Long-range RNA-RNA interaction between the 5′ nontranslated region and the core-coding sequences of hepatitis C virus modulates the IRES-dependent translation

RNA

Volumn 9, Issue 5, 2003, Pages 599-606

  Kim, Yoon Ki ^a   Lee, Song Hee ^a   Kim, Chon Saeng ^a   Seol, Su Kyoung ^a   Jang, Sung Key ^a  

^a Pohang University of Science and Technology (POSTECH)   (South Korea)

Author keywords

Core; HCV; IRES; Translation

Indexed keywords

VIRUS RNA;

5' UNTRANSLATED REGION; ARTICLE; GENE EXPRESSION REGULATION; HEPATITIS C VIRUS; HUMAN; HUMAN CELL; INTERNAL RIBOSOME ENTRY SITE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA BINDING; SITE DIRECTED MUTAGENESIS; VIRUS GENOME;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; BINDING SITES; CELL LINE; CONSERVED SEQUENCE; HEPACIVIRUS; HUMANS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PHYLOGENY; PROTEIN BIOSYNTHESIS; RNA, VIRAL;

HEPATITIS C VIRUS; ORYCTOLAGUS CUNICULUS; RNA VIRUSES;

EID: 0037407151     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.2185603     Document Type: Article

References (38)

1. Back, S.H., Kim, Y.K., Kim, W.J., Cho, S., Oh, H.R., Kim, J.E., and Jang, S.K. 2002. Translation of polioviral mRNA is inhibited by cleavage of polypyrimidine tract-binding proteins executed by polioviral 3C(pro). J. Virol. 76: 2529-2542.
2. Bartenschlager, R. and Lohmann, V. 2000. Replication of hepatitis C virus. J. Gen. Virol. 81: 1631-1648.
3. Barton, D.J., Morasco, B.J., and Flanegan, J.B. 1999. Translating ribosomes inhibit poliovirus negative-strand RNA synthesis. J. Virol. 73: 10104-10112.
4. Blyn, L.B., Swiderek, K.M., Richards, O., Stahl, D.C., Semler, B.L., and Ehrenfeld, E. 1996. Poly(rC) binding protein 2 binds to stem-loop IV of the poliovirus RNA 5′ noncoding region: Identification by automated liquid chromatography-tandem mass spectrometry. Proc. Natl. Acad. Sci. 93: 11115-11120.
5. Blyn, L.B., Towner, J.S., Semler, B.L., and Ehrenfeld, E. 1997. Requirement of poly(rC) binding protein 2 for translation of poliovirus RNA. J. Virol. 71: 6243-6246.
6. Gamarnik, A.V. and Andino, R. 1997. Two functional complexes formed by KH domain containing proteins with the 5′ noncoding region of poliovirus RNA. RNA 3: 882-892.
7. -. 1998. Switch from translation to RNA replication in a positive-stranded RNA virus. Genes & Dev. 12: 2293-2304.
8. -. 2000. Interactions of viral protein 3CD and poly(rC) binding protein with the 5′ untranslated region of the poliovirus genome. J. Virol. 74: 2219-2226.
9. Graff, J., Cha, J., Blyn, L.B., and Ehrenfeld, E. 1998. Interaction of poly(rC) binding protein 2 with the 5′ noncoding region of hepatitis A virus RNA and its effects on translation. J. Virol. 72: 9668-9675.
10. Hahm, B., Kim, Y.K., Kim, J.H., Kim, T.Y., and Jang, S.K. 1998. Heterogeneous nuclear ribonucleoprotein L interacts with the 3′ border of the internal ribosomal entry site of hepatitis C virus. J. Virol. 72: 8782-8788.
11. Herold, J. and Andino, R. 2001. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol. Cell 7: 581-591.
12. Honda, M., Brown, E.A., and Lemon, S.M. 1996a. Stability of a stem-loop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA. RNA 2: 955-968.
13. Honda, M., Ping, L.H., Rijnbrand, R.C., Amphlett, E., Clarke, B., Rowlands, D., and Lemon, S.M. 1996b. Structural requirements for initiation of translation by internal ribosome entry within genome-length hepatitis C virus RNA. Virology 222: 31-42.
14. Honda, M., Rijnbrand, R., Abell, G., Kim, D., and Lemon, S.M. 1999. Natural variation in translational activities of the 5′ nontranslated RNAs of hepatitis C virus genotypes 1a and 1b: Evidence for a long-range RNA-RNA interaction outside of the internal ribosomal entry site. J. Virol. 73: 4941-4951.
15. Hwang, L.H., Hsieh, C.L., Yen, A., Chung, Y.L., and Chen, D.S. 1998. Involvement of the 5′ proximal coding sequences of hepatitis C virus with internal initiation of viral translation. Biochem. Biophys. Res. Commun. 252: 455-460.
16. Ito, T. and Lai, M.M. 1999. An internal polypyrimidine-tract-binding protein-binding site in the hepatitis C virus RNA attenuates translation, which is relieved by the 3′-untranslated sequence. Virology 254: 288-296.
17. Kamoshita, N., Tsukiyama-Kohara, K., Kohara, M., and Nomoto, A. 1997. Genetic analysis of internal ribosomal entry site on hepatitis C virus RNA: Implication for involvement of the highly ordered structure an a cell type-specific transacting factors. Virology 233: 9-18.
18. Kim, Y.K., Hahm, B., and Jang, S.K. 2000. Polypyrimidine tract-binding protein inhibits translation of bip mRNA. J. Mol. Biol. 304: 119-133.
19. Kim, Y.K., Back, S.H., Rho, J., Lee, S.H., and Jang, S.K. 2001. La autoantigen enhances translation of BiP mRNA. Nucleic Acids Res. 29: 5009-5016.
20. Lu, H.H. and Wimmer, E, 1996. Poliovirus chimeras replicating under the translational control of genetic elements of hepatitis C virus reveal unusual properties of the internal ribosomal entry site of hepatitis C virus. Proc. Natl. Acad. Sci. 93: 1412-1417.
21. Parsley, T.B., Towner, J.S., Blyn, L.B., Ehrenfeld, E., and Semler, B.L. 1997. Poly (rC) binding protein 2 forms a ternary complex with the 5±-terminal sequences of poliovirus RNA and the viral 3CD proteinase. RNA 3: 1124-1134.
22. Reed, K.E. and Rice, C.M. 2000. Overview of hepatitis C virus genome structure, polyprotein processing, and protein properties. Curr. Top Microbiol. Immunol. 242: 55-84.
23. Reynolds, J.E., Kaminski, A., Kettinen, H.J., Grace, K., Clarke, B.E., Carroll, A.R., Rowlands, D.J., and Jackson, R.J. 1995. Unique features of internal initiation of hepatitis C virus RNA translation. EMBO J. 14: 6010-6020.
24. Rice, C.M. 1996. Flaviviridae: The viruses and their replication. In Fields virology (eds. B.N. Field et al.) pp. 931-959, Raven Press, Philadelphia, PA.
25. Rijnbrand, R.C. and Lemon, S.M. 2000. Internal ribosome entry site-mediated translation in hepatitis C virus replication. Curr. Top. Microbiol. Immunol. 242: 85-116.
26. Rijnbrand, R., Bredenbeek, P., van der Straaten, T., Whetter, L., Inchauspe, G., Lemon, S., and Spaan, W. 1995. Almost the entire 5′ non-translated region of hepatitis C virus is required for cap-independent translation. FEBS Lett. 365: 115-119.
27. Rijnbrand, R., Abell, G., and Lemon, S.M. 2000. Mutational analysis of the GB virus B internal ribosome entry site. J. Virol. 74: 773-783.
28. Rijnbrand, R., Bredenbeek, P.J., Haasnoot, P.C., Kieft, J.S., Spaan, W.J., and Lemon, S.M. 2001. The influence of downstream protein-coding sequence on internal ribosome entry on hepatitis C virus and other flavivirus RNAS. RNA 7: 585-597.
29. Silvera, D., Gamarnik, A.V., and Andino, R. 1999. The N-terminal K homology domain of the poly(rC)-binding protein is a major determinant for binding to the poliovirus 5′-untranslated region and acts as an inhibitor of viral translation. J. Biol. Chem. 274: 38163-38170.
30. Smith, D.B. and Simmonds, P. 1997. Characteristics of nucleotide substitution in the Hepatitis C Virus genome: Constraints on sequence change in coding region at both ends of the genome. J. Mol. Evol. 45: 238-246.
31. Tuplin, A., Wood, J., Evans, D.J., Patel, A.H., and Simmonds, P. 2002. Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of Hepatitis C Virus. RNA 8: 824-841.
32. Tsukiyama-Kohara, K., Iizuka, N., Kohara, M., and Nomoto, A. 1992. Internal ribosome entry site within hepatitis C virus RNA. J. Virol. 66: 1476-1483.
33. Walter, B.L., Nguyen, J.H., Ehrenfeld, E., and Semler, B.L. 1999. Differential utilization of poly(rC) binding protein 2 in translation directed by picornavirus IRES elements. RNA 5: 1570-1585.
34. Wang, C., Sarnow, P., and Siddiqui, A. 1994. A conserved helical element is essential for internal initiation of translation of hepatitis C virus RNA. J. Virol. 68: 7301-7307.
35. Wang, C., Le, S.Y., Ali, N., and Siddiqui, A. 1995. An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5′ noncoding region. RNA 1: 526-537.
36. Wang, T.H., Rijnbrand, R.C., and Lemon, S.M. 2000. Core protein-coding sequence, but not core protein, modulates the efficiency of cap-independent translation directed by the internal ribosome entry site of hepatitis C virus. J. Virol. 74: 11347-11358.
37. Zhao, W.D. and Wimmer, E. 2001. Genetic analysis of a poliovirus/hepatitis C virus chimera: New structure for domain II of the internal ribosomal entry site of hepatitis C virus. J. Virol. 75: 3719-3730.
38. Zhao, W.D., Lahser, F.C., and Wimmer, E. 2000. Genetic analysis of a poliovirus/hepatitis C virus (HCV) chimera: Interaction between the poliovirus cloverleaf and a sequence in the HCV 5′ nontranslated region results in a replication phenotype. J. Virol. 74: 6223-6226.