1887

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Volume 91, Issue 5

RNA-dependent RNA polymerase of hepatitis C virus binds to its coding region RNA stem–loop structure, 5BSL3.2, and its negative strand Free

Abstract

The hepatitis C virus NS5B RNA-dependent RNA polymerase (RdRp) is a key enzyme involved in viral replication. Interaction between NS5B RdRp and the viral RNA sequence is likely to be an important step in viral RNA replication. The C-terminal half of the NS5B-coding sequence, which contains the important -acting replication element, has been identified as an NS5B-binding sequence. In the present study, we confirm the specific binding of NS5B to one of the RNA stem–loop structures in the region, 5BSL3.2. In addition, we show that NS5B binds to the complementary strand of 5BSL3.2 (5BSL3.2N). The bulge structure of 5BSL3.2N was shown to be indispensable for tight binding to NS5B. RdRp activity was inhibited by 5BSL3.2N, indicating the importance of the RNA element in the polymerization by RdRp. These results suggest the involvement of the RNA stem–loop structure of the negative strand in the replication process.

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2010-05-01
2024-04-23
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References

  1. Astier-Gin, T., Bellecave, P., Litvak, S. & Ventura, M.(2005). Template requirements and binding of hepatitis C virus NS5B polymerase during in vitro RNA synthesis from the 3′-end of virus minus-strand RNA. FEBS J 272, 3872–3886.[CrossRef] [Google Scholar]
  2. Behrens, S. E., Tomei, L. & De Francesco, R.(1996). Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus. EMBO J 15, 12–22. [Google Scholar]
  3. Biroccio, A., Hamm, J., Incitti, I., De Francesco, R. & Tomei, L.(2002). Selection of RNA aptamers that are specific and high-affinity ligands of the hepatitis C virus RNA-dependent RNA polymerase. J Virol 76, 3688–3696.[CrossRef] [Google Scholar]
  4. Bukh, J., Purcell, R. H. & Miller, R. H.(1992). Sequence analysis of the 5′ noncoding region of hepatitis C virus. Proc Natl Acad Sci U S A 89, 4942–4946.[CrossRef] [Google Scholar]
  5. Cheng, J. C., Chang, M. F. & Chang, S. C.(1999). Specific interaction between the hepatitis C virus NS5B RNA polymerase and the 3′ end of the viral RNA. J Virol 73, 7044–7049. [Google Scholar]
  6. De Francesco, R., Behrens, S. E., Tomei, L., Altamura, S. & Jiricny, J.(1996). RNA-dependent RNA polymerase of hepatitis C virus. Methods Enzymol 275, 58–67. [Google Scholar]
  7. Diviney, S., Tuplin, A., Struthers, M., Armstrong, V., Elliott, R. M., Simmonds, P. & Evans, D. J.(2008). A hepatitis C virus cis-acting replication element forms a long-range RNA–RNA interaction with upstream RNA sequences in NS5B. J Virol 82, 9008–9022.[CrossRef] [Google Scholar]
  8. Ferrari, E., Wright-Minogue, J., Fang, J. W., Baroudy, B. M., Lau, J. Y. & Hong, Z.(1999). Characterization of soluble hepatitis C virus RNA-dependent RNA polymerase expressed in Escherichia coli. J Virol 73, 1649–1654. [Google Scholar]
  9. Friebe, P., Boudet, J., Simorre, J. P. & Bartenschlager, R.(2005). Kissing-loop interaction in the 3′ end of the hepatitis C virus genome essential for RNA replication. J Virol 79, 380–392.[CrossRef] [Google Scholar]
  10. Hamamoto, I., Nishimura, Y., Okamoto, T., Aizaki, H., Liu, M., Mori, Y., Abe, T., Suzuki, T., Lai, M. M. & other authors(2005). Human VAP-B is involved in hepatitis C virus replication through interaction with NS5A and NS5B. J Virol 79, 13473–13482.[CrossRef] [Google Scholar]
  11. Holland, J., Spindler, K., Horodyski, F., Grabau, E., Nichol, S. & VandePol, S.(1982). Rapid evolution of RNA genomes. Science 215, 1577–1585.[CrossRef] [Google Scholar]
  12. Kanamori, H., Yuhashi, K., Uchiyama, Y., Kodama, T. & Ohnishi, S.(2009).In vitro selection of RNA aptamers that bind the RNA-dependent RNA polymerase of hepatitis C virus: a possible role of GC-rich RNA motifs in NS5B binding. Virology 388, 91–102.[CrossRef] [Google Scholar]
  13. Kim, M., Kim, H., Cho, S. P. & Min, M. K.(2002). Template requirements for de novo RNA synthesis by hepatitis C virus nonstructural protein 5B polymerase on the viral X RNA. J Virol 76, 6944–6956.[CrossRef] [Google Scholar]
  14. Kolykhalov, A. A., Feinstone, S. M. & Rice, C. M.(1996). Identification of a highly conserved sequence element at the 3′ terminus of hepatitis C virus genome RNA. J Virol 70, 3363–3371. [Google Scholar]
  15. Lee, H., Shin, H., Wimmer, E. & Paul, A. V.(2004).cis-Acting RNA signals in the NS5B C-terminal coding sequence of the hepatitis C virus genome. J Virol 78, 10865–10877.[CrossRef] [Google Scholar]
  16. Lohmann, V., Korner, F., Herian, U. & Bartenschlager, R.(1997). Biochemical properties of hepatitis C virus NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity. J Virol 71, 8416–8428. [Google Scholar]
  17. Miller, R. H. & Purcell, R. H.(1990). Hepatitis C virus shares amino acid sequence similarity with pestiviruses and flaviviruses as well as members of two plant virus supergroups. Proc Natl Acad Sci U S A 87, 2057–2061.[CrossRef] [Google Scholar]
  18. Oh, J. W., Ito, T. & Lai, M. M.(1999). A recombinant hepatitis C virus RNA-dependent RNA polymerase capable of copying the full-length viral RNA. J Virol 73, 7694–7702. [Google Scholar]
  19. Oh, J. W., Sheu, G. T. & Lai, M. M.(2000). Template requirement and initiation site selection by hepatitis C virus polymerase on a minimal viral RNA template. J Biol Chem 275, 17710–17717.[CrossRef] [Google Scholar]
  20. Simmonds, P., Holmes, E. C., Cha, T. A., Chan, S. W., McOmish, F., Irvine, B., Beall, E., Yap, P. L., Kolberg, J. & Urdea, M. S.(1993). Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J Gen Virol 74, 2391–2399.[CrossRef] [Google Scholar]
  21. Smith, D. B., Mellor, J., Jarvis, L. M., Davidson, F., Kolberg, J., Urdea, M., Yap, P. L. & Simmonds, P.(1995). Variation of the hepatitis C virus 5′ non-coding region: implications for secondary structure, virus detection and typing. The International HCV Collaborative Study Group. J Gen Virol 76, 1749–1761.[CrossRef] [Google Scholar]
  22. Tanaka, T., Kato, N., Cho, M. J. & Shimotohno, K.(1995). A novel sequence found at the 3′ terminus of hepatitis C virus genome. Biochem Biophys Res Commun 215, 744–749.[CrossRef] [Google Scholar]
  23. Tu, H., Gao, L., Shi, S. T., Taylor, D. R., Yang, T., Mircheff, A. K., Wen, Y., Gorbalenya, A. E., Hwang, S. B. & Lai, M. M.(1999). Hepatitis C virus RNA polymerase and NS5A complex with a SNARE-like protein. Virology 263, 30–41.[CrossRef] [Google Scholar]
  24. Uchiyama, Y., Huang, Y., Kanamori, H., Uchida, M., Doi, T., Takamizawa, A., Hamakubo, T. & Kodama, T.(2002). Measurement of HCV RdRp activity with C-terminal 21 aa truncated NS5b protein: optimization of assay conditions. Hepatol Res 23, 90–97.[CrossRef] [Google Scholar]
  25. Vo, N. V., Oh, J. W. & Lai, M. M.(2003). Identification of RNA ligands that bind hepatitis C virus polymerase selectively and inhibit its RNA synthesis from the natural viral RNA templates. Virology 307, 301–316.[CrossRef] [Google Scholar]
  26. Walewski, J. L., Keller, T. R., Stump, D. D. & Branch, A. D.(2001). Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame. RNA 7, 710–721.[CrossRef] [Google Scholar]
  27. Wang, C., Gale, M., Jr, Keller, B. C., Huang, H., Brown, M. S., Goldstein, J. L. & Ye, J.(2005). Identification of FBL2 as a geranylgeranylated cellular protein required for hepatitis C virus RNA replication. Mol Cell 18, 425–434.[CrossRef] [Google Scholar]
  28. Watashi, K., Ishii, N., Hijikata, M., Inoue, D., Murata, T., Miyanari, Y. & Shimotohno, K.(2005). Cyclophilin B is a functional regulator of hepatitis C virus RNA polymerase. Mol Cell 19, 111–122.[CrossRef] [Google Scholar]
  29. Yamada, N., Tanihara, K., Takada, A., Yorihuzi, T., Tsutsumi, M., Shimomura, H., Tsuji, T. & Date, T.(1996). Genetic organization and diversity of the 3′ noncoding region of the hepatitis C virus genome. Virology 223, 255–261.[CrossRef] [Google Scholar]
  30. You, S., Stump, D. D., Branch, A. D. & Rice, C. M.(2004). A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication. J Virol 78, 1352–1366.[CrossRef] [Google Scholar]
  31. Zhang, J., Yamada, O., Sakamoto, T., Yoshida, H., Araki, H., Murata, T. & Shimotohno, K.(2005). Inhibition of hepatitis C virus replication by pol III-directed overexpression of RNA decoys corresponding to stem-loop structures in the NS5B coding region. Virology 342, 276–285.[CrossRef] [Google Scholar]
  32. Zuker, M.(2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406–3415.[CrossRef] [Google Scholar]
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RNA-dependent RNA polymerase of hepatitis C virus binds to its coding region RNA stem–loop structure, 5BSL3.2, and its negative strand
J. Gen. Virol. 91, 1207 (2010); https://doi.org/10.1099/vir.0.016907-0
/content/journal/jgv/10.1099/vir.0.016907-0
/content/journal/jgv/10.1099/vir.0.016907-0
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