1887

Abstract

Previously, it was shown that the 3′ untranslated region (3′UTR) of Kamiti River virus (KRV) is nearly twice as long as the 3′UTR of other flaviviruses (1208 nucleotides compared with 730 nucleotides for the longest 3′UTR of any virus in the species). Additionally, KRV and the closely related Cell fusing agent virus (CFAV) were shown to contain two short, almost perfect repeat sequences of 67 nucleotides. However, the construction of a robust comparative nucleotide alignment has now revealed that the double-length 3′UTR and the direct repeats resulted from the virtually complete duplication of a primordial KRV 3′UTR. We also propose that the CFAV 3′UTR was derived from a KRV-like precursor sequence with a large deletion that nevertheless preserved the two direct repeat sequences. These data provide new insights into the evolution of the flavivirus 3′UTR.

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2006-09-01
2019-11-18
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References

  1. Bredenbeek, P. J., Kooi, E. A., Lindenbach, B., Huijkman, N., Rice, C. M. & Spaan, W. J. ( 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.[CrossRef]
    [Google Scholar]
  2. Bryant, J. E., Vasconcelos, P. F., Rijnbrand, R. C., Mutebi, J. P., Higgs, S. & Barrett, A. D. ( 2005; ). Size heterogeneity in the 3′ noncoding region of South American isolates of yellow fever virus. J Virol 79, 3807–3821.[CrossRef]
    [Google Scholar]
  3. Cammisa-Parks, H., Cisar, L. A., Kane, A. & Stollar, V. ( 1992; ). The complete nucleotide sequence of cell fusing agent (CFA): homology between the nonstructural proteins encoded by CFA and the nonstructural proteins encoded by arthropod-borne flaviviruses. Virology 189, 511–524.[CrossRef]
    [Google Scholar]
  4. Charlier, N., Leyssen, P., Pleij, C. W. A. & 7 other authors ( 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.
    [Google Scholar]
  5. Chastel, C., Bailly-Choumara, H., Bach-Hamba, D., Le Lay, G., Legrand, M. C., Le Goff, F. & Vermeil, C. ( 1995; ). Tick-transmitted arbovirus in Maghreb. Bull Soc Pathol Exot 88, 81–85 (in French).
    [Google Scholar]
  6. 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.[CrossRef]
    [Google Scholar]
  7. Crabtree, M. B., Sang, R. C., Stollar, V., Dunster, L. M. & Miller, B. R. ( 2003; ). Genetic and phenotypic characterization of the newly described insect flavivirus, Kamiti River virus. Arch Virol 148, 1095–1118.[CrossRef]
    [Google Scholar]
  8. Crochu, S., Cook, S., Attoui, H., Charrel, R. N., De Chesse, R., Belhouchet, M., Lemasson, J. J., de Micco, P. & de Lamballerie, X. ( 2004; ). Sequences of flavivirus-related RNA viruses persist in DNA form integrated in the genome of Aedes spp. mosquitoes. J Gen Virol 85, 1971–1980.[CrossRef]
    [Google Scholar]
  9. Deas, T. S., Binduga-Gajewska, I., Tilgner, M. & 7 other authors ( 2005; ). Inhibition of flavivirus infections by antisense oligomers specifically suppressing viral translation and RNA replication. J Virol 79, 4599–4609.[CrossRef]
    [Google Scholar]
  10. de Lamballerie, X., Crochu, S., Billoir, F., Neyts, J., de Micco, P., Holmes, E. C. & Gould, E. A. ( 2002; ). Genome sequence analysis of Tamana bat virus and its relationship with the genus Flavivirus. J Gen Virol 83, 2443–2454.
    [Google Scholar]
  11. Gritsun, T. S., Venugopal, K., Zanotto, P. M. & 8 other authors ( 1997; ). 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, 27–39.[CrossRef]
    [Google Scholar]
  12. Gritsun, T. S., Tuplin, A. K. & Gould, E. A. ( 2006; ). Origin, evolution and function of flavivirus RNA in untranslated and coding regions: implications for virus transmission. In Flaviviridae: Pathogenesis, Molecular Biology and Genetics. Edited by M. Kalitzky & P. Borowski. Norwich, UK: Horizon Scientific Press (in press).
  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.[CrossRef]
    [Google Scholar]
  14. Hall, T. A. ( 1999; ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98.
    [Google Scholar]
  15. Heinz, F. X., Collett, M. S., Purcell, R. H., Gould, E. A., Howard, C. R., Houghton, M., Moormann, R. J. M., Rice, C. M. & Thiel, H. J. ( 2000; ). Family Flaviviridae. In Virus Taxonomy, 7th Report of the International Committee for the Taxonomy of Viruses, pp. 859–878. Edited by M. H. V. van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. Carstens, M. K. Estes, S. Lemon, J. Maniloff, M. A. Mayo, D. McGeogh, C. R. Pringle & R. B. Wickner. San Diego: Academic Press.
  16. Khromykh, A. A. & Westaway, E. G. ( 1997; ). Subgenomic replicons of the flavivirus Kunjin: construction and applications. J Virol 71, 1497–1505.
    [Google Scholar]
  17. Kinney, R. M., Huang, C. Y., Rose, B. C., Kroeker, A. D., Dreher, T. W., Iversen, P. L. & Stein, D. A. ( 2005; ). Inhibition of dengue virus serotypes 1 to 4 in vero cell cultures with morpholino oligomers. J Virol 79, 5116–5128.[CrossRef]
    [Google Scholar]
  18. Leyssen, P., Charlier, N., Lemey, P., Billoir, F., Vandamme, A. M., De Clercq, E., de Lamballerie, X. & Neyts, J. ( 2002; ). Complete genome sequence, taxonomic assignment, and comparative analysis of the untranslated regions of the Modoc virus, a flavivirus with no known vector. Virology 293, 125–140.[CrossRef]
    [Google Scholar]
  19. Lindenbach, B. D. & Rice, C. M. ( 2001; ). Flaviviridae: the viruses and their replication. In Fields Virology, 4th edn, pp. 991–1042. Edited by D. M. Knipe & P. M. Howley. London, New York & Tokyo: Lippincott Williams & Wilkins.
  20. 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.[CrossRef]
    [Google Scholar]
  21. Mandl, C. W., Kunz, C. & Heinz, F. X. ( 1991; ). Presence of poly(A) in a flavivirus: significant differences between the 3′ noncoding regions of the genomic RNAs of tick-borne encephalitis virus strains. J Virol 65, 4070–4077.
    [Google Scholar]
  22. Mandl, C. W., Holzmann, H., Meixner, T., Rauscher, S., Stadler, P. F., Allison, S. L. & Heinz, F. X. ( 1998; ). 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, 2132–2140.
    [Google Scholar]
  23. Markoff, L. ( 2003; ). 5′- and 3′-noncoding regions in flavivirus RNA. Adv Virus Res 59, 177–228.
    [Google Scholar]
  24. Men, R., Bray, M., Clark, D., Chanock, R. M. & Lai, C. J. ( 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.
    [Google Scholar]
  25. Mutebi, J. P., Rijnbrand, R. C., Wang, H., Ryman, K. D., Wang, E., Fulop, L. D., Titball, R. & Barrett, A. D. ( 2004; ). Genetic relationships and evolution of genotypes of yellow fever virus and other members of the yellow fever virus group within the Flavivirus genus based on the 3′ noncoding region. J Virol 78, 9652–9665.[CrossRef]
    [Google Scholar]
  26. Pilipenko, E. V., Gmyl, A. P. & Agol, V. I. ( 1995; ). A model for rearrangements in RNA genomes. Nucleic Acids Res 23, 1870–1875.[CrossRef]
    [Google Scholar]
  27. Pletnev, A. G. ( 2001; ). 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, 288–300.[CrossRef]
    [Google Scholar]
  28. Proutski, V., Gaunt, M. W., Gould, E. A. & Holmes, E. C. ( 1997a; ). Secondary structure of the 3′-untranslated region of yellow fever virus: implications for virulence, attenuation and vaccine development. J Gen Virol 78, 1543–1549.
    [Google Scholar]
  29. Proutski, V., Gould, E. A. & Holmes, E. C. ( 1997b; ). Secondary structure of the 3′ untranslated region of flaviviruses: similarities and differences. Nucleic Acids Res 25, 1194–1202.[CrossRef]
    [Google Scholar]
  30. Proutski, V., Gritsun, T. S., Gould, E. A. & Holmes, E. C. ( 1999; ). Biological consequences of deletions within the 3′-untranslated region of flaviviruses may be due to rearrangements of RNA secondary structure. Virus Res 64, 107–123.[CrossRef]
    [Google Scholar]
  31. Rauscher, S., Flamm, C., Mandl, C. W., Heinz, F. X. & Stadler, P. F. ( 1997; ). Secondary structure of the 3′-noncoding region of flavivirus genomes: comparative analysis of base pairing probabilities. RNA 3, 779–791.
    [Google Scholar]
  32. Sang, R. C., Gichogo, A., Gachoya, J., Dunster, M. D., Ofula, V., Hunt, A. R., Crabtree, M. B., Miller, B. R. & Dunster, L. M. ( 2003; ). Isolation of a new flavivirus related to cell fusing agent virus (CFAV) from field-collected flood-water Aedes mosquitoes sampled from a dambo in central Kenya. Arch Virol 148, 1085–1093.[CrossRef]
    [Google Scholar]
  33. Thompson, J. D., Gibson, T. J., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  34. Thurner, C., Witwer, C., Hofacker, I. L. & Stadler, P. F. ( 2004; ). Conserved RNA secondary structures in Flaviviridae genomes. J Gen Virol 85, 1113–1124.[CrossRef]
    [Google Scholar]
  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.[CrossRef]
    [Google Scholar]
  36. Wallner, G., Mandl, C. W., Kunz, C. & Heinz, F. X. ( 1995; ). The flavivirus 3′-noncoding region: extensive size heterogeneity independent of evolutionary relationships among strains of tick-borne encephalitis virus. Virology 213, 169–178.[CrossRef]
    [Google Scholar]
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