Nucleic Acids Research, 1992, Vol. 20, No. 19 5041-5045
© 1992
GENOME STRUCTURE AND MAPPING |
Secondary structure of the 5' nontranslated regions of hepatitis C virus and pestivirus genomic RNAs
Department of Medicine, 547 Burnett-Womack CSB, CB # 7030, The University of North Carolina at Chapel Hill Chapel Hill, NC 27599-7030, USA
Received July 20, 1992. Revised September 4, 1992. Accepted September 4, 1992.
The RNA genomes of human hepatitis C virus (HCV) and the animal pestiviruses responsible for bovine viral diarrhea (BVDV) and hog cholera (HChV) have relatively lengthy 5' nontranslated regions (5'NTRs) sharing short segments of conserved primary nucleotlde sequence. The functions of these 5'NTRs are poorly understood. By comparative sequence analysis and thermodynamic modeling of the 5'NTRs of multiple BVDV and HChV strains, we developed models of the secondary structures of these RNAs. These pestiviral 5'NTRs are highly conserved structurally, despite substantial differences in their primary nucleotlde sequences. The assignment of similar structures to conserved segments of primary nucleotide sequence present in the 5'NTR of HCV resulted in a model of the secondary structure of the HCV 5'NTR which was refined by determining sites at which synthetic HCV RNA was cleaved by double- and single-strand specific RNases. These studies indicate the existence of a large conserved stem-loop structure within the 3' 200 bases of the 5'NTRs of both HCV and pestiviruses which corresponds to the ribosomal landing pad (Internal ribosomal entry site) of HCV. This structure shows little relatedness to the ribosomal landing pad of hepatitis A virus, suggesting that these functionally similar structures may have evolved independently.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. Roy, N. Gupta, N. Subramanian, T. Mondal, A. C. Banerjea, and S. Das Sequence-specific cleavage of hepatitis C virus RNA by DNAzymes: inhibition of viral RNA translation and replication J. Gen. Virol., July 1, 2008; 89(7): 1579 - 1586. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. M. Hales, N. J. Knowles, P. S. Reddy, L. Xu, C. Hay, and P. L. Hallenbeck Complete genome sequence analysis of Seneca Valley virus-001, a novel oncolytic picornavirus J. Gen. Virol., May 1, 2008; 89(5): 1265 - 1275. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Guerniou, R. Gillet, F. Berree, B. Carboni, and B. Felden Targeted inhibition of the hepatitis C internal ribosomal entry site genomic RNA with oligonucleotide conjugates Nucleic Acids Res., November 29, 2007; 35(20): 6778 - 6787. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. D. Baird, S. M. Lewis, M. Turcotte, and M. Holcik A search for structurally similar cellular internal ribosome entry sites Nucleic Acids Res., July 9, 2007; 35(14): 4664 - 4677. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. U. T. Hellen and S. de Breyne A Distinct Group of Hepacivirus/Pestivirus-Like Internal Ribosomal Entry Sites in Members of Diverse Picornavirus Genera: Evidence for Modular Exchange of Functional Noncoding RNA Elements by Recombination J. Virol., June 1, 2007; 81(11): 5850 - 5863. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. L. Burch, S. Guyader, D. Samarov, and H. Shen Experimental Estimate of the Abundance and Effects of Nearly Neutral Mutations in the RNA Virus {phi}6 Genetics, May 1, 2007; 176(1): 467 - 476. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Kanda, R. Steele, R. Ray, and R. B. Ray Small Interfering RNA Targeted to Hepatitis C Virus 5' Nontranslated Region Exerts Potent Antiviral Effect J. Virol., January 15, 2007; 81(2): 669 - 676. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Song, P. Friebe, E. Tzima, C. Junemann, R. Bartenschlager, and M. Niepmann The Hepatitis C Virus RNA 3'-Untranslated Region Strongly Enhances Translation Directed by the Internal Ribosome Entry Site J. Virol., December 1, 2006; 80(23): 11579 - 11588. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. D. Baird, M. Turcotte, R. G. Korneluk, and M. Holcik Searching for IRES RNA, October 1, 2006; 12(10): 1755 - 1785. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. L. Tellinghuisen, M. S. Paulson, and C. M. Rice The NS5A Protein of Bovine Viral Diarrhea Virus Contains an Essential Zinc-Binding Site Similar to That of the Hepatitis C Virus NS5A Protein. J. Virol., August 1, 2006; 80(15): 7450 - 7458. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. I. Gismondi, P. D. Becker, P. Valva, C. A. Guzman, and M. V. Preciado Phylogenetic analysis of previously nontypeable hepatitis C virus isolates from Argentina. J. Clin. Microbiol., June 1, 2006; 44(6): 2229 - 2232. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. W.-L. Li, J. Li, S. L. Timmerman, L. A. Krushel, and S. L. Martin The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition Nucleic Acids Res., February 6, 2006; 34(3): 853 - 864. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Hazari, A. Patil, V. Joshi, D. E. Sullivan, C. D. Fermin, R. F. Garry, R. M. Elliott, and S. Dash Alpha interferon inhibits translation mediated by the internal ribosome entry site of six different hepatitis C virus genotypes J. Gen. Virol., November 1, 2005; 86(11): 3047 - 3053. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Pudi, S. S. Ramamurthy, and S. Das A Peptide Derived from RNA Recognition Motif 2 of Human La Protein Binds to Hepatitis C Virus Internal Ribosome Entry Site, Prevents Ribosomal Assembly, and Inhibits Internal Initiation of Translation J. Virol., August 1, 2005; 79(15): 9842 - 9853. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Pankraz, H.-J. Thiel, and P. Becher Essential and Nonessential Elements in the 3' Nontranslated Region of Bovine Viral Diarrhea Virus J. Virol., July 15, 2005; 79(14): 9119 - 9127. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Boni, J.-P. Lavergne, S. Boulant, and A. Cahour Hepatitis C Virus Core Protein Acts as a trans-Modulating Factor on Internal Translation Initiation of the Viral RNA J. Biol. Chem., May 6, 2005; 280(18): 17737 - 17748. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Girard, M. Ravallec, M. Mariller, J.-P. Bossy, A. Cahour, M. Lopez-Ferber, G. Devauchelle, G. Inchauspe, and M. Duonor-Cerutti Effect of the 5' non-translated region on self-assembly of hepatitis C virus genotype 1a structural proteins produced in insect cells J. Gen. Virol., December 1, 2004; 85(12): 3659 - 3670. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Li, W. B. Lott, J. Martyn, G. Haqshenas, and E. J. Gowans Differential Effects on the Hepatitis C Virus (HCV) Internal Ribosome Entry Site by Vitamin B12 and the HCV Core Protein J. Virol., November 1, 2004; 78(21): 12075 - 12081. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Pudi, P. Srinivasan, and S. Das La Protein Binding at the GCAC Site Near the Initiator AUG Facilitates the Ribosomal Assembly on the Hepatitis C Virus RNA to Influence Internal Ribosome Entry Site-mediated Translation J. Biol. Chem., July 16, 2004; 279(29): 29879 - 29888. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Martell, C. Briones, A. de Vicente, M. Piron, J. I. Esteban, R. Esteban, J. Guardia, and J. Gomez Structural analysis of hepatitis C RNA genome using DNA microarrays Nucleic Acids Res., June 24, 2004; 32(11): e90 - e90. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. M. Forton, P. Karayiannis, N. Mahmud, S. D. Taylor-Robinson, and H. C. Thomas Identification of Unique Hepatitis C Virus Quasispecies in the Central Nervous System and Comparative Analysis of Internal Translational Efficiency of Brain, Liver, and Serum Variants J. Virol., May 15, 2004; 78(10): 5170 - 5183. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Thurner, C. Witwer, I. L. Hofacker, and P. F. Stadler Conserved RNA secondary structures in Flaviviridae genomes J. Gen. Virol., May 1, 2004; 85(5): 1113 - 1124. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. S. Ray and S. Das Inhibition of hepatitis C virus IRES-mediated translation by small RNAs analogous to stem-loop structures of the 5'-untranslated region Nucleic Acids Res., March 12, 2004; 32(5): 1678 - 1687. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. E. MELCHER, T. J. WILSON, and D. M.J. LILLEY The dynamic nature of the four-way junction of the hepatitis C virus IRES RNA, July 1, 2003; 9(7): 809 - 820. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Luo, S. Xin, and Z. Cai Role of the 5'-Proximal Stem-Loop Structure of the 5' Untranslated Region in Replication and Translation of Hepatitis C Virus RNA J. Virol., March 1, 2003; 77(5): 3312 - 3318. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. R. Jones, R. Zandomeni, and E. L. Weber Quasispecies in the 5' untranslated genomic region of bovine viral diarrhoea virus from a single individual J. Gen. Virol., September 1, 2002; 83(9): 2161 - 2168. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. M. Smith, C. M. Walton, C. H. Wu, and G. Y. Wu Secondary Structure and Hybridization Accessibility of Hepatitis C Virus 3'-Terminal Sequences J. Virol., August 28, 2002; 76(19): 9563 - 9574. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Schuster, C. Isel, I. Imbert, C. Ehresmann, R. Marquet, and M. P. Kieny Secondary Structure of the 3' Terminus of Hepatitis C Virus Minus-Strand RNA J. Virol., July 17, 2002; 76(16): 8058 - 8068. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Casacuberta and M.-L. Pardue Coevolution of the Telomeric Retrotransposons Across Drosophila Species Genetics, July 1, 2002; 161(3): 1113 - 1124. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. P. Fletcher and R. J. Jackson Pestivirus Internal Ribosome Entry Site (IRES) Structure and Function: Elements in the 5' Untranslated Region Important for IRES Function J. Virol., April 16, 2002; 76(10): 5024 - 5033. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Odreman-Macchioli, F. E. Baralle, and E. Buratti Mutational Analysis of the Different Bulge Regions of Hepatitis C Virus Domain II and Their Influence on Internal Ribosome Entry Site Translational Ability J. Biol. Chem., November 2, 2001; 276(45): 41648 - 41655. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. Lytle, L. Wu, and H. D. Robertson The Ribosome Binding Site of Hepatitis C Virus mRNA J. Virol., August 15, 2001; 75(16): 7629 - 7636. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Lyons, J. R. Lytle, J. Gomez, and H. D. Robertson Hepatitis C virus internal ribosome entry site RNA contains a tertiary structural element in a functional domain of stem-loop II Nucleic Acids Res., June 15, 2001; 29(12): 2535 - 2541. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. D. Zhao and E. Wimmer 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., April 15, 2001; 75(8): 3719 - 3730. [Abstract] [Full Text]
|
|
|
|
|
|
M. Kunkel, M. Lorinczi, R. Rijnbrand, S. M. Lemon, and S. J. Watowich Self-Assembly of Nucleocapsid-Like Particles from Recombinant Hepatitis C Virus Core Protein J. Virol., March 1, 2001; 75(5): 2119 - 2129. [Abstract] [Full Text]
|
|
|
|
|
|
R. Banerjee and A. Dasgupta Specific Interaction of Hepatitis C Virus Protease/Helicase NS3 with the 3'-Terminal Sequences of Viral Positive- and Negative-Strand RNA J. Virol., February 15, 2001; 75(4): 1708 - 1721. [Abstract] [Full Text]
|
|
|
|
|
|
R. Jubin, N. E. Vantuno, J. S. Kieft, M. G. Murray, J. A. Doudna, J. Y. N. Lau, and B. M. Baroudy Hepatitis C Virus Internal Ribosome Entry Site (IRES) Stem Loop IIId Contains a Phylogenetically Conserved GGG Triplet Essential for Translation and IRES Folding J. Virol., November 15, 2000; 74(22): 10430 - 10437. [Abstract] [Full Text]
|
|
|
|
|
|
P. Becher, M. Orlich, and H.-J. Thiel Mutations in the 5' Nontranslated Region of Bovine Viral Diarrhea Virus Result in Altered Growth Characteristics J. Virol., September 1, 2000; 74(17): 7884 - 7894. [Abstract] [Full Text]
|
|
|
|
|
|
V. G. Kolupaeva, T. V. Pestova, and C. U. T. Hellen An Enzymatic Footprinting Analysis of the Interaction of 40S Ribosomal Subunits with the Internal Ribosomal Entry Site of Hepatitis C Virus J. Virol., July 15, 2000; 74(14): 6242 - 6250. [Abstract] [Full Text]
|
|
|
|
|
|
H. Yu, O. Isken, C. W. Grassmann, and S.-E. Behrens A Stem-Loop Motif Formed by the Immediate 5' Terminus of the Bovine Viral Diarrhea Virus Genome Modulates Translation as well as Replication of the Viral RNA J. Virol., July 1, 2000; 74(13): 5825 - 5835. [Abstract] [Full Text]
|
|
|
|
 |
|
 R. Gosert, K. H. Chang, R. Rijnbrand, M. Yi, D. V. Sangar, and S. M. Lemon Transient Expression of Cellular Polypyrimidine-Tract Binding Protein Stimulates Cap-Independent Translation Directed by Both Picornaviral and Flaviviral Internal Ribosome Entry Sites In Vivo Mol. Cell. Biol., March 1, 2000; 20(5): 1583 - 1595. [Abstract] [Full Text]
|
|
|
|
|
|
F. E. Odreman-Macchioli, S. G. Tisminetzky, M. Zotti, F. E. Baralle, and E. Buratti Influence of correct secondary and tertiary RNA folding on the binding of cellular factors to the HCV IRES Nucleic Acids Res., February 15, 2000; 28(4): 875 - 885. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Rijnbrand, G. Abell, and S. M. Lemon Mutational Analysis of the GB Virus B Internal Ribosome Entry Site J. Virol., January 1, 2000; 74(2): 773 - 783. [Abstract] [Full Text]
|
|
|
|
|
|
G. Luo, R. K. Hamatake, D. M. Mathis, J. Racela, K. L. Rigat, J. Lemm, and R. J. Colonno De Novo Initiation of RNA Synthesis by the RNA-Dependent RNA Polymerase (NS5B) of Hepatitis C Virus J. Virol., January 1, 2000; 74(2): 851 - 863. [Abstract] [Full Text]
|
|
|
|
|
|
J.-W. Oh, T. Ito, and M. M. C. Lai A Recombinant Hepatitis C Virus RNA-Dependent RNA Polymerase Capable of Copying the Full-Length Viral RNA J. Virol., September 1, 1999; 73(9): 7694 - 7702. [Abstract] [Full Text]
|
|
|
|
|
|
T. Isoyama, N. Kamoshita, K. Yasui, A. Iwai, K. Shiroki, H. Toyoda, A. Yamada, Y. Takasaki, and A. Nomoto Lower concentration of La protein required for internal ribosome entry on hepatitis C virus RNA than on poliovirus RNA J. Gen. Virol., September 1, 1999; 80(9): 2319 - 2327. [Abstract] [Full Text]
|
|
|
|
|
|
M. Honda, R. Rijnbrand, G. Abell, D. Kim, and S. M. Lemon 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., June 1, 1999; 73(6): 4941 - 4951. [Abstract] [Full Text]
|
|
|
|
|
|
K Spangberg and S Schwartz Poly(C)-binding protein interacts with the hepatitis C virus 5' untranslated region J. Gen. Virol., June 1, 1999; 80(6): 1371 - 1376. [Abstract]
|
|
|
|
|
|
H. Yu, C. W. Grassmann, and S.-E. Behrens Sequence and Structural Elements at the 3' Terminus of Bovine Viral Diarrhea Virus Genomic RNA: Functional Role during RNA Replication J. Virol., May 1, 1999; 73(5): 3638 - 3648. [Abstract] [Full Text]
|
|
|
|
|
|
S. Jang, L. Wang, M Radkowski, J Rakela, and T Laskus Differences between hepatitis C virus 5' untranslated region quasispecies in serum and liver J. Gen. Virol., March 1, 1999; 80(3): 711 - 716. [Abstract]
|
|
|
|
|
|
S. Tang, A. J. Collier, and R. M. Elliott Alterations to both the Primary and Predicted Secondary Structure of Stem-Loop IIIc of the Hepatitis C Virus 1b 5' Untranslated Region (5'UTR) Lead to Mutants Severely Defective in Translation Which Cannot Be Complemented in trans by the Wild-Type 5'UTR Sequence J. Virol., March 1, 1999; 73(3): 2359 - 2364. [Abstract] [Full Text]
|
|
|
|
|
|
M. Honda, M. R. Beard, L.-H. Ping, and S. M. Lemon 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 J. Virol., February 1, 1999; 73(2): 1165 - 1174. [Abstract] [Full Text]
|
|
|
|
|
|
W. D. Zhao, E. Wimmer, and F. C. Lahser Poliovirus/Hepatitis C Virus (Internal Ribosomal Entry Site-Core) Chimeric Viruses: Improved Growth Properties through Modification of a Proteolytic Cleavage Site and Requirement for Core RNA Sequences but Not for Core-Related Polypeptides J. Virol., February 1, 1999; 73(2): 1546 - 1554. [Abstract] [Full Text]
|
|
|
|
|
|
B. Hahm, Y. K. Kim, J. H. Kim, T. Y. Kim, and S. K. Jang Heterogeneous Nuclear Ribonucleoprotein L Interacts with the 3' Border of the Internal Ribosomal Entry Site of Hepatitis C Virus J. Virol., November 1, 1998; 72(11): 8782 - 8788. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Ito, S. M. Tahara, and M. M. C. Lai The 3'-Untranslated Region of Hepatitis C Virus RNA Enhances Translation from an Internal Ribosomal Entry Site J. Virol., November 1, 1998; 72(11): 8789 - 8796. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. O'Meara, Z. Yun, A. Sönnerborg, and J. Lundeberg Cooperative Oligonucleotides Mediating Direct Capture of Hepatitis C Virus RNA from Serum J. Clin. Microbiol., September 1, 1998; 36(9): 2454 - 2459. [Abstract] [Full Text]
|
|
|
|
|
|
D. V. Sizova, V. G. Kolupaeva, T. V. Pestova, I. N. Shatsky, and C. U. T. Hellen Specific Interaction of Eukaryotic Translation Initiation Factor 3 with the 5' Nontranslated Regions of Hepatitis C Virus and Classical Swine Fever Virus RNAs J. Virol., June 1, 1998; 72(6): 4775 - 4782. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. V. Pestova, I. N. Shatsky, S. P. Fletcher, R. J. Jackson, and C. U.T. Hellen A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initation of hepatitis C and classical swine fever virus RNAs Genes & Dev., January 1, 1998; 12(1): 67 - 83. [Abstract] [Full Text]
|
|
|
|
 |
|
 N. Ali and A. Siddiqui 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 PNAS, March 18, 1997; 94(6): 2249 - 2254. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. F. Lima, V. Brown-Driver, M. Fox, R. Hanecak, and T. W. Bruice Combinatorial Screening and Rational Optimization for Hybridization to Folded Hepatitis C Virus RNA of Oligonucleotides with Biological Antisense Activity J. Biol. Chem., January 3, 1997; 272(1): 626 - 638. [Abstract] [Full Text] [PDF]
|
|