1887

Abstract

Epstein–Barr virus (EBV) nuclear antigen 1 (EBNA-1) plays key roles in both the regulation of gene expression and the replication of the EBV genome in latently infected cells. To characterize the RNA-binding activity of EBNA-1, it was demonstrated that EBNA-1 binds efficiently to RNA homopolymers that are composed of poly(G) and weakly to those composed of poly(U). All three RGG boxes of EBNA-1 contributed additively to poly(G)-binding activity and could mediate RNA binding when attached to a heterologous protein in an RNA gel mobility-shift assay. -transcribed EBV and non-EBV RNA probes revealed that EBNA-1 bound to most RNAs examined and the affinity increased as the content of G and U increased, as demonstrated in competition assays. Among these probes, the 5′ non-coding region (NCR) (nt 131–278) of hepatitis C virus RNA appeared to be the strongest competitor for EBNA-1 binding to the EBV-encoded small nuclear RNA 1 (EBER1) probe, whereas a mutant 5′ NCR RNA with partially disrupted secondary structure was a weak competitor. Furthermore, the interaction of endogenous EBNA-1 and EBER1 in EBV-infected cells was demonstrated by a ribonucleoprotein immunoprecipitation assay. These results revealed that EBNA-1 is a DNA-binding protein with strong binding activity to a relatively broad spectrum of RNA and suggested an additional biological impact of EBNA-1 through its ability to bind to RNA.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.80239-0
2004-10-01
2019-09-22
Loading full text...

Full text loading...

/deliver/fulltext/jgv/85/10/vir852755.html?itemId=/content/journal/jgv/10.1099/vir.0.80239-0&mimeType=html&fmt=ahah

References

  1. Ali, N. & Siddiqui, A. ( 1997; ). The La antigen binds 5′ noncoding region of the hepatitis C virus RNA in the context of the initiator AUG codon and stimulates internal ribosome entry site-mediated translation. Proc Natl Acad Sci U S A 94, 2249–2254.[CrossRef]
    [Google Scholar]
  2. Ambinder, R. F., Shah, W. A., Rawlins, D. R., Hayward, G. S. & Hayward, S. D. ( 1990; ). Definition of the sequence requirements for binding of the EBNA-1 protein to its palindromic target sites in Epstein-Barr virus DNA. J Virol 64, 2369–2379.
    [Google Scholar]
  3. Ambinder, R. F., Mullen, M. A., Chang, Y.-N., Hayward, G. S. & Hayward, S. D. ( 1991; ). Functional domains of Epstein-Barr virus nuclear antigen EBNA-1. J Virol 65, 1466–1478.
    [Google Scholar]
  4. Attrill, H. L., Cumming, S. A., Clements, J. B. & Graham, S. V. ( 2002; ). The herpes simplex virus type 1 US11 protein binds the coterminal UL12, UL13, and UL14 RNAs and regulates UL13 expression in vivo. J Virol 76, 8090–8100.[CrossRef]
    [Google Scholar]
  5. Belsham, G. J., Sonenberg, N. & Svitkin, Y. V. ( 1995; ). The role of the La autoantigen in internal initiation. Curr Top Microbiol Immunol 203, 85–98.
    [Google Scholar]
  6. Bochkarev, A., Barwell, J. A., Pfuetzner, R. A., Bochkareva, E., Frappier, L. & Edwards, A. M. ( 1996; ). Crystal structure of the DNA-binding domain of the Epstein–Barr virus origin binding protein, EBNA1, bound to DNA. Cell 84, 791–800.[CrossRef]
    [Google Scholar]
  7. Cassiday, L. A. & Maher, L. J., III ( 2002; ). Having it both ways: transcription factors that bind DNA and RNA. Nucleic Acids Res 30, 4118–4126.[CrossRef]
    [Google Scholar]
  8. Chang, Y., Tung, C.-H., Huang, Y.-T., Lu, J., Chen, J.-Y. & Tsai, C.-H. ( 1999; ). Requirement for cell-to-cell contact in Epstein-Barr virus infection of nasopharyngeal carcinoma cells and keratinocytes. J Virol 73, 8857–8866.
    [Google Scholar]
  9. Chen, M.-R., Hsu, T.-Y., Chen, J.-Y. & Yang, C.-S. ( 1990; ). Molecular characterization of a cDNA clone encoding the Epstein-Barr virus (EBV) DNase. J Virol Methods 29, 127–141.[CrossRef]
    [Google Scholar]
  10. Chen, M.-R., Middeldorp, J. M. & Hayward, S. D. ( 1993; ). Separation of the complex DNA binding domain of EBNA-1 into DNA recognition and dimerization subdomains of novel structure. J Virol 67, 4875–4885.
    [Google Scholar]
  11. Chen, M.-R., Zong, J. & Hayward, S. D. ( 1994; ). Delineation of a 16 amino acid sequence that forms a core DNA recognition motif in the Epstein-Barr virus EBNA-1 protein. Virology 205, 486–495.[CrossRef]
    [Google Scholar]
  12. Chen, M.-R., Yang, J.-F., Wu, C.-W., Middeldorp, J. M. & Chen, J.-Y. ( 1998; ). Physical association between the EBV protein EBNA-1 and P32/TAP/hyaluronectin. J Biomed Sci 5, 173–179.[CrossRef]
    [Google Scholar]
  13. Chen, M.-R., Tsai, C.-H., Wu, F.-F., Kan, S.-H., Yang, C.-S. & Chen, J.-Y. ( 1999; ). The major immunogenic epitopes of Epstein–Barr virus (EBV) nuclear antigen 1 are encoded by sequence domains which vary among nasopharyngeal carcinoma biopsies and EBV-associated cell lines. J Gen Virol 80, 447–455.
    [Google Scholar]
  14. Chen, M.-R., Liu, M.-Y., Hsu, S.-M., Fong, C.-C., Chen, C.-J., Chen, I.-H., Hsu, M.-M., Yang, C.-S. & Chen, J.-Y. ( 2001; ). Use of bacterially expressed EBNA-1 protein cloned from a nasopharyngeal carcinoma (NPC) biopsy as a screening test for NPC patients. J Med Virol 64, 51–57.[CrossRef]
    [Google Scholar]
  15. Cobianchi, F., Karpel, R. L., Williams, K. R., Notario, V. & Wilson, S. H. ( 1988; ). Mammalian heterogeneous nuclear ribonucleoprotein complex protein A1. Large-scale overproduction in Escherichia coli and cooperative binding to single-stranded nucleic acids. J Biol Chem 263, 1063–1071.
    [Google Scholar]
  16. Fu, X.-D. ( 1995; ). The superfamily of arginine/serine-rich splicing factors. RNA 1, 663–680.
    [Google Scholar]
  17. Hearing, J. C. & Levine, A. J. ( 1985; ). The Epstein-Barr virus nuclear antigen (BamHI K antigen) is a single-stranded DNA binding phosphoprotein. Virology 145, 105–116.[CrossRef]
    [Google Scholar]
  18. Helbig, R. & Fackelmayer, F. O. ( 2003; ). Scaffold attachment factor A (SAF-A) is concentrated in inactive X chromosome territories through its RGG domain. Chromosoma 112, 173–182.[CrossRef]
    [Google Scholar]
  19. Holcik, M. & Korneluk, R. G. ( 2000; ). Functional characterization of the X-linked inhibitor of apoptosis (XIAP) internal ribosome entry site element: role of La autoantigen in XIAP translation. Mol Cell Biol 20, 4648–4657.[CrossRef]
    [Google Scholar]
  20. Huber, M. D., Dworet, J. H., Shire, K., Frappier, L. & McAlear, M. A. ( 2000; ). The budding yeast homolog of the human EBNA1-binding protein 2 (Ebp2p) is an essential nucleolar protein required for pre-rRNA processing. J Biol Chem 275, 28764–28773.[CrossRef]
    [Google Scholar]
  21. Kapoor, P. & Frappier, L. ( 2003; ). EBNA1 partitions Epstein-Barr virus plasmids in yeast cells by attaching to human EBNA1-binding protein 2 on mitotic chromosomes. J Virol 77, 6946–6956.[CrossRef]
    [Google Scholar]
  22. Kieff, E. ( 1996; ). Epstein-Barr virus and its replication. In Fields Virology, 3rd edn, pp. 2343–2396. Edited by B. N. Fields, D. M. Knipe & P. M. Howley. Philadelphia, PA: Lippincott-Raven.
  23. Kienzle, N., Young, D. B., Liaskou, D., Buck, M., Greco, S. & Sculley, T. B. ( 1999; ). Intron retention may regulate expression of Epstein-Barr virus nuclear antigen 3 family genes. J Virol 73, 1195–1204.
    [Google Scholar]
  24. Kiledjian, M. & Dreyfuss, G. ( 1992; ). Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. EMBO J 11, 2655–2664.
    [Google Scholar]
  25. Krainer, A. R., Conway, G. C. & Kozak, D. ( 1990; ). Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells. Genes Dev 4, 1158–1171.[CrossRef]
    [Google Scholar]
  26. Kube, D., Vockerodt, M., Weber, O. & 8 other authors ( 1999; ). Expression of Epstein-Barr virus nuclear antigen 1 is associated with enhanced expression of CD25 in the Hodgkin cell line L428. J Virol 73, 1630–1636.
    [Google Scholar]
  27. Lerga, A., Hallier, M., Delva, L., Orvain, C., Gallais, I., Marie, J. & Moreau-Gachelin, F. ( 2001; ). Identification of an RNA binding specificity for the potential splicing factor TLS. J Biol Chem 276, 6807–6816.[CrossRef]
    [Google Scholar]
  28. Li, C., Ai, L.-S., Lin, C.-H., Hsieh, M., Li, Y.-C. & Li, S.-Y. ( 1998; ). Protein N-arginine methylation in adenosine dialdehyde-treated lymphoblastoid cells. Arch Biochem Biophys 351, 53–59.[CrossRef]
    [Google Scholar]
  29. Mackey, D., Middleton, T. & Sugden, B. ( 1995; ). Multiple regions within EBNA1 can link DNAs. J Virol 69, 6199–6208.
    [Google Scholar]
  30. Manley, J. L. & Tacke, R. ( 1996; ). SR proteins and splicing control. Genes Dev 10, 1569–1579.[CrossRef]
    [Google Scholar]
  31. Maraia, R. J. & Intine, R. V. A. ( 2001; ). Recognition of nascent RNA by the human La antigen: conserved and divergent features of structure and function. Mol Cell Biol 21, 367–379.[CrossRef]
    [Google Scholar]
  32. Marechal, V., Dehee, A., Chikhi-Brachet, R., Piolot, T., Coppey-Moisan, M. & Nicolas, J.-C. ( 1999; ). Mapping EBNA-1 domains involved in binding to metaphase chromosomes. J Virol 73, 4385–4392.
    [Google Scholar]
  33. Mears, W. E. & Rice, S. A. ( 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.
    [Google Scholar]
  34. Middleton, T. & Sugden, B. ( 1992; ). EBNA1 can link the enhancer element to the initiator element of the Epstein-Barr virus plasmid origin of DNA replication. J Virol 66, 489–495.
    [Google Scholar]
  35. Miller, M. M. & Read, L. K. ( 2003; ). Trypanosoma brucei: functions of RBP16 cold shock and RGG domains in macromolecular interactions. Exp Parasitol 105, 140–148.[CrossRef]
    [Google Scholar]
  36. Niranjanakumari, S., Lasda, E., Brazas, R. & Garcia-Blanco, M. A. ( 2002; ). Reversible cross-linking combined with immunoprecipitation to study RNA–protein interactions in vivo. Methods 26, 182–190.[CrossRef]
    [Google Scholar]
  37. Pannone, B. K., Xue, D. & Wolin, S. L. ( 1998; ). A role for the yeast La protein in U6 snRNP assembly: evidence that the La protein is a molecular chaperone for RNA polymerase III transcripts. EMBO J 17, 7442–7453.[CrossRef]
    [Google Scholar]
  38. Petersen-Mahrt, S. K., Estmer, C., Öhrmalm, C., Matthews, D. A., Russell, W. C. & Akusjärvi, G. ( 1999; ). The splicing factor-associated protein, p32, regulates RNA splicing by inhibiting ASF/SF2 RNA binding and phosphorylation. EMBO J 18, 1014–1024.[CrossRef]
    [Google Scholar]
  39. Polvino-Bodnar, M., Kiso, J. & Schaffer, P. A. ( 1988; ). Mutational analysis of Epstein–Barr virus nuclear antigen 1 (EBNA 1). Nucleic Acids Res 16, 3415–3435.[CrossRef]
    [Google Scholar]
  40. Ramos, A., Hollingworth, D. & Pastore, A. ( 2003; ). G-quartet-dependent recognition between the FMRP RGG box and RNA. RNA 9, 1198–1207.[CrossRef]
    [Google Scholar]
  41. Rawlins, D. R., Milman, G., Hayward, S. D. & Hayward, G. S. ( 1985; ). Sequence-specific DNA binding of the Epstein-Barr virus nuclear antigen (EBNA-1) to clustered sites in the plasmid maintenance region. Cell 42, 859–868.[CrossRef]
    [Google Scholar]
  42. Sandri-Goldin, R. M. ( 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.[CrossRef]
    [Google Scholar]
  43. Shah, W. A., Ambinder, R. F., Hayward, G. S. & Hayward, S. D. ( 1992; ). Binding of EBNA-1 to DNA creates a protease-resistant domain that encompasses the DNA recognition and dimerization functions. J Virol 66, 3355–3362.
    [Google Scholar]
  44. Shire, K., Ceccarelli, D. F. J., Avolio-Hunter, T. M. & Frappier, L. ( 1999; ). EBP2, a human protein that interacts with sequences of the Epstein–Barr virus nuclear antigen 1 important for plasmid maintenance. J Virol 73, 2587–2595.
    [Google Scholar]
  45. Snudden, D. K., Hearing, J., Smith, P. R., Grasser, F. A. & Griffin, B. E. ( 1994; ). EBNA-1, the major nuclear antigen of Epstein-Barr virus, resembles ‘RGG’ RNA binding proteins. EMBO J 13, 4840–4847.
    [Google Scholar]
  46. Srinivas, S. K. & Sixbey, J. W. ( 1995; ). Epstein-Barr virus induction of recombinase-activating genes RAG1 and RAG2. J Virol 69, 8155–8158.
    [Google Scholar]
  47. Sugawara, Y., Makuuchi, M., Kato, N., Shimotohno, K. & Takada, K. ( 1999a; ). Enhancement of hepatitis C virus replication by Epstein-Barr virus-encoded nuclear antigen 1. EMBO J 18, 5755–5760.[CrossRef]
    [Google Scholar]
  48. Sugawara, Y., Mizugaki, Y., Uchida, T., Torii, T., Imai, S., Makuuchi, M. & Takada, K. ( 1999b; ). Detection of Epstein–Barr virus (EBV) in hepatocellular carcinoma tissue: a novel EBV latency characterized by the absence of EBV-encoded small RNA expression. Virology 256, 196–202.[CrossRef]
    [Google Scholar]
  49. Swanson, M. S. & Dreyfuss, G. ( 1988; ). Classification and purification of proteins of heterogeneous nuclear ribonucleoprotein particles by RNA-binding specificities. Mol Cell Biol 8, 2237–2241.
    [Google Scholar]
  50. Vanhamme, L., Perez-Morga, D., Marchal, C. & 8 other authors ( 1998; ). Trypanosoma brucei TBRGG1, a mitochondrial oligo(U)-binding protein that co-localizes with an in vitro RNA editing activity. J Biol Chem 273, 21825–21833.[CrossRef]
    [Google Scholar]
  51. Van Horn, D. J., Yoo, C. J., Xue, D., Shi, H. & Wolin, S. L. ( 1997; ). The La protein in Schizosaccharomyces pombe: a conserved yet dispensable phosphoprotein that functions in tRNA maturation. RNA 3, 1434–1443.
    [Google Scholar]
  52. Van Scoy, S., Watakabe, I., Krainer, A. R. & Hearing, J. ( 2000; ). Human p32: a coactivator for Epstein–Barr virus nuclear antigen-1-mediated transcriptional activation and possible role in viral latent cycle DNA replication. Virology 275, 145–157.[CrossRef]
    [Google Scholar]
  53. Wang, Y., Finan, J. E., Middeldorp, J. M. & Hayward, S. D. ( 1997; ). P32/TAP, a cellular protein that interacts with EBNA-1 of Epstein–Barr virus. Virology 236, 18–29.[CrossRef]
    [Google Scholar]
  54. Yang, T.-H., Tsai, W.-H., Lee, Y.-M., Lei, H.-Y., Lai, M.-Y., Chen, D.-S., Yeh, N.-H. & Lee, S.-C. ( 1994; ). Purification and characterization of nucleolin and its identification as a transcription repressor. Mol Cell Biol 14, 6068–6074.[CrossRef]
    [Google Scholar]
  55. Yates, J. L. & Camiolo, S. M. ( 1988; ). Dissection of DNA replication and enhancer activation functions of Epstein-Barr virus nuclear antigen 1. Cancer Cells 6, 197–205.
    [Google Scholar]
  56. Yen, J.-H., Chang, S. C., Hu, C.-R., Chu, S.-C., Lin, S.-S., Hsieh, Y.-S. & Chang, M.-F. ( 1995; ). Cellular proteins specifically bind to the 5′-noncoding region of hepatitis C virus RNA. Virology 208, 723–732.[CrossRef]
    [Google Scholar]
  57. Zetterberg, H., Jansson, A., Rymo, L., Chen, F., Karlsson, A., Klein, G. & Brodin, B. ( 2002; ). The Epstein–Barr virus ZEBRA protein activates transcription from the early lytic F promoter by binding to a promoter-proximal AP-1-like site. J Gen Virol 83, 2007–2014.
    [Google Scholar]
  58. Zuker, M. ( 2003; ). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406–3415.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.80239-0
Loading
/content/journal/jgv/10.1099/vir.0.80239-0
Loading

Data & Media loading...

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error