Molecular biology of flaviviruses

Novartis Foundation Symposium

Volumn 277, Issue , 2006, Pages 23-29

  Harris, Eva ^a   Holden, Katherine L ^a   Edgil, Dianna ^a   Polacek, Charlotta ^a   Clyde, Karen ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS PROTEIN; VIRUS RNA;

ANIMAL; CHEMISTRY; FLAVIVIRUS; GENETICS; HUMAN; METABOLISM; REVIEW; RNA TRANSLATION; VIRUS GENOME; VIRUS INFECTION; VIRUS REPLICATION;

ANIMALS; FLAVIVIRUS; FLAVIVIRUS INFECTIONS; GENOME, VIRAL; HUMANS; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; RNA, VIRAL; VIRAL PROTEINS; VIRUS REPLICATION;

EID: 33947546643     PISSN: 15282511     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Conference Paper

References (76)

1. Alvarez DE, De Lella Ezcurra AL, Fucito S, Gamarnik AV 2005a Role of RNA structures present at the 3′ UTR of dengue virus on translation, RNA synthesis, and viral replication. Virology 339:200-212
2. Alvarez DE, Lodeiro MF, Ludueña SJ, Pietrasanta LI, Gamarnik AG 2005b Long-range RNA-RNA interactions circularize the dengue virus genome. J Virol 79:6631-6643
3. Blackwell JL, Brinton MA 1995 BHK cell proteins that bind to the 3′ stem-loop structure of the West Nile Virus genome RNA. J Virol 69:5650-5658
4. Blackwell JL, Brinton MA 1997 Translation elongation factor-1 alpha interacts with the 3′ stem-loop region of West Nile Virus genomic RNA. J Virol 71:6433-6444
5. Borman AM, Michel YM, Malnou CE, Kean KM 2002 Free poly(A) stimulates capped mRNA translation in vitro through the eIF4G-PABP interaction. J Biol Chem 277:36818-36824
6. Brinton MA, Fernandez AV, Dispoto JH 1986 The 3′-nucleotides of flavivirus genomic RNA form a conserved secondary structure. Virology 153:113-121
7. Cahour A, Pletnev A, Vazeille-Flacoz M, Rosen L, Lai C-J 1995 Growth-restricted dengue virus mutants containing deletions in the 5′ noncoding region of the RNA genome. Virology 207:68-76
8. Chambers TJ, Hahn CS, Galler R, Rice CM 1990 Flavivirus genome organization, expression, and replication. Annu Rev Microbiol 44:649-688
9. Chen CJ, Ku MD, Chien LJ, Hsu SL, Wang YM, Lin JH 1997 RNA-protein interactions: involvement of NS3, NS5, and 3′ noncoding regions of Japanese encephalitis virus genomic RNA. J Virol 71:3466-3473
10. Chiu WW, Kinney RM, Dreher TW 2005 Control of translation by the 5′- and 3′-terminal regions of the dengue virus genome. J Virol 79:8303-8315
11. Clyde K, Harris E 2006 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 80:2170-2182
12. Craig AW, Haghighat A, Yu AT, Sonenberg N 1998 Interaction of polyadenylate-binding protein with the eIF4G homologue PAIP enhances translation. Nature 392:520-523
13. De Nova-Ocampo M, Villegas-Sepulveda N, del Angel RM 2002 Translation elongation factor-1alpha, La, and PTB interact with the 3′ untranslated region of dengue 4 virus RNA. Virology 295:337-347
14. Deas TS, Binduga-Gajewska I, Tilgner M et al 2005 Inhibition of flavivirus infections by antisense oligomers specifically suppressing viral translation and RNA replication. J Virol 79:4599-4609
15. Diamond MS, Zachariah M, Harris E 2002 Mycophenolic acid potently inhibits dengue viral infection by preventing replication of viral RNA. Virology 304:211-221
16. Edgil D, Harris E 2006 End-to-end communication in the modulation of translation by mammalian RNA viruses. Virus Res 119:43-51
17. Edgil D, Diamond MS, Holden KL, Paranjape SM, Harris E 2003 Differences in cellular infection among dengue virus type 2 strains correlate with efficiency of translation. Virology 317:275-290
18. Edgil D, Polacek C, Harris E 2006 Dengue virus utilizes a novel strategy for translation initiation when cap-dependent translation is inhibited. J Virol 80:2976-2986
19. Falgout B, Markoff L 1995 Evidence that flavivirus NS1-NS2A cleavage is mediated by a membrane-bound host protease in the endoplasmic reticulum. J Virol 69:7232-7243
20. Gale M, Tan S-L, Katze MG 2000 Translational control of viral gene expression in eukaryotes. Microbiol Mol Biol Rev 64:239-280
21. Gamarnik AV, Andino R 1998 Switch from translation to RNA replication in a positivestranded RNA virus. Genes Dev 12:2293-2304
22. Garcia-Montalvo BM, Medina F, Del Angel RM 2004 La protein binds to NS5 and NS3 and to the 5′ and 3′ ends of Dengue 4 virus RNA. Virus Res 102:141-150
23. Grolleau A, Sonenberg N, Wietzerbin J, Beretta L 1999 Differential regulation of 4E-BP1 and 4E-BP2, two repressors of translation initiation, during human myeloid cell differentiation. J Immunol 162:3491-3497
24. Gubler DJ 1997 Dengue and dengue hemorrhagic fever: Its history and resurgence as a global public health problem. In: Gubler DJ, Kuno G (eds) Dengue and dengue hemorrhagic fever. CAB International, New York
25. Guo L, Allen AM, Miller WA 2001 Base-pairing between untranslated regions facilitates translation of uncapped, nonpolyadenylated viral RNA. Mol Cell 7:1103-1109
26. Hahn CS, Hahn YS, Rice CM et al 1987 Conserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequences. J Mol Biol 198:33-41
27. Heinz F, Auer G, Stiasny K et al 1994a The interactions of the flavivirus envelope proteins: implications for virus entry and release. Arch Virol 9:339-348
28. Heinz F, Stiasny K, Puschner-Auer G et al 1994b Structural changes and functional control of the tick-borne encephalitis virus glycoprotein E by the heterodimeric association with the protein prM. Virology 198:109-117
29. Ho LJ, Wang JJ, Shaio MF et al 2001 Infection of human dendritic cells by dengue virus causes cell maturation and cytokine production. J Immunol 166:1499-1506
30. Holden KL, 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
31. Holden KL, Stein D, Pierson TC et al 2006 Inhibition of dengue virus translation and RNA synthesis by a morpholino oligomer to the top of the 3′ stem-loop structure. Virology 344:439-452
32. Jessie K, Fong MY, Devi S, Lam SK, Wong KT 2004 Localization of dengue virus in naturally infected human tissues, by immunohistochemistry and in situ hybridization. J Infect Dis 189:1411-1418
33. Khromykh AA, Sedlak PL, Westaway EG 1999 trans-Complementation analysis of the flavivirus Kunjin ns5 gene reveals an essential role for translation of its N-terminal half in RNA replication. J Virol 73:9247-9255
34. Khromykh AA, Sedlak PL, Westaway EG 2000 cis-and trans-acting elements in flavivirus RNA replication. J Virol 74:3253-3263
35. Khromykh AA, Meka H, Guyatt KJ, Westway EG 2001a Essential role of cyclization domains in flavivirus RNA replication. J Virol 75:6719-6728
36. Khromykh AA, Varnavski AN, Sedlak PL, Westaway EG 2001b Coupling between replication and packaging of flavivirus RNA: evidence derived from the use of DNA-based full-length cDNA clones of Kunjin virus. J Virol 75:4633-4640
37. Kinney RM, Huang CY-H, Rose BC et al 2005 Inhibition of dengue virus serotypes 1 to 4 in Vero cell cultures with morpholino oligomers. J Virol 79:5116-5128
38. Kozak M 1989 Context effects and inefficient initiation at non-AUG codons in eucaryotic cellfree translation systems. Mol Cell Biol 9:5073-5080
39. Kozak M 1990 Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes. Proc Natl Acad Sci USA 87:8301-8305
40. Kozak M 1991 Structural features in eukaryotic mRNAs that modulate the initiation of translation. J Biol Chem 266:19867-19870
41. Krichevsky AM, Metzer E, Rosen H 1999 Translational control of specific genes during differentiation of HL-60 cells. J Biol Chem 274:14295-14305
42. Li W, Li Y, Kedersha N et al 2002 Cell proteins TIA-1 and TIAR interact with the 3′ stem-loop of the West Nile virus complementary minus-strand RNA and facilitate virus replication. J Virol 76:11989-12000
43. Lin C, Amberg SM, Chambers TJ, Rice CM 1993 Cleavage at a novel site in the NS4A region by the yellow fever virus NS2B-3 proteinase is a prerequisite for processing at the downstream 4A/4B signalase site. J Virol 67:2327-2335
44. Lindenbach BD, Rice CM 2001 Flaviviridae: The viruses and their replication. In: Knipe DM, Howley PM (eds) Fields Virology. Vol. 1 Lippincott Williams and Wilkins, Philadelphia, p 991-1041
45. Lo M, Tilgner M, Bernard KA, 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
46. Lyle JM, Bullitt E, Bienz K, Kirkegaard K 2002 Visualization and functional analysis of RNA-dependent RNA polymerase lattices. Science 296:2218-2222
47. Mackenzie JM, Khromykh AA, Jones MK, Westaway EG 1998 Subcellular localization and some biochemical properties of the flavivirus Kunjin nonstructural proteins NS2A and NS4A. Virology 245:203-215
48. Mackenzie JM, Jones MK, Westaway EG 1999 Markers for trans-Golgi membranes and the intermediate compartment localize to induced membranes with distinct replication functions in flavivirus-infected cells. J Virol 73:9555-9567
49. Markoff L, Chang A, Falgout B 1994 Processing of flavivirus structural glycoproteins: stable membrane insertion of premembrane requires the envelope signal peptide. Virology 204:526-540
50. Men R, Bray M, Clark D, Chanock RM, 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
51. Michel YM, Borman AM, Paulous S, Kean KM 2001 Eukaryotic initiation factor 4G-poly(A) binding protein interaction is required for poly(A) tail-mediated stimulation of picornavirus internal ribosome entry segment-driven translation but not for X-mediated stimulation of hepatitis C virus translation. Mol Cell Biol 21:4097-4109
52. Mohan PM, Padmanabhan R 1991 Detection of stable secondary structure at the 3′ terminus of dengue virus type 2 RNA. Gene 108:185-191
53. Noueiry AO, Diez J, Falk SP, Chen J, Ahlquist P 2003 Yeast Lsm1p-7p/Pat1p deadenylation-dependent mRNA-decapping factors are required for brome mosaic virus genomic RNA translation. Mol Cell Biol 23:4094-4106
54. Novak JE, Kirkegaard K 1994 Coupling between genome translation and replication in an RNA virus. Genes Dev 8:1726-1737
55. Nugent CI, Johnson KL, Sarnow P, Kirkegaard K 1999 Functional coupling between replication and packaging of poliovirus replicon RNA. J Virol 73:427-435
56. Olsthoorn RC, Bol JF 2001 Sequence comparison and secondary structure analysis of the 3′ noncoding region of flavivirus genomes reveals multiple pseudoknots. RNA 7:1370-1377
57. Piron M, Vende P, Cohen J, Poncet D 1998 Rotavirus RNA-binding protein NSP3 interacts with eIF4GI and evicts the poly(A) binding protein from eIF4F. EMBO J 17:5811-5821
58. Proutski V, Gould EA, Holmes EC 1997 Secondary structure of the 3′ untranslated region of flaviviruses: similarities and differences. Nucleic Acids Res 25:1194-1202
59. Proutski V, Gritsun TS, Gould EA, Holmes EC 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
60. Proweller A, Butler JS 1996 Ribosomal association of poly(A)-binding protein in poly(A)-deficient Saccharomyces cerevisiae. J Biol Chem 271:10859-10865
61. Sachs A 2000 Physical and functional interactions between the mRNA cap structure and the poly(A) tail. In: Sonenberg N, Hershey JWB, Matthews MB (eds) Translational control of gene expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, p 447-465
62. Sachs AB, Sarnow P, Hentze MW 1997 Starting at the beginning, middle, and end: Translation initiation in eukaryotes. Cell 89:831-838
63. Shi P-Y, Brinton MA, Veal JM, Zhong YY, Wilson WD 1996a Evidence for the existence of a pseudoknot structure at the 3′ terminus of the flavivirus genomic RNA. Biochemistry 35:4222-4230
64. Shi P-Y, Li W, Brinton MA 1996b Cell proteins bind specifically to West Nile Virus minusstrand 3′ stem-loop RNA. J Virol 70:6278-6287
65. Tarun S, Sachs AB 1995 A common function for mRNA 5′ and 3′ ends in translation initiation in yeast. Genes Dev 9:2997-3007
66. Tarun SZ, Sachs AB 1996 Association of the yeast poly(A) tail binding protein with translation initiation factor eIF4G. EMBO J 15:7168-7177
67. Tilgner M, Shi PY 2004 Structure and function of the 3′ terminal six nucleotides of the West Nile virus genome in viral replication. J Virol 78:8159-8171
68. Tilgner M, Deas TS, Shi PY 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
69. Vanhaesebroeck B, Leevers SJ, Ahmadi K et al 2001 Synthesis and function of 3-phosphorylated inositol lipids. Annu Rev Biochem 70:535-602
70. Vaughn DW, Green S, Kalayanarooj S et al 2000 Dengue viremia titer, antibody response pattern, and virus serotype correlate with disease severity. J Infect Dis 181:2-9
71. Westaway EG, Mackenzie JM, Kenney MT, Jones MK, Khromykh AA 1997 Ultrastructure of Kunjin virus-infected cells: Colocalization of NS1 and NS3 with double-stranded RNA, and of NS2B with NS3, in virus-induced membrane structures. J Virol 71:6650-6661
72. Wu SJ, Grouard-Vogel G, Sun W et al 2000 Human skin Langerhans cells are targets of dengue virus infection. Nat Med 6:816-820
73. Yocupicio-Monroy RM, Medina F, Reyes-del Valle J, del Angel RM 2003 Cellular proteins from human monocytes bind to dengue 4 virus minus-strand 3′ untranslated region RNA. J Virol 77:3067-3076
74. You S, Falgout B, Markoff L, Padmanabhan R 2001 In vitro RNA synthesis from exogenous dengue viral RNA templates requires long range interactions netween 5′- and 3′-terminal regions that influence RNA structure. J Biol Chem 276:15581-15591
75. Zeng L, Falgout B, Markoff L 1998 Identification of specific nucleotide sequences within conserved 3′-SL in the dengue type 2 virus genome required for replication. J Virol 72:7510-7522
76. Zuker M 2003 Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406-3415