Requirements for de novo initiation of RNA synthesis by recombinant flaviviral RNA-dependent RNA polymerases

Journal of Virology

Volumn 76, Issue 24, 2002, Pages 12526-12536

  Ranjith Kumar, C T ^a   Gutshall, Les ^b   Kim, Min Ju ^a   Sarisky, Robert T ^b   Kao, C Cheng ^a  

^a INDIANA UNIVERSITY   (United States)

^b GLAXOSMITHKLINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MAGNESIUM ION; MANGANESE; METAL ION; RNA DIRECTED RNA POLYMERASE;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; ENZYME MECHANISM; ENZYME MODIFICATION; ENZYME STRUCTURE; FLAVIVIRUS; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; RNA SYNTHESIS;

BROMOVIRUS; DIARRHEA VIRUSES, BOVINE VIRAL; FLAVIVIRUS; GB VIRUS B; HEPACIVIRUS; MANGANESE; RECOMBINANT PROTEINS; RNA REPLICASE; RNA, VIRAL;

EID: 0036892593     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.76.24.12526-12536.2002     Document Type: Article

References (48)

1. Ackermann, M., and R. Padmanabhan. 2001. De novo synthesis of RNA by the dengue virus RNA-dependent RNA polymerase exhibits temperature dependence at the initiation, but not the elongation phase. J. Biol. Chem. 276:39926-39937.
2. Adkins, S., and C. Kao. 1998. Subgenomic RNA promoters dictate the mode of recognition by bromoviral RNA-dependent RNA polymerases. Virology 252:1-8.
3. Adkins, S., S. Stawicki, G. Faurote, R. Siegel, and C. Kao. 1998. Mechanistic analysis of RNA synthesis by RNA-dependent RNA polymerase from two promoters reveals similarities to DNA-dependent RNA polymerase. RNA 4:455-470.
4. Behrens S.-E., L. Tomei, and R. De Francesco. 1996. Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus. EMBO J. 15:12-22.
5. Bressanelli, S., L. Tomei, A. Roussel, I. Incitti, R. L. Vitale, M. Mathieu, and R. DeFrancesco. 1999. Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Proc. Natl. Acad. Sci. USA 96:13034-13039.
6. Bressanelli, S., L. Tomei, F. A. Rey, and R. DeFrancesco. 2002. Structural analysis of the hepatitis C virus RNA polymerase in complex with ribonucleotides. J. Virol. 76:3482-3492.
7. Butcher, S. J., J. M. Grimes, E. V. Makeyev, D. H. Bramford, and D. I. Stuart. 2001. A mechanism for initiating RNA-dependent RNA polymerization. Nature 410:235-240.
8. Chen, D., and J. T. Patton. 2000. De novo synthesis of minus-strand RNA by the rotavirus RNA polymerase in a cell-free system involves a novel mechanism of initiation. RNA 6:1455-1467.
9. Garcin, D., M. Lezzi, M, Dobbs, R. M. Elliott, C. Schmaljohn, C. Y. Kang, and D. Kolakofsky. 1995. The 5′ ends of Hantaan virus (Bunyaviridae) RNAs suggest a prime-and-realign mechanism for the initiation of RNA synthesis. J. Virol. 69:5754-5762.
10. Honda, A., K. Mizumoto, and A. Ishihama. 1986. RNA polymerase of influenza virus: dinucleotide-primed initiation of transcription at specific positions on viral RNA. J. Biol. Chem. 261:5987-5991.
11. 2+ and deoxynucleoside monophosphate incorporation into transcripts. Biochemistry 36:13718-13728.
12. Joyce, C. M., and T. A. Steitz. 1995. Polymerase structure and function: Variations on a theme? J. Bacteriol. 177:6321-6329.
13. Kao, C. 2002. Lessons learned from the core RNA promoters of Brome mosaic virus and Cucumber mosaic virus. Mol. Plant Pathol. 3:55-62.
14. Kao, C., and J. H. Sun. 1996. Initiation of minus-strand RNA synthesis by the brome mosaic virus RNA-dependent RNA polymerase: Use of oligoribonucleotide primers. J. Virol. 70:6826-6830.
15. Kao, C. C., X. Yang, A. Kline, Q. M. Wang, D. Barket, and B. A. Heinz. 2000. Template requirements for RNA synthesis by a recombinant hepatitis C virus RNA-dependent RNA polymerase. J. Virol. 74:11121-11128.
16. Kao, C. C., A. M. Del Vecchio, and W. Zhong. 1999. De novo initiation of RNA synthesis by a recombinant Flaviviridae RNA-dependent RNA polymerase. Virology 253:1-7.
17. Kao, C. C., D. Ecker, and P. Singh. 2001. De novo initiation of viral RNA-dependent RNA synthesis. Virology 287:252-260.
18. Kim, M.-J., W. Zhong, Z. Hong, and C. C. Kao. 2000. Template nucleotide moieties for de novo initiation of RNA synthesis by a recombinant RNA- dependent RNA polymerase. J. Virol. 74:10312-10322.
19. Kuo, L., R. Fearns, and P. L. Collins. 1997. Analysis of the gene start and gene end signals of human respiratory syncytial virus: Quasi-templated initiation at position 1 of the encoded mRNA. J. Virol. 71:4944-4953.
20. Lesberg, C. A., M. B. Cable, E. Ferrari, Z. Hong, A. F. Mannarino, and P. C. Weber. 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.
21. Lohmann, V., H. Overton, and R. Bartenschlager. 1999. Selective stimulation of hepatitis C virus and pestivirus NS5B RNA polymerase activity by GTP. J. Biol. Chem. 274:10807-10815.
22. Luo, G., R. K. Hamatake, D. M. Mathis, J. Racela, K. L. Rigat, J. Lemm, and R. J. Colonno. 2000. De novo initiation of RNA synthesis by the RNA- dependent RNA polymerase (NS5B) of hepatitis C virus. J. Virol. 74:851- 863.
23. Martin, C. T., and J. E. Coleman. 1989. T7 RNA polymerase does not interact with the 5′-phosphate of the initiating nucleotide. Biochemistry 28:2760-2762.
24. Muller, D. K., C. T. Martin, and J. E. Coleman. 1989. T7 RNA polymerase interacts with its promoter from one side of the DNA helix. Biochemistry 28:3306-3313.
25. Ng, K., M., Cherney, A., López-Vázquez, A., Machin, J. Alonso, F., Parra, and M. James. 2002. Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase. J. Biol. Chem. 277:1381-1387.
26. Oh, J.-W., G.-T. Sheu, and M. M. C. Lai. 2000. Template requirement and initiation site selection by hepatitis C virus polymerase on a minimal viral RNA template. J. Biol. Chem. 275:17710-17717.
27. Pata, J. D., S. C. Schultz, and K. Kirkegaard. 1995. Functional oligomerization of poliovirus RNA-dependent RNA polymerase. RNA 1:466-477.
28. Pei, Y., K. Lehman, L. Tian, and S. Shuman. 2000. Characterization of Candida albicans RNA triphosphatase and mutational analysis of its active site. Nucleic Acids Res. 28:1885-1892.
29. Pezo, V., and S. Wain-Hobson. 1997. Hypermutagenic in vitro transcription employing biased NTP pools and manganese cations. Gene 186:67-72.
30. Pinto, D., M. T. Sarocchi-Landousy, and W. Guschlbacher. 1979. 2′-deoxy2′fluorouridine-5′-triphosphates: a possible substrate for E. coli RNA polymerase. Nucleic Acids Res. 6:1041-1048.
31. 2+ changes in a vascular smooth muscle cell line. Am. J. Physiol. 265:H281-H288.
32. Ranjith-Kumar, C. T., Y.-C. Kim, L. Gutshall, C. Silverman, S. Khandekar, R. T. Sarisky, and C. C. Kao. 2002. Mechanism of de novo initiation by the hepatitis C virus RNA-dependent RNA polymerase: Role of divalent metals. J. Virol. 76:12513-12525.
33. Ranjith-Kumar, C. T., J. Gajewski, L. Gutshall, R. Maley, R. Sarisky, and C. C. Kao. 2001. Terminal nucleotidyl transferase activity of recombinant Flaviviridae RNA-dependent RNA polymerases: Implication for viral RNA synthesis. J. Virol. 75:8615-8623.
34. Reddy, P. S., and D. Chatterji. 1994. Evidence for a pyrimidine nucleotidespecific initiation site (the i site) on Escherichia coli RNA polymerase. Eur. J. Biochem. 225:737-745.
35. Shuman, S., and B. Schwer. 1995. RNA capping enzyme and DNA ligase: A superfamily of covalent nucleotidyl transferases. Mol. Microbiol. 17:405-410.
36. Siegel, R., L. Bellon, L. Beigelman, and C. Kao. 1999. Use of RNA, DNA and chimeric templates revealed that a viral RNA-dependent RNA polymerase can bridge the gap from the RNA to the DNA world. J. Virol. 73:6424-6429.
37. Siegel, R., S. Adkins, and C. Kao. 1997. Sequence-specific recognition of an RNA promoter by a viral RNA polymerase. Proc. Natl. Acad. Sci. USA 94:11238-11243.
38. Sivakumaran, K., Y. Bao, M. Roossnick, and C. Kao. 2000. Recognition of the core RNA promoter for minus-strand RNA synthesis by the brome mosaic virus and Cucumber mosaic virus RNA replicases. J. Virol. 74:10323-10331.
39. Sivakumaran, K., C. H. Kim, R. Tayon, and C. Kao. 1999. RNA sequence and structural determinants for the recognition and efficiency of RNA synthesis by a viral RNA replicase. J. Mol. Biol. 294:667-682.
40. Sun, J. H., S. Adkins, G. Faurote, and C. Kao. 1996. Initiation of (-)-strand RNA synthesis catalyzed by the BMV RNA-dependent RNA polymerase: Synthesis of oligonucleotides. Virology 226:1-12.
41. Tabor, S., and C. Richardson. 1989. Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I. Proc. Natl. Acad. Sci. USA 86:4076-4080.
42. Tayon, Jr. R., M.-J. Kim, and C. Kao. 2001. Nucleotides near the 5′-terminus of the template contributes to the completion of RNA synthesis by viral RNA replicases. Nucleic Acids Res. 29:3583-3594.
43. Testa, D., and A. K. Banerjee. 1979. Initiation of RNA synthesis in vitro by vesicular stomatitis virus. Role of ATP. J. Biol. Chem. 254:2053-2058.
44. Trujillo, K. M., S. S. Yuan, E. Y. Lee, and P. Sung. 1998. Nuclease activities in a complex of human recombination and DNA repair factors Rad50, Mre11, and p95. J. Biol. Chem. 273:21447-21450.
45. Wang, Q. M., M. A. Hockman, K. Staschke, R. B. Johnson, K. A. Case, J. Lu, S. Parson, F. Zhang, R. Rathnachalam, K. Kirkegaard, and J. Colacino. 2002. Oligomerization and cooperative RNA synthesis activity of hepatitis C virus RNA-dependent RNA polymerase. J. Virol 76:3865-3872.
46. Zhang, R., and K. Ellis. 1989. In vivo measurement of total body magnesium and manganese in rats. Am. J. Physiol. 257:R1136-R1140.
47. Zhong, W., E. Ferrari, C. A. Lesburg, D. Maag, A. Gosh, C. Cameron, J. Lau, and Z. Hong. 2000. Template-primer requirements and single-nucleotide incorporation by hepatitis C virus nonstructural protein 5B polymerase. J. Virol. 74:9134-9143.
48. Zhong, W., P. Ingravallo, J. Wright-Minogue, A. S. Uss, A. Skelton, E. Ferrari, J. Y. Lau, and Z. Hong. 2000. RNA-dependent RNA polymerase activity encoded by GB virus-B nonstructural protein 5B. J. Viral Hepat. 7:335-342.