Repair and polyadenylation of a naturally occurring hepatitis C virus 3′ nontranslated region-shorter variant in selectable replicon cell lines

Journal of Virology

Volumn 80, Issue 9, 2006, Pages 4336-4343

  Van Leeuwen, Hans C ^a   Liefhebber, Jolanda M P ^a   Spaan, Willy J M ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EXORIBONUCLEASE; POLYADENYLIC ACID;

3' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; BLOOD SAMPLING; CELL LINE; CHRONIC HEPATITIS; COLONY FORMATION; DNA REPAIR; GENETIC CONSERVATION; GENETIC VARIABILITY; HEPATITIS C VIRUS; MOLECULAR CLONING; NONHUMAN; POLYADENYLATION; PRIORITY JOURNAL; REPLICON; RNA REPLICATION; SEQUENCE ANALYSIS; VIRUS GENOME; VIRUS REPLICATION;

3' UNTRANSLATED REGIONS; BASE SEQUENCE; CELL LINE, TUMOR; GENOME, VIRAL; GENOTYPE; HEPACIVIRUS; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; POLY A; POLYADENYLATION; REPLICON; VARIATION (GENETICS);

HEPATITIS C VIRUS; HEPATITIS C VIRUS GENOTYPE 3; RNA VIRUSES;

EID: 33646192965     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.80.9.4336-4343.2006     Document Type: Article

References (45)

1. Behrens, S. E., L. Tomei, and R. DeFrancesco. 1996. Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus. EMBO J. 15:12-22.
2. Blight, K. J., and C. M. Rice. 1997. Secondary structure determination of the conserved 98-base sequence at the 3′ terminus of hepatitis C virus genome RNA. J. Virol. 71:7345-7352.
3. Burgyan, J., and F. Garcia-Arenal. 1998. Template-independent repair of the 3′ end of cucumber mosaic virus satellite RNA controlled by RNAs 1 and 2 of helper virus. J. Virol. 72:5061-5066.
4. Cai, Z. H., T. J. Liang, and G. X. Luo. 2004. Effects of mutations of the initiation nucleotides on hepatitis C virus RNA replication in the cell. J. Virol. 78:3633-3643.
5. Chen, M. H., and T. K. Frey. 1999. Mutagenic analysis of the 3′ cis-acting elements of the rubella virus genome. J. Virol. 73:3386-3403.
6. Cheng, J. H., C. W. Peng, Y. H. Hsu, and C. H. Tsai. 2002. The synthesis of minus-strand RNA of bamboo mosaic potexvirus initiates from multiple sites within the poly(A) tail. J. Virol. 76:6114-6120.
7. Dreher, T. W., C. H. Tsai, and J. M. Skuzeski. 1996. Aminoacylation identity switch of turnip yellow mosaic virus RNA from valine to methionine results in an infectious virus. Proc. Natl. Acad. Sci. USA 93:12212-12216.
8. Friebe, P., and R. Bartenschlager. 2002. Genetic analysis of sequences in the 3′ nontranslated region of hepatitis C virus that are important for RNA replication. J. Virol. 76:5326-5338.
9. Frolov, I., R. Hardy, and C. M. Rice. 2001. cis-Acting RNA elements at the 5′ end of Sindbis virus genome RNA regulate minus- and plus-strand RNA synthesis. RNA 7:1638-1651.
10. Gallei, A., M. Orlich, H. J. Thiel, and P. Becher. 2005. Noncytopathogenic pestivirus strains generated by nonhomologous RNA recombination: alterations in the NS4A/NS4B coding region. J. Virol. 79:14261-14270.
11. Gamarnik, A. V., and R. Andino. 1998. Switch from translation to RNA replication in a positive-stranded RNA virus. Genes Dev. 12:2293-2304.
12. Guilford, P. J., D. L. Beck, and R. L. S. Forster. 1991. Influence of the poly(A) tail and putative polyadenylation signal on the infectivity of white clover mosaic potexvirus. Virology 182:61-67.
13. Hardy, R. W., and C. M. Rice. 2005. Requirements at the 3′ end of the Sindbis virus genome for efficient synthesis of minus-strand RNA. J. Virol. 79:4630-4639.
14. Hill, K. R., M. Hajjou, J. Y. Hu, and R. Raju. 1997. RNA-RNA recombina-tion in Sindbis virus: roles of the 3′ conserved motif, poly(A) tail, and nonviral sequences of template RNAs in polymerase recognition and template switching. J. Virol. 71:2693-2704.
15. Hofmann, M. A., and D. A. Brian. 1991. The 5′ end of coronavirus minus-strand RNAs contains a short poly(U) tract. J. Virol. 65:6331-6333.
16. Jupin, I., S. Bouzoubaa, K. Richards, G. Jonard, and H. Guilley. 1990. Multiplication of beet necrotic yellow vein virus RNA-3 lacking a 3′ poly(A) tail is accompanied by reappearance of the poly(A) tail and a novel short U-rich tract preceding it. Virology 178:281-284.
17. Kao, C. C., P. Singh, and D. J. Ecker. 2001. De novo initiation of viral RNA-dependent RNA synthesis. Virology 287:251-260.
18. Kim, M., H. Kim, S. P. Cho, and M. K. Min. 2002. Template requirements for de novo RNA synthesis by hepatitis C virus nonstructural protein 5B polymerase on the viral X RNA. J. Virol. 76:6944-6956.
19. Kolykhalov, A. A., S. M. Feinstone, and C. M. Rice. 1996. Identification of a highly conserved sequence element at the 3′ terminus of hepatitis C virus genome RNA. J. Virol. 70:3363-3371.
20. Kolykhalov, A. A., K. Mihalik, S. M. Feinstone, and C. M. Rice. 2000. Hepatitis C virus-encoded enzymatic activities and conserved RNA elements in the 3′ nontranslated region are essential for virus replication in vivo. J. Virol. 74:2046-2051.
21. Krieger, N., V. Lohmann, and R. Bartenschlager. 2001. Enhancement of hepatitis C virus RNA replication by cell culture-adaptive mutations. J. Virol. 75:4614-4624.
22. Lin, Y. J., C. L. Liao, and M. M. Lai. 1994. Identification of the cis-acting signal for minus-strand RNA synthesis of a murine coronavirus: implications for the role of minus-strand RNA in RNA replication and transcription. J. Virol. 68:8131-8140.
23. Lohmann, V., F. Korner, U. Herian, and R. Bartenschlager. 1997. Biochemical properties of hepatitis C virus NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity. J. Virol. 71:8416-8428.
24. Lohmann, V., F. Korner, J. O. Koch, U. Herian, L. Theilmann, and R. Bartenschlager. 1999. Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line. Science 285:110-113.
25. Luo, G. X., R. K. Hamatake, D. M. Mathis, J. Racela, K. L. Rigat, J. Lemm, and R. J. Colonno. 2000. De novo initiation of RNA synthesis by the RNA-dependent RNA polymerase (NS5B) of hepatitis C virus. J. Virol. 74:851-863.
26. Mandl, C. W., C. Kunz, and F. X. Heinz. 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.
27. Nagy, P. D., C. D. Carpenter, and A. E. Simon. 1997. A novel 3′-end repair mechanism in an RNA virus. Proc. Natl. Acad. Sci. USA 94:1113-1118.
28. Oh, J. W., G. T. Sheu, and M. M. C. Lai. 2000. Template requirement and initiation site selection by hepatitis C virus polymerase on a minimal viral RNA template. J. Biol. Chem. 275:17710-17717.
29. Raju, R., M. Hajjou, K. R. Hill, V. Botta, and S. Botta. 1999. In vivo addition of poly(A) tail and AU-rich sequences to the 3′ terminus of the Sindbis virus RNA genome: a novel 3′-end repair pathway. J. Virol. 73:2410-2419.
30. Ranjith-Kumar, C. T., J. Gajewski, L. Gutshall, D. Maley, R. T. Sarisky, and C. C. Kao. 2001. Terminal nucleotidyl transferase activity of recombinant Flaviviridae RNA-dependent RNA polymerases: implication for viral RNA synthesis. J. Virol. 75:8615-8623.
31. Sheets, M. D., and M. Wickens. 1989. Two phases in the addition of a poly(A) tail. Genes Dev. 3:1401-1412.
32. Shim, J. H., G. Larson, J. Z. Wu, and Z. Hong. 2002. Selection of 3′-template bases and initiating nucleotides by hepatitis C virus NS5B RNA-dependent RNA polymerase. J. Virol. 76:7030-7039.
33. Spagnolo, J. F., and B. G. Hogue. 2000. Host protein interactions with the 3′ end of bovine coronavirus RNA and the requirement of the poly(A) tail for coronavirus defective genome replication. J. Virol. 74:5053-5065.
34. Sun, X. P., G. H. Zhang, and A. E. Simon. 2005. Short internal sequences involved in replication and virion accumulation in a subviral RNA of Turnip crinkle virus. J. Virol. 79:512-524.
35. Tanaka, T., N. Kato, M. J. Cho, K. Sugiyama, and K. Shimotohno. 1996. Structure of the 3′ terminus of the hepatitis C virus genome. J. Virol. 70: 3307-3312.
36. Uchil, P. D., and V. Satchidanandam. 2003. Architecture of the flaviviral replication complex: protease, nuclease, and detergents reveal encasement within double-layered membrane compartments. J. Biol. Chem. 278:24388-24398.
37. van Leeuwen, H. C., C. B. E. M. Reusken, M. Roeten, T. J. Dalebout, J. I. Riezu-Boj, J. Ruiz, and W. J. M. Spaan. 2004. Evolution of naturally occurring 5′ non-translated region variants of hepatitis C virus genotype 1b in selectable replicons. J. Gen. Virol. 85:1859-1866.
38. Vo, N. V., J. R. Tuler, and M. M. C. Lai. 2004. Enzymatic characterization of the full-length and C-terminally truncated hepatitis C virus RNA polymerases: function of the last 21 amino acids of the C terminus in template binding and RNA synthesis. Biochemistry 43:10579-10591.
39. Wahle, E., and U. Ruegsegger. 1999. 3′-End processing of pre-mRNA in eukaryotes. FEMS Microbiol. Rev. 23:277-295.
40. Yamada, N., K. Tanihara, A. Takada, T. Yorihuzi, M. Tsutsumi, H. Shimomura, T. Tsuji, and T. Date. 1996. Genetic organization and diversity of the 3′ noncoding region of the hepatitis C virus genome. Virology 223:255-261.
41. Yanagi, M., M. St. Claire, S. U. Emerson, R. H. Purcell, and J. Bukh. 1999. In vivo analysis of the 3′ untranslated region of the hepatitis C virus after in vitro mutagenesis of an infectious cDNA clone. Proc. Natl. Acad. Sci. USA 96:2291-2295.
42. Yi, M. K., and S. M. Lemon. 2003. 3′ Nontranslated RNA signals required for replication of hepatitis C virus RNA. J. Virol. 77:3557-3568.
43. Zheng, H. Y., H. A. Lee, P. Palese, and A. Garcia-Sastre. 1999. Influenza A virus RNA polymerase has the ability to stutter at the polyadenylation site of a viral RNA template during RNA replication. J. Virol. 73:5240-5243.
44. Zhong, W. D., A. S. Uss, E. Ferrari, J. Y. N. Lau, and Z. Hong. 2000. De novo initiation of RNA synthesis by hepatitis C virus nonstructural protein 5B polymerase. J. Virol. 74:2017-2022.
45. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.