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Competitive and Cooperative Interactions Mediate RNA Transfer from Herpesvirus Saimiri ORF57 to the Mammalian Export Adaptor ALYREF


The essential herpesvirus adaptor protein HVS ORF57, which has homologs in all other herpesviruses, promotes viral mRNA export by utilizing the cellular mRNA export machinery. ORF57 protein specifically recognizes viral mRNA transcripts, and binds to proteins of the cellular transcription-export (TREX) complex, in particular ALYREF. This interaction introduces viral mRNA to the NXF1 pathway, subsequently directing it to the nuclear pore for export to the cytoplasm. Here we have used a range of techniques to reveal the sites for direct contact between RNA and ORF57 in the absence and presence of ALYREF. A binding site within ORF57 was characterized which recognizes specific viral mRNA motifs. When ALYREF is present, part of this ORF57 RNA binding site, composed of an α-helix, binds preferentially to ALYREF. This competitively displaces viral RNA from the α-helix, but contact with RNA is still maintained by a flanking region. At the same time, the flexible N-terminal domain of ALYREF comes into contact with the viral RNA, which becomes engaged in an extensive network of synergistic interactions with both ALYREF and ORF57. Transfer of RNA to ALYREF in the ternary complex, and involvement of individual ORF57 residues in RNA recognition, were confirmed by UV cross-linking and mutagenesis. The atomic-resolution structure of the ORF57-ALYREF interface was determined, which noticeably differed from the homologous ICP27-ALYREF structure. Together, the data provides the first site-specific description of how viral mRNA is locked by a herpes viral adaptor protein in complex with cellular ALYREF, giving herpesvirus access to the cellular mRNA export machinery. The NMR strategy used may be more generally applicable to the study of fuzzy protein-protein-RNA complexes which involve flexible polypeptide regions.


Vyšlo v časopise: Competitive and Cooperative Interactions Mediate RNA Transfer from Herpesvirus Saimiri ORF57 to the Mammalian Export Adaptor ALYREF. PLoS Pathog 10(2): e32767. doi:10.1371/journal.ppat.1003907
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1003907

Souhrn

The essential herpesvirus adaptor protein HVS ORF57, which has homologs in all other herpesviruses, promotes viral mRNA export by utilizing the cellular mRNA export machinery. ORF57 protein specifically recognizes viral mRNA transcripts, and binds to proteins of the cellular transcription-export (TREX) complex, in particular ALYREF. This interaction introduces viral mRNA to the NXF1 pathway, subsequently directing it to the nuclear pore for export to the cytoplasm. Here we have used a range of techniques to reveal the sites for direct contact between RNA and ORF57 in the absence and presence of ALYREF. A binding site within ORF57 was characterized which recognizes specific viral mRNA motifs. When ALYREF is present, part of this ORF57 RNA binding site, composed of an α-helix, binds preferentially to ALYREF. This competitively displaces viral RNA from the α-helix, but contact with RNA is still maintained by a flanking region. At the same time, the flexible N-terminal domain of ALYREF comes into contact with the viral RNA, which becomes engaged in an extensive network of synergistic interactions with both ALYREF and ORF57. Transfer of RNA to ALYREF in the ternary complex, and involvement of individual ORF57 residues in RNA recognition, were confirmed by UV cross-linking and mutagenesis. The atomic-resolution structure of the ORF57-ALYREF interface was determined, which noticeably differed from the homologous ICP27-ALYREF structure. Together, the data provides the first site-specific description of how viral mRNA is locked by a herpes viral adaptor protein in complex with cellular ALYREF, giving herpesvirus access to the cellular mRNA export machinery. The NMR strategy used may be more generally applicable to the study of fuzzy protein-protein-RNA complexes which involve flexible polypeptide regions.


Zdroje

1. GlisovicT, BachorikJL, YongJ, DreyfussG (2008) RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett 582: 1977–1986.

2. StrasserK, MasudaS, MasonP, PfannstielJ, OppizziM, et al. (2002) TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417: 304–308.

3. MasudaS, DasR, ChengH, HurtE, DormanN, et al. (2005) Recruitment of the human TREX complex to mRNA during splicing. Genes Dev 19: 1512–1517.

4. HautbergueGM, HungML, WalshMJ, SnijdersAP, ChangCT, et al. (2009) UIF, a New mRNA Export Adaptor that Works Together with REF/ALY, Requires FACT for Recruitment to mRNA. Curr Biol 19: 1918–1924.

5. HautbergueGM, HungML, GolovanovAP, LianLY, WilsonSA (2008) Mutually exclusive interactions drive handover of mRNA from export adaptors to TAP. Proc Natl Acad Sci USA 105: 5154–5159.

6. ViphakoneN, HautbergueGM, WalshM, ChangCT, HollandA, et al. (2012) TREX exposes the RNA-binding domain of Nxf1 to enable mRNA export. Nat Commun 3: 1006.

7. StutzF, BachiA, DoerksT, BraunIC, SeraphinB, et al. (2000) REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. RNA 6: 638–650.

8. RodriguesJP, RodeM, GatfieldD, BlencoweBJ, Carmo-FonsecaM, et al. (2001) REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus. Proc Natl Acad Sci USA 98: 1030–1035.

9. Perez-AlvaradoGC, Martinez-YamoutM, AllenMM, GrosschedlR, DysonHJ, et al. (2003) Structure of the nuclear factor ALY: insights into post-transcriptional regulatory and mRNA nuclear export processes. Biochemistry 42: 7348–7357.

10. GolovanovAP, HautbergueGM, TintaruAM, LianLY, WilsonSA (2006) The solution structure of REF2-I reveals interdomain interactions and regions involved in binding mRNA export factors and RNA. RNA 12: 1933–1948.

11. HungML, HautbergueGM, SnijdersAP, DickmanMJ, WilsonSA (2010) Arginine methylation of REF/ALY promotes efficient handover of mRNA to TAP/NXF1. Nucleic Acids Research 38: 3351–3361.

12. BachiA, BraunIC, RodriguesJP, PanteN, RibbeckK, et al. (2000) The C-terminal domain of TAP interacts with the nuclear pore complex and promotes export of specific CTE-bearing RNA substrates. RNA 6: 136–158.

13. FribourgS, BraunIC, IzaurraldeE, ContiE (2001) Structural basis for the recognition of a nucleoporin FG repeat by the NTF2-like domain of the TAP/p15 mRNA nuclear export factor. Mol Cell 8: 645–656.

14. GrantRP, HurtE, NeuhausD, StewartM (2002) Structure of the C-terminal FG-nucleoporin binding domain of Tap/NXF1. Nature Struct Biol 9: 247–251.

15. KoffaMD, ClementsJB, IzaurraldeE, WaddS, WilsonSA, et al. (2001) Herpes simplex virus ICP27 protein provides viral mRNAs with access to the cellular mRNA export pathway. EMBO J 20: 5769–5778.

16. ChenIH, SciabicaKS, Sandri-GoldinRM (2002) ICP27 interacts with the RNA export factor Aly/REF to direct herpes simplex virus type 1 intronless mRNAs to the TAP export pathway. J Virol 76: 12877–12889.

17. MalikP, BlackbournDJ, ClementsJB (2004) The evolutionarily conserved Kaposi's sarcoma-associated herpesvirus ORF57 protein interacts with REF protein and acts as an RNA export factor. J Biol Chem 279: 33001–33011.

18. HiriartE, FarjotG, GruffatH, NguyenMV, SergeantA, et al. (2003) A novel nuclear export signal and a REF interaction domain both promote mRNA export by the Epstein-Barr virus EB2 protein. J Biol Chem 278: 335–342.

19. JacksonBR, BoyneJR, NoerenbergM, TaylorA, HautbergueGM, et al. (2011) An Interaction between KSHV ORF57 and UIF Provides mRNA-Adaptor Redundancy in Herpesvirus Intronless mRNA Export. PLoS Pathog 7: e1002138.

20. GoodwinDJ, HallKT, StevensonAJ, MarkhamAF, WhitehouseA (1999) The open reading frame 57 gene product of herpesvirus saimiri shuttles between the nucleus and cytoplasm and is involved in viral RNA nuclear export. J Virol 73: 10519–10524.

21. WilliamsBJ, BoyneJR, GoodwinDJ, RoadenL, HautbergueGM, et al. (2005) The prototype gamma-2 herpesvirus nucleocytoplasmic shuttling protein, ORF 57, transports viral RNA through the cellular mRNA export pathway. Biochem J 387: 295–308.

22. BoyneJR, ColganKJ, WhitehouseA (2008) Recruitment of the complete hTREX complex is required for Kaposi's sarcoma-associated herpesvirus intronless mRNA nuclear export and virus replication. PLoS Pathog 4: e1000194.

23. BoyneJR, ColganKJ, WhitehouseA (2008) Herpesvirus saimiri ORF57: a post-transcriptional regulatory protein. Front Biosci 13: 2928–2938.

24. StubbsSH, HunterOV, HooverA, ConradNK (2012) Viral Factors Reveal a Role for REF/Aly in Nuclear RNA Stability. Mol Cell Biol 32: 1260–1270.

25. Sandri-GoldinRM (2011) The many roles of the highly interactive HSV protein ICP27, a key regulator of infection. Future Microbiol 6: 1261–1277.

26. TaylorA, JacksonBR, NoerenbergM, HughesDJ, BoyneJR, et al. (2011) Mutation of a C-Terminal Motif Affects Kaposi's Sarcoma-Associated Herpesvirus ORF57 RNA Binding, Nuclear Trafficking, and Multimerization. J Virol 85: 7881–7891.

27. SchumannS, JacksonBR, Baquero-PerezB, WhitehouseA (2013) Kaposi's Sarcoma-Associated Herpesvirus ORF57 Protein: Exploiting All Stages of Viral mRNA Processing. Viruses 5: 1901–1923.

28. HiriartE, BardouilletL, ManetE, GruffatH, PeninF, et al. (2003) A region of the Epstein-Barr virus (EBV) mRNA export factor EB2 containing an arginine-rich motif mediates direct binding to RNA. J Biol Chem 278: 37790–37798.

29. TothZ, StammingerT (2008) The human cytomegalovirus regulatory protein UL69 and its effect on mRNA export. Front Biosci 13: 2939–2949.

30. TunnicliffeRB, HautbergueGM, KalraP, JacksonBR, WhitehouseA, et al. (2011) Structural basis for the recognition of cellular mRNA export factor REF by herpes viral proteins HSV-1 ICP27 and HVS ORF57. PLoS Pathog 7: e1001244.

31. GrayKA, DaughertyLC, GordonSM, SealRL, WrightMW, et al. (2013) Genenames.org: the HGNC resources in 2013. Nucleic Acids Res 41: D545–D552.

32. ColganKJ, BoyneJR, WhitehouseA (2009) Identification of a response element in a herpesvirus saimiri mRNA recognized by the ORF57 protein. J Gen Virol 90: 596–601.

33. MearsWE, RiceSA (1996) The RGG box motif of the herpes simplex virus ICP27 protein mediates an RNA-binding activity and determines in vivo methylation. J Virol 70: 7445–7453.

34. Sandri-GoldinRM (1998) ICP27 mediates HSV RNA export by shuttling through a leucine-rich nuclear export signal and binding viral intronless RNAs through an RGG motif. Genes Dev 12: 868–879.

35. MackerethCD, SattlerM (2012) Dynamics in multi-domain protein recognition of RNA. Curr Opin Struct Biol 22: 287–296.

36. ValkovE, DeanJC, JaniD, KuhlmannSI, StewartM (2012) Structural basis for the assembly and disassembly of mRNA nuclear export complexes. Biochim Biophys Acta 1819: 578–592.

37. TakahashiH, NakanishiT, KamiK, ArataY, ShimadaI (2000) A novel NMR method for determining the interfaces of large protein-protein complexes. Nat Struct Biol 7: 220–223.

38. GolovanovAP, BlankleyRT, AvisJM, BermelW (2007) Isotopically discriminated NMR spectroscopy: a tool for investigating complex protein interactions in vitro. J Am Chem Soc 129: 6528–6535.

39. LaneAN, KellyG, RamosA, FrenkielTA (2001) Determining binding sites in protein-nucleic acid complexes by cross-saturation. J Biomol NMR 21: 127–139.

40. JonesDT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292: 195–202.

41. LacroixE, VigueraAR, SerranoL (1998) Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol 284: 173–191.

42. ShenY, DelaglioF, CornilescuG, BaxA (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44: 213–223.

43. KuzmicP (1996) Program DYNAFIT for the analysis of enzyme kinetic data: Application to HIV proteinase. Analytical Biochemistry 237: 260–273.

44. WilliamsonJR (2008) Cooperativity in macromolecular assembly. Nature Chem Biol 4: 458–465.

45. BorgM, MittagT, PawsonT, TyersM, Forman-KayJD, et al. (2007) Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity. Proc Natl Acad Sci USA 104: 9650–9655.

46. CalnanBJ, BiancalanaS, HudsonD, FrankelAD (1991) Analysis of arginine-rich peptides from the HIV Tat protein reveals unusual features of RNA-protein recognition. Genes Dev 5: 201–210.

47. WilkinsonTA, ZhuLY, HuWD, ChenY (2004) Retention of conformational flexibility in HIV-1 Rev-RNA complexes. Biochemistry 43: 16153–16160.

48. BayerTS, BoothLN, KnudsenSM, EllingtonAD (2005) Arginine-rich motifs present multiple interfaces for specific binding by RNA. RNA 11: 1848–1857.

49. LundeBM, MooreC, VaraniG (2007) RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol 8: 479–490.

50. KielkopfCL, RodionovaNA, GreenMR, BurleySK (2001) A novel peptide recognition mode revealed by the X-ray structure of a core U2AF-(35)/U2AF(65) heterodimer. Cell 106: 595–605.

51. KielkopfCL, LuckeS, GreenAR (2004) U2AF homology motifs: protein recognition in the RRM world. Genes & Dev 18: 1513–1526.

52. CleryA, BlatterM, AllainFH (2008) RNA recognition motifs: boring? Not quite. Curr Opin Struct Biol 18: 290–298.

53. MajerciakV, YamanegiK, NieSH, ZhengZM (2006) Structural and functional analyses of Kaposi sarcoma-associated herpesvirus ORF57 nuclear localization signals in living cells. J Biol Chem 281: 28365–28378.

54. TianX, Devi-RaoG, GolovanovAP, Sandri-GoldinRM (2013) The Interaction of the Cellular Export Adaptor Protein Aly/REF with ICP27 Contributes to the Efficiency of Herpes Simplex Virus 1 mRNA Export. J Virol 87: 7210–7217.

55. TompaP, FuxreiterM (2008) Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. Trends Biochem Sci 33: 2–8.

56. TompaP (2011) Unstructural biology coming of age. Curr Opin Struct Biol 21: 419–425.

57. BoehrDD, NussinovR, WrightPE (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 5: 789–796.

58. MittagT, KayLE, Forman-KayJD (2010) Protein dynamics and conformational disorder in molecular recognition. J Mol Recogn 23: 105–116.

59. DaveyNE, TraveG, GibsonTJ (2011) How viruses hijack cell regulation. Trends Biochem Sci 36: 159–169.

60. EllisdonAM, DimitrovaL, HurtE, StewartM (2012) Structural basis for the assembly and nucleic acid binding of the TREX-2 transcription-export complex. Nature Struct Mol Biol 19: 328–U390.

61. MarshJA, TeichmannSA, Forman-KayJD (2012) Probing the diverse landscape of protein flexibility and binding. Curr Opin Struct Biol 22: 643–650.

62. GolovanovAP, HautbergueGM, WilsonSA, LianLY (2004) A simple method for improving protein solubility and long-term stability. J Am Chem Soc 126: 8933–8939.

63. DelaglioF, GrzesiekS, VuisterGW, ZhuG, PfeiferJ, et al. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6: 277–293.

64. GuntertP (2004) Automated NMR structure calculation with CYANA. Methods Mol Biol 278: 353–378.

65. StuartAC, BorzilleriKA, WithkaJM, PalmerAG (1999) Compensating for Variations in 1H-13C Scalar Coupling Constants in Isotope-Filtered NMR Experiments. J Am Chem Soc 121: 5346–5347.

66. ZwahlenC, LegaultP, VincentSbJF, GreenblattJ, KonratR, et al. (1997) Methods for Measurement of Intermolecular NOEs by Multinuclear NMR Spectroscopy: Application to a bacteriophage λ N-peptide/boxB RNA complex. J Am Chem Soc 119: 6711–6721.

67. HoopsS, SahleS, GaugesR, LeeC, PahleJ, et al. (2006) COPASI - A COmplex PAthway SImulator. Bioinformatics 22: 3067–3074.

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