1887

Abstract

Since the first report of frameshifting in HCV-1, its sequence has been the paradigm for examining the mechanism that directs alternative translation of the hepatitis C virus (HCV) genome. The region encoding the core protein from this strain contains a cluster of 10 adenines at codons 8–11, which is thought to direct programmed ribosomal frameshifting (PRF), but formal evidence for this process has not been established unequivocally. To identify the mechanisms of frameshifting, this study used a bicistronic dual luciferase reporter system in a coupled transcription/translation assay. This approach revealed +1 as well as –1 frameshifting, whereas point mutations, selectively introduced between codons 8 and 11, demonstrated that PRF did not readily account for frameshifting in strain HCV-1. Sequence analysis of cDNAs derived from RNA transcribed by T7 RNA polymerase in the dual luciferase reporter system, as well as in both a subgenomic replicon and an infectious clone derived from strain JFH1, identified additions and deletions of adenines between codons 8 and 11 due to transcriptional slippage (TS). Moreover, RNA isolated from cells infected with virus generated by JFH1 containing the A-rich tract also contained heterogeneity in the adenine sequence, strongly suggesting TS by the NS5B viral polymerase. These findings have important implications for insight into frameshifting events in HCV-1 and demonstrate for the first time the involvement of transcriptional slippage in this recoding event.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.83614-0
2008-07-01
2019-11-18
Loading full text...

Full text loading...

/deliver/fulltext/jgv/89/7/1569.html?itemId=/content/journal/jgv/10.1099/vir.0.83614-0&mimeType=html&fmt=ahah

References

  1. Agris, P. F. ( 2004; ). Decoding the genome: a modified view. Nucleic Acids Res 32, 223–238.[CrossRef]
    [Google Scholar]
  2. Bain, C., Parroche, P., Lavergne, J. P., Duverger, B., Vieux, C., Dubois, V., Komurian-Pradel, F., Trepo, C., Gebuhrer, L. & other authors ( 2004; ). Memory T-cell-mediated immune responses specific to an alternative core protein in hepatitis C virus infection. J Virol 78, 10460–10469.[CrossRef]
    [Google Scholar]
  3. Baranov, P. V., Gesteland, R. F. & Atkins, J. F. ( 2002; ). Recoding: translational bifurcations in gene expression. Gene 286, 187–201.[CrossRef]
    [Google Scholar]
  4. Baril, M. & Brakier-Gingras, L. ( 2005; ). Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein. Nucleic Acids Res 33, 1474–1486.[CrossRef]
    [Google Scholar]
  5. Boulant, S., Becchi, M., Penin, F. & Lavergne, J. P. ( 2003; ). Unusual multiple recoding events leading to alternative forms of hepatitis C virus core protein from genotype 1b. J Biol Chem 278, 45785–45792.[CrossRef]
    [Google Scholar]
  6. Choi, J., Xu, Z. & Ou, J. H. ( 2003; ). Triple decoding of hepatitis C virus RNA by programmed translational frameshifting. Mol Cell Biol 23, 1489–1497.[CrossRef]
    [Google Scholar]
  7. Combet, C., Blanchet, C., Geourjon, C. & Deleage, G. ( 2000; ). [email protected]: network protein sequence analysis. Trends Biochem Sci 25, 147–150.[CrossRef]
    [Google Scholar]
  8. Conti, E. & Izaurralde, E. ( 2005; ). Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr Opin Cell Biol 17, 316–325.[CrossRef]
    [Google Scholar]
  9. Dinman, J. D., Ruiz-Echevarria, M. J. & Peltz, S. W. ( 1998; ). Translating old drugs into new treatments: ribosomal frameshifting as a target for antiviral agents. Trends Biotechnol 16, 190–196.[CrossRef]
    [Google Scholar]
  10. Farabaugh, P. J. ( 1996; ). Programmed translational frameshifting. Microbiol Rev 60, 103–134.
    [Google Scholar]
  11. Farabaugh, P. J. ( 2000; ). Translational frameshifting: implications for the mechanism of translational frame maintenance. Prog Nucleic Acid Res Mol Biol 64, 131–170.
    [Google Scholar]
  12. Fiorucci, M., Boulant, S., Fournillier, A., Abraham, J. D., Lavergne, J. P., Paranhos-Baccala, G., Inchauspe, G. & Bain, C. ( 2007; ). Expression of the alternative reading frame protein of hepatitis C virus induces cytokines involved in hepatic injuries. J Gen Virol 88, 1149–1162.[CrossRef]
    [Google Scholar]
  13. Gesteland, R. F. & Atkins, J. F. ( 1996; ). Recoding: dynamic reprogramming of translation. Annu Rev Biochem 65, 741–768.[CrossRef]
    [Google Scholar]
  14. Giannini, C. & Brechot, C. ( 2003; ). Hepatitis C virus biology. Cell Death Differ 10 (Suppl 1), S27–S38.[CrossRef]
    [Google Scholar]
  15. Jones, D. M., Gretton, S. N., McLauchlan, J. & Targett-Adams, P. ( 2007; ). Mobility analysis of an NS5A–GFP fusion protein in cells actively replicating hepatitis C virus subgenomic RNA. J Gen Virol 88, 470–475.[CrossRef]
    [Google Scholar]
  16. Komurian-Pradel, F., Rajoharison, A., Berland, J. L., Khouri, V., Perret, M., Van Roosmalen, M., Pol, S., Negro, F. & Paranhos-Baccala, G. ( 2004; ). Antigenic relevance of F protein in chronic hepatitis C virus infection. Hepatology 40, 900–909.[CrossRef]
    [Google Scholar]
  17. Laporte, J., Malet, I., Andrieu, T., Thibault, V., Toulme, J. J., Wychowski, C., Pawlotsky, J. M., Huraux, J. M., Agut, H. & Cahour, A. ( 2000; ). Comparative analysis of translation efficiencies of hepatitis C virus 5′ untranslated regions among intraindividual quasispecies present in chronic infection: opposite behaviors depending on cell type. J Virol 74, 10827–10833.[CrossRef]
    [Google Scholar]
  18. Lim, V. I. & Curran, J. F. ( 2001; ). Analysis of codon : anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure. RNA 7, 942–957.[CrossRef]
    [Google Scholar]
  19. Lindenbach, B. D., Evans, M. J., Syder, A. J., Wolk, B., Tellinghuisen, T. L., Liu, C. C., Maruyama, T., Hynes, R. O., Burton, D. R. & other authors ( 2005; ). Complete replication of hepatitis C virus in cell culture. Science 309, 623–626.[CrossRef]
    [Google Scholar]
  20. Lohmann, V., Korner, F., Koch, J., Herian, U., Theilmann, L. & Bartenschlager, R. ( 1999; ). Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line. Science 285, 110–113.[CrossRef]
    [Google Scholar]
  21. Martell, M., Esteban, J. I., Quer, J., Genesca, J., Weiner, A., Esteban, R., Guardia, J. & Gomez, J. ( 1992; ). Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution. J Virol 66, 3225–3229.
    [Google Scholar]
  22. Moradpour, D., Penin, F. & Rice, C. M. ( 2007; ). Replication of hepatitis C virus. Nat Rev Microbiol 5, 453–463.[CrossRef]
    [Google Scholar]
  23. Namy, O., Rousset, J. P., Napthine, S. & Brierley, I. ( 2004; ). Reprogrammed genetic decoding in cellular gene expression. Mol Cell 13, 157–168.[CrossRef]
    [Google Scholar]
  24. Penin, F. ( 2003; ). Structural biology of hepatitis C virus. Clin Liver Dis 7, 1–21. (vii)[CrossRef]
    [Google Scholar]
  25. Reed, K. E. & Rice, C. M. ( 2000; ). Overview of hepatitis C virus genome structure, polyprotein processing, and protein properties. Curr Top Microbiol Immunol 242, 55–84.
    [Google Scholar]
  26. Roussel, J., Pillez, A., Montpellier, C., Duverlie, G., Cahour, A., Dubuisson, J. & Wychowski, C. ( 2003; ). Characterization of the expression of the hepatitis C virus F protein. J Gen Virol 84, 1751–1759.[CrossRef]
    [Google Scholar]
  27. Schaller, T., Appel, N., Koutsoudakis, G., Kallis, S., Lohmann, V., Pietschmann, T. & Bartenschlager, R. ( 2007; ). Analysis of hepatitis C virus superinfection exclusion by using novel fluorochrome gene-tagged viral genomes. J Virol 81, 4591–4603.[CrossRef]
    [Google Scholar]
  28. Targett-Adams, P. & McLauchlan, J. ( 2005; ). Development and characterization of a transient-replication assay for the genotype 2a hepatitis C virus subgenomic replicon. J Gen Virol 86, 3075–3080.[CrossRef]
    [Google Scholar]
  29. Troesch, M., Jalbert, E., Canobio, S., Boulassel, M. R., Routy, J. P., Bernard, N. F., Bruneau, J., Lapointe, N., Boucher, M. & Soudeyns, H. ( 2005; ). Characterization of humoral and cell-mediated immune responses directed against hepatitis C virus F protein in subjects co-infected with hepatitis C virus and HIV-1. AIDS 19, 775–784.[CrossRef]
    [Google Scholar]
  30. Varaklioti, A., Vassilaki, N., Georgopoulou, U. & Mavromara, P. ( 2002; ). Alternate translation occurs within the core coding region of the hepatitis C viral genome. J Biol Chem 277, 17713–17721.[CrossRef]
    [Google Scholar]
  31. Vassilaki, N. & Mavromara, P. ( 2003; ). Two alternative translation mechanisms are responsible for the expression of the HCV ARFP/F/core+1 coding open reading frame. J Biol Chem 278, 40503–40513.[CrossRef]
    [Google Scholar]
  32. Volchkov, V. E., Becker, S., Volchkova, V. A., Ternovoj, V. A., Kotov, A. N., Netesov, S. V. & Klenk, H. D. ( 1995; ). GP mRNA of Ebola virus is edited by the Ebola virus polymerase and by T7 and vaccinia virus polymerases. Virology 214, 421–430.[CrossRef]
    [Google Scholar]
  33. Wagner, L. A., Weiss, R. B., Driscoll, R., Dunn, D. S. & Gesteland, R. F. ( 1990; ). Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli. Nucleic Acids Res 18, 3529–3535.[CrossRef]
    [Google Scholar]
  34. Wakita, T., Pietschmann, T., Kato, T., Date, T., Miyamoto, M., Zhao, Z., Murthy, K., Habermann, A., Krausslich, H. G. & other authors ( 2005; ). Production of infectious hepatitis C virus in tissue culture from a cloned viral genome. Nat Med 11, 791–796.[CrossRef]
    [Google Scholar]
  35. 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]
  36. Weiner, A. J., Brauer, M. J., Rosenblatt, J., Richman, K. H., Tung, J., Crawford, K., Bonino, F., Saracco, G., Choo, Q. L. & other authors ( 1991; ). Variable and hypervariable domains are found in the regions of HCV corresponding to the flavivirus envelope and NS1 proteins and the pestivirus envelope glycoproteins. Virology 180, 842–848.[CrossRef]
    [Google Scholar]
  37. Weischenfeldt, J., Lykke-Andersen, J. & Porse, B. ( 2005; ). Messenger RNA surveillance: neutralizing natural nonsense. Curr Biol 15, R559–R562.[CrossRef]
    [Google Scholar]
  38. Xu, Z., Choi, J., Yen, T. S., Lu, W., Strohecker, A., Govindarajan, S., Chien, D., Selby, M. J. & Ou, J. ( 2001; ). Synthesis of a novel hepatitis C virus protein by ribosomal frameshift. EMBO J 20, 3840–3848.[CrossRef]
    [Google Scholar]
  39. Zhong, J., Gastaminza, P., Cheng, G., Kapadia, S., Kato, T., Burton, D. R., Wieland, S. F., Uprichard, S. L., Wakita, T. & Chisari, F. V. ( 2005; ). Robust hepatitis C virus infection in vitro. Proc Natl Acad Sci U S A 102, 9294–9299.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.83614-0
Loading
/content/journal/jgv/10.1099/vir.0.83614-0
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