Structural characterization of the highly conserved 98-base sequence at the 3′ end of HCV RNA genome and the complementary sequence located at the 5′ end of the replicative viral strand

Nucleic Acids Research

Volumn 33, Issue 2, 2005, Pages 693-703

  Dutkiewicz, Mariola ^a   Ciesiołka, Jerzy ^a  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; LEAD; NUCLEASE; OLIGOMER; SHORT HAIRPIN RNA; VIRUS RNA; OLIGORIBONUCLEOTIDE;

ARTICLE; BASE PAIRING; CHEMICAL MODIFICATION; CONTROLLED STUDY; GENETIC CONSERVATION; HEPATITIS C VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; RNA ANALYSIS; RNA CLEAVAGE; RNA FINGERPRINTING; RNA STRUCTURE; STRUCTURE ANALYSIS; TERMINAL SEQUENCE; UNTRANSLATED REGION; VIRUS GENOME; VIRUS REPLICATION; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; METABOLISM; MOLECULAR GENETICS;

HEPATITIS C VIRUS;

BASE SEQUENCE; CONSERVED SEQUENCE; GENOME, VIRAL; HEPACIVIRUS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGORIBONUCLEOTIDES; RNA, VIRAL; VIRUS REPLICATION;

EID: 13844310890     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki218     Document Type: Article

References (58)

1. World Health Organization (1999), Hepatitis C: global prevalence (update). Weakly Epidemiol. Rec., 49, 425-427.
2. 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.
3. Branch,A.D. (2000) Hepatitis C virus RNA codes for proteins and replicates: does it also trigger the interferon response? Semin. LiverDis., 20, 57-68.
4. Shi,S.T. and Lai,M.M. (2001) Hepatitis C viral RNA: challenges and promises. Cell. Mol. Life Sci., 58, 1276-1295.
5. Penin,F., Dubuisson,J., Rey,F.A., Moradpour,D. and Pawlotsky,J.M. (2004) Structural biology of hepatitis C virus. Hepatology, 39, 5-19.
6. Gowans,E.J. (2000) Distribution of markers of hepatitis C virus infection throughout the body. Semin. Liver Dis., 20, 85-102.
7. Cohen,J. (1999) The scientific challenge of hepatitis C. Science, 285, 26-30.
8. 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.
9. Behrens,S.E., Tomei,L. and De Francesco,R. (1996) Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus. EMBO J., 15, 12-22.
10. Lohmann,V., Korner,F., Herian,U. and Bartenschlager,R. (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.
11. Tanaka,T., Kato,N., Cho,M.J. and Shimotohno,K. (1995) A novel sequence found at the 3′ terminus of hepatitis C virus genome. Biochem. Biophys. Res. Commun., 215, 744-749.
12. Kolykhalov,A.A., Feinstone,S.M. and Rice,C.M. (1996) Identification of a highly conserved sequence element at the 3′ terminus of hepatitis C virus genome RNA. J. Virol., 70, 3363-3371.
13. Tanaka,T., Kato,N., Cho,M.J., Sugiyama,K. and Shimotohno,K. (1996) Structure of the 3′ terminus of the hepatitis C virus genome. J. Virol., 70, 3307-3312.
14. Schuster,C., Isel,C., Imbert,I., Ehresmann,C., Marquet,R. and Kieny,M.P. (2002) Secondary structure of the 3′ terminus of hepatitis C virus minus-strand RNA. J. Virol., 76, 8058-8068.
15. Smith,R.M., Walton,C.M., Wu,C.H. and Wu,G.Y. (2002) Secondary structure and hybridization accessibility of hepatitis C virus 3′-terminal sequences. J. Virol., 76, 9563-9574.
16. Blight,K.J. and Rice,C.M. (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.
17. Ito,T. and Lai,M.M. (1997) Determination of the secondary structure of and cellular protein binding to the 3′-untranslated region of the hepatitis C virus RNA genome. J. Virol., 71, 8698-8706.
18. Wood,J., Frederickson,R.M., Fields,S. and Patel,A.H. (2001) Hepatitis C virus 3′X region interacts with human ribosomal proteins. J. Virol., 75, 1348-1358.
19. Smith,R.M. and Wu,G.Y. (2004) Secondary structure and hybridization accessibility of the hepatitis C virus negative strand RNA 5′-terminus. J. Viral Hepat., 11, 115-123.
20. Matysiak,M., Wrzesinski,J. and Ciesiołka,J. (1999) Sequential folding of the genomic ribozyme of the hepatitis delta virus: structural analysis of RNA transcription intermediates. J. Mol. Biol. 291, 283-294.
21. Wrzesinski,J., Łegiewicz,M., Smólska,B. and Ciesiołka,J. (2001) Catalytic cleavage of cis- and trans acting antigenomic delta ribozymes in the presence of various divalent metal ions. Nucleic Acids Res., 29, 4482-4492.
22. Krol,A. and Carbon,P. (1989) A guide for probing native small nuclear RNA and ribonucleoprotein structures. Methods Enzymol., 180, 212-226.
23. Zuker,M., Mathews,D.H. and Turner,D.H. (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In Barciszewski,J. and Clark,B.F.C. (eds), RNA Biochemistry and Biotechnology. NATO ASI Series, Kluwer Academic Publishers, pp. 11-43.
24. Chadalavada,D.M., Knudsen,S.M., Nakano,S. and Bevilacqua,P.C. (2000) A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme. J. Mol. Biol., 301, 349-367.
25. Górnicki,P., Baudin,F., Romby,P., Wiewiórowski,M., Krzyzosiak,W.J., Ebel,J.P., Ehresmann,C.H. and Ehresmann,B. (1989) Use of lead (II) to probe the structure of large RNA's. Conformation of the 3′ terminal domain of E.coli 16S rRNA and its involvement in building the tRNA binding sites. J. Biomol. Struct. Dyn., 6, 971-984.
26. Brunel,C.H., Romby,P., Westhof,E., Ehresmann,C. and Ehresmann,B. (1991) Three-dimensional model of Escherichia coli ribosomal 5S RNA as deduced from structure probing in solution and computer modeling. J. Mol. Biol., 221, 293-308.
27. Ciesiołka,J., Lorenz,S. and Erdmann,V.A. (1992) Structural analysis of three prokaryotic 5S rRNA species and selected 5S rRNA-ribosomal-protein complexes by means of Pb(II)-induced hydrolysis. Eur. J. Biochem., 204, 575-581.
28. Ciesiołka,J., Lorenz,S. and Erdmann,V.A. (1992) Different conformational forms of Escherichia coli and rat liver 5S rRNA revealed by Pb(II)-induced hydrolysis. Eur. J. Biochem., 204, 583-589.
29. Ciesiołka,J., Michałowski,D., Wrzesinski,J., Krajewski,J. and Krzyzosiak,W.J. (1998) Patterns of cleavages induced by lead ions in defined RNA secondary structure motifs. J. Mol. Biol., 275, 211-220.
30. Ciesiołka,J. (1999) Metal ion-induced cleavages in probing of RNA structure. In Barciszewski,J. and Clark,B.F.C. (eds), RNA Biochemistry and Biotechnology. NATO ASI Series, Kluwer Academic Publishers, pp. 111-121.
31. Ciesiołka,J. and Krzyzosiak,W.J. (1996) Structural analysis of two plant 5S rRNA species and fragments thereof by lead-induced hydrolysis. Biochem. Mol. Biol. Int., 39, 319-328.
32. Traut,T.W. (1994) Physiological concentrations of purines and pyrimidines. Mol. Cell. Biochem., 140, 1-22.
33. Shi,P.-Y., Brinton,M.A., Veal,J.M., Zhong,Y.Y. and Wilson,W.D. (1996) Evidence for the existence of a pseudoknot structure at the 3′ terminus ofthe flavivirus genomic RNA. Biochemistry, 35, 4222-4230.
34. Cheng,J.C., Chang,M.F. and Chang,S.C. (1999) Specific interaction betweenthe hepatitis C virus NS5B RNApolymerase and the 3′ end of the viral RNA. J. Virol., 73, 7044-7049.
35. Oh,J.W., Sheu,G.T. and Lai,M.M. (2000) Template requirement and initiation site selection by hepatitis C virus polymerase on a minimal viral RNA template. J. Biol. Chem., 275, 17710-17717.
36. Kolykhalov,A.A., Mihalik,K., Feinstone,S.M. and Rice,C.M. (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.
37. Cui,T. and Porter,A.G. (1995) Localization of binding site for encephalomyocarditis virus RNA polymerase in the 3′-noncoding region of the viral RNA. Nucleic Acids Res., 23, 377-382.
38. Osman,T.A., Hemenway,C.L. and Buck,K.W. (2000) Role of the 3′ tRNA-like structure in tobacco mosaic virus minus-strand RNA synthesis by the viral RNA-dependent RNA polymerase in vitro. J. Virol., 74, 11671-11680.
39. Kim,M., Kim,H., Cho,S.P. and Min,M.K. (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.
40. Hong,Z., Cameron,C.E., Walker,M.P., Castro,C., Yao,N., Lau,J.Y. and Zhong,W. (2001) A novel mechanism to ensure terminal initiation by hepatitis C virus NS5B polymerase. Virology, 285 6-11.
41. Kao,C.C., Yang,X., Kline,A., Wang,Q.M., Barket,D. and Heinz,B.A. (2000) Template requirements for RNA synthesis by a recombinant hepatitis C virus RNA-dependent RNA polymerase. J. Virol. 74, 11121-11128.
42. Shim,J.H., Larson,G., Wu,J.Z. and Hong,Z. (2002) Selection of 3′-template bases and initiating nucleotides by hepatitis C virus NS5B RNA-dependent RNA polymerase. J. Virol., 76, 7030-7039.
43. Butcher,S.J., Grimes,J.M., Makeyev,E.V., Bamford,D.H. and Stuart,D.I. (2001) A mechanism for initiating RNA-dependent RNA polymerization. Nature, 410, 235-240.
44. Yi,M. and Lemon,S.M. (2003) Structure-function analysis of the 3′ stem-loop of hepatitis C virus genomic RNA and its role in viral RNA replication. RNA, 9, 331-345.
45. Oh,J.W., Ito,T. and Lai,M.M. (1999) A recombinant hepatitis C virus RNA-dependent RNA polymerase capable of copying the full-length viral RNA. J. Virol., 73, 7694-7702.
46. Reigadas,S., Ventura,M., Sarih-Cottin,L., Castroviejo,M., Litvak,S. and Astier-Gin,T. (2001) HCV RNA-dependent RNA polymerase replicates in vitro the 3′ terminal region of the minus-strand viral RNA more efficiently than the 3′ terminal region of the plus RNA. Eur. J. Biochem., 268, 5857-5867.
47. Yi,M. and Lemon,S.M. (2003) 3′ nontranslated RNA signals required for replication of hepatitis C virus RNA. J. Virol., 77 3557-3568.
48. Friebe,P. and Bartenschlager,R. (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.
49. Banerjee,R. and Dasgupta,A. (2001) Specific interaction of hepatitis C virus protease/helicase NS3 with the 3′-terininal sequences of viral positive- and negative-strand RNA. J. Virol., 75, 1708-1721.
50. Inoue,Y., Miyazaki,M., Ohashi,R., Tsuji,T., Fukaya,K., Kouchi,H., Uemura,T., Mihara,K. and Namba,M. (1998) Ubiquitous presence of cellular proteins that specifically bind to the 3′ terminal region of hepatitis C virus. Biochem. Biophys. Res. Commun., 245, 198-203.
51. Toczyski,D.P. and Steitz,J.A. (1991) EAP, a highly conserved cellular protein associated with Epstein-Barr virus small RNAs (EBERs). EMBO J., 10, 459-466.
52. Senear,A.W. and Steitz,J.A. (1976) Site-specific interaction of Qbeta host factor and ribosomal protein S1 with Qbeta and R17 bacteriophage RNAs. J. Biol. Chem., 251, 1902-1912.
53. Tsuchihara,K., Tanaka,T., Hijikata,M., Kuge,S., Toyoda,H., Nomoto,A., Yamamoto,N. and Shimotohno,K. (1997) Specific interaction of polypyrimidine tract-binding protein with the extreme 3′-terminal structure of the hepatitis C virus genome, the 3′X. J. Virol., 71, 6720-6726.
54. 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.
55. Olsthoorn,R.C., Mertens,S., Brederode,F.T. and Bol,J.F. (1999) A conformational switch at the 3′ end of a plant virus RNA regulates viral replication. EMBO J., 18, 4856-4864.
56. Gallego,J. and Varani,G. (2002) The hepatitis C virus internal ribosome-entry site: a new target for antiviral research. Biochem. Soc. Trans., 30, 140-145.
57. Mandal,M. and Breaker,R.R. (2004) Gene regulation by riboswitches. Nat. Rev. Mol. Cell. Biol., 5, 451-463.
58. Nudler,E. and Mironov,A.S. (2004) The riboswitch control of bacterial metabolism. Trends Biochem. Sci., 29, 11-17.