation of inflammatory pathways. J. Immunol. 185, 1681–1691 (2010).

    Article  CAS  PubMed  Google Scholar 

  10. Cui, J. et al. NLRC5 negatively regulates the NF-κB and type I interferon signaling pathways. Cell 141, 483–496 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Jounai, N. et al. NLRP4 negatively regulates autophagic processes through an association with beclin1. J. Immunol. 186, 1646–1655 (2011).

    Article  CAS  PubMed  Google Scholar 

  12. Fiorentino, L. et al. A novel PAAD-containing protein that modulates NF-κB induction by cytokines tumor necrosis factor-alpha and interleukin-1beta. J. Biol. Chem. 277, 35333–35340 (2002).

    Article  CAS  PubMed  Google Scholar 

  13. Li, S., Wang, L., Berman, M., Kong, Y.Y. & Dorf, M.E. Mapping a dynamic innate immunity protein interaction network regulating type I interferon production. Immunity 35, 426–440 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Wang, C. et al. The E3 ubiquitin ligase Nrdp1 'preferentially' promotes TLR-mediated production of type I interferon. Nat. Immunol. 10, 744–752 (2009).

    Article  CAS  PubMed  Google Scholar 

  15. Honda, K. & Taniguchi, T. IRFs: master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors. Nat. Rev. Immunol. 6, 644–658 (2006).

    Article  CAS  PubMed  Google Scholar 

  16. Honda, K. et al. Spatiotemporal regulation of MyD88-IRF-7 signalling for robust type-I interferon induction. Nature 434, 1035–1040 (2005).

    Article  CAS  PubMed  Google Scholar 

  17. Radivojac, P. et al. Identification, analysis, and prediction of protein ubiquitination sites. Proteins 78, 365–380 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Xue, Y., Li, A., Wang, L., Feng, H. & Yao, X. PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. BMC Bioinformatics 7, 163 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  20. Thurston, T.L., Ryzhakov, G., Bloor, S., von Muhlinen, N. & Randow, F. The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria. Nat. Immunol. 10, 1215–1221 (2009).

    Article  CAS  PubMed  Google Scholar 

  21. Weidberg, H. & Elazar, Z. TBK1 mediates crosstalk between the innate immune response and autophagy. Sci. Signal. 4, pe39 (2011).

    Article  PubMed  Google Scholar 

  22. Ryzhakov, G. & Randow, F. SINTBAD, a novel component of innate antiviral immunity, shares a TBK1-binding domain with NAP1 and TANK. EMBO J. 26, 3180–3190 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Chau, T.L. et al. Are the IKKs and IKK-related kinases TBK1 and IKK-ɛ similarly activated? Trends Biochem. Sci. 33, 171–180 (2008).

    Article  CAS  PubMed  Google Scholar 

  24. Lei, C.Q. et al. Glycogen synthase kinase 3β regulates IRF3 transcription factor-mediated antiviral response via activation of the kinase TBK1. Immunity 33, 878–889 (2010).

    Article  CAS  PubMed  Google Scholar 

  25. Liew, F.Y., Xu, D., Brint, E.K. & O'Neill, L.A. Negative regulation of Toll-like receptor-mediated immune responses. Nat. Rev. Immunol. 5, 446–458 (2005).

    Article  CAS  PubMed  Google Scholar 

  26. Karin, M., Lawrence, T. & Nizet, V. Innate immunity gone awry: linking microbial infections to chronic inflammation and cancer. Cell 124, 823–835 (2006).

    Article  CAS  PubMed  Google Scholar 

  27. You, F. et al. PCBP2 mediates degradation of the adaptor MAVS via the HECT ubiquitin ligase AIP4. Nat. Immunol. 10, 1300–1308 (2009).

    Article  CAS  PubMed  Google Scholar 

  28. O'Neill, L.A. When signaling pathways collide: positive and negative regulation of toll-like receptor signal transduction. Immunity 29, 12–20 (2008).

    Article  CAS  PubMed  Google Scholar 

  29. Xia, X. et al. NLRX1 negatively regulates TLR-induced NF-κB signaling by targeting TRAF6 and IKK. Immunity 34, 843–853 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Barbie, D.A. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 462, 108–112 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Meylan, E. et al. Requirement for NF-κB signalling in a mouse model of lung adenocarcinoma. Nature 462, 104–107 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Ou, Y.H. et al. TBK1 directly engages Akt/PKB survival signaling to support oncogenic transformation. Mol. Cell 41, 458–470 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank S. Balachandran (Fox Chase Cancer Center) for VSV-eGFP; Y.-J. Liu and Z. Zhang (The University of Texas MD Anderson Cancer Center) for the STING expression plasmid; and A.A. Ajibade for critical reading of the manuscript. Supported by the National Natural Science Foundation of China (31000394 to J.C.), the National Cancer Institute, the US National Institutes of Health (CA090327, CA101795, CA121191, CA116408 and CA094327 to R.-F.W.), the Cancer Research Institute and The Methodist Hospital Research Institute.

Author information

Author notes

  1. Jun Cui and Yinyin Li: These authors contributed equally to this work.

Authors and Affiliations

  1. The Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA

    Jun Cui, Yinyin Li, Liang Zhu, Helen Y Wang & Rong-Fu Wang

  2. Department of Biochemistry, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China

    Jun Cui

  3. Center for Inflammation and Epigenetics, The Methodist Hospital Research Institute, Houston, Texas, USA

    Jun Cui, Yinyin Li, Helen Y Wang & Rong-Fu Wang

  4. Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas, USA

    Yinyin Li

  5. Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

    Dan Liu & Zhou Songyang

  6. Department of Pathology and Department of Immunology, Baylor College of Medicine, Houston, Texas, USA

    Rong-Fu Wang

Authors
  1. Jun Cui
    View author publications

    Search author on:PubMed Google Scholar

  2. Yinyin Li
    View author publications

    Search author on:PubMed Google Scholar

  3. Liang Zhu
    View author publications

    Search author on:PubMed Google Scholar

  4. Dan Liu
    View author publications

    Search author on:PubMed Google Scholar

  5. Zhou Songyang
    View author publications

    Search author on:PubMed Google Scholar

  6. Helen Y Wang
    View author publications

    Search author on:PubMed Google Scholar

  7. Rong-Fu Wang
    View author publications

    Search author on:PubMed Google Scholar

Contributions

J.C., Y.L. and L.Z. designed and did the experiments, J.C. and R.-F.W. wrote the manuscript; D.L. and Z.S. provided reagents and technical assistance; and H.Y.W. and R.-F.W. supervised the project.

Corresponding author

Correspondence to Rong-Fu Wang.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–14 and Methods (PDF 2668 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cui, J., Li, Y., Zhu, L. et al. NLRP4 negatively regulates type I interferon signaling by targeting the kinase TBK1 for degradation via the ubiquitin ligase DTX4. Nat Immunol 13, 387–395 (2012). https://doi.org/10.1038/ni.2239

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/ni.2239

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing