A Crystal Structure of the Dengue Virus NS5 Protein Reveals a Novel Inter-domain Interface Essential for Protein Flexibility and Virus Replication
DENV causes widespread mosquito-borne viral infections worldwide and nearly 40% of the world’s population is at risk of being infected. Currently, no licensed vaccines or specific drugs are available to treat severe infections by DENV. NS5 is a large protein of 900 amino acids composed of two domains with several key enzymatic activities for viral RNA replication in the host cell and constitutes a prime target for the design of antiviral inhibitors. We succeeded in trapping a stable conformation of the full-length NS5 protein and report its crystal structure at a resolution of 2.3 Å. This conformation reveals the entire inter-domain region and clarifies the determinants of NS5 flexibility. The inter-domain interface is stabilized by several polar contacts between residues projecting from the MTase and RdRp domains of NS5. Several evolutionarily conserved residues at the interface play a crucial role for virus replication as shown by reverse genetics, although the analogous mutations mostly do not abolish the in vitro enzymatic activities of the recombinant proteins.
Vyšlo v časopise:
A Crystal Structure of the Dengue Virus NS5 Protein Reveals a Novel Inter-domain Interface Essential for Protein Flexibility and Virus Replication. PLoS Pathog 11(3): e32767. doi:10.1371/journal.ppat.1004682
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.ppat.1004682
Souhrn
DENV causes widespread mosquito-borne viral infections worldwide and nearly 40% of the world’s population is at risk of being infected. Currently, no licensed vaccines or specific drugs are available to treat severe infections by DENV. NS5 is a large protein of 900 amino acids composed of two domains with several key enzymatic activities for viral RNA replication in the host cell and constitutes a prime target for the design of antiviral inhibitors. We succeeded in trapping a stable conformation of the full-length NS5 protein and report its crystal structure at a resolution of 2.3 Å. This conformation reveals the entire inter-domain region and clarifies the determinants of NS5 flexibility. The inter-domain interface is stabilized by several polar contacts between residues projecting from the MTase and RdRp domains of NS5. Several evolutionarily conserved residues at the interface play a crucial role for virus replication as shown by reverse genetics, although the analogous mutations mostly do not abolish the in vitro enzymatic activities of the recombinant proteins.
Zdroje
1. Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, et al. (2013) The global distribution and burden of dengue. Nature 496: 504–507. doi: 10.1038/nature12060 23563266
2. Mackenzie J (2005) Wrapping things up about virus RNA replication. Traffic 6: 967–977. 16190978
3. Miller S, Krijnse-Locker J (2008) Modification of intracellular membrane structures for virus replication. Nat Rev Microbiol 6: 363–374. doi: 10.1038/nrmicro1890 18414501
4. Salonen A, Ahola T, Kaariainen L (2005) Viral RNA replication in association with cellular membranes. Curr Top Microbiol Immunol 285: 139–173. 15609503
5. Egloff MP, Benarroch D, Selisko B, Romette JL, Canard B (2002) An RNA cap (nucleoside-2′-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J 21: 2757–2768. 12032088
6. Ferron F, Decroly E, Selisko B, Canard B (2012) The viral RNA capping machinery as a target for antiviral drugs. Antiviral Res 96: 21–31. doi: 10.1016/j.antiviral.2012.07.007 22841701
7. Zhou Y, Ray D, Zhao Y, Dong H, Ren S, et al. (2007) Structure and function of flavivirus NS5 methyltransferase. J Virol 81: 3891–3903. 17267492
8. Ray D, Shah A, Tilgner M, Guo Y, Zhao Y, et al. (2006) West Nile virus 5′-cap structure is formed by sequential guanine N-7 and ribose 2′-O methylations by nonstructural protein 5. J Virol 80: 8362–8370. 16912287
9. Dong H, Ren S, Zhang B, Zhou Y, Puig-Basagoiti F, et al. (2008) West Nile virus methyltransferase catalyzes two methylations of the viral RNA cap through a substrate-repositioning mechanism. J Virol 82: 4295–4307. doi: 10.1128/JVI.02202-07 18305027
10. Issur M, Geiss BJ, Bougie I, Picard-Jean F, Despins S, et al. (2009) The flavivirus NS5 protein is a true RNA guanylyltransferase that catalyzes a two-step reaction to form the RNA cap structure. RNA 15: 2340–2350. doi: 10.1261/rna.1609709 19850911
11. Bollati M, Milani M, Mastrangelo E, Ricagno S, Tedeschi G, et al. (2009) Recognition of RNA cap in the Wesselsbron virus NS5 methyltransferase domain: implications for RNA-capping mechanisms in Flavivirus. J Mol Biol 385: 140–152. doi: 10.1016/j.jmb.2008.10.028 18976670
12. Malet H, Egloff MP, Selisko B, Butcher RE, Wright PJ, et al. (2007) Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5. J Biol Chem 282: 10678–10689. 17287213
13. Yap TL, Xu T, Chen YL, Malet H, Egloff MP, et al. (2007) Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution. J Virol 81: 4753–4765. 17301146
14. Zou G, Chen YL, Dong H, Lim CC, Yap LJ, et al. (2011) Functional analysis of two cavities in flavivirus NS5 polymerase. J Biol Chem 286: 14362–14372. doi: 10.1074/jbc.M110.214189 21349834
15. Brooks AJ, Johansson M, John AV, Xu Y, Jans DA, et al. (2002) The interdomain region of dengue NS5 protein that binds to the viral helicase NS3 contains independently functional importin beta 1 and importin alpha/beta-recognized nuclear localization signals. J Biol Chem 277: 36399–36407. 12105224
16. Johansson M, Brooks AJ, Jans DA, Vasudevan SG (2001) A small region of the dengue virus-encoded RNA-dependent RNA polymerase, NS5, confers interaction with both the nuclear transport receptor importin-beta and the viral helicase, NS3. J Gen Virol 82: 735–745. 11257177
17. Tay MYF, Saw WG, Zhao Y, Chan WKK, Singh D, et al. (2014) The C-terminal 50 amino acid residues of Dengue NS3 protein are important for NS3-NS5 interaction and viral replication J Biol Chem In press. doi: 10.1074/jbc.M114.607341 25488659
18. Fernandez-Garcia MD, Meertens L, Bonazzi M, Cossart P, Arenzana-Seisdedos F, et al. (2011) Appraising the roles of CBLL1 and the ubiquitin/proteasome system for flavivirus entry and replication. J Virol 85: 2980–2989. doi: 10.1128/JVI.02483-10 21191016
19. Gomila RC, Martin GW, Gehrke L (2011) NF90 binds the dengue virus RNA 3′ terminus and is a positive regulator of dengue virus replication. PLoS One 6: e16687. doi: 10.1371/journal.pone.0016687 21386893
20. Davis WG, Blackwell JL, Shi PY, Brinton MA (2007) Interaction between the cellular protein eEF1A and the 3′-terminal stem-loop of West Nile virus genomic RNA facilitates viral minus-strand RNA synthesis. J Virol 81: 10172–10187. 17626087
21. Ashour J, Laurent-Rolle M, Shi PY, Garcia-Sastre A (2009) NS5 of dengue virus mediates STAT2 binding and degradation. J Virol 83: 5408–5418. doi: 10.1128/JVI.02188-08 19279106
22. Hannemann H, Sung PY, Chiu HC, Yousuf A, Bird J, et al. (2013) Serotype-specific differences in dengue virus non-structural protein 5 nuclear localization. J Biol Chem 288: 22621–22635. doi: 10.1074/jbc.M113.481382 23770669
23. Tay MY, Fraser JE, Chan WK, Moreland NJ, Rathore AP, et al. (2013) Nuclear localization of dengue virus (DENV) 1–4 non-structural protein 5; protection against all 4 DENV serotypes by the inhibitor Ivermectin. Antiviral Res 99: 301–306. doi: 10.1016/j.antiviral.2013.06.002 23769930
24. Keller TH, Chen YL, Knox JE, Lim SP, Ma NL, et al. (2006) Finding new medicines for flaviviral targets. Novartis Found Symp 277: 102–114; discussion 114–109, 251–103. 17319157
25. Yin Z, Chen YL, Kondreddi RR, Chan WL, Wang G, et al. (2009) N-sulfonylanthranilic acid derivatives as allosteric inhibitors of dengue viral RNA-dependent RNA polymerase. J Med Chem 52: 7934–7937. doi: 10.1021/jm901044z 20014868
26. Yin Z, Chen YL, Schul W, Wang QY, Gu F, et al. (2009) An adenosine nucleoside inhibitor of dengue virus. Proc Natl Acad Sci U S A 106: 20435–20439. doi: 10.1073/pnas.0907010106 19918064
27. Noble CG, Shi PY (2012) Structural biology of dengue virus enzymes: towards rational design of therapeutics. Antiviral Res 96: 115–126. doi: 10.1016/j.antiviral.2012.09.007 22995600
28. Lim SP, Wang QY, Noble CG, Chen YL, Dong H, et al. (2013) Ten years of dengue drug discovery: progress and prospects. Antiviral Res 100: 500–519. doi: 10.1016/j.antiviral.2013.09.013 24076358
29. Bussetta C, Choi KH (2012) Dengue virus nonstructural protein 5 adopts multiple conformations in solution. Biochemistry 51: 5921–5931. 22757685
30. Selisko B, Dutartre H, Guillemot JC, Debarnot C, Benarroch D, et al. (2006) Comparative mechanistic studies of de novo RNA synthesis by flavivirus RNA-dependent RNA polymerases. Virology 351: 145–158. 16631221
31. Lu G, Gong P (2013) Crystal Structure of the full-length Japanese encephalitis virus NS5 reveals a conserved methyltransferase-polymerase interface. PLoS Pathog 9: e1003549. doi: 10.1371/journal.ppat.1003549 23950717
32. Lim SP, Koh JH, Seh CC, Liew CW, Davidson AD, et al. (2013) A crystal structure of the dengue virus non-structural protein 5 (NS5) polymerase delineates interdomain amino acid residues that enhance its thermostability and de novo initiation activities. J Biol Chem 288: 31105–31114. doi: 10.1074/jbc.M113.508606 24025331
33. Potisopon S, Priet S, Collet A, Decroly E, Canard B, et al. (2014) The methyltransferase domain of dengue virus protein NS5 ensures efficient RNA synthesis initiation and elongation by the polymerase domain. Nucleic Acids Res.
34. Aslanidis C, de Jong PJ (1990) Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res 18: 6069–6074. 2235490
35. (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50: 760–763. 15299374
36. Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33: 491–497. 5700707
37. Storoni LC, McCoy AJ, Read RJ (2004) Likelihood-enhanced fast rotation functions. Acta Crystallogr D Biol Crystallogr 60: 432–438. 14993666
38. Lim SP, Sonntag LS, Noble C, Nilar SH, Ng RH, et al. (2011) Small molecule inhibitors that selectively block dengue virus methyltransferase. J Biol Chem 286: 6233–6240. doi: 10.1074/jbc.M110.179184 21147775
39. Collaborative Computational Project N (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50: 760–763. 15299374
40. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66: 213–221. doi: 10.1107/S0907444909052925 20124702
41. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126–2132. 15572765
42. Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66: 12–21. doi: 10.1107/S0907444909042073 20057044
43. Schrödinger L (2010) The PyMOL Molecular Graphics System, Version 1.5.0.4
44. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774–797. 17681537
45. Hayward S, Lee RA (2002) Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J Mol Graph Model 21: 181–183. 12463636
46. Pascal BD, Chalmers MJ, Busby SA, Griffin PR (2009) HD desktop: an integrated platform for the analysis and visualization of H/D exchange data. J Am Soc Mass Spectrom 20: 601–610. doi: 10.1016/j.jasms.2008.11.019 19135386
47. Avis JM, Conn GL, Walker SC (2012) Cis-acting ribozymes for the production of RNA in vitro transcripts with defined 5′ and 3′ ends. Methods Mol Biol 941: 83–98. doi: 10.1007/978-1-62703-113-4_7 23065555
48. Lim SP, Wen D, Yap TL, Yan CK, Lescar J, et al. (2008) A scintillation proximity assay for dengue virus NS5 2′-O-methyltransferase-kinetic and inhibition analyses. Antiviral Res 80: 360–369. doi: 10.1016/j.antiviral.2008.08.005 18809436
49. Niyomrattanakit P, Chen YL, Dong H, Yin Z, Qing M, et al. (2010) Inhibition of dengue virus polymerase by blocking of the RNA tunnel. J Virol 84: 5678–5686. doi: 10.1128/JVI.02451-09 20237086
50. Hung M, Gibbs CS, Tsiang M (2002) Biochemical characterization of rhinovirus RNA-dependent RNA polymerase. Antiviral Res 56: 99–114. 12367717
51. Johnson BW, Russell BJ, Lanciotti RS (2005) Serotype-specific detection of dengue viruses in a fourplex real-time reverse transcriptase PCR assay. J Clin Microbiol 43: 4977–4983. 16207951
52. Moreland NJ, Tay MY, Lim E, Rathore AP, Lim AP, et al. (2012) Monoclonal antibodies against dengue NS2B and NS3 proteins for the study of protein interactions in the flaviviral replication complex. J Virol Methods 179: 97–103. doi: 10.1016/j.jviromet.2011.10.006 22040846
53. Benarroch D, Egloff MP, Mulard L, Guerreiro C, Romette JL, et al. (2004) A structural basis for the inhibition of the NS5 dengue virus mRNA 2′-O-methyltransferase domain by ribavirin 5′-triphosphate. J Biol Chem 279: 35638–35643. 15152003
54. Egloff MP, Decroly E, Malet H, Selisko B, Benarroch D, et al. (2007) Structural and functional analysis of methylation and 5′-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5. J Mol Biol 372: 723–736. 17686489
55. Iglesias NG, Filomatori CV, Gamarnik AV (2011) The F1 motif of dengue virus polymerase NS5 is involved in promoter-dependent RNA synthesis. J Virol 85: 5745–5756. doi: 10.1128/JVI.02343-10 21471248
56. Konermann L, Pan J, Liu YH (2011) Hydrogen exchange mass spectrometry for studying protein structure and dynamics. Chem Soc Rev 40: 1224–1234. doi: 10.1039/c0cs00113a 21173980
57. Bollati M, Alvarez K, Assenberg R, Baronti C, Canard B, et al. (2010) Structure and functionality in flavivirus NS-proteins: perspectives for drug design. Antiviral Res 87: 125–148. doi: 10.1016/j.antiviral.2009.11.009 19945487
58. Zhang X, Chien EY, Chalmers MJ, Pascal BD, Gatchalian J, et al. (2010) Dynamics of the beta2-adrenergic G-protein coupled receptor revealed by hydrogen-deuterium exchange. Anal Chem 82: 1100–1108. doi: 10.1021/ac902484p 20058880
59. Zheng J, Yong HY, Panutdaporn N, Liu C, Tang K, et al. (2014) High resolution HDX-MS reveals distinct mechanisms of RNA recognition and activation by RIG-I and MDA5. Nucleic Acids Res Accepted.
60. Tan CS, Hobson-Peters JM, Stoermer MJ, Fairlie DP, Khromykh AA, et al. (2013) An interaction between the methyltransferase and RNA dependent RNA polymerase domains of the West Nile virus NS5 protein. J Gen Virol 94: 1961–1971. doi: 10.1099/vir.0.054395-0 23740481
61. Vieira-Pires RS, Morais-Cabral JH (2010) 3(10) helices in channels and other membrane proteins. J Gen Physiol 136: 585–592. doi: 10.1085/jgp.201010508 21115694
62. Jones S, Thornton JM (1996) Principles of protein-protein interactions. Proc Natl Acad Sci U S A 93: 13–20. 8552589
63. Armon A, Graur D, Ben-Tal N (2001) ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 307: 447–463. 11243830
64. Li XD, Shan C, Deng CL, Ye HQ, Shi PY, et al. (2014) The interface between methyltransferase and polymerase of NS5 is essential for flavivirus replication. PLoS Negl Trop Dis 8: e2891. doi: 10.1371/journal.pntd.0002891 24852307
65. Wu J, Lu G, Zhang B, Gong P (2014) Perturbation in the conserved methyltransferase-polymerase interface of flavivirus NS5 differentially affects polymerase initiation and elongation. J Virol.
66. Li K, Phoo WW, Luo D (2014) Functional interplay among the flavivirus NS3 protease, helicase, and cofactors. Virologica Sinica: 1–12. doi: 10.1007/s12250-014-3437-7 24470264
67. Luo D, Lim SP, Lescar J (2012) The Flavivirus NS3 Protein: Structure and Functions. Molecular Virology and Control of Flaviviruses: 77.
68. Luo D, Wei N, Doan DN, Paradkar PN, Chong Y, et al. (2010) Flexibility between the protease and helicase domains of the dengue virus NS3 protein conferred by the linker region and its functional implications. Journal of biological chemistry 285: 18817–18827. doi: 10.1074/jbc.M109.090936 20375022
69. Assenberg R, Mastrangelo E, Walter TS, Verma A, Milani M, et al. (2009) Crystal structure of a novel conformational state of the flavivirus NS3 protein: implications for polyprotein processing and viral replication. J Virol 83: 12895–12906. doi: 10.1128/JVI.00942-09 19793813
70. Luo D, Xu T, Hunke C, Grüber G, Vasudevan SG, et al. (2008) Crystal structure of the NS3 protease-helicase from dengue virus. Journal of virology 82: 173–183. 17942558
71. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188–1190. 15173120
72. Selisko B, Wang C, Harris E, Canard B (2014) Regulation of Flavivirus RNA synthesis and replication. Curr Opin Virol 9C: 74–83.
Štítky
Hygiena a epidemiológia Infekčné lekárstvo LaboratóriumČlánok vyšiel v časopise
PLOS Pathogens
2015 Číslo 3
- Parazitičtí červi v terapii Crohnovy choroby a dalších zánětlivých autoimunitních onemocnění
- Očkování proti virové hemoragické horečce Ebola experimentální vakcínou rVSVDG-ZEBOV-GP
- Koronavirus hýbe světem: Víte jak se chránit a jak postupovat v případě podezření?
Najčítanejšie v tomto čísle
- Bacterial Immune Evasion through Manipulation of Host Inhibitory Immune Signaling
- Antimicrobial-Induced DNA Damage and Genomic Instability in Microbial Pathogens
- Is Antigenic Sin Always “Original?” Re-examining the Evidence Regarding Circulation of a Human H1 Influenza Virus Immediately Prior to the 1918 Spanish Flu
- An 18 kDa Scaffold Protein Is Critical for Biofilm Formation