RESEARCH ARTICLE

SARS coronavirus papain-like protease inhibits the type I interferon signaling pathway through interaction with the STING-TRAF3-TBK1 complex

  • Xiaojuan Chen 1 ,
  • Xingxing Yang 1,2 ,
  • Yang Zheng 1 ,
  • Yudong Yang 1 ,
  • Yaling Xing 1 ,
  • Zhongbin Chen , 1,2
Expand
  • 1. Division of Infection and Immunity, Department of Electromagnetic and Laser Biology, Beijing Institute of Radiation Medicine, Beijing 100850, China
  • 2. Anhui Medical University, Hefei 230032, China

Received date: 11 Dec 2013

Accepted date: 13 Jan 2014

Published date: 25 Jun 2014

Copyright

2014 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

SARS coronavirus (SARS-CoV) develops an antagonistic mechanism by which to evade the antiviral activities of interferon (IFN). Previous studies suggested that SARS-CoV papain-like protease (PLpro) inhibits activation of the IRF3 pathway, which would normally elicit a robust IFN response, but the mechanism(s) used by SARS PLpro to inhibit activation of the IRF3 pathway is not fully known. In this study, we uncovered a novel mechanism that may explain how SARS PLpro efficiently inhibits activation of the IRF3 pathway. We found that expression of the membrane-anchored Plpro domain (PLpro-TM) from SARS-CoV inhibits STING/TBK1/IKKϵ-mediated activation of type I IFNs and disrupts the phosphorylation and dimerization of IRF3, which are activated by STING and TBK1. Meanwhile, we showed that PLpro-TM physically interacts with TRAF3, TBK1, IKKϵ, STING, and IRF3, the key components that assemble the STING-TRAF3-TBK1 complex for activation of IFN expression. However, the interaction between the components in STING-TRAF3-TBK1 complex is disrupted by PLpro-TM. Furthermore, SARS PLpro-TM reduces the levels of ubiquitinated forms of RIG-I, STING, TRAF3, TBK1, and IRF3 in the STING-TRAF3- TBK1 complex. These results collectively point to a new mechanism used by SARS-CoV through which Plpro negatively regulates IRF3 activation by interaction with STING-TRAF3-TBK1 complex, yielding a SARS-CoV countermeasure against host innate immunity.

Cite this article

Xiaojuan Chen , Xingxing Yang , Yang Zheng , Yudong Yang , Yaling Xing , Zhongbin Chen . SARS coronavirus papain-like protease inhibits the type I interferon signaling pathway through interaction with the STING-TRAF3-TBK1 complex[J]. Protein & Cell, 2014 , 5(5) : 369 -381 . DOI: 10.1007/s13238-014-0026-3

1
Alff PJ, Sen N, Gorbunova E, Gavrilovskaya IN, Mackow ER (2008) The NY-1 hantavirus Gn cytoplasmic tail coprecipitates TRAF3 and inhibits cellular interferon responses by disrupting TBK1-TRAF3 complex formation. J Virol82: 9115-9122

DOI

2
Barral PM, Sarkar D, Su ZZ, Barber GN, DeSalle R, Racaniello VR, Fisher PB (2009) Functions of the cytoplasmic RNA sensors RIGI and MDA-5: key regulators of innate immunity. Pharmacol Ther124: 219-234

DOI

3
Barretto N, Jukneliene D, Ratia K, Chen Z, Mesecar AD, Baker SC (2005) The papain-like protease of severe acute respiratory syndrome coronavirus has deubiquitinating activity. J Virol79: 15189-15198

DOI

4
Barretto N, Jukneliene D, Ratia K, Chen Z, Mesecar AD, Baker SC (2006) Deubiquitinating activity of the SARS-CoV papain-like protease. Adv Exp Med Biol581: 37-41

DOI

5
Bhoj VG, Chen ZJ (2009) Ubiquitylation in innate and adaptive immunity. Nature458: 430-437

DOI

6
Bibeau-Poirier A, Servant MJ (2008) Roles of ubiquitination in pattern-recognition receptors and type I interferon receptor signaling. Cytokine43: 359-367

DOI

7
Chen H, Jiang Z (2013) The essential adaptors of innate immune signaling. Protein Cell4: 27-39

DOI

8
Chen Z, Wang Y, Ratia K, Mesecar AD, Wilkinson KD, Baker SC (2007) Proteolytic processing and deubiquitinating activity of papain-like proteases of human coronavirus NL63. J Virol81: 6007-6018

DOI

9
Chen X, Chou CY, Chang GG (2009) Thiopurine analogue inhibitors of severe acute respiratory syndrome-coronavirus papain-like protease, a deubiquitinating and deISGylating enzyme. Antivir Chem Chemother19: 151-156

10
Chen Z, Zhou X, Lunney JK, Lawson S, Sun Z, Brown E, Christopher-Hennings J, Knudsen D, Nelson E, Fang Y (2010) Immunodominant epitopes in nsp2 of porcine reproductive and respiratory syndrome virus are dispensable for replication, but play an important role in modulation of the host immune response. J Gen Virol91: 1047-1057

DOI

11
Clementz MA, Chen Z, Banach BS, Wang Y, Sun L, Ratia K, Baez-Santos YM, Wang J, Takayama J, Ghosh AK (2010) Deubiquitinating and interferon antagonism activities of coronavirus papain-like proteases. J Virol84: 4619-4629

DOI

12
Coornaert B, Carpentier I, Beyaert R (2009) A20: central gatekeeper in inflammation and immunity. J Biol Chem284: 8217-8221

DOI

13
Devaraj SG, Wang N, Chen Z, Chen Z, Tseng M, Barretto N, Lin R, Peters CJ, Tseng CT, Baker SC (2007) Regulation of IRF-3-dependent innate immunity by the papain-like protease domain of the severe acute respiratory syndrome coronavirus. J Biol Chem282: 32208-32221

DOI

14
Evans PC, Ovaa H, Hamon M, Kilshaw PJ, Hamm S, Bauer S, Ploegh HL, Smith TS (2004) Zinc-finger protein A20, a regulator of inflammation and cell survival, has de-ubiquitinating activity. Biochem J378: 727-734

DOI

15
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 Immunol4: 491-496

DOI

16
Frieman M, Yount B, Heise M, Kopecky-Bromberg SA, Palese P, Baric RS (2007) Severe acute respiratory syndrome coronavirus ORF6 antagonizes STAT1 function by sequestering nuclear import factors on the rough endoplasmic reticulum/Golgi membrane. J Virol81: 9812-9824

DOI

17
Frieman M, Ratia K, Johnston RE, Mesecar AD, Baric RS (2009) Severe acute respiratory syndrome coronavirus papain-like protease ubiquitin-like domain and catalytic domain regulate antagonism of IRF3 and NF-kappaB signaling. J Virol83: 6689-6705

DOI

18
Gack MU, Shin YC, Joo CH, Urano T, Liang C, Sun L, Takeuchi O, Akira S, Chen Z, Inoue S (2007) TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity. Nature446: 916-920

DOI

19
He JQ, Oganesyan G, Saha SK, Zarnegar B, Cheng G (2007) TRAF3 and its biological function. Adv Exp Med Biol597: 48-59

DOI

20
Hornung V, Ellegast J, Kim S, Brzozka K, Jung A, Kato H, Poeck H, Akira S, Conzelmann KK, Schlee M (2006) 5′-Triphosphate RNA is the ligand for RIG-I. Science314: 994-997

DOI

21
Huang YH, Liu XY, Du XX, Jiang ZF, Su XD (2012) The structural basis for the sensing and binding of cyclic di-GMP by STING. Nat Struct Mol Biol19: 728-730

DOI

22
Isaacson MK, Ploegh HL (2009) Ubiquitination, ubiquitin-like modifiers, and deubiquitination in viral infection. Cell Host Microbe5: 559-570

DOI

23
Ishikawa H, Barber GN (2008) STING is an endoplasmic reticulum adaptor that facilitates innate immune signalling. Nature455: 674-678

DOI

24
Kamitani W, Narayanan K, Huang C, Lokugamage K, Ikegami T, Ito N, Kubo H, Makino S (2006) Severe acute respiratory syndrome coronavirus nsp1 protein suppresses host gene expression by promoting host mRNA degradation. Proc Natl Acad Sci USA103: 12885-12890

DOI

25
Kattenhorn LM, Korbel GA, Kessler BM, Spooner E, Ploegh HL (2005) A deubiquitinating enzyme encoded by HSV-1 belongs to a family of cysteine proteases that is conserved across the family Herpesviridae. Mol Cell19: 547-557

DOI

26
Kawai T, Akira S (2007) Antiviral signaling through pattern recognition receptors. J Biochem141: 137-145

DOI

27
Kayagaki N, Phung Q, Chan S, Chaudhari R, Quan C, O’Rourke KM, Eby M, Pietras E, Cheng G, Bazan J F (2007) DUBA: a deubiquitinase that regulates type I interferon production. Science318: 1628-1632

DOI

28
Kopecky-Bromberg SA, Martinez-Sobrido L, Frieman M, Baric RA, Palese P (2007) Severe acute respiratory syndrome coronavirus open reading frame (ORF) 3b, ORF 6, and nucleocapsid proteins function as interferon antagonists. J Virol81: 548-557

DOI

29
Lindner HA, Fotouhi-Ardakani N, Lytvyn V, Lachance P, Sulea T, Menard R (2005) The papain-like protease from the severe acute respiratory syndrome coronavirus is a deubiquitinating enzyme. J Virol79: 15199-15208

DOI

30
Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, Khattra J, Asano JK, Barber SA, Chan SY (2003) The genome sequence of the SARS-associated coronavirus. Science300: 1399-1404

DOI

31
Matthys V, Mackow ER (2012) Hantavirus regulation of type I interferon responses. Adv Virol2012: 524024

DOI

32
Narayanan K, Huang C, Lokugamage K, Kamitani W, Ikegami T, Tseng CT, Makino S (2008) Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells. J Virol82: 4471-4479

DOI

33
Oganesyan G, Saha SK, Guo B, He JQ, Shahangian A, Zarnegar B, Perry A, Cheng G (2006) Critical role of TRAF3 in the Toll-like receptor-dependent and-independent antiviral response. Nature439: 208-211

DOI

34
Ouyang S, Song X, Wang Y, Ru H, Shaw N, Jiang Y, Niu F, Zhu Y, Qiu W, Parvatiyar K (2012) Structural analysis of the STING adaptor protein reveals a hydrophobic dimer interface and mode of cyclic di-GMP binding. Immunity36: 1073-1086

DOI

35
Perlman S, Netland J (2009) Coronaviruses post-SARS: update on replication and pathogenesis. Nat Rev Microbiol7: 439-450

DOI

36
Pichlmair A, Schulz O, Tan CP, Naslund TI, Liljestrom P, Weber F, Reis e Sousa C (2006) RIG-I-mediated antiviral responses to singlestranded RNA bearing 5′-phosphates. Science314: 997-1001

DOI

37
Ratia K, Saikatendu KS, Santarsiero BD, Barretto N, Baker SC, Stevens RC, Mesecar AD (2006) Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme. Proc Natl Acad Sci USA103: 5717-5722

DOI

38
Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Penaranda S, Bankamp B, Maher K, Chen MH (2003) Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science300: 1394-1399

DOI

39
Saha SK, Cheng G (2006) TRAF3: a new regulator of type I interferons. Cell Cycle5: 804-807

DOI

40
Saitoh T, Fujita N, Yoshimori T, Akira S (2010) Regulation of dsDNAinduced innate immune responses by membrane trafficking. Autophagy6: 430-432

DOI

41
Schindler C, Levy DE, Decker T (2007) JAK-STAT signaling: from interferons to cytokines. J Biol Chem282: 20059-20063

DOI

42
Shang G, Zhu D, Li N, Zhang J, Zhu C, Lu D, Liu C, Yu Q, Zhao Y, Xu S (2012) Crystal structures of STING protein reveal basis for recognition of cyclic di-GMP. Nat Struct Mol Biol19: 725-727

DOI

43
Shu C, Yi G, Watts T, Kao CC, Li P (2012) Structure of STING bound to cyclic di-GMP reveals the mechanism of cyclic dinucleotide recognition by the immune system. Nat Struct Mol Biol19: 722-724

DOI

44
Siu KL, Kok KH, Ng MH, Poon VK, Yuen KY, Zheng BJ, Jin DY (2009) Severe acute respiratory syndrome coronavirus M protein inhibits type I interferon production by impeding the formation of TRAF3. TANK.TBK1/IKKepsilon complex. J Biol Chem284: 16202-16209

DOI

45
Sulea T, Lindner HA, Purisima EO, Menard R (2005) Deubiquitination, a new function of the severe acute respiratory syndrome coronavirus papain-like protease? J Virol79: 4550-4551

DOI

46
Sun W, Li Y, Chen L, Chen H, You F, Zhou X, Zhai Z, Chen D (2009) ERIS, an endoplasmic reticulum IFN stimulator, activiates innate immune signaling through dimerization. Pro Natl Acad Sci USA106: 8653-8658

DOI

47
Sun Z, Chen Z, Lawson SR, Fang Y (2010) The cysteine protease domain of porcine reproductive and respiratory syndrome virus nonstructural protein 2 possesses deubiquitinating and interferon antagonism functions. J Virol84: 7832-7846

DOI

48
Sun L, Xing Y, Chen X, Zheng Y, Yang Y, Nichols DB, Clementz MA, Banach BS, Li K, Baker SC (2012) Coronavirus papain-like proteases negatively regulate antiviral innate immune response through disruption of STING-mediated signaling. PLoS One7: e30802

DOI

49
Tanaka Y, Chen ZJ (2012) STING specifies IRF3 phosphorylation by TBK1 in the cytosolic DNA signaling pathway. Sci Signal5: ra20

DOI

50
Thiel V, Weber F (2008) Interferon and cytokine responses to SARScoronavirus infection. Cytokine Growth Factor Rev19: 121-132

DOI

51
van Kasteren PB, Bailey-Elkin BA, James TW, Ninaber DK, Beugeling C, Khajehpour M, Snijder EJ, Mark BL, Kikkert M (2013) Deubiquitinase function of arterivirus papain-like protease 2 suppresses the innate immune response in infected host cells. Proc Natl Acad Sci USA110: E838-E847

DOI

52
van Zuylen WJ, Doyon P, Clement JF, Khan KA, D’Ambrosio LM, Do F, St-Amant-Verret M, Wissanji T, Emery G, Gingras AC (2012) Proteomic profiling of the TRAF3 interactome network reveals a new role for the ER-to-Golgi transport compartments in innate immunity. PLoS Pathog8: e1002747

DOI

53
Vaux DL, Fidler F, Cumming G (2012) Replicates and repeats—what is the difference and is it significant? A brief discussion of statistics and experimental design. EMBO Rep13: 291-296

DOI

54
Wang G, Chen G, Zheng D, Cheng G, Tang H (2011) PLP2 of mouse hepatitis virus A59 (MHV-A59) targets TBK1 to negatively regulate cellular type I interferon signaling pathway. PLoS One6: e17192

DOI

55
Wathelet MG, Orr M, Frieman MB, Baric RS (2007) Severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp1 and rational design of an attenuated strain. J Virol81: 11620-11633

DOI

56
Yin Q, Tian Y, Kabaleeswaran V, Jiang X, Tu D, Eck MJ, Chen ZJ, Wu H (2012) Cyclic di-GMP sensing via the innate immune signaling protein STING. Mol Cell46: 735-745

DOI

57
Yoneyama M, Fujita T (2009) RNA recognition and signal transduction by RIG-I-like receptors. Immunol Rev227: 54-65

DOI

58
Zeng W, Sun L, Jiang X, Chen X, Hou F, Adhikari A, Xu M, Chen ZJ (2010) Reconstitution of the RIG-I pathway reveals a signaling role of unanchored polyubiquitin chains in innate immunity. Cell141: 315-330

DOI

59
hong B, Yang Y, Li S, Wang YY, Li Y, Diao F, Lei C, He X, Zhang L, Tien P (2008) The adaptor protein MITA links virus-sensing receptors to IRF3 transcription factor activation. Immunity29: 538-550

60
Zhong B, Zhang Y, Tan B, Liu TT, Wang YY, Shu HB (2010) The E3 ubiquitin ligase RNF5 targets virus-induced signaling adaptor for ubiquitination and degradation. J Immunol184: 6249-6255

DOI

61
Zielecki F, Weber M, Eickmann M, Spiegelberg L, Zaki AM, Matrosovich M, Becker S, Weber F (2013) Human cell tropism and innate immune system interactions of human respiratory coronavirus EMC compared to those of severe acute respiratory syndrome coronavirus. J Virol87: 5300-5304

DOI

62
Zust R, Cervantes-Barragan L, Kuri T, Blakqori G, Weber F, Ludewig B, Thiel V (2007) Coronavirus non-structural protein 1 is a major pathogenicity factor: implications for the rational design of coronavirus vaccines. PLoS Pathog3: e109

DOI

Outlines

/