Functional analysis of mosquito-borne flavivirus conserved sequence elements within 3′ untranslated region of West Nile virus by use of a reporting replicon that differentiates between viral translation and RNA replication

Journal of Virology

Volumn 77, Issue 18, 2003, Pages 10004-10014

  Lo, Michael K ^a   Tilgner, Mark ^a   Bernard, Kristen A ^a,b   Shi, Pei Yong ^a,b  

^a WADSWORTH CENTER   (United States)

^b STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; BASE PAIRING; FLAVIVIRUS; GENETIC CONSERVATION; GENETIC TRANSFECTION; IMMUNOFLUORESCENCE; MOSQUITO; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN PROCESSING; REPORTER GENE; RNA REPLICATION; RNA TRANSLATION; SEQUENCE ANALYSIS; VIRUS CAPSID; VIRUS REPLICATION; VIRUS TRANSCRIPTION; WEST NILE FLAVIVIRUS;

3' UNTRANSLATED REGIONS; ANIMALS; CONSERVED SEQUENCE; CULICIDAE; LUCIFERASES; OPEN READING FRAMES; PROTEIN BIOSYNTHESIS; REPLICON; RNA, VIRAL; VIRUS REPLICATION; WEST NILE VIRUS;

EID: 0141570502     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.77.18.10004-10014.2003     Document Type: Article

References (33)

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 elongation phase. J. Biol. Chem. 276:39926-39937.
2. Barton, D. J., B. J. O'Donnell, and J. B. Flanegan. 2001. 5′ Cloverleaf in poliovirus RNA is a cis-acting replication element required for negative-strand synthesis. EMBO J. 20:1439-1448.
3. Berthet, F. X., H. G. Zeller, M. T. Drouet, J. Rauzier, J. P. Digoutte, and V. Deubel. 1997. Extensive nucleotide changes and deletions within the envelope glycoprotein gene of Euro-African West Nile viruses. J. Gen. Virol. 78:2293-2297.
4. Brinton, M. A., and J. H. Dispoto. 1988. Sequence and secondary structure analysis of the 5′-terminal region of flavivirus genome RNA. Virology 162:290-299.
5. Brinton, M. A., A. V. Fernandez, and J. H. Dispoto. 1986. The 3′-nucleotides of flavivirus genomic RNA form a conserved secondary structure. Virology 153:113-121.
6. Burke, D. S., and T. P. Monath. 2001. Flaviviruses, p. 1043-1126. In D. M. Knipe, and P. M. Howley (ed.), Fields virology, 4th ed., vol. 1. Lippincott Williams & Wilkins, Philadelphia, Pa.
7. Centers for Disease Control and Prevention. 2002. Provisional surveillance summary of the West Nile virus epidemic - United States, January-November 2002. Morb. Mortal. Wkly. Rep. 51:1129-1133.
8. Chambers, T. J., C. S. Hahn, R. Galler, and C. M. Rice. 1990. Flavivirus genome organization, expression, and replication. Annu. Rev. Microbiol. 44:649-688.
9. Chu, P. W., and E. G. Westaway. 1987. Characterization of Kunjin virus RNA-dependent RNA polymerase: reinitiation of synthesis in vitro. Virology 157:330-337.
10. Corver, J., E. Lenches, K. Smith, R. Robison, T. Sando, E. Strauss, and J. Strauss. 2003. Fine mapping of a cis-acting sequence element in yellow fever virus RNA that is required for RNA replication and cyclization. J. Virol. 77:2265-2270.
11. Diamond, M. S., D. Edgil, T. G. Roberts, B. Lu, and E. Harris. 2000. Infection of human cells by dengue virus is modulated by different cell types and viral strains. J. Virol. 74:7814-7823.
12. Diez, J., M. Ishikawa, M. Kaido, and P. Ahlquist. 2000. Identification and characterization of a host protein required for efficient template selection in viral RNA replication. Proc. Natl. Acad. Sci. USA 97:3913-3918.
13. Hahn, C. S., Y. S. Hahn, C. M. Rice, E. Lee, L. Dalgarno, E. G. Strauss, and J. H. Strauss. 1987. Conserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequences. J. Mol. Biol. 198:33-41.
14. Herold, J., and R. Andino. 2001. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol. Cell 7:581-591.
15. Huang, P., and M. M. C. Lai. 2001. Heterogeneous nuclear ribonucleoprotein A1 binds to the 3′-untranslated region and mediates potential 5′-3′-end cross talks of mouse hepatitis virus RNA. J. Virol. 75:5009-5017.
16. Khromykh, A. A., H. Meka, K. J. Guyatt, and E. G. Westaway. 2001. Essential role of cyclization sequences in flavivirus RNA replication. J. Virol. 75:6719-6728.
17. Khromykh, A. A., and E. G. Westaway. 1997. Subgenomic replicons of the flavivirus Kunjin: construction and applications. J. Virol. 71:1497-1505.
18. Klovins, J., and J. van Duin. 1999. A long-range pseudoknot in Qbeta RNA is essential for replication. J. Mol. Biol. 294:875-884.
19. Lahser, F. C., L. E. Marsh, and T. C. Hall. 1993. Contributions of the brome mosaic virus RNA-3 3′-nontranslated region to replication and translation. J. Virol. 67:3295-3303.
20. Lanciotti, R. S., J. T. Roehrig, V. Deubel, J. Smith, M. Parker, K. Steele, B. Crise, K. E. Volpe, M. B. Crabtree, J. H. Scherret, R. A. Hall, J. S. MacKenzie, C. B. Cropp, B. Panigrahy, E. Ostlund, B. Schmitt, M. Malkinson, C. Banet, J. Weissman, N. Komar, H. M. Savage, W. Stone, T. McNamara, and D. J. Gubler. 1999. Origin of the West Nile virus responsible for an outbreak of encephalitis in the northeastern United States. Science 286:2333-2337.
21. Men, R., M. Bray, D. Clark, R. M. Chanock, and C. J. Lai. 1996. Dengue type 4 virus mutants containing deletions in the 3′ noncoding region of the RNA genome: analysis of growth restriction in cell culture and altered viremia pattern and immunogenicity in rhesus monkeys. J. Virol. 70:3930-3937.
22. Molenkamp, R., E. Kooi, M. Lucassen, S. Greve, J. Thijssen, W. Spaan, and P. Bredenbeek. 2003. Yellow fever virus replicons as an expression system for hepatitis C virus structural proteins. J. Virol. 77:1644-1648.
23. Muylaert, I. R., T. J. Chambers, R. Galler, and C. M. Rice. 1996. Mutagenesis of the N-linked glycosylation sites of the yellow fever virus NS1 protein: effects on virus replication and mouse neurovirulence. Virology 222:159-168.
24. Rice, C. M., E. M. Lenches, S. R. Eddy, S. J. Shin, R. L. Sheets, and J. H. Strauss. 1985. Nucleotide sequence of yellow fever virus: implications for flavivirus gene expression and evolution. Science 229:726-733.
25. Sambrook, J., and D. W. Russel. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
26. Shi, P. Y., M. A. Brinton, J. M. Veal, Y. Y. Zhong, and W. D. Wilson. 1996. Evidence for the existence of a pseudoknot structure at the 3′ terminus of the flavivirus genomic RNA. Biochemistry 35:4222-4230.
27. Shi, P. Y., E. B. Kauffman, P. Ren, A. Felton, J. H. Tai, A. P. Dupuis II, S. A. Jones, K. A. Ngo, D. C. Nicholas, J. Maffel, G. D. Ebel, K. A. Bernard, and L. D. Kramer. 2001. High-throughput detection of West Nile virus RNA. J. Clin. Microbiol. 39:1264-1271.
28. Shi, P. Y., M. Tilgner, and M. K. Lo. 2002. Construction and characterization of subgenomic replicons of New York strain of West Nile virus. Virology 296:219-233.
29. Shi, P. Y., M. Tilgner, M. K. Lo, K. A. Kent, and K. A. Bernard. 2002. Infectious cDNA clone of the epidemic West Nile virus from New York City. J. Virol. 76:5847-5856.
30. Spagnolo, J. F., and B. G. Hogue. 2000. Host protein interactions with the 3′ end of bovine coronavirus RNA and the requirement of the poly(A) tail for coronavirus defective genome replication. J. Virol. 74:5053-5065.
31. Wallner, G., C. W. Mandl, C. Kunz, and F. X. Heinz. 1995. The flavivirus 3′-noncoding region: extensive size heterogeneity independent of evolutionary relationships among strains of tick-borne encephalitis virus. Virology 213:169-178.
32. Yamshchikov, V. F., G. Wengler, A. A. Perelygin, M. A. Brinton, and R. W. Compans. 2001. An infectious clone of the West Nile flavivirus. Virology 281:294-304.
33. You, S., and R. Padmanabhan. 1999. A novel in vitro replication system for Dengue virus. Initiation of RNA synthesis at the 3′ end of exogenous viral RNA templates requires 5′- and 3′-terminal complementary sequence motifs of the viral RNA. J. Biol. Chem. 274:33714-33722.