1887

Abstract

Japanese encephalitis virus (JEV) genome is a single-stranded, positive-sense RNA with non-coding regions (NCRs) of 95 and 585 bases at its 5′ and 3′ ends, respectively. These may bind to viral or host proteins important for viral replication. It has been shown previously that three proteins of 32, 35 and 50 kDa bind the 3′ stem–loop (SL) structure of the JEV 3′ NCR, and one of these was identified as 36 kDa Mov34 protein. Using electrophoretic mobility-shift and UV cross-linking assays, as well as a yeast three-hybrid system, it was shown here that La protein binds to the 3′ SL of JEV. The binding was stable under high-salt conditions (300 mM KCl) and the affinity of the RNA–protein interaction was high; the dissociation constant ( ) for binding of La protein to the 3′ SL was 12 nM, indicating that this RNA–protein interaction is physiologically plausible. Only the N-terminal half of La protein containing RNA recognition motifs 1 and 2 interacted with JEV RNA. An RNA toe-printing assay followed by deletion mutagenesis showed that La protein bound to predicted loop structures in the 3′ SL RNA. Furthermore, it was shown that small interfering RNA-mediated downregulation of La protein resulted in repression of JEV replication in cultured cells.

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2009-06-01
2019-11-22
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References

  1. Ali, N., Pruijn, G. J., Kenan, D. J., Keene, J. D. & Siddiqui, A. ( 2000; ). Human La antigen is required for the hepatitis C virus internal ribosome entry site-mediated translation. J Biol Chem 275, 27531–27540.
    [Google Scholar]
  2. Bachmann, M., Pfeifer, K., Schroder, H. C. & Muller, W. E. ( 1990; ). Characterization of the autoantigen La as a nucleic acid-dependent ATPase/dATPase with melting properties. Cell 60, 85–93.[CrossRef]
    [Google Scholar]
  3. Behrens, S. E., Grassmann, C. W., Thiel, H. J., Meyers, G. & Tautz, N. ( 1998; ). Characterization of an autonomous subgenomic pestivirus RNA replicon. J Virol 72, 2364–2372.
    [Google Scholar]
  4. Blackwell, J. L. & Brinton, M. A. ( 1997; ). Translation elongation factor-1 alpha interacts with the 3′ stem–loop region of West Nile virus genomic RNA. J Virol 71, 6433–6444.
    [Google Scholar]
  5. Blumenthal, T. & Carmichael, G. G. ( 1979; ). RNA replication: function and structure of Qβ-replicase. Annu Rev Biochem 48, 525–548.[CrossRef]
    [Google Scholar]
  6. Brinton, M. A., Fernandez, A. V. & Dispoto, J. H. ( 1986; ). The 3′-nucleotides of flavivirus genomic RNA form a conserved secondary structure. Virology 153, 113–121.[CrossRef]
    [Google Scholar]
  7. Chambers, T. J., Hahn, C. S., Galler, R. & Rice, C. M. ( 1990; ). Flavivirus genome organization, expression, and replication. Annu Rev Microbiol 44, 649–688.[CrossRef]
    [Google Scholar]
  8. Chang, Y. N., Kenan, D. J., Keene, J. D., Gatignol, A. & Jeang, K. T. ( 1994; ). Direct interactions between autoantigen La and human immunodeficiency virus leader RNA. J Virol 68, 7008–7020.
    [Google Scholar]
  9. Chen, C. J., Kuo, M. D., Chien, L. J., Hsu, S. L., Wang, Y. M. & Lin, J. H. ( 1997; ). RNA–protein interactions: involvement of NS3, NS5, and 3′ noncoding regions of Japanese encephalitis virus genomic RNA. J Virol 71, 3466–3473.
    [Google Scholar]
  10. Costa-Mattioli, M., Svitkin, Y. & Sonenberg, N. ( 2004; ). La autoantigen is necessary for optimal function of the poliovirus and hepatitis C virus internal ribosome entry site in vivo and in vitro. Mol Cell Biol 24, 6861–6870.[CrossRef]
    [Google Scholar]
  11. Craig, A. W., Svitkin, Y. V., Lee, H. S., Belsham, G. J. & Sonenberg, N. ( 1997; ). The La autoantigen contains a dimerization domain that is essential for enhancing translation. Mol Cell Biol 17, 163–169.
    [Google Scholar]
  12. Domitrovich, A. M., Diebel, K. W., Ali, N., Sarker, S. & Siddiqui, A. ( 2005; ). Role of La autoantigen and polypyrimidine tract-binding protein in HCV replication. Virology 335, 72–86.[CrossRef]
    [Google Scholar]
  13. Duncan, R. C. & Nakhasi, H. L. ( 1997; ). La autoantigen binding to a 5′ cis-element of rubella virus RNA correlates with element function in vivo. Gene 201, 137–149.[CrossRef]
    [Google Scholar]
  14. Ehlers, I., Horke, S., Reumann, K., Rang, A., Grosse, F., Will, H. & Heise, T. ( 2004; ). Functional characterization of the interaction between human La and hepatitis B virus RNA. J Biol Chem 279, 43437–43447.[CrossRef]
    [Google Scholar]
  15. Fan, H., Goodier, J. L., Chamberlain, J. R., Engelke, D. R. & Maraia, R. J. ( 1998; ). 5′ Processing of tRNA precursors can be modulated by the human La antigen phosphoprotein. Mol Cell Biol 18, 3201–3211.
    [Google Scholar]
  16. Francoeur, A. M. & Mathews, M. B. ( 1982; ). Interaction between VA RNA and the lupus antigen La: formation of a ribonucleoprotein particle in vitro. Proc Natl Acad Sci U S A 79, 6772–6776.[CrossRef]
    [Google Scholar]
  17. Garcia-Montalvo, B. M., Medina, F. & del Angel, R. M. ( 2004; ). La protein binds to NS5 and NS3 and to the 5′ and 3′ ends of dengue 4 virus RNA. Virus Res 102, 141–150.[CrossRef]
    [Google Scholar]
  18. Gietz, R. D. & Woods, R. A. ( 2002; ). Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol 350, 87–96.
    [Google Scholar]
  19. Goodier, J. L., Fan, H. & Maraia, R. J. ( 1997; ). A carboxy-terminal basic region controls RNA polymerase III transcription factor activity of human La protein. Mol Cell Biol 17, 5823–5832.
    [Google Scholar]
  20. Gottlieb, E. & Steitz, J. A. ( 1989a; ). Function of the mammalian La protein: evidence for its action in transcription termination by RNA polymerase III. EMBO J 8, 851–861.
    [Google Scholar]
  21. Gottlieb, E. & Steitz, J. A. ( 1989b; ). The RNA binding protein La influences both the accuracy and the efficiency of RNA polymerase III transcription in vitro. EMBO J 8, 841–850.
    [Google Scholar]
  22. Gutiérrez-Escolano, A. L., Brito, Z. U., del Angel, R. M. & Jiang, X. ( 2000; ). Interaction of cellular proteins with the 5′ end of Norwalk virus genomic RNA. J Virol 74, 8558–8562.[CrossRef]
    [Google Scholar]
  23. Gutiérrez-Escolano, A. L., Vázquez-Ochoa, M., Escobar-Herrera, J. & Hernández-Acosta, J. ( 2003; ). La, PTB, and PAB proteins bind to the 3′ untranslated region of Norwalk virus genomic RNA. Biochem Biophys Res Commun 311, 759–766.[CrossRef]
    [Google Scholar]
  24. Harris, K. S., Xiang, W., Alexander, L., Lane, W. S., Paul, A. V. & Wimmer, E. ( 1994; ). Interaction of poliovirus polypeptide 3CDpro with the 5′ and 3′ termini of the poliovirus genome. Identification of viral and cellular cofactors needed for efficient binding. J Biol Chem 269, 27004–27014.
    [Google Scholar]
  25. Hayes, R. J. & Buck, K. W. ( 1990; ). Complete replication of a eukaryotic virus RNA in vitro by a purified RNA-dependent RNA polymerase. Cell 63, 363–368.[CrossRef]
    [Google Scholar]
  26. Horke, S., Reumann, K., Schulze, C., Grosse, F. & Heise, T. ( 2004; ). The La motif and the RNA recognition motifs of human La autoantigen contribute individually to RNA recognition and subcellular localization. J Biol Chem 279, 50302–50309.[CrossRef]
    [Google Scholar]
  27. Huhn, P., Pruijn, G. J., van Venrooij, W. J. & Bachmann, M. ( 1997; ). Characterization of the autoantigen La (SS-B) as a dsRNA unwinding enzyme. Nucleic Acids Res 25, 410–416.[CrossRef]
    [Google Scholar]
  28. Ito, T. & Lai, M. M. ( 1997; ). Determination of the secondary structure of and cellular protein binding to the 3′-untranslated region of the hepatitis C virus RNA genome. J Virol 71, 8698–8706.
    [Google Scholar]
  29. Izumi, R. E., Das, S., Barat, B., Raychaudhuri, S. & Dasgupta, A. ( 2004; ). A peptide from autoantigen La blocks poliovirus and hepatitis C virus cap-independent translation and reveals a single tyrosine critical for La RNA binding and translation stimulation. J Virol 78, 3763–3776.[CrossRef]
    [Google Scholar]
  30. Joshi, R. L., Ravel, J. M. & Haenni, A. L. ( 1986; ). Interaction of turnip yellow mosaic virus Val-RNA with eukaryotic elongation factor EF-1α. Search for a function. EMBO J 5, 1143–1148.
    [Google Scholar]
  31. Kaur, R., Sachdeva, G. & Vrati, S. ( 2002; ). Plasmid DNA immunization against Japanese encephalitis virus: immunogenicity of membrane-anchored and secretory envelope protein. J Infect Dis 185, 1–12.[CrossRef]
    [Google Scholar]
  32. Kenan, D. J. ( 1995; ). Recognition by the human La protein and its role in transcription, translation, and viral infectivity. PhD thesis, Duke University, Raleigh, NC, USA.
  33. Kim, S. M. & Jeong, Y. S. ( 2006; ). Polypyrimidine tract-binding protein interacts with the 3′ stem-loop region of Japanese encephalitis virus negative-strand RNA. Virus Res 115, 131–140.[CrossRef]
    [Google Scholar]
  34. Maraia, R. J., Kenan, D. J. & Keene, J. D. ( 1994; ). Eukaryotic transcription termination factor La mediates transcript release and facilitates reinitiation by RNA polymerase III. Mol Cell Biol 14, 2147–2158.
    [Google Scholar]
  35. McLaren, R. S., Caruccio, N. & Ross, J. ( 1997; ). Human La protein: a stabilizer of histone mRNA. Mol Cell Biol 17, 3028–3036.
    [Google Scholar]
  36. Meerovitch, K., Svitkin, Y. V., Lee, H. S., Lejbkowicz, F., Kenan, D. J., Chan, E. K., Agol, V. I., Keene, J. D. & Sonenberg, N. ( 1993; ). La autoantigen enhances and corrects aberrant translation of poliovirus RNA in reticulocyte lysate. J Virol 67, 3798–3807.
    [Google Scholar]
  37. Moyer, S. A., Baker, S. C. & Horikami, S. M. ( 1990; ). Host cell proteins required for measles virus reproduction. J Gen Virol 71, 775–783.[CrossRef]
    [Google Scholar]
  38. Nova-Ocampo, M., Villegas-Sepulveda, N. & del Angel, R. M. ( 2002; ). Translation elongation factor-1α, La, and PTB interact with the 3′ untranslated region of dengue 4 virus RNA. Virology 295, 337–347.[CrossRef]
    [Google Scholar]
  39. O'Neill, R. E. & Palese, P. ( 1994; ). Cis-acting signals and trans-acting factors involved in influenza virus RNA synthesis. Infect Agents Dis 3, 77–84.
    [Google Scholar]
  40. Osman, T. A. & Buck, K. W. ( 1997; ). The tobacco mosaic virus RNA polymerase complex contains a plant protein related to the RNA-binding subunit of yeast eIF-3. J Virol 71, 6075–6082.
    [Google Scholar]
  41. Pardigon, N. & Strauss, J. H. ( 1996; ). Mosquito homolog of the La autoantigen binds to Sindbis virus RNA. J Virol 70, 1173–1181.
    [Google Scholar]
  42. Pestova, T. V., Shatsky, I. N., Fletcher, S. P., Jackson, R. J. & Hellen, C. U. ( 1998; ). A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes Dev 12, 67–83.[CrossRef]
    [Google Scholar]
  43. Pudi, R., Abhiman, S., Srinivasan, N. & Das, S. ( 2003; ). Hepatitis C virus internal ribosome entry site-mediated translation is stimulated by specific interaction of independent regions of human La autoantigen. J Biol Chem 278, 12231–12240.[CrossRef]
    [Google Scholar]
  44. Quadt, R., Kao, C. C., Browning, K. S., Hershberger, R. P. & Ahlquist, P. ( 1993; ). Characterization of a host protein associated with brome mosaic virus RNA-dependent RNA polymerase. Proc Natl Acad Sci U S A 90, 1498–1502.[CrossRef]
    [Google Scholar]
  45. Rosa, M. D., Gottlieb, E., Lerner, M. R. & Steitz, J. A. ( 1981; ). Striking similarities are exhibited by two small Epstein–Barr virus-encoded ribonucleic acids and the adenovirus-associated ribonucleic acids VAI and VAII. Mol Cell Biol 1, 785–796.
    [Google Scholar]
  46. Rutjes, S.A., van der Heijden, A., Utz, P. J., van Venrooij, W. J. & Pruijn, G. J. ( 1999; ). Rapid nucleolytic degradation of the small cytoplasmic Y RNAs during apoptosis. J Biol Chem 274, 24799–24807.[CrossRef]
    [Google Scholar]
  47. Shi, P. Y., Brinton, M. A., Veal, J. M., Zhong, Y. Y. & Wilson, W. D. ( 1996; ). Evidence for the existence of a pseudoknot structure at the 3′ terminus of the flavivirus genomic RNA. Biochemistry 35, 4222–4230.[CrossRef]
    [Google Scholar]
  48. Silva, P. A., Molenkamp, R., Dalebout, T. J., Charlier, N., Neyts, J. H., Spaan, W. J. & Bredenbeek, P. J. ( 2007; ). Conservation of the pentanucleotide motif at the top of the yellow fever virus 17D 3′ stem–loop structure is not required for replication. J Gen Virol 88, 1738–1747.[CrossRef]
    [Google Scholar]
  49. Spangberg, K., Wiklund, L. & Schwartz, S. ( 2001; ). Binding of the La autoantigen to the hepatitis C virus 3′ untranslated region protects the RNA from rapid degradation in vitro. J Gen Virol 82, 113–120.
    [Google Scholar]
  50. Svitkin, Y. V., Pause, A. & Sonenberg, N. ( 1994; ). La autoantigen alleviates translational repression by the 5′ leader sequence of the human immunodeficiency virus type 1 mRNA. J Virol 68, 7001–7007.
    [Google Scholar]
  51. Ta, M. & Vrati, S. ( 2000; ). Mov34 protein from mouse brain interacts with the 3′ noncoding region of Japanese encephalitis virus. J Virol 74, 5108–5115.[CrossRef]
    [Google Scholar]
  52. Takegami, T., Washizu, M. & Yasui, K. ( 1986; ). Nucleotide sequence at the 3′ end of Japanese encephalitis virus genomic RNA. Virology 152, 483–486.[CrossRef]
    [Google Scholar]
  53. Tilgner, M. & Shi, P. Y. ( 2004; ). Structure and function of the 3′ terminal six nucleotides of the West Nile virus genome in viral replication. J Virol 78, 8159–8171.[CrossRef]
    [Google Scholar]
  54. Tsuchihara, K., Tanaka, T., Hijikata, M., Kuge, S., Toyoda, H., Nomoto, A., Yamamoto, N. & Shimotohno, K. ( 1997; ). Specific interaction of polypyrimidine tract-binding protein with the extreme 3′-terminal structure of the hepatitis C virus genome, the 3′X. J Virol 71, 6720–6726.
    [Google Scholar]
  55. Vrati, S., Agarwal, V., Malik, P., Wani, S. A. & Saini, M. ( 1999; ). Molecular characterization of an Indian isolate of Japanese encephalitis virus that shows an extended lag phase during growth. J Gen Virol 80, 1665–1671.
    [Google Scholar]
  56. Wilusz, J., Kurilla, M. G. & Keene, J. D. ( 1983; ). A host protein (La) binds to a unique species of minus-sense leader RNA during replication of vesicular stomatitis virus. Proc Natl Acad Sci U S A 80, 5827–5831.[CrossRef]
    [Google Scholar]
  57. Wolin, S. L. & Cedervall, T. ( 2002; ). The La protein. Annu Rev Biochem 71, 375–403.[CrossRef]
    [Google Scholar]
  58. Xiao, Q., Sharp, T. V., Jeffrey, I. W., James, M. C., Pruijn, G. J., van Venrooij, W. J. & Clemens, M. J. ( 1994; ). The La antigen inhibits the activation of the interferon-inducible protein kinase PKR by sequestering and unwinding double-stranded RNA. Nucleic Acids Res 22, 2512–2518.[CrossRef]
    [Google Scholar]
  59. Yocupicio-Monroy, R. M., Medina, F., Reyes-del Valle, J. & del Angel, R. M. ( 2003; ). Cellular proteins from human monocytes bind to dengue 4 virus minus-strand 3′ untranslated region RNA. J Virol 77, 3067–3076.[CrossRef]
    [Google Scholar]
  60. You, S. & Padmanabhan, R. ( 1999; ). A novel in vitro replication system for dengue virus. Initiation of RNA synthesis at the 3′-end of exogenous viral RNA templates requires 5′- and 3′-terminal complementary sequence motifs of the viral RNA. J Biol Chem 274, 33714–33722.[CrossRef]
    [Google Scholar]
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