The 3′ untranslated region of tick-borne flaviviruses originated by the duplication of long repeat sequences within the open reading frame (DOI:10.1016/j.virol.2006.03.002)

Virology

Volumn 354, Issue 1, 2006, Pages 217-223

  Gritsun, T S ^a   Gould, E A ^a  

^a CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

Author keywords

3 UTR; Direct repeats; Tick borne flaviviruses; Untranslated regions

Indexed keywords

3' UNTRANSLATED REGION; ANIMAL; ARTICLE; FLAVIVIRUS; GENETICS; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TICK; TICK BORNE ENCEPHALITIS FLAVIVIRUS; VIROLOGY;

3' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; ENCEPHALITIS VIRUSES, TICK-BORNE; EVOLUTION, MOLECULAR; FLAVIVIRUS; MOLECULAR SEQUENCE DATA; MUTATION; OPEN READING FRAMES; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; TERMINAL REPEAT SEQUENCES; TICKS;

EID: 33748970298     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2006.03.052     Document Type: Erratum

References (26)

1. Bredenbeek P.J., Kooi E.A., Lindenbach B., Huijkman N., Rice C.M., and Spaan W.J. A stable full-length yellow fever virus cDNA clone and the role of conserved RNA elements in flavivirus replication. J. Gen. Virol. 84 Pt. 5 (2003) 1261-1268
2. 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
3. Charlier N., Leyssen P., Pleij C.W.A., Lemey P., Billoir F., Van Laethem K., Vandamme A.M., De Clercq E., de Lamballerie X., and Neyts J. 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 Pt. 8 (2002) 1875-1885
4. Crabtree M.B., Sang R.C., Stollar V., Dunster L.M., and Miller B.R. Genetic and phenotypic characterization of the newly described insect flavivirus, Kamiti River virus. Arch. Virol. 148 6 (2003) 1095-1118
5. Gould E.A., de Lamballerie X., Zanotto P.M., and Holmes E.C. Origins, evolution, and vector/host coadaptations within the genus Flavivirus. Adv. Virus Res. 59 (2003) 277-314
6. Gritsun T.S., Holmes E.C., and Gould E.A. Analysis of flavivirus envelope proteins reveals variable domains that reflect their antigenicity and may determine their pathogenesis. Virus Res. 35 3 (1995) 307-321
7. Gritsun T.S., Venugopal K., Zanotto P.M., Mikhailov M.V., Sall A.A., Holmes E.C., Polkinghorne I., Frolova T.V., Pogodina V.V., Lashkevich V.A., and Gould E.A. Complete sequence of two tick-borne flaviviruses isolated from Siberia and the UK: analysis and significance of the 5′ and 3′-UTRs. Virus Res. 49 1 (1997) 27-39
8. Gritsun T.S., Lashkevich V.A., and Gould E.A. Tick-borne encephalitis. Antiviral Res. 57 1-2 (2003) 129-146
9. Gritsun, T.S., Tuplin, A.K., Gould, E.A., in press. Origin, evolution and function of flavivirus RNA in untranslated and coding regions: implications for virus transmission. In: Kalitzky, M., Borowski, P. (Eds.), Flaviviridae: Pathogenesis, Molecular Biology and Genetics. Horizon Scientific Press, Norwich, UK.
10. 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
11. Hayasaka D., Ivanov L., Leonova G.N., Goto A., Yoshii K., Mizutani T., Kariwa H., and Takashima I. Distribution and characterization of tick-borne encephalitis viruses from Siberia and far-eastern Asia. J. Gen. Virol. 82 Pt. 6 (2001) 1319-1328
12. Heinz F.X., Collett M.S., Purcell R.H., Gould E.A., Howard C.R., Houghton M., Moormann R.J.M., Rice C.M., and Thiel H.J. Family Flaviviridae. In: van Regenmortel M.H.V., Fauquet C.M., Bishop D.H.L., Carstens E., Estes M.K., Lemon S., Maniloff J., Mayo M.A., McGeogch D., Pringle C.R., and Wickner R.B. (Eds). Virus Taxonomy. 7th International Committee for the Taxonomy of Viruses (2000), Academic Press, San Diego 859-878
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. Mandl C.W., Holzmann H., Meixner T., Rauscher S., Stadler P.F., Allison S.L., and Heinz F.X. Spontaneous and engineered deletions in the 3′ noncoding region of tick-borne encephalitis virus: construction of highly attenuated mutants of a flavivirus. J. Virol. 72 3 (1998) 2132-2140
15. Markoff L. 5′- and 3′-noncoding regions in flavivirus RNA. Adv. Virus Res. 59 (2003) 177-228
16. 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
17. Olsthoorn R.C., and Bol J.F. Sequence comparison and secondary structure analysis of the 3′ noncoding region of flavivirus genomes reveals multiple pseudoknots. RNA 7 10 (2001) 1370-1377
18. Pilipenko E.V., Gmyl A.P., and Agol V.I. A model for rearrangements in RNA genomes. Nucleic Acids Res. 23 11 (1995) 1870-1875
19. Pletnev A.G. Infectious cDNA clone of attenuated Langat tick-borne flavivirus (strain E5) and a 3′ deletion mutant constructed from it exhibits decreased neuroinvasiveness in immunodeficient mice. Virology 282 2 (2001) 288-300
20. Proutski V., Gould E.A., and Holmes E.C. Secondary structure of the 3′ untranslated region of flaviviruses: similarities and differences. Nucleic Acids Res. 25 6 (1997) 1194-1202
21. Proutski V., Gritsun T.S., Gould E.A., and Holmes E.C. Biological consequences of deletions within the 3′-untranslated region of flaviviruses may be due to rearrangements of RNA secondary structure. Virus Res. 64 2 (1999) 107-123
22. Rauscher S., Flamm C., Mandl C.W., Heinz F.X., and Stadler P.F. Secondary structure of the 3′-noncoding region of flavivirus genomes: comparative analysis of base pairing probabilities. RNA 3 7 (1997) 779-791
23. Thompson J.D., Gibson T.J., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
24. Wallner G., Mandl C.W., Kunz C., and Heinz F.X. The flavivirus 3′-noncoding region: extensive size heterogeneity independent of evolutionary relationships among strains of tick-borne encephalitis virus. Virology 213 1 (1995) 169-178
25. Warren C.E., and Murphy J.F. The complete nucleotide sequence of Pepper mottle virus-Florida RNA. Arch. Virol. 148 1 (2003) 189-197
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