The majority of the nucleotides in the top loop of the genomic 3′ terminal stem loop structure are cis-acting in a West Nile virus infectious clone

Virology

Volumn 331, Issue 2, 2005, Pages 238-246

  Elghonemy, Salwa ^a   Davis, William G ^a   Brinton, Margo A ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

Author keywords

3 cis acting nucleotides; 3 Stem loop structure; Infectious clone; West Nile virus

Indexed keywords

GENOMIC RNA; NUCLEOTIDE; VIRUS PROTEIN; VIRUS RNA;

ACCURACY; ANIMAL CELL; ANIMAL MODEL; ARTICLE; CONTROLLED STUDY; GENE LOCATION; GENE MUTATION; GENE STRUCTURE; GENETIC CONSERVATION; HAMSTER; MOLECULAR CLONING; MOSQUITO; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; RNA VIRUS INFECTION; TICK; VIRUS GENOME; VIRUS REPLICATION; WEST NILE FLAVIVIRUS;

ANIMALS; CONSERVED SEQUENCE; CRICETINAE; GENOME, VIRAL; KIDNEY; MUTATION; NUCLEIC ACID CONFORMATION; RNA, VIRAL; STRUCTURE-ACTIVITY RELATIONSHIP; VIRUS REPLICATION; WEST NILE VIRUS;

ACARI; FLAVIVIRUS; MOSQUITO-BORNE VIRUSES; TICK-BORNE FLAVIVIRUS; WEST NILE VIRUS;

EID: 11344274983     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virol.2004.11.008     Document Type: Article

References (23)

1. J.L. Blackwell, and M.A. Brinton BHK cell proteins that bind to the 3′ stem loop structure of the West Nile virus genome RNA J. Virol. 69 1995 5650 5658
2. J.L. Blackwell, and M.A. Brinton Translation elongation factor-1 alpha interacts with the 3′ stem-loop region of West Nile virus genomic RNA J. Virol. 71 1997 6433 6444
3. P.J. Bredenbeek, E.A. Kooi, B. Lindenbach, N. Huijkman, C.M. Rice, and W.J. Spaan A stable full length yellow fever virus cDNA clone and the role of conserved RNA elements in flavivirus replication J. Gen. Virol. 84 2003 1261 1268
4. M.A. Brinton Replication of flavivirus S. Schlesinger M. Schlesinger The Togaviridae and Flaviviridae 1986 Plenum Press New York 327 365
5. M.A. Brinton The molecular biology of West Nile Virus: a new invader of the Western hemisphere Annu. Rev. Microbiol. 56 2002 371 402
6. M.A. Brinton, A.V. Fernandez, and J.H. Dispoto The 3′ nucleotides of flavivirus genomic RNA form a conserved secondary structure Virology 153 1986 113 121
7. C.J. Chen, M.D. Kuo, L.J. Chien, S.L. Hsu, Y.M. Wang, and J.H. Lin RNA-protein interactions: involvement of NS3, NS5, and 3′ noncoding regions of Japanese encephalitis virus genomic RNA J. Virol. 71 1997 3466 3473
8. T. Grange, M. Bouloy, and M. Girard Stable secondary structures at the 3′ end of the genome of yellow fever virus (17 D vaccine strain) FEBS Lett. 188 1985 159 163
9. C.S. Hahn, Y.S. Hahn, C.M. Rice, E. Lee, L. Dalgarno, E.G. Strauss, and J.H. Strauss Conserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequences J. Mol. Biol. 198 1987 33 41
10. A.A. Khromykh, N. Kondratieva, J.Y. Sgro, A. Palmenberg, and E.G. Westaway Significance in replication of the terminal nucleotides of the flavivirus genome J. Virol. 77 2003 10623 10629
11. B.D. Lindenbach, and C.M. Rice Flaviviridae: the viruses and their replication B.N. Fields D.N. Knipe P.M. Howley D.E. Griffin M.A. Martin R.A. Lamb B. Roizman S.E. Straus Fields Virology 4th ed. 2001 Lippincott Williams and Wilkins Philadelphia 991 1024
12. L. Markoff 5′- and 3′-noncoding regions of flavivirus RNA Adv. Virus Res. 59 2003 177 228
13. L.R. Petersen, and J.T. Roehrig West Nile Virus: a reemerging global pathogen Emerging Infect. Dis. 7 2001 611 614
14. V. Proutski, E.A. Gould, and E.C. Holmes Secondary structure of the 3′ untranslated region of flaviviruses: similarities and differences Nucleic Acids Res. 25 1997 1194 1202
15. J.H. Rappole, S.R. Derrickson, and Z. Hubalek Migratory birds and spread of West Nile in the Western Hemisphere Emerging Infect. Dis. 6 2000 319 328
16. S. Rauscher, C. Flamm, C.W. Mandl, F.X. Heinz, and P.F. Stadler Secondary structure of the 3′-noncoding region of flavivirus genomes: comparative analysis of base pairing probabilities RNA 3 1997 779 791
17. M. Tilgner, T.S. Deas, and P.-Y. Shi The flavivirus-conserved penta-nucleotide in the 3′ stem-loop of the West Nile virus genome requires a specific sequence and structure for RNA synthesis, but not for viral translation Virology 331 2004 375 386
18. A. Vaheri, W.D. Sedwick, S.A. Plotkin, and R. Maes Cytopathic effect of rubella virus in BHK21 cells and growth to high titers in suspension culture Virology 27 1965 239 241
19. G. Wengler, and E. Castle Analysis of structural properties which possibly are characteristic for the 3′-terminal sequence of the genome RNA of flaviviruses J. Gen. Virol. 67 1986 1183 1188
20. V.F. Yamshchikov, G. Wengler, A.A. Perelygin, M.A. Brinton, and R.W. Compans An infectious clone of the West Nile Flavivirus Virology 281 2001 294 304
21. L. Zeng, B. Flagout, and L. Markoff Identification of specific nucleotide sequences within the conserved 3′ SL in the dengue type-2 virus genome required for replication J. Virol. 72 1998 7510 7522
22. M. Zuker M fold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 31 2003 3406 3415
23. M. Zuker, and A.B. Jacobson Well-determined regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA Nucleic Acids Res. 23 1995 2791 2798