Histone deacetylase 3 promotes innate antiviral immunity through deacetylation of TBK1

Jie-lin Tang, Qi Yang, Chong-hui Xu, He Zhao, Ya-ling Liu, Can-yu Liu, Yuan Zhou, Dong-wei Gai, Rong-juan Pei, Yun Wang, Xue Hu, Bo Zhong, Yan-yi Wang, Xin-wen Chen, Ji-zheng Chen

PDF(1790 KB)
PDF(1790 KB)
Protein Cell ›› 2021, Vol. 12 ›› Issue (4) : 261-278. DOI: 10.1007/s13238-020-00751-5
RESEARCH ARTICLE
RESEARCH ARTICLE

Histone deacetylase 3 promotes innate antiviral immunity through deacetylation of TBK1

Author information +
History +

Abstract

TANK-binding kinase 1 (TBK1), a core kinase of antiviral pathways, activates the production of interferons (IFNs). It has been reported that deacetylation activates TBK1; however, the precise mechanism still remains to be uncovered. We show here that during the early stage of viral infection, the acetylation of TBK1 was increased, and the acetylation of TBK1 at Lys241 enhanced the recruitment of IRF3 to TBK1. HDAC3 directly deacetylated TBK1 at Lys241 and Lys692, which resulted in the activation of TBK1. Deacetylation at Lys241 and Lys692 was critical for the kinase activity and dimerization of TBK1 respectively. Using knockout cell lines and transgenic mice, we confirmed that a HDAC3 null mutant exhibited enhanced susceptibility to viral challenge via impaired production of type I IFNs. Furthermore, activated TBK1 phosphorylated HDAC3, which promoted the deacetylation activity of HDAC3 and formed a feedback loop. In this study, we illustrated the roles the acetylated and deacetylated forms of TBK1 play in antiviral innate responses and clarified the post-translational modulations involved in the interaction between TBK1 and HDAC3.

Keywords

TBK1 / HDAC3 / deacetylation / IRF3 / innate immune

Cite this article

Download citation ▾
Jie-lin Tang, Qi Yang, Chong-hui Xu, He Zhao, Ya-ling Liu, Can-yu Liu, Yuan Zhou, Dong-wei Gai, Rong-juan Pei, Yun Wang, Xue Hu, Bo Zhong, Yan-yi Wang, Xin-wen Chen, Ji-zheng Chen. Histone deacetylase 3 promotes innate antiviral immunity through deacetylation of TBK1. Protein Cell, 2021, 12(4): 261‒278 https://doi.org/10.1007/s13238-020-00751-5

References

[1]
Akira S,Uematsu S, Takeuchi O (2006) Pathogen recognition and innate immunity. Cell 124:783–801
CrossRef Google scholar
[2]
An T, Li S, Pan W, Tien P, Zhong B, Shu HB, Wu S (2015) DYRK2 negatively regulates type I interferon induction by promoting TBK1 degradation via Ser527 phosphorylation. PLoS Pathog 11: e1005179
CrossRef Google scholar
[3]
Aung HT, Schroder K, Himes SR, Brion K, van Zuylen W, Trieu A, Suzuki H, Hayashizaki Y, Hume DA, Sweet MJ (2006) LPS regulates proinflammatory gene expression in macrophages by altering histone deacetylase expression. FASEB J 20:1315–1327
CrossRef Google scholar
[4]
Cao W, Bao C, Padalko E, Lowenstein CJ (2008) Acetylation of mitogen-activated protein kinase phosphatase-1 inhibits Toll-like receptor signaling. J Exp Med 205:1491–1503
CrossRef Google scholar
[5]
Chen J, Wang N, Dong M, Guo M, Zhao Y, Zhuo Z, Zhang C, Chi X, Pan Y, Jiang J(2015) The metabolic regulator histone deacetylase 9 contributes to glucose homeostasis abnormality induced by hepatitis C virus infection. Am Diabetes Assoc 64:4088
CrossRef Google scholar
[6]
Chini CC, Escande C, Nin V, Chini EN (2010) HDAC3 is negatively regulated by the nuclear protein DBC1. J Biol Chem 285:40830–40837
CrossRef Google scholar
[7]
Dai J, Huang YJ, He X, Zhao M, Wang X, Liu ZS, Xue W, Cai H, Zhan XY, Huang SY(2019) Acetylation blocks cGAS activity and inhibits Self-DNA-induced autoimmunity. Cell 176(1447–1460):e1414
CrossRef Google scholar
[8]
Feng Q, Miao Y, Ge J,Yuan Y, Zuo Y, Qian L, Liu J, Cheng Q, Guo T, Zhang L (2018) ATXN3 positively regulates type I IFN antiviral response by deubiquitinating and stabilizing HDAC3. J Immunol 201:675–687
CrossRef Google scholar
[9]
Fischle W, Dequiedt F, Hendzel MJ, Guenther MG, Lazar MA, Voelter W,Verdin E (2002) Enzymatic activity associated with class II HDACs is dependent on a multiprotein complex containing HDAC3 and SMRT/N-CoR. Mol Cell 9:45
CrossRef Google scholar
[10]
Fitzgerald KA, McWhirter SM, Faia KL, Rowe DC, Latz E, Golenbock DT, Coyle AJ, Liao SM, Maniatis T (2003) IKKepsilon and TBK1 are essential components of the IRF3 signaling pathway. Nat Immunol 4:491–496
CrossRef Google scholar
[11]
Halili MA, Andrews MR, Labzin LI, Schroder K, Matthias G, Cao C, Lovelace E,Reid RC , Le GT, Hume DA (2010) Differential effects of selective HDAC inhibitors on macrophage inflammatory responses to the Toll-like receptor 4 agonist LPS. J Leukoc Biol 87:1103–1114
CrossRef Google scholar
[12]
Honda K, Taniguchi T (2006) IRFs: master regulators of signalling by toll-like receptors and cytosolic pattern-recognition receptors. Nat Rev Immunol 6:644–658
CrossRef Google scholar
[13]
Karagianni P, Wong J (2009) HDAC3: taking the SMRT-N-CoRrect road to repression. Oncogene 26:5439
CrossRef Google scholar
[14]
Klampfer L, Huang J, Swaby LA, Augenlicht L (2004) Requirement of histone deacetylase activity for signaling by STAT1. J Biol Chem 279:30358–30368
CrossRef Google scholar
[15]
Lahm A, Paolini C, Pallaoro M, Nardi MC, Jones P, Neddermann P, Sambucini S, Bottomley MJ, Lo Surdo P,Carfi A (2007) Unraveling the hidden catalytic activity of vertebrate class IIa histone deacetylases. Proc Natl Acad Sci USA 104:17335–17340
CrossRef Google scholar
[16]
Larabi A, Devos JM, Ng SL, Nanao MH, Round A, Maniatis T, Panne D (2013) Crystal structure and mechanism of activation of TANKbinding kinase 1. Cell Rep 3:734–746
CrossRef Google scholar
[17]
Li S, Wang L, Berman M, Kong YY, Dorf ME (2011) Mapping a dynamic innate immunity protein interaction network regulating type I interferon production. Immunity 35:426–440
CrossRef Google scholar
[18]
Li X, Zhang Q, Ding Y, Liu Y, Zhao D, Zhao K, Shen Q, Liu X, Zhu X,Li N (2016) Methyltransferase Dnmt3a upregulates HDAC9 to deacetylate the kinase TBK1 for activation of antiviral innate immunity. Nat Immunol 17:806–815
CrossRef Google scholar
[19]
Liu HM, Jiang F, Loo YM, Hsu S, Hsiang TY, Marcotrigiano J, Gale M Jr (2016) Regulation of retinoic acid inducible gene-I (RIG-I) activation by the histone deacetylase 6. EBioMedicine 9:195–206
CrossRef Google scholar
[20]
Liu S, Chen S, Li X, Wu S, Zhang Q, Jin Q, Hu L, Zhou R, Yu Z, Meng F et al (2017) Lck/Hck/Fgr-mediated tyrosine phosphorylation negatively regulates TBK1 to restrain innate antiviral responses. Cell Host Microbe 21(754–768):e755
CrossRef Google scholar
[21]
Ma X, Helgason E, Phung QT, Quan CL, Iyer RS, Lee MW, Bowman KK, Starovasnik MA, Dueber EC (2012) Molecular basis of tankbinding kinase 1 activation by transautophosphorylation. Proc Natl Acad Sci USA 109:9378–9383
CrossRef Google scholar
[22]
Medzhitov R (2007) Recognition of microorganisms and activation of the immune response. Nature 449:819–826
CrossRef Google scholar
[23]
Meng J, Liu X, Zhang P, Li D, Xu S, Zhou Q, Guo M, Huai W, Chen X, Wang Q(2016) Rb selectively inhibits innate IFN-beta production by enhancing deacetylation of IFN-beta promoter through HDAC1 and HDAC8. J Autoimmun 73:42–53
CrossRef Google scholar
[24]
Mihaylova MM, Vasquez DS, Ravnskjaer K, Denechaud PD, Yu RT, Alvarez JG, Downes M, Evans RM, Montminy M, Shaw RJ (2011) Class IIa histone deacetylases are hormone-activated regulators of FOXO and mammalian glucose homeostasis. Cell 145:607–621
CrossRef Google scholar
[25]
Mowen KA, David M (2014) Unconventional post-translational modifications in immunological signaling. Nat Immunol 15:512–520
CrossRef Google scholar
[26]
Nusinzon I,Horvath CM (2006) Positive and negative regulation of the innate antiviral response and beta interferon gene expression by deacetylation. Mol Cell Biol 26:3106–3113
CrossRef Google scholar
[27]
Park H, Kim Y, Park D, Jeoung D (2014) Nuclear localization signal domain of HDAC3 is necessary and sufficient for the expression regulation of MDR1. BMB Rep 47:342–347
CrossRef Google scholar
[28]
Saul VV, Niedenthal R, Pich A, Weber F, Schmitz ML (2015) SUMO modification of TBK1 at the adaptor-binding C-terminal coiled-coil domain contributes to its antiviral activity. Biochim Biophys Acta 1853:136–143
CrossRef Google scholar
[29]
Shevtsova AS, Motuzova OV, Kuragina VM, Akhmatova NK, Gmyl LV, Kondrat’eva YI, Kozlovskaya LI, Rogova YV, Litov AG, Romanova LI (2016) Lethal experimental tick-borne encephalitis infection: influence of two strains with similar virulence on the immune response. Front Microbiol 7:2172
CrossRef Google scholar
[30]
Smale ST, Tarakhovsky A, Natoli G (2014) Chromatin contributions to the regulation of innate immunity. Annu Rev Immunol 32:489–511
CrossRef Google scholar
[31]
Song G, Liu B, Li Z, Wu H, Wang P,Zhao K, Jiang G, Zhang L, Gao C (2016) E3 ubiquitin ligase RNF128 promotes innate antiviral immunity through K63-linked ubiquitination of TBK1. Nat Immunol 17:1342–1351
CrossRef Google scholar
[32]
Suhara W, Yoneyama M, Iwamura T, Yoshimura S, Tamura K, Namiki H, Aimoto S, Fujita T (2000) Analyses of virus-induced homomeric and heteromeric protein associations between IRF-3 and coactivator CBP/p300. J Biochem 128:301–307
CrossRef Google scholar
[33]
Takeuchi O, Akira S (2010) Pattern recognition receptors and inflammation. Cell 140:805–820
CrossRef Google scholar
[34]
Tu D, Zhu Z, Zhou AY, Yun CH, Lee KE, Toms AV, Li Y, Dunn GP, Chan E, Thai T (2013) Structure and ubiquitination-dependent activation of TANK-binding kinase 1. Cell Rep 3:747–758
CrossRef Google scholar
[35]
Wang C, Chen T, Zhang J, Yang M, Li N, Xu X, Cao X (2009) The E3 ubiquitin ligase Nrdp1 ‘preferentially’ promotes TLR-mediated production of type I interferon. Nat Immunol 10:744–752
CrossRef Google scholar
[36]
Yang Q, Tang J, Pei R, Gao X, Guo J, Xu C, Wang Y, Wang Q, Wu C, Zhou Y (2018) Host HDAC4 regulates the antiviral response by inhibiting the phosphorylation of IRF3. J Mol Cell Biol 11:158
CrossRef Google scholar
[37]
Yang WM, Tsai SC, Wen YD, Fejer G, Seto E (2002) Functional domains of histone deacetylase-3. J Biol Chem 277:9447–9454
CrossRef Google scholar
[38]
Zhang X, Ozawa Y, Lee H, Wen YD, Tan TH, Wadzinski BE, Seto E (2005) Histone deacetylase 3 (HDAC3) activity is regulated by interaction with protein serine/threonine phosphatase 4. Genes Dev 19:827–839
CrossRef Google scholar

RIGHTS & PERMISSIONS

2020 The Author(s)
AI Summary AI Mindmap
PDF(1790 KB)

Accesses

Citations

Detail

Sections
Recommended

/