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The methyltransferase PRMT6 attenuates antiviral innate immunity by blocking TBK1–IRF3 signaling

A Correction to this article was published on 27 November 2019

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Abstract

Protein arginine methyltransferases (PRMTs) play diverse biological roles and are specifically involved in immune cell development and inflammation. However, their role in antiviral innate immunity has not been elucidated. Viral infection triggers the TBK1–IRF3 signaling pathway to stimulate the production of type-I interferon, which mediates antiviral immunity. We performed a functional screen of the nine mammalian PRMTs for regulators of IFN-β expression and found that PRMT6 inhibits the antiviral innate immune response. Viral infection also upregulated PRMT6 protein levels. We generated PRMT6-deficient mice and found that they exhibited enhanced antiviral innate immunity. PRMT6 deficiency promoted the TBK1–IRF3 interaction and subsequently enhanced IRF3 activation and type-I interferon production. Mechanistically, viral infection enhanced the binding of PRMT6 to IRF3 and inhibited the interaction between IRF3 and TBK1; this mechanism was independent of PRMT6 methyltransferase activity. Thus, PRMT6 inhibits antiviral innate immunity by sequestering IRF3, thereby blocking TBK1-IRF3 signaling. Our work demonstrates a methyltransferase-independent role for PRMTs. It also identifies a negative regulator of the antiviral immune response, which may protect the host from the damaging effects of an overactive immune system and/or be exploited by viruses to escape immune detection.

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  • 27 November 2019

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

References

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

    Article  CAS  PubMed  Google Scholar 

  2. Cao, X. Self-regulation and cross-regulation of pattern-recognition receptor signalling in health and disease. Nat. Rev. Immunol. 16, 35–50 (2016).

    Article  CAS  PubMed  Google Scholar 

  3. Gurtler, C. & Bowie, A. G. Innate immune detection of microbial nucleic acids. Trends Microbiol. 21, 413–420 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Goubau, D., Deddouche, S. & Reis e Sousa, C. Cytosolic sensing of viruses. Immunity 38, 855–869 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Paludan, S. R. & Bowie, A. G. Immune sensing of DNA. Immunity 38, 870–880 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. 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 

  7. 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  PubMed  PubMed Central  Google Scholar 

  8. Loo, Y. M. & Gale, M. Jr. Immune signaling by RIG-I-like receptors. Immunity 34, 680–692 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Goubau, D. et al. Antiviral immunity via RIG-I-mediated recognition of RNA bearing 5’-diphosphates. Nature 514, 372–375 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Cai, X., Chiu, Y. H. & Chen, Z. J. The cGAS-cGAMP-STING pathway of cytosolic DNA sensing and signaling. Mol. Cell 54, 289–296 (2014).

    Article  CAS  PubMed  Google Scholar 

  11. 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 

  12. 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 

  13. Chen, K., Liu, J. & Cao, X. Regulation of type I interferon signaling in immunity and inflammation: a comprehensive review. J. Autoimmun. 83, 1–11 (2017).

    Article  PubMed  CAS  Google Scholar 

  14. Liu, J., Qian, C. & Cao, X. Post-translational modification control of innate immunity. Immunity 45, 15–30 (2016).

    Article  PubMed  CAS  Google Scholar 

  15. Li X., et al. The tyrosine kinase Src promotes phosphorylation of the kinase TBK1 to facilitate type I interferon production after viral infection. Sci Signal 10, eaae0435 (2017).

  16. Gabhann, J. N. et al. Absence of SHIP-1 results in constitutive phosphorylation of tank-binding kinase 1 and enhanced TLR3-dependent IFN-beta production. J. Immunol. 184, 2314–2320 (2010).

    Article  CAS  PubMed  Google Scholar 

  17. Zhao, Y. et al. PPM1B negatively regulates antiviral response via dephosphorylating TBK1. Cell. Signal. 24, 2197–2204 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. McCoy, C. E., Carpenter, S., Palsson-McDermott, E. M., Gearing, L. J. & O’Neill, L. A. Glucocorticoids inhibit IRF3 phosphorylation in response to Toll-like receptor-3 and -4 by targeting TBK1 activation. J. Biol. Chem. 283, 14277–14285 (2008).

    Article  CAS  PubMed  Google Scholar 

  19. 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 

  20. Cui, J. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Zhang, M. et al. TRAF-interacting protein (TRIP) negatively regulates IFN-beta production and antiviral response by promoting proteasomal degradation of TANK-binding kinase 1. J. Exp. Med. 209, 1703–1711 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Li, X. et al. Methyltransferase Dnmt3a upregulates HDAC9 to deacetylate the kinase TBK1 for activation of antiviral innate immunity. Nat. Immunol. 17, 806–815 (2016).

    Article  CAS  PubMed  Google Scholar 

  23. Saitoh, T. et al. Negative regulation of interferon-regulatory factor 3-dependent innate antiviral response by the prolyl isomerase Pin1. Nat. Immunol. 7, 598–605 (2006).

    Article  CAS  PubMed  Google Scholar 

  24. Li, S. et al. The tumor suppressor PTEN has a critical role in antiviral innate immunity. Nat. Immunol. 17, 241–249 (2015).

    Article  PubMed  CAS  Google Scholar 

  25. Blanc, R. S. & Richard, S. Arginine methylation: the coming of age. Mol. Cell 65, 8–24 (2017).

    Article  CAS  PubMed  Google Scholar 

  26. Biggar, K. K. & Li, S. S. Non-histone protein methylation as a regulator of cellular signalling and function. Nat. Rev. Mol. Cell Biol. 16, 5–17 (2015).

    Article  CAS  PubMed  Google Scholar 

  27. Wei, H., Mundade, R., Lange, K. C. & Lu, T. Protein arginine methylation of non-histone proteins and its role in diseases. Cell Cycle 13, 32–41 (2014).

    Article  PubMed  CAS  Google Scholar 

  28. Yang, Y. & Bedford, M. T. Protein arginine methyltransferases and cancer. Nat. Rev. Cancer 13, 37–50 (2012).

    Article  CAS  PubMed  Google Scholar 

  29. Greenblatt, S. M., Liu, F. & Nimer, S. D. Arginine methyltransferases in normal and malignant hematopoiesis. Exp. Hematol. 44, 435–441 (2016).

    Article  CAS  PubMed  Google Scholar 

  30. Liu, F. et al. Arginine methyltransferase PRMT5 is essential for sustaining normal adult hematopoiesis. J. Clin. Invest. 125, 3532–3544 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  31. Kim, J. H. et al. The role of protein arginine methyltransferases in inflammatory responses. Mediat. Inflamm. 2016, 4028353 (2016).

    Google Scholar 

  32. Infantino, S. et al. Arginine methylation of the B cell antigen receptor promotes differentiation. J. Exp. Med. 207, 711–719 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Ying, Z. et al. Histone arginine methylation by PRMT7 controls germinal center formation via regulating Bcl6 transcription. J. Immunol. 195, 1538–1547 (2015).

    Article  CAS  PubMed  Google Scholar 

  34. Guccione, E. et al. Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature 449, 933–937 (2007).

    Article  CAS  PubMed  Google Scholar 

  35. Hyllus, D. et al. PRMT6-mediated methylation of R2 in histone H3 antagonizes H3 K4 trimethylation. Genes Dev. 21, 3369–3380 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Waldmann, T. et al. Methylation of H2AR29 is a novel repressive PRMT6 target. Epigenetics Chromatin 4, 11 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Poulard, C., Corbo, L., & Le Romancer, M. Protein arginine methylation/demethylation and cancer. Oncotarget 7, 67532–67550 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  38. Di Lorenzo, A., Yang, Y., Macaluso, M. & Bedford, M. T. A gain-of-function mouse model identifies PRMT6 as a NF-kappaB coactivator. Nucleic Acids Res. 42, 8297–8309 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Liu, X. et al. Intracellular MHC class II molecules promote TLR-triggered innate immune responses by maintaining activation of the kinase Btk. Nat. Immunol. 12, 416–424 (2011).

    Article  CAS  PubMed  Google Scholar 

  40. Han, C. et al. Integrin CD11b negatively regulates TLR-triggered inflammatory responses by activating Syk and promoting degradation of MyD88 and TRIF via Cbl-b. Nat. Immunol. 11, 734–742 (2010).

    Article  CAS  PubMed  Google Scholar 

  41. Chen, W. et al. Induction of Siglec-G by RNA viruses inhibits the innate immune response by promoting RIG-I degradation. Cell 152, 467–478 (2013).

    Article  CAS  PubMed  Google Scholar 

  42. Neault, M., Mallette, F. A., Vogel, G., Michaud-Levesque, J. & Richard, S. Ablation of PRMT6 reveals a role as a negative transcriptional regulator of the p53 tumor suppressor. Nucleic Acids Res. 40, 9513–9521 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Phalke, S. et al. p53-Independent regulation of p21Waf1/Cip1 expression and senescence by PRMT6. Nucleic Acids Res. 40, 9534–9542 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Nakakido, M. et al. PRMT6 increases cytoplasmic localization of p21CDKN1A in cancer cells through arginine methylation and makes more resistant to cytotoxic agents. Oncotarget 6, 30957–30967 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  45. Chen, L. T., Hu, M. M., Xu, Z. S., Liu, Y. & Shu, H. B. MSX1 modulates RLR-mediated innate antiviral signaling by facilitating assembly of TBK1-associated complexes. J. Immunol. 197, 199–207 (2016).

    Article  CAS  PubMed  Google Scholar 

  46. Wang, F. et al. S6K-STING interaction regulates cytosolic DNA-mediated activation of the transcription factor IRF3. Nat. Immunol. 17, 514–522 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Gates, L. T. & Shisler, J. L. cFLIPL Interrupts IRF3-CBP-DNA Interactions To Inhibit IRF3-Driven Transcription. J. Immunol. 197, 923–933 (2016).

    Article  CAS  PubMed  Google Scholar 

  48. Uhlmann, T. et al. A method for large-scale identification of protein arginine methylation. Mol. Cell. Proteomics 11, 1489–1499 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Guo, A. et al. Immunoaffinity enrichment and mass spectrometry analysis of protein methylation. Mol. Cell. Proteomics 13, 372–387 (2014).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported by grants from the National Key R&D program of China (2018YFA0507401), National Natural Science Foundation of China (31390431, 31522019, 81471568, 80178104, and 31770945), and the CAMS Innovation Fund for Medical Sciences (2016-12M-1-003). We thank Ms. Xiaofei Li for technical assistance and Life Science Editors for editing assistance.

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X.C. designed and supervised the study. H.Z., C.H., T.L., and N.L. performed the experiments. H.Z., C.H., and X.C. analyzed the data and wrote the paper.

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Correspondence to Xuetao Cao.

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Zhang, H., Han, C., Li, T. et al. The methyltransferase PRMT6 attenuates antiviral innate immunity by blocking TBK1–IRF3 signaling. Cell Mol Immunol 16, 800–809 (2019). https://doi.org/10.1038/s41423-018-0057-4

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