Origin and Evolution of 3′Utr of Flaviviruses: Long Direct Repeats as A Basis for the Formation of Secondary Structures and Their Significance for Virus Transmission

Advances in Virus Research

Volumn 69, Issue , 2006, Pages 203-248

  Gritsun, T S ^a   Gould, E A ^a  

^a CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA;

3' UNTRANSLATED REGION; CHEMISTRY; DISEASE TRANSMISSION; FLAVIVIRUS; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; REVIEW; SEQUENCE ALIGNMENT; VIRUS INFECTION;

3' UNTRANSLATED REGIONS; BASE SEQUENCE; EVOLUTION, MOLECULAR; FLAVIVIRUS; FLAVIVIRUS INFECTIONS; MOLECULAR SEQUENCE DATA; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA, VIRAL; SEQUENCE ALIGNMENT;

EID: 33845988056     PISSN: 00653527     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-3527(06)69005-2     Document Type: Review

References (74)

1. Ackermann M., and Padmanabhan R. De novo synthesis of RNA by the dengue virus RNA-dependent RNA polymerase exhibits temperature dependence at the initiation but not elongation phase. J. Biol. Chem. 276 (2001) 39926-39937
2. Blackwell J.L., and Brinton M.A. BHK cell proteins that bind to the 3′ stem-loop structure of the West Nile virus genome RNA. J. Virol. 69 (1995) 5650-5658
3. Blackwell J.L., and Brinton M.A. Translation elongation factor-1 alpha interacts with the 3′ stem-loop region of West Nile virus genomic RNA. J. Virol. 71 (1997) 6433-6444
4. Boguszewska-Chachulska A.M., and Haenni A.L. RNA viruses redirect host factors to better amplify their genome. Adv. Virus Res. 65 (2005) 29-61
5. 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 (2003) 1261-1268
6. Brinton M.A., Fernandez A.V., and Dispoto J.H. The 3′-nucleotides of flavivirus genomic RNA form a conserved secondary structure. Virology 153 (1986) 113-121
7. Bryan G.T., Gardner R.C., and Forster R.L. Nucleotide sequence of the coat protein gene of a strain of clover yellow vein virus from New Zealand: Conservation of a stem-loop structure in the 3′ region of potyviruses. Arch. Virol. 124 (1992) 133-146
8. Bryant J.E., Vasconcelos P.F., Rijnbrand R.C., Mutebi J.P., Higgs S., and Barrett A.D. Size heterogeneity in the 3′ noncoding region of South American isolates of yellow fever virus. J. Virol. 79 (2005) 3807-3821
9. Charlier N., Leyssen P., Pleij C.W.A., Lemey P., Billoir F., Van Laethem K., Vandamme A.M., De Clercq E., deLamballerie 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 (2002) 1875-1885
10. Chen C.J., Kuo M.D., Chien L.J., Hsu S.L., Wang Y.M., and Lin J.H. RNA-protein interactions: Involvement of NS3, NS5, and 3′ noncoding regions of Japanese encephalitis virus genomic RNA. J. Virol. 71 (1997) 3466-3473
11. Chiu W.W., Kinney R.M., and Dreher T.W. Control of translation by the 5′- and 3′-terminal regions of the dengue virus genome. J. Virol. 79 (2005) 8303-8315
12. Copper P.D., Steiner-Pryor A., Scotti P.D., and Delong D. On the nature of poliovirus genetic recombinants. J. Gen. Virol. 23 (1974) 41-49
13. 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 (2003) 1095-1118
14. Cui T., Sugrue R.J., Xu Q., Lee A.K., Chan Y.C., and Fu J. Recombinant dengue virus type 1 NS3 protein exhibits specific viral RNA binding and NTPase activity regulated by the NS5 protein. Virology 246 (1998) 409-417
15. de Lamballerie X., Crochu S., Billoir F., Neyts J., de Micco P., Holmes E.C., and Gould E.A. Genome sequence analysis of Tamana bat virus and its relationship with the genus Flavivirus. J. Gen. Virol. 83 (2002) 2443-2454
16. De Nova Ocampo M., Villegas Sepulveda N., and del Angel R.M. Translation elongation factor-1alpha, La, and PTB interact with the 3′ untranslated region of dengue 4 virus RNA. Virology 295 (2002) 337-347
17. Deas T.S., Binduga-Gajewska I., Tilgner M., Ren P., Stein D.A., Moulton H.M., Iversen P.L., Kauffman E.B., Kramer L.D., and Shi P.Y. Inhibition of flavivirus infections by antisense oligomers specifically suppressing viral translation and RNA replication. J. Virol. 79 (2005) 4599-4609
18. Faragher S.G., and Dalgarno L. Regions of conservation and divergence in the 3′ untranslated sequences of genomic RNA from Ross River virus isolates. J. Mol. Biol. 190 (1986) 141-148
19. 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
20. Gritsun T.S., and Gould E.A. The 3′ untranslated region of Kamiti River virus and Cell fusing agent virus originated by self-duplication. J. Gen. Virol. 87 (2006) 2615-2619
21. Gritsun T.S., and Gould E.A. The origin, evolution and functional significance of direct repeats in the 3′ untranslated regions of mosquito-borne flaviviruses: Possible implications for virus transmission. J. Gen. Virol. 87 (2006) 3297-3305
22. Gritsun T.S., and Gould E.A. The 3′ untranslated region of tick-borne flaviviruses originated by the duplication of long repeat sequences within the open reading frame. Virology 350 (2006) 269-275
23. Gritsun T.S., and Gould E.A. Direct repeats in the flavivirus 3′ untranslated region; a strategy for survival in the environment. Virology (2006) (in press)
24. 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 (1995) 307-321
25. 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 (1997) 27-39
26. Gritsun T.S., Desai A., and Gould E.A. The degree of attenuation of tick-borne encephalitis virus depends on the cumulative effects of point mutations. J. Gen. Virol. 82 (2001) 1667-1675
27. Gritsun T.S., Tuplin A.K., and Gould E.A. Origin, evolution and function of flavivirus RNA in untranslated and coding regions: Implications for virus transmission. In: Kalitzky M., and Borowski P. (Eds). "Flaviviridae: Pathogenesis, Molecular Biology and Genetics" (2006), Horizon Scientific Press, Norwich, UK 47-99
28. 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 (1987) 33-41
29. Hajjou M., Hill K.R., Subramaniam S.V., Hu J.Y., and Raju R. Nonhomologous RNA-RNA recombination events at the 3′ nontranslated region of the Sindbis virus genome: Hot spots and utilization of nonviral sequences. J. Virol. 70 (1996) 5153-5164
30. 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 (2001) 1319-1328
31. 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: 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
32. Jones L.D., Gaunt M., Hails R.S., Laurenson K., Hudson P.J., Reid H., Henbest P., and Gould E.A. Transmission of louping ill virus between infected and uninfected ticks co-feeding on mountain hares. Med. Vet. Entomol. 11 (1997) 172-176
33. Khromykh A.A., and Westaway E.G. Subgenomic replicons of the flavivirus Kunjin: Construction and applications. J. Virol. 71 (1997) 1497-1505
34. Khromykh A.A., Meka H., Guyatt K.J., and Westaway E.G. Essential role of cyclization sequences in flavivirus RNA replication. J. Virol. 75 (2001) 6719-6728
35. Khromykh A.A., Kondratieva N., Sgro J.Y., Palmenberg A., and Westaway E.G. Significance in replication of the terminal nucleotides of the flavivirus genome. J. Virol. 77 (2003) 10623-10629
36. Kinney R.M., Huang C.Y., Rose B.C., Kroeker A.D., Dreher T.W., Iversen P.L., and Stein D.A. Inhibition of dengue virus serotypes 1 to 4 in vero cell cultures with morpholino oligomers. J. Virol. 79 (2005) 5116-5128
37. Kofler R.M., Heinz F.X., and Mandl C.W. Capsid protein C of tick-borne encephalitis virus tolerates large internal deletions and is a favorable target for attenuation of virulence. J. Virol. 76 (2002) 3534-3543
38. Labuda M., Austyn J.M., Zuffova E., Kozuch O., Fuchsberger N., Lysy J., and Nuttall P.A. Importance of localized skin infection in tick-borne encephalitis virus transmission. Virology 219 (1996) 357-366
39. Lai M.M. RNA recombination in animal and plant viruses. Microbiol. Rev. 56 (1992) 61-79
40. Lai M.M. Cellular factors in the transcription and replication of viral RNA genomes: A parallel to DNA-dependent RNA transcription. Virology 244 (1998) 1-12
41. Leyssen P., Charlier N., Lemey P., Billoir F., Vandamme A.M., De Clercq E., de Lamballerie X., and Neyts J. Complete genome sequence, taxonomic assignment, and comparative analysis of the untranslated regions of the Modoc virus, a flavivirus with no known vector. Virology 293 (2002) 125-140
42. Lindenbach B.D., and Rice C.M. Flaviviridae: The viruses and their replication. In: Knippe D.M., and Howley P.M. (Eds). "Fields Virology" (2001), Lippincott Williams and Wilkins, London, New York, Tokyo 991-1042
43. 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 (2003) 10004-10014
44. Mandl C.W., Kunz C., and Heinz F.X. 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 (1991) 4070-4077
45. 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 (1998) 2132-2140
46. Markoff L. 5′- and 3′-noncoding regions in flavivirus RNA. Adv. Virus Res. 59 (2003) 177-228
47. 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 (1996) 3930-3937
48. Mohan P.M., and Padmanabhan R. Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA. Gene 108 (1991) 185-191
49. Mutebi J.P., Rijnbrand R.C., Wang H., Ryman K.D., Wang E., Fulop L.D., Titball R., and Barrett A.D. 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 (2004) 9652-9665
50. 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 (2001) 1370-1377
51. Peerenboom E., Jacobi V., Cartwright E.J., Adams M.J., Steinbiss H.H., and Antoniw J.F. A large duplication in the 3′-untranslated region of a subpopulation of RNA2 of the UK-M isolate of barley mild mosaic bymovirus. Virus Res. 47 (1997) 1-6
52. Pilipenko E.V., Gmyl A.P., and Agol V.I. A model for rearrangements in RNA genomes. Nucleic Acids Res. 23 (1995) 1870-1875
53. 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 (2001) 288-300
54. Pletnev A.G., Bray M., Hanley K.A., Speicher J., and Elkins R. Tick-borne Langat/mosquito-borne dengue flavivirus chimera, a candidate live attenuated vaccine for protection against disease caused by members of the tick-borne encephalitis virus complex: Evaluation in rhesus monkeys and in mosquitoes. J. Virol. 75 (2001) 8259-8267
55. Proutski V., Gaunt M.W., Gould E.A., and Holmes E.C. Secondary structure of the 3′-untranslated region of yellow fever virus: Implications for virulence, attenuation and vaccine development. J. Gen. Virol. 78 (1997) 1543-1549
56. 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 (1997) 1194-1202
57. 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 (1999) 107-123
58. 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 (1997) 779-791
59. Santagati M.G., Itaranta P.V., Koskimies P.R., Maatta J.A., Salmi A.A., and Hinkkanen A.E. Multiple repeating motifs are found in the 3′-terminal non-translated region of Semliki Forest virus A7 variant genome. J. Gen. Virol. 75 Pt. 6 (1994) 1499-1504
60. Shi B., Ding S., and Symons R.H. Two novel subgenomic RNAs derived from RNA 3 of tomato aspermy cucumovirus. J. Gen. Virol. 78 Pt. 3 (1997) 505-510
61. Shi P.Y., Brinton M.A., Veal J.M., Zhong Y.Y., and Wilson W.D. Evidence for the existence of a pseudoknot structure at the 3′ terminus of the flavivirus genomic RNA. Biochemistry 35 (1996) 4222-4230
62. Ta M., and Vrati S. Mov34 protein from mouse brain interacts with the 3′ noncoding region of Japanese encephalitis virus. J. Virol. 74 (2000) 5108-5115
63. Tajima S., Takasaki T., Matsuno S., Nakayama M., and Kurane I. Genetic characterization of Yokose virus, a flavivirus isolated from the bat in Japan. Virology 332 (2005) 38-44
64. Tan B.H., Fu J., Sugrue R.J., Yap E.H., Chan Y.C., and Tan Y.H. Recombinant dengue type 1 virus NS5 protein expressed in Escherichia coli exhibits RNA-dependent RNA polymerase activity. Virology 216 (1996) 317-325
65. Thurner C., Witwer C., Hofacker I.L., and Stadler P.F. Conserved RNA secondary structures in Flaviviridae genomes. J. Gen. Virol. 85 (2004) 1113-1124
66. 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 (2005) 375-386
67. 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 (1995) 169-178
68. Wang E., Weaver S.C., Shope R.E., Tesh R.B., Watts D.M., and Barrett A.D. Genetic variation in yellow fever virus: Duplication in the 3′ noncoding region of strains from Africa. Virology 225 (1996) 274-281
69. Warren C.E., and Murphy J.F. The complete nucleotide sequence of Pepper mottle virus-Florida RNA. Arch. Virol. 148 (2003) 189-197
70. Westaway E.G., Mackenzie J.M., and Khromykh A.A. Replication and gene function in Kunjin virus. Curr. Top. Microbiol. Immunol. 267 (2002) 323-351
71. Westaway E.G., Mackenzie J.M., and Khromykh A.A. Kunjin RNA replication and applications of Kunjin replicons. Adv. Virus Res. 59 (2003) 99-140
72. 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 (1999) 33714-33722
73. 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 (2001) 15581-15591
74. Zanotto P.M., Gould E.A., Gao G.F., Harvey P.H., and Holmes E.C. Population dynamics of flaviviruses revealed by molecular phylogenies. Proc. Natl. Acad. Sci. USA 93 (1996) 548-553