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De novo polymerase activity and oligomerization of Hepatitis C Virus RNA-dependent RNApolymerases from genotypes 1 to 5. Clemente-Casares, P., López-Jiménez, A.J., Bellón-Echeverría, I., Encinar, J.A., Martínez-Alfaro, E., Pérez-Flores, R., & Mas, A. 2011. PLoS ONE 6(4): e18515.


  1. Martell M, Esteban JI, Quer J, Genescà J, Weiner A, et al. (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.
  2. Perelson AS, Herrmann E, Micol F, Zeuzem S (2005) New kinetic models for the hepatitis C virus. Hepatol 42: 749-754.
  3. Domingo E, Gomez J (2007) Quasispecies and its impact on viral hepatitis. Virus Res 127: 131-150.
  4. Kuiken C, Yusim K, Boykin L, Richardson R (2005) The Los Alamos HCV Sequence Database. Bioinformatics 21: 379-384.
  5. Kuiken C, Simmonds P (2009) Nomenclature and numbering of the hepatitis C virus. Methods Mol Biol 510: 33-53.
  6. Simmonds P, Bukh J, Combet C, Deléage N, Enomoto S, et al. (2005) Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42: 962-973.
  7. Zeuzem S (2008) Interferon-based therapy for chronic hepatitis C: current and future perspectives. Nat Clin Pract Gastroenterol Hepatol 5: 610-622.
  8. Nguyen MH, Keeffe EB (2005) Prevalence and treatment of hepatitis C virus genotypes 4, 5, and 6. Clin Gastroenterol Hepatol 3: S97-S101.
  9. Lindenbach BD, Rice CM (2005) Unravelling hepatitis C virus replication from genome to function. Nature 436: 933-938.
  10. Behrens SE, Tomei L, De Francesco R (1996) Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus. EMBO J 15: 12-22.
  11. Lohmann V, Körner 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.
  12. Luo G, Hamatake RK, Mathis DM, Racela J, Rigat KL, et al. (2000) De novo initiation of RNA synthesis by the RNA-dependent RNA polymerase (NS5B) of hepatitis C virus. J Virol 2000; 74: 851-863.
  13. Zhong W, Uss AS, Ferrari E, Lau JY, Hong Z (2000) De novo initiation of RNA synthesis by hepatitis C virus nonstructural protein 5B polymerase. J Virol 74: 2017-2022.
  14. Ranjith-Kumar CT, Kim YC, Gutshall L, Silverman C, Khandekar S, et al. (2002) Mechanism of de novo initiation by the hepatitis C virus RNA-dependent RNA polymerase: role of divalent metals. J Virol 76: 12513-12525.
  15. Ahmed-Belkacem A, Ahnou N, Barbotte L, Wychowski C, Pallier C, et al. (2010) Silibinin and related compounds are direct inhibitors of hepatitis C virus RNA-dependent RNA polymerase. Gastroenterology 138: 1112-1122.
  16. Heck JA, Lam AM, Narayanan N, Frick DN (2008) Effects of mutagenic and chain-terminating nucleotide analogs on enzymes isolated from hepatitis C virus strains of various genotypes. Antimicrob Agents Chemother 52: 1901-1911.
  17. Huang P, Goff DA, Huang Q, Martinez A, Xu X, et al. (2008) Discovery and characterization of substituted diphenyl heterocyclic compounds as potent and selective inhibitors of hepatitis C virus replication. Antimicrob Agents Chemother 52: 1419-1429.
  18. Lam AM, Murakami E, Espiritu C, Steuer HM, Niu Cetal (2010) PSI-7851, a Pronucleotide of {beta}-D-2'-deoxy-2'-fluoro-2'-C-methylu?ridinemonophosphate, is a potent and pan-genotype inhibitor of hepatitis C virus replication. Antimicrob Agents Chemother 54: 3187-3196.
  19. Liu Y, Donner PL, Pratt JK, Jiang WW, Ng T, et al. (2008) Identification of halosalicylamide derivatives as a novel class of allosteric inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett 18: 3173-3177.
  20. Pauwels F, Mostmans W, Quirynen LM, van der Helm L, Boutton CW, et al. (2007) Binding-site identification and genotypic profiling of hepatitis C virus polymerase inhibitors. J Virol 81: 6909-6919.
  21. Quinkert D, Bartenschlager R, Lohmann V (2005) Quantitative analysis of the hepatitis C virus replication complex. J Virol 79: 13594-13605.
  22. Wang QM, Hockman MA, Staschke K, Johnson RB, Case KA, et al. (2002) Oligomerization and cooperative RNA synthesis activity of Hepatitis C virus RNA-dependent RNA polymerase. J Virol 76: 3865-3872.
  23. Bellon-Echeverria I, Lopez-Jimenez AJ, Clemente-Casares P, Mas A (2010) Monitoring hepatitis C virus (HCV) RNA-dependent RNA polymerase oligomerization by a FRET-based in vitro system. Antiviral Res 87: 57-66.
  24. Qin W, Luo H, Nomura T, Hayashi N, Yamashita T, et al. (2002) Oligomeric interaction of hepatitis C virus NS5B is critical for catalytic activity of RNA-dependent RNA polymerase. J Biol Chem 277: 2132-2137.
  25. Biswal BK, Wang M, Cherney MM, Chan L, Yannopoulos CG, et al. (2006) Non-nucleoside inhibitors binding to hepatitis C virus NS5B polymerase reveal a novel mechanism of inhibition. J Mol Biol 361: 33-45.
  26. Love RA, Parge HE, Yu X, Hickey MJ, Diehl W, et al. (2003) Crystallographic identification of a noncompetitive inhibitor binding site on the hepatitis C virus NS5B RNA polymerase enzyme. J Virol 77: 7575-7581.
  27. Fan X, Xu Y, Di Bisceglie AM (2006) Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples. Biochem Biophys Res Commun 346: 1163-1172.
  28. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
  29. Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22: 521-565.
  30. Carroll SS, Sardana V, Yang Z, Jacobs AR, Mizenko C, et al. (2000) Only a small fraction of purified hepatitis C RNA-dependent RNA polymerase is catalytically competent: implications for viral replication and in vitro assays. Biochemistry 18: 8243-8249.
  31. Copeland RA (1996) Enzymes. New York: Wiley-VCH Press.
  32. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci 98: 10037-10041.
  33. DeLano WL (2010) The PyMOL Molecular Graphics System, Version 1.3, Schrödinger, LLC. Accessed 2011 Feb 25.
  34. Guerois R, Nielsen JE, Serrano L (2002) Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations. J Mol Biol 320: 369-387.
  35. Tovchigrechko A, Vakser IA (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Res 34: W310-4.
  36. Tina KG, Bhadra R, Srinivasan N (2007) Protein Interactions Calculator. Nucleic Acids Res 35: W473-W476.
  37. Maulik A, Ghosh H, Basu S (2009) Comparative study of protein-protein interaction observed in PolyGalacturonase-Inhibiting Proteins from Phaseolus vulgaris and Glycine max and PolyGalacturonase from Fusarium moniliforme. BMC Genomics 3: Suppl 3S19.
  38. Ferrari E, He Z, Palermo RE, Huang HC (2008) Hepatitis C virus NS5B polymerase exhibits distinct nucleotide requirements for initiation and elongation. J Biol Chem 283: 33893-33901.
  39. Selisko B, Dutartre H, Guillemot JC, Debarnot C, et al. (2006) Comparative mechanistic studies of de novo RNA synthesis by flavivirus RNA-dependent RNA polymerases. Virology 351: 145-58.
  40. Poranen MM, Salgado PS, Koivunen MR, Wright S, Bamford DH, et al. (2008) Structural explanation for the role of Mn2+ in the activity of phi6 RNA-dependent RNA polymerase. Nucleic Acids Res 36: 6633-44.
  41. Bougie I, Charpentier S, Bisaillon M (2003) Characterization of the metal ion binding properties of the hepatitis C virus RNA polymerase. J Biol Chem 278: 3868-75.
  42. Versieck J, Cornelis R (1989) Trace Elements in Human Plasma or Serum. Boca Raton, FL: CRC Press.
  43. Ferrari E, Wright-Minogue J, Fang JWS, Baroudy BM, Lau JY, et al. (1999) Characterization of soluble Hepatitis C virus RNA-Dependent RNA polymerase expressed in Escherichia coli. J Virol 73: 1649-1654.
  44. Schmitt M, Scrima N, Radujkovic D, Caillet-Saguy C, Simister PC, et al. (2011) A comprehensive structure-function comparison of hepatitis C virus strains JFH1 and J6 polymerases reveals a key residue stimulating replication in cell culture across genotypes. J Virol 85: 2565-2581.
  45. Högbom M, Jäger K, Robel I, Unge T, Rohayem J (2009) The active form of the norovirus RNA-dependent RNA polymerase is a homodimer with cooperative activity. J Gen Virol 90: 281-291.
  46. Jorba N, Area E, Ortín J (2008) Oligomerization of the influenza virus polymerase complex in vivo. J Gen Virol 89: 520-524.
  47. Kaiser WJ, Chaudhry Y, Sosnovtsev SV, Goodfellow IG (2006) Analysis of protein-protein interactions in the feline calicivirus replication complex. J Gen Virol 87: 363-368.
  48. Pata JD, Schultz SC, Kirkegaard K (1995) Functional oligomerization of poliovirus RNA-dependent RNA polymerase. RNA 1: 466-477.
  49. Spagnolo JF, Rossignol E, Bullitt E, Kirkegaard K (2010) Enzymatic and nonenzymatic functions of viral RNA-dependent RNA polymerases within oligomeric arrays. RNA 16: 382-393.
  50. Egger D, Wölk B, Gosert R, Bianchi L, Blum HE, et al. (2002) Expression of hepatitis C virus proteins induces distinct membrane alterations including a candidate viral replication complex. J Virol 76: 5974-5984.
  51. Gosert R, Egger D, Lohmann V, Bartenschlager R, Blum HE, et al. (2003) Identification of the hepatitis C virus RNA replication complex in Huh-7 cells harboring subgenomic replicons. J Virol 77: 5487-5492.
  52. Chinnaswamy S, Murali A, Li P, Fujisaki K, Kao CC (2010) Regulation of de novo-initiated RNA synthesis in hepatitis C virus RNA-dependent RNA polymerase by intermolecular interactions. J Virol 84: 5923-5935.
  53. Cramer J, Jaeger J, Restle T (2006) Biochemical and pre-steady-state kinetic characterization of the hepatitis C virus RNA polymerase (NS5Bdelta21, HC-J4). Biochemistry 45: 3610-3619.
  54. Ago H, Adachi T, Yoshida A, Yamamoto M, Habuka N, et al. (1999) Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Structure 7: 1417-1426.
  55. Biswal BK, Cherney MM, Wang M, Chan L, Yannopoulos CG, et al. (2005) Crystal structures of the RNA-dependent RNA polymerase genotype 2a of hepatitis C virus reveal two conformations and suggest mechanisms of inhibition by non-nucleoside inhibitors. J Biol Chem 280: 18202-18210.
  56. Bressanelli S, Tomei L, Roussel A, Incitti I, Vitali RL, et al. (1999) Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Proc Natl Acad Sci USA 96: 13034-13039.
  57. Bressanelli S, Tomei L, Rey FA, De Francesco R (2002) Structural Analysis of the Hepatitis C Virus RNA Polymerase in Complex with Ribonucleotides. J Virol 76: 3482-3492.
  58. Lesburg CA, Cable MB, Ferrari E, Hong Z, Mandarino AF, et al. (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.
  59. O'Farrell D, Trowbridge R, Rowlands D, Jäger J (2003) Substrate complexes of hepatitis C virus RNA polymerase (HC-J4): structural evidence for nucleotide import and de-novo initiation. J Mol Biol 326: 1025-1035.