A phylogenetically conserved stem-loop structure at the 5' border of the internal ribosome entry site of hepatitis C virus is required for cap- independent viral translation

Journal of Virology

Volumn 73, Issue 2, 1999, Pages 1165-1174

  Honda, Masao ^a   Beard, Michael R ^b   Ping, Li Hua ^c   Lemon, Stanley M ^b  

^a KANAZAWA UNIVERSITY   (Japan)

^b University of Texas Medical Branch School of Medicine   (United States)

^c UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; PROTEIN; RNA;

ANIMAL CELL; ARTICLE; BASE PAIRING; CERCOPITHECIDAE; HEPATITIS C VIRUS; HUMAN; HUMAN CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RIBOSOME; RNA STRUCTURE; VIRUS TRANSCRIPTION;

EID: 0032903304     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.73.2.1165-1174.1999     Document Type: Article

References (32)

1. Ali, N., and A. Siddiqui. 1997. The La antigen binds 5′ noncoding region of the hepatitis C virus RNA in the context of the initiator AUG codon and stimulates internal ribosome entry site-mediated translation. Proc. Natl. Acad. Sci. USA 94:2249-2254.
2. Brown, E. A., H. Zhang, L. H. Ping, and S. M. Lemon. 1992. Secondary structure of the 5′ nontranslated regions of hepatitis C virus and pestivirus genomic RNAs. Nucleic Acids Res. 20:5041-5045.
3. Choo, Q. L., G. Kuo, A. J. Weiner, L. R. Overby, D. W. Bradley, and M. Houghton. 1989. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244:359-362.
4. Davidson, F., P. Simmonds, J. C. Ferguson, L. M. Jarvis, B. C. Dow, E. A. Follett, C. R. Seed, T. Krusius, C. Lin, G. A. Medgyesi, H. Kiyokawa, G. Olim, G. Duraisamy, T. Cuypers, A. A. Saeed, D. Teo, J. Conradie, M. C. Kew, M. Lin, C. Nuchaprayoon, O. K. Ndimbie, and P. L. Yap. 1995. Survey of major genotypes and subtypes of hepatitis C virus using RFLP of sequences amplified from the 5′ non-coding region. J. Gen. Virol. 76:1197-1204.
5. Fuerst, T., E. G. Niles, F. W. Studier, and B. Moss. 1986. Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase. Proc. Natl. Acad. Sci. USA 83:8122-8126.
6. Fukushi, S., K. Katayama, C. Kurihara, N. Ishiyama, F. B. Hoshino, T. Ando, and A. Oya. 1994. Complete 5′ noncoding region is necessary for the efficient internal initiation of hepatitis C virus RNA. Biochem. Biophys. Res. Commun. 199:425-432.
7. Hayashi, N., H. Higashi, K. Kaminaka, H. Sugimoto, M. Esumi, K. Komatsu, K. Hayashi, M. Sugitani, K. Suzuki, O. Tadao, C. Nozaki, K. Mizuno, and T. Shikata. 1993. Molecular cloning and heterogeneity of the human hepatitis C virus (HCV) genome. J. Hepatol. 17:S94-S107.
8. Honda, M., G. Abell, D. Kim, and S. M. Lemon. Natural variation in translational activities of the 5′ nontranslated RNAs of genotypes 1a and 1b hepatitis C virus: evidence for a long range RNA-RNA interaction outside of the internal ribosomal entry site. Submitted for publication.
9. Honda, M., E. A. Brown, and S. M. Lemon. 1996. 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.
10. Honda, M., S. Kaneko, A. Sakai, M. Unoura, S. Murakami, and K. Kobayashi. 1994. Degree of diversity of hepatitis C virus quasispecies and progression of liver disease. Hepatology 20:1144-1151.
11. Honda, M., L.-H. Ping, R. Rijnbrand, E. Amphlett, B. Clarke, D. Rowlands, and S. M. Lemon. 1996. Structural requirements for initiation of translation by internal ribosome entry within genome-length hepatitis C virus RNA. Virology 222:31-42.
12. Kiyosawa, K., T. Sodeyama, E. Tanaka, Y. Gibo, K. Yoshizawa, Y. Nakano, S. Furuta, Y. Akahane, K. Nishioka, R. H. Purcell, and H. J. Alter. 1990. Interrelationship of blood transfusion, non-A, non-B hepatitis and hepatocellular carcinoma: analysis by detection of antibody to hepatitis C virus. Hepatology 12:671-675.
13. Lowman, H. B., and D. E. Draper. 1986. On the recognition of helical RNA by cobra venom V1 nuclease. J. Biol. Chem. 261:5396-5403.
14. Pestova, T. V., I. N. Shatsky, S. P. Fletcher, R. J. Jackson, and C. U. Hellen. 1998. A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes Dev. 12:67-83.
15. Reynolds, J. E., A. Kaminski, A. R. Carroll, B. E. Clarke, D. J. Rowlands, and R. J. Jackson. 1996. Internal initiation of translation of hepatitis C virus RNA: the ribosome entry site is at the authentic initiation codon. RNA 2: 867-878.
16. Reynolds, J. E., A. Kaminski, H. Kettinen, A. R. Carroll, D. J. Rowlands, and R. J. Jackson. 1995. Unique features of internal initiation of hepatitis C virus RNA translation. EMBO J. 14:5016-6020.
17. Rijnbrand, K., P. Bredenbeek, T. van der Straaten, L. Whetter, G. Inchauspe, S. Lemon, and W. Spaan. 1995. Almost the entire 5′ non-translated region of hepatitis C virus is required for cap-independent translation. FEBS Lett. 365:115-119.
18. Rijnbrand, R., T. van der Stratten, P. A. van Rijn, W. J. M. Spaan, and P. J. Bredenbeek. 1997. Internal entry of ribosomes is directed by the 5′ noncoding region of classical swine fever virus and is dependent on the presence of RNA pseudoknot upstream of the initiation codon. J. Virol. 71:451-457.
19. Rijnbrand, R. C., T. E. Abbink, P. C. Haasnoot, W. J. Spaan, and P. J. Bredenbeek. 1996. The influence of AUG codons in the hepatitis C virus 5′ nontranslated region on translation and mapping of the translation initiation window. Virology 226:47-56.
20. Schultz, D. E., M. Honda, L. E. Whetter, K. L. McKnight, and S. M. Lemon. 1996. Mutations within the 5′ nontranslated RNA of cell culture-adapted hepatitis A virus which enhance cap-independent translation in cultured African green monkey kidney cells. J. Virol. 70:1041-1049.
21. Simmonds. P., E. C. Holmes, T. A. Cha, S. W. Chan, F. McOmish, B. Irvine. E. Beall, P. L. Yap, J. Kolberg, and M. S. Urdea. 1993. Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J. Gen. Virol. 74:2391-2399.
22. Simons, J. N., S. M. Desai, D. E. Schultz, S. M. Lemon, and I. K. Mushahwar. 1996. Translation initiation in GB viruses A and C: evidence for internal ribosome entry and implications on genome organization. J, Virol. 70:6126-6135.
23. Simons, J. N., T. J. Pilot-Matias, T. P. Leary, G. J. Dawson, S. M. Desai, G. G. Schleuder, A. S. Muerhoff, J. C. Erker, S. L. Buijk, M. L. Chalmers, C. L. Van Sant, and I. K. Mushahwar. 1995. Identification of two flavivirus-like genomes in the GB hepatitis agent. Proc. Natl. Acad. Sci. USA 92:3401-3405.
24. Smith, D. B, J. Mellor, L. M. Jarvis, F. Davidson, J. Kolberg, M. Urdea, P.-L. Yap, P. Sinimonds, and International HCV Collaborative Study Group. 1995. Variation of the hepatitis C virus 5′ non-coding region: implications for secondary structure, virus detection and typing. J. Gen. Virol. 76:1749-1761.
25. Strauss, J. H., E. G. Strauss, C. S. Hahn, and C. M. Rice. 1987. The genomes of alphaviruses and flaviviruses: organization and translation, p. 75-104. In D. J. Rowlands, M. A. Mayo, and B. W. J. Mahy (ed.), The molecular biology of the positive strand RNA viruses. Academic Press, London, England.
26. Tinoco, I. 1993. Structure of base pairs involving at least two hydrogen bonds, p. 603-7. In R. F. Gesteland and J. F. Atkins (ed.). The RNA world. Cold Spring Harbor Press, Cold Spring Harbor, N.Y.
27. Tsukiyama, K. K., N. Iizuka, M. Kohara, and A. Nomoto. 1992. Internal ribosome entry site within hepatitis C virus RNA. J. Virol. 66:1476-1483.
28. Wang, C., S. Y. Le, N. Ali, and A. Siddiqui. 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.
29. Wang, C., P. Sarnow, and A. Siddiqui. 1994. A conserved helical element is essential for internal initiation of translation of hepatitis C virus RNA. J. Virol. 68:7301-7307.
30. Wang, C., P. Sarnow, and A. Siddiqui. 1993. Translation of human hepatitis C virus RNA in cultured cells is mediated by an internal ribosome-binding mechanism. J. Virol. 67:3338-3344.
31. Weiner, A. J., H. M. Geysen, C. Christopherson, J. E. Hall, T. J. Mason, G. Saracco, F. Bonino, K. Crawford, C. D. Marion, K. A. Crawford, et al. 1992. Evidence for immune selection of hepatitis C virus (HCV) putative envelope glycoprotein variants: potential role in chronic HCV infections. Proc. Natl. Acad. Sci. USA 89:3468-3472.
32. Whetter, L. E., S. P. Day, O. Elroy-Stein, E. A, Brown, and S. M. Lemon. 1994. Low efficiency of the 5′ nontranslated region of hepatitis A virus RNA in directing cap-independent translation in permissive monkey kidney cells. J. Virol. 68:5253-5263.