Functional analysis of dengue virus cyclization sequences located at the 5′ and 3′UTRs

Virology

Volumn 375, Issue 1, 2008, Pages 223-235

  Alvarez, Diego E ^a   Filomatori, Claudia V ^a   Gamarnik, Andrea V ^a  

^a FUNDACIÓN INSTITUTO LELOIR   (Argentina)

Author keywords

3 UTR; 5 UTR; Cyclization sequences; Dengue virus; Flavivirus; Plus strand RNA virus; RNA cyclization; RNA replication; RNA RNA interactions; Viral RNA synthesis

Indexed keywords

NUCLEOTIDE; VIRUS RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CYCLIZATION; DENGUE VIRUS; GENE AMPLIFICATION; GENE MUTATION; GENE SEQUENCE; GENOMICS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA REPLICATION; RNA SYNTHESIS; VIRAL GENETICS; VIRUS GENOME; VIRUS REPLICATION;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ANIMALS; CELL LINE; CRICETINAE; DENGUE VIRUS; MODELS, MOLECULAR; MUTATION; NUCLEIC ACID CONFORMATION; RNA; RNA, COMPLEMENTARY; RNA, VIRAL; SUPPRESSION, GENETIC; VIRUS REPLICATION;

DENGUE VIRUS; FLAVIVIRUS; RNA VIRUSES;

EID: 42749084987     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2008.01.014     Document Type: Article

References (31)

1. Alvarez D.E., De Lella Ezcurra A.L., Fucito S., and Gamarnik A.V. Role of RNA structures present at the 3′UTR of dengue virus on translation, RNA synthesis, and viral replication. Virology 339 2 (2005) 200-212
2. Alvarez D.E., Lodeiro M.F., Luduena S.J., Pietrasanta L.I., and Gamarnik A.V. Long-range RNA-RNA interactions circularize the dengue virus genome. J. Virol. 79 11 (2005) 6631-6643
3. Brinton M.A., and Dispoto J.H. Sequence and secondary structure analysis of the 5′-terminal region of flavivirus genome RNA. Virology 162 2 (1988) 290-299
4. Brinton M.A., Fernandez A.V., and Dispoto J.H. The 3′-nucleotides of flavivirus genomic RNA form a conserved secondary structure. Virology 153 1 (1986) 113-121
5. Cahour A., Pletnev A., Vazielle-Falcoz M., Rosen L., and Lai C.J. Growth-restricted dengue virus mutants containing deletions in the 5′ noncoding region of the RNA genome. Virology 207 1 (1995) 68-76
6. Clyde K., and Harris E. RNA secondary structure in the coding region of dengue virus type 2 directs translation start codon selection and is required for viral replication. J. Virol. 80 5 (2006) 2170-2182
7. Corver J., Lenches E., Smith K., Robison R.A., Sando T., Strauss E.G., and Strauss J.H. Fine mapping of a cis-acting sequence element in yellow fever virus RNA that is required for RNA replication and cyclization. J. Virol. 77 3 (2003) 2265-2270
8. Elghonemy S., Davis W.G., and Brinton M.A. 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 2 (2005) 238-246
9. Filomatori C.V., Lodeiro M.F., Alvarez D.E., Samsa M.M., Pietrasanta L., and Gamarnik A.V. A 5′ RNA element promotes dengue virus RNA synthesis on a circular genome. Genes Dev. 20 16 (2006) 2238-2249
10. Gritsun T.S., and Gould E.A. Origin and evolution of flavivirus 5′UTRs and panhandles: trans-terminal duplications?. Virology 366 1 (2007) 8-15
11. Hahn C.S., Hahn Y.S., Rice C.M., Lee E., Dalgarno L., Strauss E.G., and Strauss J.H. Conserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequences. J. Mol. Biol. 198 1 (1987) 33-41
12. Jaeger L., Michel F., and Westhof E. Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol. Biol. 236 5 (1994) 1271-1276
13. Khromykh A.A., Meka H., Guyatt K.J., and Westaway E.G. Essential role of cyclization sequences in flavivirus RNA replication. J. Virol. 75 14 (2001) 6719-6728
14. Kinney R.M., Butrapet S., Chang G.J., Tsuchiya K.R., Roehrig J.T., Bhamarapravati N., and Gubler D.J. Construction of infectious cDNA clones for dengue 2 virus: strain 16681 and its attenuated vaccine derivative, strain PDK-53. Virology 230 2 (1997) 300-308
15. Legault P., Li J., Mogridge J., Kay L.E., and Greenblatt J. NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell 93 2 (1998) 289-299
16. Leitmeyer K.C., Vaughn D.W., Watts D.M., Salas R., Villalobos I., de C., Ramos C., and Rico-Hesse R. Dengue virus structural differences that correlate with pathogenesis. J. Virol. 73 6 (1999) 4738-4747
17. Lindenbach B., and Rice C. Flaviviridae: the viruses and their replication. Fields Virology 1 (2001), Lippincott-Raven, Philadelphia
18. Lo M.K., Tilgner M., Bernard K.A., and Shi P.Y. 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 18 (2003) 10004-10014
19. Markoff L. 5′ and 3′ NCRs in Flavivirus RNA. In: Chambers T.J., and Monath T.P. (Eds). Flaviviruses. Adv. Virus Res. 60 (2003), Elsevier Academic Press
20. Men R., Bray M., Clark D., Chanock R.M., and Lai C.J. 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 6 (1996) 3930-3937
21. Olsthoorn R.C., Mertens S., Brederode F.T., and Bol J.F. A conformational switch at the 3′ end of a plant virus RNA regulates viral replication. EMBO J. 18 17 (1999) 4856-4864
22. Pogany J., Fabian M.R., White K.A., and Nagy P.D. A replication silencer element in a plus-strand RNA virus. EMBO J. 22 20 (2003) 5602-5611
23. Thurner C., Witwer C., Hofacker I.L., and Stadler P.F. Conserved RNA secondary structures in Flaviviridae genomes. J. Gen. Virol. 85 Pt 5 (2004) 1113-1124
24. Tilgner M., Deas T.S., and Shi P.Y. 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 2 (2005) 375-386
25. You S., and Padmanabhan R. 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 47 (1999) 33714-33722
26. You S., Falgout B., Markoff L., and Padmanabhan R. In vitro RNA synthesis from exogenous dengue viral RNA templates requires long range interactions between 5′- and 3′-terminal regions that influence RNA structure. J. Biol. Chem. 276 19 (2001) 15581-15591
27. Yu L., and Markoff L. The topology of bulges in the long stem of the flavivirus 3′ stem-loop is a major determinant of RNA replication competence. J. Virol. 79 4 (2005) 2309-2324
28. Zeng L., Falgout B., and Markoff L. Identification of specific nucleotide sequences within the conserved 3′-SL in the dengue type 2 virus genome required for replication. J. Virol. 72 9 (1998) 7510-7522
29. Zhang G., Zhang J., and Simon A.E. Repression and derepression of minus-strand synthesis in a plus-strand RNA virus replicon. J. Virol. 78 14 (2004) 7619-7633
30. Zhang G., Zhang J., George A.T., Baumstark T., and Simon A.E. Conformational changes involved in initiation of minus-strand synthesis of a virus-associated RNA. RNA 12 1 (2006) 147-162
31. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids. Res. 31 (2003) 3406-3415