1887

Abstract

The RNA-dependent RNA polymerase of the double-stranded RNA bacteriophage 6 is capable of primer-independent initiation, as are many RNA polymerases. The structure of this polymerase revealed an initiation platform, composed of a loop in the C-terminal domain (QYKW, aa 629–632), that was essential for de novo initiation. A similar element has been identified in hepatitis C virus RNA-dependent RNA polymerase. Biochemical studies have addressed the role of this platform, revealing that a mutant version can utilize a back-priming initiation mechanism, where the 3′ terminus of the template adopts a hairpin-like conformation. Here, the mechanism of back-primed initiation is studied further by biochemical and structural methods.

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2005-02-01
2020-10-21
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References

  1. Ago H., Adachi T., Yoshida A., Yamamoto M., Habuka N., Yatsunami K., Miyano M. 1999; Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Structure Fold Des 7:1417–1426 [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. Bressanelli S., Tomei L., Roussel A., Incitti I., Vitale R. L., Mathieu M., De Francesco R., Rey F. A. 1999; Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Proc Natl Acad Sci U S A 96:13034–13039 [CrossRef]
    [Google Scholar]
  4. Bressanelli S., Tomei L., Rey F. A., De Francesco R. 2002; Structural analysis of the hepatitis C virus RNA polymerase in complex with ribonucleotides. J Virol 76:3482–3492 [CrossRef]
    [Google Scholar]
  5. Brunger A. T., Adams P. D., Clore G. M. 11 other authors 1998; Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921
    [Google Scholar]
  6. Butcher S. J., Grimes J. M., Makeyev E. V., Bamford D. H., Stuart D. I. 2001; A mechanism for initiating RNA-dependent RNA polymerization. Nature 410:235–240 [CrossRef]
    [Google Scholar]
  7. Cheetham G. M. T., Steitz T. A. 2000; Insights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases. Curr Opin Struct Biol 10:117–123 [CrossRef]
    [Google Scholar]
  8. Choi K. H., Groarke J. M., Young D. C., Kuhn R. J., Smith J. L., Pevear D. C., Rossmann M. G. 2004; The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation. Proc Natl Acad Sci U S A 101:4425–4430 [CrossRef]
    [Google Scholar]
  9. Doublie S., Sawaya M. R., Ellenberger T. 1999; An open and closed case for all polymerases. Structure Fold Des 7:R31–R35 [CrossRef]
    [Google Scholar]
  10. Esnouf R. M. 1997; Polyalanine reconstruction from C α positions using the program CALPHA can aid initial phasing of data by molecular replacement procedures. Acta Crystallogr D Biol Crystallogr 53:665–672 [CrossRef]
    [Google Scholar]
  11. Esnouf R. M. 1999; Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallogr D Biol Crystallogr 55:938–940 [CrossRef]
    [Google Scholar]
  12. Hong Z., Cameron C. E., Walker M. P., Castro C., Yao N., Lau J. Y. N., Zhong W. 2001; A novel mechanism to ensure terminal initiation by hepatitis C virus NS5B polymerase. Virology 285:6–11 [CrossRef]
    [Google Scholar]
  13. Kao C. C., Singh P., Ecker D. J. 2001; De novo initiation of viral RNA-dependent RNA synthesis. Virology 287:251–260 [CrossRef]
    [Google Scholar]
  14. Koonin E. V. 1991; The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J Gen Virol 72:2197–2206 [CrossRef]
    [Google Scholar]
  15. Laurila M. R. L., Makeyev E. V., Bamford D. H. 2002; Bacteriophage ϕ 6 RNA-dependent RNA polymerase: molecular details of initiating nucleic acid synthesis without primer. J Biol Chem 277:17117–17124 [CrossRef]
    [Google Scholar]
  16. Lesburg C. A., Cable M. B., Ferrari E., Hong Z., Mannarino A. F., Weber P. C. 1999; Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site. Nat Struct Biol 6:937–943 [CrossRef]
    [Google Scholar]
  17. Luo G., Hamatake R. K., Mathis D. M., Racela J., Rigat K. L., Lemm J., Colonno R. J. 2000; De novo initiation of RNA synthesis by the RNA-dependent RNA polymerase (NS5B) of hepatitis C virus. J Virol 74:851–863 [CrossRef]
    [Google Scholar]
  18. Makeyev E. V. 2001; RNA-dependent RNA polymerase of bacteriophage ϕ6 . PhD thesis University of Helsinki;
  19. Makeyev E. V., Bamford D. H. 2000a; Replicase activity of purified recombinant protein P2 of double-stranded RNA bacteriophage ϕ 6. EMBO J 19:124–133 [CrossRef]
    [Google Scholar]
  20. Makeyev E. V., Bamford D. H. 2000b; The polymerase subunit of a dsRNA virus plays a central role in the regulation of viral RNA metabolism. EMBO J 19:6275–6284 [CrossRef]
    [Google Scholar]
  21. Makeyev E. V., Bamford D. H. 2001; Primer-independent RNA sequencing with bacteriophage ϕ 6 RNA polymerase and chain terminators. RNA 7:774–781 [CrossRef]
    [Google Scholar]
  22. Merritt E. A., Bacon D. J. 1997; Raster3D: photorealistic molecular graphics. Methods Enzymol 277:505–524
    [Google Scholar]
  23. Mindich L., Qiao X., Onodera S., Gottlieb P., Frilander M. 1994; RNA structural requirements for stability and minus-strand synthesis in the dsRNA bacteriophage ϕ 6. Virology 202:258–263 [CrossRef]
    [Google Scholar]
  24. Ollis D. L., Kline C., Steitz T. A. 1985; Domain of E. coli DNA polymerase I showing sequence homology to T7 DNA polymerase. Nature 313:818–819 [CrossRef]
    [Google Scholar]
  25. Otwinowski Z., Minor W. 1997; Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307–326
    [Google Scholar]
  26. Pagratis N., Revel H. R. 1990; Detection of bacteriophage ϕ 6 minus-strand RNA and novel mRNA isoconformers synthesized in vivo and in vitro , by strand-separating agarose gels. Virology 177:273–280 [CrossRef]
    [Google Scholar]
  27. Ranjith-Kumar C. T., Kim Y.-C., Gutshall L., Silverman C., Khandekar S., Sarisky R. T., Kao C. C. 2002a; Mechanism of de novo initiation by the hepatitis C virus RNA-dependent RNA polymerase: role of divalent metals. J Virol 76:12513–12525 [CrossRef]
    [Google Scholar]
  28. Ranjith-Kumar C. T., Gutshall L., Kim M.-J., Sarisky R. T., Kao C. C. 2002b; Requirements for de novo initiation of RNA synthesis by recombinant flaviviral RNA-dependent RNA polymerases. J Virol 76:12526–12536 [CrossRef]
    [Google Scholar]
  29. Ranjith-Kumar C. T., Gutshall L., Sarisky R. T., Kao C. C. 2003; Multiple interactions within the hepatitis C virus RNA polymerase repress primer-dependent RNA synthesis. J Mol Biol 330:675–685 [CrossRef]
    [Google Scholar]
  30. Salgado P. S., Makeyev E. V., Butcher S. J., Bamford D. H., Stuart D. I., Grimes J. M. 2004; The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase. Structure (Camb) 12:307–316
    [Google Scholar]
  31. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual , 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  32. Sun X.-L., Johnson R. B., Hockman M. A., Wang Q. M. 2000; De novo RNA synthesis catalyzed by HCV RNA-dependent RNA polymerase. Biochem Biophys Res Commun 268:798–803 [CrossRef]
    [Google Scholar]
  33. van Dijk A. A., Makeyev E. V., Bamford D. H. 2004; Initiation of viral RNA-dependent RNA polymerization. J Gen Virol 85:1077–1093 [CrossRef]
    [Google Scholar]
  34. Yang H., Makeyev E. V., Bamford D. H. 2001; Comparison of polymerase subunits from double-stranded RNA bacteriophages. J Virol 75:11088–11095 [CrossRef]
    [Google Scholar]
  35. Zhong W., Gutshall L. L., Del Vecchio A. M. 1998; Identification and characterization of an RNA-dependent RNA polymerase activity within the nonstructural protein 5B region of bovine viral diarrhea virus. J Virol 72:9365–9369
    [Google Scholar]
  36. Zhong W., Ferrari E., Lesburg C. A., Maag D., Ghosh S. K. B., Cameron C. E., Lau J. Y. N., Hong Z. 2000a; Template/primer requirements and single nucleotide incorporation by hepatitis C virus nonstructural protein 5B polymerase. J Virol 74:9134–9143 [CrossRef]
    [Google Scholar]
  37. Zhong W., Uss A. S., Ferrari E., Lau J. Y. N., Hong Z. 2000b; De novo initiation of RNA synthesis by hepatitis C virus nonstructural protein 5B polymerase. J Virol 74:2017–2022 [CrossRef]
    [Google Scholar]
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