Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5 Reveals a Conserved Methyltransferase-Polymerase Interface
The flavivirus NS5 harbors a methyltransferase (MTase) in its N-terminal ≈265 residues and an RNA-dependent RNA polymerase (RdRP) within the C-terminal part. One of the major interests and challenges in NS5 is to understand the interplay between RdRP and MTase as a unique natural fusion protein in viral genome replication and cap formation. Here, we report the first crystal structure of the full-length flavivirus NS5 from Japanese encephalitis virus. The structure completes the vision for polymerase motifs F and G, and depicts defined intra-molecular interactions between RdRP and MTase. Key hydrophobic residues in the RdRP-MTase interface are highly conserved in flaviviruses, indicating the biological relevance of the observed conformation. Our work paves the way for further dissection of the inter-regulations of the essential enzymatic activities of NS5 and exploration of possible other conformations of NS5 under different circumstances.
Vyšlo v časopise:
Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5 Reveals a Conserved Methyltransferase-Polymerase Interface. PLoS Pathog 9(8): e32767. doi:10.1371/journal.ppat.1003549
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.ppat.1003549
Souhrn
The flavivirus NS5 harbors a methyltransferase (MTase) in its N-terminal ≈265 residues and an RNA-dependent RNA polymerase (RdRP) within the C-terminal part. One of the major interests and challenges in NS5 is to understand the interplay between RdRP and MTase as a unique natural fusion protein in viral genome replication and cap formation. Here, we report the first crystal structure of the full-length flavivirus NS5 from Japanese encephalitis virus. The structure completes the vision for polymerase motifs F and G, and depicts defined intra-molecular interactions between RdRP and MTase. Key hydrophobic residues in the RdRP-MTase interface are highly conserved in flaviviruses, indicating the biological relevance of the observed conformation. Our work paves the way for further dissection of the inter-regulations of the essential enzymatic activities of NS5 and exploration of possible other conformations of NS5 under different circumstances.
Zdroje
1. CleavesGR, DubinDT (1979) Methylation status of intracellular dengue type 2 40 S RNA. Virology 96: 159–165.
2. EgloffMP, BenarrochD, SeliskoB, RometteJL, CanardB (2002) An RNA cap (nucleoside-2′-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J 21: 2757–2768.
3. LiuL, DongH, ChenH, ZhangJ, LingH, et al. (2010) Flavivirus RNA cap methyltransferase: structure, function, and inhibition. Front Biol 5: 286–303.
4. GeissBJ, ThompsonAA, AndrewsAJ, SonsRL, GariHH, et al. (2009) Analysis of flavivirus NS5 methyltransferase cap binding. J Mol Biol 385: 1643–1654.
5. RayD, ShahA, TilgnerM, GuoY, ZhaoY, 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.
6. IssurM, GeissBJ, BougieI, Picard-JeanF, DespinsS, 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.
7. MaletH, EgloffMP, SeliskoB, ButcherRE, WrightPJ, 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.
8. YapTL, XuT, ChenYL, MaletH, EgloffMP, 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.
9. LesburgCA, CableMB, FerrariE, HongZ, MannarinoAF, et al. (1999) Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site. Nat Struct Biol 6: 937–943.
10. ChoiKH, GroarkeJM, YoungDC, KuhnRJ, SmithJL, et al. (2004) The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation. Proc Natl Acad Sci U S A 101: 4425–4430.
11. ThompsonAA, PeersenOB (2004) Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase. EMBO J 23: 3462–3471.
12. GongP, PeersenOB (2010) Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase. Proc Natl Acad Sci U S A 107: 22505–22510.
13. ZhangB, DongH, ZhouY, ShiPY (2008) Genetic interactions among the West Nile virus methyltransferase, the RNA-dependent RNA polymerase, and the 5′ stem-loop of genomic RNA. J Virol 82: 7047–7058.
14. FilomatoriCV, LodeiroMF, AlvarezDE, SamsaMM, PietrasantaL, et al. (2006) A 5′ RNA element promotes dengue virus RNA synthesis on a circular genome. Genes Dev 20: 2238–2249.
15. RawlinsonSM, PryorMJ, WrightPJ, JansDA (2009) CRM1-mediated nuclear export of dengue virus RNA polymerase NS5 modulates interleukin-8 induction and virus production. J Biol Chem 284: 15589–15597.
16. BrooksAJ, JohanssonM, JohnAV, XuY, JansDA, 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.
17. VasudevanSG, JohanssonM, BrooksAJ, LlewellynLE, JansDA (2001) Characterisation of inter- and intra-molecular interactions of the dengue virus RNA dependent RNA polymerase as potential drug targets. Farmaco 56: 33–36.
18. ForwoodJK, BrooksA, BriggsLJ, XiaoCY, JansDA, et al. (1999) The 37-amino-acid interdomain of dengue virus NS5 protein contains a functional NLS and inhibitory CK2 site. Biochem Biophys Res Commun 257: 731–737.
19. BussettaC, ChoiKH (2012) Dengue virus nonstructural protein 5 adopts multiple conformations in solution. Biochemistry 51: 5921–5931.
20. AssenbergR, RenJ, VermaA, WalterTS, AldertonD, et al. (2007) Crystal structure of the Murray Valley encephalitis virus NS5 methyltransferase domain in complex with cap analogues. J Gen Virol 88: 2228–2236.
21. ButcherSJ, GrimesJM, MakeyevEV, BamfordDH, StuartDI (2001) A mechanism for initiating RNA-dependent RNA polymerization. Nature 410: 235–240.
22. JohanssonM, BrooksAJ, JansDA, VasudevanSG (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.
23. PryorMJ, RawlinsonSM, ButcherRE, BartonCL, WaterhouseTA, et al. (2007) Nuclear localization of dengue virus nonstructural protein 5 through its importin alpha/beta-recognized nuclear localization sequences is integral to viral infection. Traffic 8: 795–807.
24. WuY, LouZ, MiaoY, YuY, DongH, et al. (2010) Structures of EV71 RNA-dependent RNA polymerase in complex with substrate and analogue provide a drug target against the hand-foot-and-mouth disease pandemic in China. Protein Cell 1: 491–500.
25. ZamyatkinDF, ParraF, AlonsoJM, HarkiDA, PetersonBR, et al. (2008) Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase. J Biol Chem 283: 7705–7712.
26. JagerJ, SmerdonSJ, WangJ, BoisvertDC, SteitzTA (1994) Comparison of three different crystal forms shows HIV-1 reverse transcriptase displays an internal swivel motion. Structure 2: 869–876.
27. ChoiKH, GalleiA, BecherP, RossmannMG (2006) The structure of bovine viral diarrhea virus RNA-dependent RNA polymerase and its amino-terminal domain. Structure 14: 1107–1113.
28. BrocchieriL, KarlinS (1994) Geometry of interplanar residue contacts in protein structures. Proc Natl Acad Sci U S A 91: 9297–9301.
29. ZhouY, RayD, ZhaoY, DongH, RenS, et al. (2007) Structure and function of flavivirus NS5 methyltransferase. J Virol 81: 3891–3903.
30. BressanelliS, TomeiL, RousselA, IncittiI, VitaleRL, et al. (1999) Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Proc Natl Acad Sci U S A 96: 13034–13039.
31. MarcotteLL, WassAB, GoharaDW, PathakHB, ArnoldJJ, et al. (2007) Crystal structure of poliovirus 3CD protein: virally encoded protease and precursor to the RNA-dependent RNA polymerase. J Virol 81: 3583–3596.
32. ChenY, SuC, KeM, JinX, XuL, et al. (2011) Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2′-O-methylation by nsp16/nsp10 protein complex. PLoS Pathog 7: e1002294.
33. MastrangeloE, BollatiM, MilaniM, SeliskoB, PeyraneF, et al. (2007) Structural bases for substrate recognition and activity in Meaban virus nucleoside-2′-O-methyltransferase. Protein Sci 16: 1133–1145.
34. BollatiM, MilaniM, MastrangeloE, RicagnoS, TedeschiG, 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.
35. WangQ, WengL, TianX, CounorD, SunJ, et al. (2012) Effect of the methyltransferase domain of Japanese encephalitis virus NS5 on the polymerase activity. Biochim Biophys Acta 1819: 411–418.
36. GongP, KortusMG, NixJC, DavisRE, PeersenOB (2013) Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts. PLoS One 8: e60272.
37. MartinCT, MullerDK, ColemanJE (1988) Processivity in early stages of transcription by T7 RNA polymerase. Biochemistry 27: 3966–3974.
38. CarpousisAJ, GrallaJD (1980) Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lac UV5 promoter. Biochemistry 19: 3245–3253.
39. KaoCC, YangX, KlineA, WangQM, BarketD, et al. (2000) Template requirements for RNA synthesis by a recombinant hepatitis C virus RNA-dependent RNA polymerase. J Virol 74: 11121–11128.
40. SeliskoB, DutartreH, GuillemotJC, DebarnotC, BenarrochD, et al. (2006) Comparative mechanistic studies of de novo RNA synthesis by flavivirus RNA-dependent RNA polymerases. Virology 351: 145–158.
41. GongP, MartinCT (2006) Mechanism of instability in abortive cycling by T7 RNA polymerase. J Biol Chem 281: 23533–23544.
42. MosleyRT, EdwardsTE, MurakamiE, LamAM, GriceRL, et al. (2012) Structure of hepatitis C virus polymerase in complex with primer-template RNA. J Virol 86: 6503–6511.
43. JinZ, LevequeV, MaH, JohnsonKA, KlumppK (2012) Assembly, purification, and pre-steady-state kinetic analysis of active RNA-dependent RNA polymerase elongation complex. J Biol Chem 287: 10674–10683.
44. GoharaDW, HaCS, KumarS, GhoshB, ArnoldJJ, et al. (1999) Production of “authentic” poliovirus RNA-dependent RNA polymerase (3D(pol)) by ubiquitin-protease-mediated cleavage in Escherichia coli. Protein Expr Purif 17: 128–138.
45. PflugrathJW (1999) The finer things in X-ray diffraction data collection. Acta Crystallogr D Biol Crystallogr 55: 1718–1725.
46. McCoyAJ, Grosse-KunstleveRW, AdamsPD, WinnMD, StoroniLC, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658–674.
47. EmsleyP, CowtanK (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126–2132.
48. AdamsPD, Grosse-KunstleveRW, HungLW, IoergerTR, McCoyAJ, et al. (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58: 1948–1954.
49. BrungerAT, AdamsPD, CloreGM, DeLanoWL, GrosP, et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54: 905–921.
Štítky
Hygiena a epidemiológia Infekčné lekárstvo LaboratóriumČlánok vyšiel v časopise
PLOS Pathogens
2013 Číslo 8
- Očkování proti virové hemoragické horečce Ebola experimentální vakcínou rVSVDG-ZEBOV-GP
- Parazitičtí červi v terapii Crohnovy choroby a dalších zánětlivých autoimunitních onemocnění
- Koronavirus hýbe světem: Víte jak se chránit a jak postupovat v případě podezření?
Najčítanejšie v tomto čísle
- Host Immune Response to Intestinal Amebiasis
- Bed Bugs and Infectious Disease: A Case for the Arboviruses
- Discovery of Anthelmintic Drug Targets and Drugs Using Chokepoints in Nematode Metabolic Pathways
- Relevance of Trehalose in Pathogenicity: Some General Rules, Yet Many Exceptions