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Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating Activity of SARS-CoV Papain-Like Protease


All coronaviruses such as the SARS virus and the recently identified Middle East Respiratory Syndrome (MERS) virus encode in their genomes at least one papain-like protease (PLpro) enzyme that has two distinct functions in viral pathogenesis. The first function is to process the viral polyprotein into individual proteins that are essential for viral replication. The second function is to remove ubiquitin and ISG15 proteins from host cell proteins, which likely helps coronaviruses short circuit the host's innate immune response. The 3-dimensional structure of SARS virus PLpro in complex with a human ubiquitin analog was determined and reveals how coronavirus PLpro enzymes strip ubiquitin and ISG15 from host cell proteins at the molecular level. A series of amino acid residues involved in interactions between PLpro and ubiquitin were mutated to identify which interactions are important only for the recognition of ubiquitin and ISG15 modified proteins by PLpro and not for recognition and cleaving of the viral polyprotein. The 3D structure of SARS PLpro with ubiquitin-aldehyde sheds significant new light into how PLpro interacts with ubiquitin-like molecules and provides a molecular road map for performing similar studies on other deadly coronaviruses such as MERS.


Vyšlo v časopise: Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating Activity of SARS-CoV Papain-Like Protease. PLoS Pathog 10(5): e32767. doi:10.1371/journal.ppat.1004113
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1004113

Souhrn

All coronaviruses such as the SARS virus and the recently identified Middle East Respiratory Syndrome (MERS) virus encode in their genomes at least one papain-like protease (PLpro) enzyme that has two distinct functions in viral pathogenesis. The first function is to process the viral polyprotein into individual proteins that are essential for viral replication. The second function is to remove ubiquitin and ISG15 proteins from host cell proteins, which likely helps coronaviruses short circuit the host's innate immune response. The 3-dimensional structure of SARS virus PLpro in complex with a human ubiquitin analog was determined and reveals how coronavirus PLpro enzymes strip ubiquitin and ISG15 from host cell proteins at the molecular level. A series of amino acid residues involved in interactions between PLpro and ubiquitin were mutated to identify which interactions are important only for the recognition of ubiquitin and ISG15 modified proteins by PLpro and not for recognition and cleaving of the viral polyprotein. The 3D structure of SARS PLpro with ubiquitin-aldehyde sheds significant new light into how PLpro interacts with ubiquitin-like molecules and provides a molecular road map for performing similar studies on other deadly coronaviruses such as MERS.


Zdroje

1. JiangX, ChenZJ (2011) The role of ubiquitylation in immune defence and pathogen evasion. Nature reviewsImmunology 12: 35–48.

2. KomanderD, RapeM (2012) The ubiquitin code. Annu Rev Biochem 81: 203–229.

3. HershkoA, CiechanoverA (1998) The ubiquitin system. Annu Rev Biochem 67: 425–479.

4. RahighiS, IkedaF, KawasakiM, AkutsuM, SuzukiN, et al. (2009) Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Cell 136: 1098–1109.

5. WelchmanRL, GordonC, MayerRJ (2005) Ubiquitin and ubiquitin-like proteins as multifunctional signals. Nat Rev Mol Cell Biol 6: 599–609.

6. HaasAL, AhrensP, BrightPM, AnkelH (1987) Interferon induces a 15-kilodalton protein exhibiting marked homology to ubiquitin. J Biol Chem 262: 11315–11323.

7. HusnjakK, DikicI (2012) Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions. Annu Rev Biochem 81: 291–322.

8. KomanderD, ClagueMJ, UrbeS (2009) Breaking the chains: structure and function of the deubiquitinases. Nat Rev Mol Cell Biol 10: 550–563.

9. SridharanH, ZhaoC, KrugRM (2010) Species specificity of the NS1 protein of influenza B virus: NS1 binds only human and non-human primate ubiquitin-like ISG15 proteins. J Biol Chem 285: 7852–7856.

10. BalakirevMY, JaquinodM, HaasAL, ChroboczekJ (2002) Deubiquitinating function of adenovirus proteinase. J Virol 76: 6323–6331.

11. KattenhornLM, KorbelGA, KesslerBM, SpoonerE, PloeghHL (2005) A deubiquitinating enzyme encoded by HSV-1 belongs to a family of cysteine proteases that is conserved across the family Herpesviridae. Mol Cell 19: 547–557.

12. SchliekerC, KorbelGA, KattenhornLM, PloeghHL (2005) A deubiquitinating activity is conserved in the large tegument protein of the herpesviridae. J Virol 79: 15582–15585.

13. LilleyCE, ChaurushiyaMS, BoutellC, LandryS, SuhJ, et al. A viral E3 ligase targets RNF8 and RNF168 to control histone ubiquitination and DNA damage responses. Embo J 29: 943–955.

14. YeY, AkutsuM, Reyes-TurcuF, EnchevRI, WilkinsonKD, et al. (2011) Polyubiquitin binding and cross-reactivity in the USP domain deubiquitinase USP21. EMBO reports 12: 350–357.

15. AkutsuM, YeY, VirdeeS, ChinJW, KomanderD (2011) Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains. Proceedings of the National Academy of Sciences of the United States of America 108: 2228–2233.

16. JamesTW, Frias-StaheliN, BacikJP, Levingston MacleodJM, KhajehpourM, et al. (2011) Structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domain-containing protease. Proceedings of the National Academy of Sciences of the United States of America 108: 2222–2227.

17. van KasterenPB, Bailey-ElkinBA, JamesTW, NinaberDK, BeugelingC, et al. (2013) Deubiquitinase function of arterivirus papain-like protease 2 suppresses the innate immune response in infected host cells. Proceedings of the National Academy of Sciences of the United States of America 110: E838–847.

18. PerlmanS, NetlandJ (2009) Coronaviruses post-SARS: update on replication and pathogenesis. Nature reviewsMicrobiology 7: 439–450.

19. ThielV, IvanovKA, PuticsA, HertzigT, SchelleB, et al. (2003) Mechanisms and enzymes involved in SARS coronavirus genome expression. J Gen Virol 84: 2305–2315.

20. HarcourtBH, JuknelieneD, KanjanahaluethaiA, BechillJ, SeversonKM, et al. (2004) Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity. J Virol 78: 13600–13612.

21. RatiaK, SaikatenduKS, SantarsieroBD, BarrettoN, BakerSC, et al. (2006) Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme. Proc Natl Acad Sci U S A 103: 5717–5722.

22. SuleaT, LindnerHA, PurisimaEO, MenardR (2005) Deubiquitination, a new function of the severe acute respiratory syndrome coronavirus papain-like protease? J Virol 79: 4550–4551.

23. LindnerHA, Fotouhi-ArdakaniN, LytvynV, LachanceP, SuleaT, et al. (2005) The papain-like protease from the severe acute respiratory syndrome coronavirus is a deubiquitinating enzyme. J Virol 79: 15199–15208.

24. LindnerHA, LytvynV, QiH, LachanceP, ZiomekE, et al. (2007) Selectivity in ISG15 and ubiquitin recognition by the SARS coronavirus papain-like protease. Arch Biochem Biophys 466: 8–14.

25. BarrettoN, JuknelieneD, RatiaK, ChenZ, MesecarAD, et al. (2005) The papain-like protease of severe acute respiratory syndrome coronavirus has deubiquitinating activity. J Virol 79: 15189–15198.

26. DevarajSG, WangN, ChenZ, ChenZ, TsengM, et al. (2007) Regulation of IRF-3-dependent innate immunity by the papain-like protease domain of the severe acute respiratory syndrome coronavirus. J Biol Chem 282: 32208–32221.

27. FriemanM, RatiaK, JohnstonRE, MesecarAD, BaricRS (2009) Severe acute respiratory syndrome coronavirus papain-like protease ubiquitin-like domain and catalytic domain regulate antagonism of IRF3 and NF-kappaB signaling. J Virol 83: 6689–6705.

28. ClementzMA, ChenZ, BanachBS, WangY, SunL, et al. Deubiquitinating and interferon antagonism activities of coronavirus papain-like proteases. J Virol 84: 4619–4629.

29. LiuYC, PenningerJ, KarinM (2005) Immunity by ubiquitylation: a reversible process of modification. Nat Rev Immunol 5: 941–952.

30. MelandriF, GrenierL, PlamondonL, HuskeyWP, SteinRL (1996) Kinetic studies on the inhibition of isopeptidase T by ubiquitin aldehyde. Biochemistry 35: 12893–12900.

31. HuM, LiP, LiM, LiW, YaoT, et al. (2002) Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell 111: 1041–1054.

32. RenatusM, ParradoSG, D'ArcyA, EidhoffU, GerhartzB, et al. (2006) Structural basis of ubiquitin recognition by the deubiquitinating protease USP2. Structure 14: 1293–1302.

33. HickeL, SchubertHL, HillCP (2005) Ubiquitin-binding domains. Nat Rev Mol Cell Biol 6: 610–621.

34. CookWJ, JeffreyLC, KasperekE, PickartCM (1994) Structure of tetraubiquitin shows how multiubiquitin chains can be formed. J Mol Biol 236: 601–609.

35. EddinsMJ, VaradanR, FushmanD, PickartCM, WolbergerC (2007) Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH. J Mol Biol 367: 204–211.

36. DattaAB, HuraGL, WolbergerC (2009) The structure and conformation of Lys63-linked tetraubiquitin. J Mol Biol 392: 1117–1124.

37. KomanderD, Reyes-TurcuF, LicchesiJD, OdenwaelderP, WilkinsonKD, et al. (2009) Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains. EMBO Rep 10: 466–473.

38. NarasimhanJ, WangM, FuZ, KleinJM, HaasAL, et al. (2005) Crystal structure of the interferon-induced ubiquitin-like protein ISG15. J Biol Chem 280: 27356–27365.

39. YeY, BlaserG, HorrocksMH, Ruedas-RamaMJ, IbrahimS, et al. (2012) Ubiquitin chain conformation regulates recognition and activity of interacting proteins. Nature 492: 266–270.

40. BealRE, Toscano-CantaffaD, YoungP, RechsteinerM, PickartCM (1998) The hydrophobic effect contributes to polyubiquitin chain recognition. Biochemistry 37: 2925–2934.

41. ClementzMA, ChenZ, BanachBS, WangY, SunL, et al. (2010) Deubiquitinating and interferon antagonism activities of coronavirus papain-like proteases. Journal of virology 84: 4619–4629.

42. SunS, ElwoodJ, GreeneWC (1996) Both amino- and carboxyl-terminal sequences within I kappa B alpha regulate its inducible degradation. Molecular and cellular biology 16: 1058–1065.

43. BorodovskyA, KesslerBM, CasagrandeR, OverkleeftHS, WilkinsonKD, et al. (2001) A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14. Embo J 20: 5187–5196.

44. HuM, LiP, SongL, JeffreyPD, ChenovaTA, et al. (2005) Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14. Embo J 24: 3747–3756.

45. KomanderD, LordCJ, ScheelH, SwiftS, HofmannK, et al. (2008) The structure of the CYLD USP domain explains its specificity for Lys63-linked polyubiquitin and reveals a B box module. Mol Cell 29: 451–464.

46. SatoY, YoshikawaA, YamagataA, MimuraH, YamashitaM, et al. (2008) Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains. Nature 455: 358–362.

47. DangLC, MelandriFD, SteinRL (1998) Kinetic and mechanistic studies on the hydrolysis of ubiquitin C-terminal 7-amido-4-methylcoumarin by deubiquitinating enzymes. Biochemistry 37: 1868–1879.

48. AvvakumovGV, WalkerJR, XueS, FinertyPJJr, MackenzieF, et al. (2006) Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8). J Biol Chem 281: 38061–38070.

49. CapodagliGC, DeatonMK, BakerEA, LumpkinRJ, PeganSD (2013) Diversity of ubiquitin and ISG15 specificity among nairoviruses' viral ovarian tumor domain proteases. Journal of virology 87: 3815–3827.

50. CapodagliGC, McKercherMA, BakerEA, MastersEM, BrunzelleJS, et al. (2011) Structural analysis of a viral ovarian tumor domain protease from the Crimean-Congo hemorrhagic fever virus in complex with covalently bonded ubiquitin. Journal of virology 85: 3621–3630.

51. DurfeeLA, LyonN, SeoK, HuibregtseJM (2010) The ISG15 conjugation system broadly targets newly synthesized proteins: implications for the antiviral function of ISG15. Mol Cell 38: 722–732.

52. Frias-StaheliN, GiannakopoulosNV, KikkertM, TaylorSL, BridgenA, et al. (2007) Ovarian tumor domain-containing viral proteases evade ubiquitin- and ISG15-dependent innate immune responses. Cell Host Microbe 2: 404–416.

53. ShiHX, YangK, LiuX, LiuXY, WeiB, et al. (2010) Positive regulation of interferon regulatory factor 3 activation by Herc5 via ISG15 modification. Mol Cell Biol 30: 2424–2436.

54. HarhajEW, DixitVM (2012) Regulation of NF-kappaB by deubiquitinases. Immunol Rev 246: 107–124.

55. SunSC (2008) Deubiquitylation and regulation of the immune response. Nat Rev Immunol 8: 501–511.

56. KayagakiN, PhungQ, ChanS, ChaudhariR, QuanC, et al. (2007) DUBA: a deubiquitinase that regulates type I interferon production. Science 318: 1628–1632.

57. SchweitzerK, BozkoPM, DubielW, NaumannM (2007) CSN controls NF-kappaB by deubiquitinylation of IkappaBalpha. Embo J 26: 1532–1541.

58. ZakiAM, van BoheemenS, BestebroerTM, OsterhausAD, FouchierRA (2012) Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. The New England journal of medicine 367: 1814–1820.

59. BollesM, DemingD, LongK, AgnihothramS, WhitmoreA, et al. (2011) A double-inactivated severe acute respiratory syndrome coronavirus vaccine provides incomplete protection in mice and induces increased eosinophilic proinflammatory pulmonary response upon challenge. Journal of virology 85: 12201–12215.

60. ErnstA, AvvakumovG, TongJ, FanY, ZhaoY, et al. (2013) A Strategy for Modulation of Enzymes in the Ubiquitin System. Science 339 (6119) 590–5.

61. WilkinsonKD, Gan-ErdeneT, KolliN (2005) Derivitization of the C-terminus of ubiquitin and ubiquitin-like proteins using intein chemistry: methods and uses. Methods Enzymol 399: 37–51.

62. StudierFW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41: 207–234.

63. Otwinowski Z, Minor W (1997) Methods in Enzymology, Volume 276: Macromolecular Crystallography. Methods in Enzymology. New York: Academic Press. pp. 307–326.

64. McCoyAJ, Grosse-KunstleveRW, AdamsPD, WinnMD, StoroniLC, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658–674.

65. MurshudovGN, VaginAA, LebedevA, WilsonKS, DodsonEJ (1999) Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr D Biol Crystallogr 55: 247–255.

66. EmsleyP, CowtanK (2004) Coot: Model-Building Tools for Molecular Graphics. Acta Crystallographica Section D - Biological Crystallography 60: 2126–2132.

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