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A deneddylase encoded by Epstein–Barr virus promotes viral DNA replication by regulating the activity of cullin-RING ligases

Abstract

The large tegument proteins of herpesviruses encode conserved cysteine proteases of unknown function. Here we show that BPLF1, the Epstein–Barr-virus-encoded member of this protease family, is a deneddylase that regulates virus production by modulating the activity of cullin-RING ligases (CRLs). BPLF1 hydrolyses NEDD8 conjugates in vitro, acts as a deneddylase in vivo, binds to cullins and stabilizes CRL substrates. Expression of BPLF1 alone or in the context of the productive virus cycle induces accumulation of the licensing factor CDT1 and deregulates S-phase DNA synthesis. Inhibition of BPLF1 during the productive virus cycle prevents cellular DNA re-replication and inhibits virus replication. Viral DNA synthesis is restored by overexpression of CDT1. Homologues encoded by other herpesviruses share the deneddylase activity. Thus, these enzymes are likely to have a key function in the virus life cycle by inducing a replication-permissive S-phase-like cellular environment.

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Figure 1: BPLF1 is a NEDD8-specific deconjugase.
Figure 2: BPLF1 deneddylates cullins and induces the accumulation of CRL substrates.
Figure 3: Expression of a catalytically active BPLF1 induces accumulation of cells with a DNA content of at least 4N.
Figure 4: Cell cycle deregulation in cells expressing BPLF1.
Figure 5: Activation of the EBV productive cycle is associated with cellular DNA re-replication.
Figure 6: Expression of BPLF1 is required for efficient EBV DNA replication.
Figure 7: Overexpression of CDT1 promotes EBV DNA replication.
Figure 8: Deneddylase activity is shared by BPLF1 homologues encoded by other herpesviruses.

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References

  1. Glickman, M.H. & Ciechanover, A. The ubiquitin–proteasome proteolytic pathway: destruction for the sake of construction. Physiol. Rev. 82, 373–428 (2002).

    Article  CAS  Google Scholar 

  2. Ciechanover, A., Orian, A. & Schwartz, A. L. The ubiquitin-mediated proteolytic pathway: mode of action and clinical implications. J Cell Biochem Suppl 34, 40–51 (2000).

    Article  CAS  Google Scholar 

  3. Reyes-Turcu, F. E., Ventii, K. H. & Wilkinson, K. D. Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes. Annu. Rev. Biochem. 78, 363–397 (2009).

    Article  CAS  Google Scholar 

  4. Kerscher, O., Felberbaum, R. & Hochstrasser, M. Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu. Rev. Cell Dev. Biol. 22, 159–180 (2006).

    Article  CAS  Google Scholar 

  5. Chiba, T. & Tanaka, K. Cullin-based ubiquitin ligase and its control by NEDD8-conjugating system. Curr. Protein Pept. Sci. 5, 177–184 (2004).

    Article  CAS  Google Scholar 

  6. Tatham, M. H. et al. RNF4 is a poly-SUMO-specific E3 ubiquitin ligase required for arsenic-induced PML degradation. Nature Cell Biol. 10, 538–546 (2008).

    Article  CAS  Google Scholar 

  7. Lallemand-Breitenbach, V. et al. Arsenic degrades PML or PML-RARα through a SUMO-triggered RNF4/ubiquitin-mediated pathway. Nature Cell Biol. 10, 547–555 (2008).

    Article  CAS  Google Scholar 

  8. Duda, D. M. et al. Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation. Cell 134, 995–1006 (2008).

    Article  CAS  Google Scholar 

  9. Pan, Z. Q., Kentsis, A., Dias, D. C., Yamoah, K. & Wu, K. Nedd8 on cullin: building an expressway to protein destruction. Oncogene 23, 1985–1997 (2004).

    Article  CAS  Google Scholar 

  10. Isaacson, M. K. & Ploegh, H. L. Ubiquitination, ubiquitin-like modifiers, and deubiquitination in viral infection. Cell Host Microbe 5, 559–570 (2009).

    Article  CAS  Google Scholar 

  11. Loureiro, J. & Ploegh, H. L. Antigen presentation and the ubiquitin–proteasome system in host–pathogen interactions. Adv. Immunol. 92, 225–305 (2006).

    Article  CAS  Google Scholar 

  12. Scheffner, M., Huibregtse, J. M., Vierstra, R. D. & Howley, P. M. The HPV-16 E6 and E6-AP complex functions as a ubiquitin-protein ligase in the ubiquitination of p53. Cell 75, 495–505 (1993).

    Article  CAS  Google Scholar 

  13. Boutell, C., Canning, M., Orr, A. & Everett, R. D. Reciprocal activities between herpes simplex virus type 1 regulatory protein ICP0, a ubiquitin E3 ligase, and ubiquitin-specific protease USP7. J. Virol. 79, 12342–12354 (2005).

    Article  CAS  Google Scholar 

  14. Saridakis, V. et al. Structure of the p53 binding domain of HAUSP/USP7 bound to Epstein–Barr nuclear antigen 1 implications for EBV-mediated immortalization. Mol. Cell 18, 25–36 (2005).

    Article  CAS  Google Scholar 

  15. Randow, F. & Lehner, P. J. Viral avoidance and exploitation of the ubiquitin system. Nature Cell Biol. 11, 527–534 (2009).

    Article  CAS  Google Scholar 

  16. Young, L. S. & Rickinson, A. B. Epstein–Barr virus: 40 years on. Nature Rev. Cancer 4, 757–768 (2004).

    Article  CAS  Google Scholar 

  17. Bishop, G. A. & Busch, L. K. Molecular mechanisms of B-lymphocyte transformation by Epstein–Barr virus. Microbes Infect. 4, 853–857 (2002).

    Article  CAS  Google Scholar 

  18. Tsurumi, T., Fujita, M. & Kudoh, A. Latent and lytic Epstein–Barr virus replication strategies. Rev. Med. Virol. 15, 3–15 (2005).

    Article  CAS  Google Scholar 

  19. Kudoh, A. et al. Epstein–Barr virus lytic replication elicits ATM checkpoint signal transduction while providing an S-phase-like cellular environment. J. Biol. Chem. 280, 8156–8163 (2005).

    Article  CAS  Google Scholar 

  20. Sompallae, R. et al. Epstein–Barr virus encodes three bona fide ubiquitin-specific proteases. J. Virol. 82, 10477–10486 (2008).

    Article  CAS  Google Scholar 

  21. Kattenhorn, L. M., Korbel, G. A., Kessler, B. M., Spooner, E. & Ploegh, H. L. 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 (2005).

    Article  CAS  Google Scholar 

  22. Mendoza, H. M. et al. NEDP1, a highly conserved cysteine protease that deNEDDylates Cullins. J. Biol. Chem. 278, 25637–25643 (2003).

    Article  CAS  Google Scholar 

  23. Borodovsky, A. et al. A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14. EMBO J. 20, 5187–5196 (2001).

    Article  CAS  Google Scholar 

  24. Nishitani, H. et al. Two E3 ubiquitin ligases, SCF-Skp2 and DDB1-Cul4, target human Cdt1 for proteolysis. EMBO J. 25, 1126–1136 (2006).

    Article  CAS  Google Scholar 

  25. Busino, L. et al. Degradation of Cdc25A by β-TrCP during S phase and in response to DNA damage. Nature 426, 87–91 (2003).

    Article  CAS  Google Scholar 

  26. Auld, C. A., Fernandes, K. M. & Morrison, R. F. Skp2-mediated p27Kip1 degradation during S/G2 phase progression of adipocyte hyperplasia. J. Cell Physiol. 211, 101–111 (2007).

    Article  CAS  Google Scholar 

  27. Ohta, T. & Xiong, Y. Phosphorylation- and Skp1-independent in vitro ubiquitination of E2F1 by multiple ROC-cullin ligases. Cancer Res. 61, 1347–1353 (2001).

    CAS  PubMed  Google Scholar 

  28. Cook, J. G. Replication licensing and the DNA damage checkpoint. Front. Biosci. 14, 5013–5030 (2009).

    Article  CAS  Google Scholar 

  29. Wilsker, D. & Bunz, F. Chk1 phosphorylation during mitosis: a new role for a master regulator. Cell Cycle 8, 1161–1163 (2009).

    Article  CAS  Google Scholar 

  30. Chen, Y. & Poon, R. Y. The multiple checkpoint functions of CHK1 and CHK2 in maintenance of genome stability. Front. Biosci. 13, 5016–5029 (2008).

    CAS  PubMed  Google Scholar 

  31. Hans, F. & Dimitrov, S. Histone H3 phosphorylation and cell division. Oncogene 20, 3021–3027 (2001).

    Article  CAS  Google Scholar 

  32. Guerreiro-Cacais, A. O., Uzunel, M., Levitskaya, J. & Levitsky, V. Inhibition of heavy chain and β2-microglobulin synthesis as a mechanism of major histocompatibility complex class I downregulation during Epstein–Barr virus replication. J. Virol. 81, 1390–1400 (2007).

    Article  CAS  Google Scholar 

  33. Daibata, M., Humphreys, R. E., Takada, K. & Sairenji, T. Activation of latent EBV via anti-IgG-triggered, second messenger pathways in the Burkitt's lymphoma cell line Akata. J. Immunol. 144, 4788–4793 (1990).

    CAS  PubMed  Google Scholar 

  34. Chrisp, P. & Clissold, S. P. Foscarnet. A review of its antiviral activity, pharmacokinetic properties and therapeutic use in immunocompromised patients with cytomegalovirus retinitis. Drugs 41, 104–129 (1991).

    Article  CAS  Google Scholar 

  35. Yuan, J., Cahir-McFarland, E., Zhao, B. & Kieff, E. Virus and cell RNAs expressed during Epstein–Barr virus replication. J. Virol. 80, 2548–2565 (2006).

    Article  CAS  Google Scholar 

  36. Kim, Y. & Kipreos, E. T. Cdt1 degradation to prevent DNA re-replication: conserved and non-conserved pathways. Cell Div. 2, 18 (2007).

    Article  Google Scholar 

  37. Shen, L. N. et al. Structural basis of NEDD8 ubiquitin discrimination by the deNEDDylating enzyme NEDP1. EMBO J. 24, 1341–1351 (2005).

    Article  CAS  Google Scholar 

  38. Schlieker, C. et al. Structure of a herpesvirus-encoded cysteine protease reveals a unique class of deubiquitinating enzymes. Mol. Cell 25, 677–687 (2007).

    Article  CAS  Google Scholar 

  39. Edelmann, M. J. et al. Structural basis and specificity of human otubain 1-mediated deubiquitination. Biochem. J. 418, 379–390 (2009).

    Article  CAS  Google Scholar 

  40. Soucy, T. A. et al. An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer. Nature 458, 732–736 (2009).

    Article  CAS  Google Scholar 

  41. Gredmark-Russ, S. et al. A gammaherpesvirus ubiquitin-specific protease is involved in the establishment of murine gammaherpesvirus 68 infection. J. Virol. 83, 10644–10652 (2009).

    Article  CAS  Google Scholar 

  42. Bottcher, S. et al. Mutagenesis of the active-site cysteine in the ubiquitin-specific protease contained in large tegument protein pUL36 of pseudorabies virus impairs viral replication in vitro and neuroinvasion in vivo. J. Virol. 82, 6009–6016 (2008).

    Article  Google Scholar 

  43. Jarosinski, K., Kattenhorn, L., Kaufer, B., Ploegh, H. & Osterrieder, N. A herpesvirus ubiquitin-specific protease is critical for efficient T cell lymphoma formation. Proc. Natl Acad. Sci. USA 104, 20025–20030 (2007).

    Article  CAS  Google Scholar 

  44. Davy, C. & Doorbar, J. G2/M cell cycle arrest in the life cycle of viruses. Virology 368, 219–226 (2007).

    Article  CAS  Google Scholar 

  45. Boehmer, P. E. & Lehman, I. R. Herpes simplex virus DNA replication. Annu. Rev. Biochem. 66, 347–384 (1997).

    Article  CAS  Google Scholar 

  46. Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283–1298 (2006).

    Article  CAS  Google Scholar 

  47. Hassink, G. C. et al. The ER-resident ubiquitin-specific protease 19 participates in the UPR and rescues ERAD substrates. EMBO Rep. 10, 755–761 (2009).

    Article  CAS  Google Scholar 

  48. Zhao, B., Schlesiger, C., Masucci, M. G. & Lindsten, K. The ubiquitin specific protease 4 (Usp4) is a new player in the Wnt signalling pathway. J. Cell. Mol. Med. 13, 1886–1895 (2009).

    Article  Google Scholar 

  49. Duda, D. M. et al. Structure of a SUMO-binding-motif mimic bound to Smt3p–Ubc9p: conservation of a non-covalent ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway. J. Mol. Biol. 369, 619–630 (2007).

    Article  CAS  Google Scholar 

  50. Yao, G. Q., Grill, S., Egan, W. & Cheng, Y. C. Potent inhibition of Epstein–Barr virus by phosphorothioate oligodeoxynucleotides without sequence specification. Antimicrob. Agents Chemother. 37, 1420–1425 (1993).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank Ron T. Hay, Frauke Melchior, Zhen-Quian-Pan, Dong-Er Zhang, Chiba Chikatumi and Jürgen Haas for providing plasmids, antibodies and technical advice. This study was supported by grants awarded by the Swedish Cancer Society, the Swedish Medical Research Council, the Karolinska Institutet, Stockholm, Sweden, and by the European Community Integrated Project INCA, contract no. LSHC-CT-2005-018704, and Network of Excellence RUBICON, contract no. LSG-CT-2005-018683. S.H. is supported by a fellowship from the European Community Marie Curie Early Training Network UbiRegulators contract no. MRTN-CT-2006-034555.

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S.G. and M.G.M. designed the experiments; O.F. produced the recombinant lentiviruses; S.H., M.P and C.D.G. performed analysis; S.C. performed bioinformatics analysis; S.G. and M.G.M. wrote the manuscript.

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Correspondence to Maria G. Masucci.

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Gastaldello, S., Hildebrand, S., Faridani, O. et al. A deneddylase encoded by Epstein–Barr virus promotes viral DNA replication by regulating the activity of cullin-RING ligases. Nat Cell Biol 12, 351–361 (2010). https://doi.org/10.1038/ncb2035

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