Conservation of the pentanucleotide motif at the top of the yellow fever virus 17D 3′ stem-loop structure is not required for replication

Journal of General Virology

Volumn 88, Issue 6, 2007, Pages 1738-1747

  Silva, Patŕicia A G C ^a   Molenkamp, Richard ^a,c   Dalebout, Tim J ^a   Charlier, Nathalie ^b   Neyts, Johan H ^b   Spaan, Willy J M ^a   Bredenbeek, Peter J ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^c ACADEMIC MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC RNA; NUCLEOTIDE;

ANIMAL CELL; ARTICLE; BASE PAIRING; CELL CULTURE; CONTROLLED STUDY; GENE MUTATION; GENETIC CONSERVATION; MOLECULAR MECHANICS; MUTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN STRUCTURE; VIRUS GENOME; VIRUS REPLICATION; WEST NILE FLAVIVIRUS; YELLOW FEVER FLAVIVIRUS;

3' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CELL LINE; CERCOPITHECUS AETHIOPS; CONSERVED SEQUENCE; CRICETINAE; GENOME, VIRAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; RNA, VIRAL; VIRUS REPLICATION; WEST NILE VIRUS; YELLOW FEVER VIRUS;

ANIMALIA; ARBOVIRUS; FLAVIVIRUS; REPLICATION COMPETENT VIRUSES; WEST NILE VIRUS; YELLOW FEVER VIRUS;

EID: 34249810901     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/vir.0.82811-0     Document Type: Article

References (38)

1. Alvarez, D. E., Ezcurra, A. L. D., Fucito, S. & Gamarnik, A. V. (2005). Role of RNA structures present at the 3′ UTR of dengue virus on translation, RNA synthesis, and viral replication. Virology 339, 200-212.
2. Ausubel, F. M., Brent, R., Kingstone, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. (2000). Current Protocols in Molecular Biology. New York: Wiley.
3. Blackwell, J. L. & Brinton, M. A. (1997). Translation elongation factor-1α interacts with the 3′ stem-loop region of West Nile virus genomic RNA. J Virol 71, 6433-6444.
4. Bredenbeek, P. J., Kooi, E. A., Lindenbach, B., Huijkman, N., Rice, C. M. & Spaan, W. J. M. (2003). A stable full-length yellow fever virus cDNA clone and the role of conserved RNA elements in flavivirus replication. J Gen Virol 84, 1261-1268.
5. Brinton, M. A., Fernandez, A. V. & Dispoto, J. H. (1986). The 3′-nucleotides of flavivirus genomic RNA form a conserved secondary structure. Virology 153, 113-121.
6. Charlier, N., Leyssen, P., Pleij, C. W. A., Lemey, P., Billoir, F., Van Laethem, K., Vandamme, A. M., De Clercq, E., de Lamballerie, X. & Neyts, J. (2002). Complete genome sequence of Montana Myotis leukoencephalitis virus, phylogenetic analysis and comparative study of the 3′ untranslated region of flaviviruses with no known vector. J Gen Virol 83, 1875-1885.
7. Charlier, N., Molenkamp, R., Leyssen, P., Paeshuyse, J., Drosten, C., Panning, M., De Clercq, E., Bredenbeek, P. J. & Neyts, J. (2004). Exchanging the yellow fever virus envelope proteins with Modoc virus prM and E proteins results in a chimeric virus that is neuroinvasive in SCID mice. J Virol 78, 7418-7426.
8. Chen, C. J., Kuo, M. D., Chien, L. J., Hsu, S. L., Wang, Y. M. & Lin, J. H. (1997). RNA-protein interactions: involvement of NS3, NS5, and 3′ noncoding regions of Japanese encephalitis virus genomic RNA. J Virol 71, 3466-3473.
9. Chiu, W. W., Kinney, R. M. & Dreher, T. W. (2005). Control of translation by the 5′- and 3′-terminal regions of the dengue virus genome. J Virol 79, 8303-8315.
10. Cook, S. & Holmes, E. C. (2006). A multigene analysis of the phylogenetic relationships among the flaviviruses (family: Flaviviridae) and the evolution of vector transmission. Arch Virol 151, 309-325.
11. Elghonemy, S., Davis, W. G. & Brinton, M. A. (2005). 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 331, 238-246.
12. Gritsun, T. S., Desai, A. & Gould, E. A. (2001). The degree of attenuation of tick-borne encephalitis virus depends on the cumulative effects of point mutations. J Gen Virol 82, 1667-1675.
13. Hahn, C. S., Hahn, Y. S., Rice, C. M., Lee, E., Dalgarno, L., Strauss, E. G. & Strauss, J. H. (1987). Conserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequences. J Mol Biol 198, 33-41.
14. Holden, K. L. & Harris, E. (2004). Enhancement of dengue virus translation: role of the 3′ untranslated region and the terminal 3′ stem-loop domain. Virology 329, 119-133.
15. Holden, K. L., Stein, D. A., Pierson, T. C., Ahmed, A. A., Clyde, K., Iversen, P. L. & Harris, E. (2006). Inhibition of dengue virus translation and RNA synthesis by a morpholino oligomer targeted to the top of the terminal 3′ stem-loop structure. Virology 344, 439-452.
16. Inoue, H., Nojima, H. & Okayama, H. (1990). High-efficiency transformation of Escherichia coli with plasmids. Gene 96, 23-28.
17. Jones, C. T., Patkar, C. G. & Kuhn, R. J. (2005). Construction and applications of yellow fever virus replicons. Virology 331, 247-259.
18. Khromykh, A. A. & Westaway, E. G. (1997). Subgenomic replicons of the flavivirus Kunjin: construction and applications. J Virol 71, 1497-1505.
19. Kim, S. M. & Jeong, Y. S. (2006). Polypyrimidine tract-binding protein interacts with the 3′ stem-loop region of Japanese encephalitis virus negative-strand RNA. Virus Res 115, 131-140.
20. Kuno, G., Chang, G. J. J., Tsuchiya, K. R., Karabatsos, N. & Cropp, C. B. (1998). Phylogeny of the genus Flavivirus. J Virol 72, 73-83.
21. Lawrie, C. H., Uzcategui, N. Y., Armesto, M., Bell-Sakyi, L. & Gould, E. A. (2004). Susceptibility of mosquito and tick cell lines to infection with various flaviviruses. Med Vet Entomol 18, 268-274.
22. Lindenbach, B. D. & Rice, C. M. (1997). trans-Complementation of yellow fever virus NS1 reveals a role in early RNA replication. J Virol 71, 9608-9617.
23. Lindenbach, B. & Rice, C. M. (2001). Flaviviridae: the viruses and their replication. In Fields Virology, 4th edn, pp. 991-1041. Edited by D. M. Knipe & P. M. Howley. Philadelphia: Lippincott, Williams, Wilkins.
24. Lo, M. K., Tilgner, M., Bernard, K. A. & Shi, P. Y. (2003). 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. J Virol 77, 10004-10014.
25. Markoff, L. (2003). 5′- and 3′-noncoding regions of flavivirus RNA. In The Flaviviruses; Structure, Replication, and Evolution, pp. 177-228. Edited by T. J. Chambers & T. P. Monath. Elsevier Academic Press.
26. Mathews, D. H., Sabina, J., Zuker, M. & Turner, D. H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288, 911-940.
27. Molenkamp, R., Kooi, E. A., Lucassen, M. A., Greve, S., Thijssen, J. C. P., Spaan, W. J. M. & Bredenbeek, P. J. (2003). Yellow fever virus replicons as an expression system for hepatitis C virus structural proteins. J Virol 77, 1644-1648.
28. Nomaguchi, M., Teramoto, T., Yu, L., Markoff, L. & Padmanabhan, R. (2004). Requirements for West Nile virus (-)- and (+)-strand subgenomic RNA synthesis in vitro by the viral RNA-dependent RNA polymerase expressed in Escherichia coli. J Biol Chem 279, 12141-12151.
29. Nova-Ocampo, M., Villegas-Sepuveda, N. & del Angel, R. M. (2002). Translation elongation factor-1α, La, and PTB interact with the 3′ untranslated region of dengue 4 virus RNA. Virology 295, 337-347.
30. Sambrook, J., Fritsch, T. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
31. Shi, P. Y., Tilgner, M. & Lo, M. K. (2002). Construction and characterization of subgenomic replicons of New York strain of West Nile virus. Virology 296, 219-233.
32. Ta, M. & Vrati, S. (2000). Mov34 protein from mouse brain interacts with the 3′ noncoding region of Japanese encephalitis virus. J Virol 74, 5108-5115.
33. Tajima, S., Takasaki, T., Matsuno, S., Nakayama, M. & Kurane, I. (2005). Genetic characterization of Yokose virus, a flavivirus isolated from the bat in Japan. Virology 332, 38-44.
34. Thiel, H.-J., Collett, M. S., Gould, E. A., Heinz, F. X., Houghton, M., Meyers, G., Purcell, R. H. & Rice, C. M. (2005). Family Flaviviridae. In Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses, pp. 981-998. Edited by C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger & L. A. Ball. San Diego: Elsevier Academic Press.
35. Tilgner, M., Deas, T. S. & Shi, P. Y. (2005). 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, 375-386.
36. van Dinten, L. C., Denboon, J. A., Wassenaar, A. L. M., Spaan, W. J. M. & Snijder, E. J. (1997). An infectious arterivirus cDNA clone: identification of a replicase point mutation that abolishes discontinuous mRNA transcription. Proc Natl Acad Sci U S A 94, 991-996.
37. Wengler, G. & Castle, E. (1986). Analysis of structural properties which possibly are characteristic for the 3′-terminal sequence of the genome RNA of flaviviruses. J Gen Virol 67, 1183-1188.
38. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415.