Secondary structure of the 3' terminus of hepatitis C virus minus-strand RNA.
The 3'-terminal ends of both the positive and negative strands of the hepatitis C virus (HCV) RNA, the latter being the replicative intermediate, are most likely the initiation sites for replication by the viral RNA-dependent RNA polymerase, NS5B. The structural features of the very conserved 3' plus [(+)] strand untranslated region [3' (+) UTR] are well established (K. J. Blight and C. M. Rice, J. Virol. 71:7345-7352, 1997). However, little information is available concerning the 3' end of the minus [(-)] strand RNA. In the present work, we used chemical and enzymatic probing to investigate the conformation of that region, which is complementary to the 5' (+) UTR and the first 74 nucleotides of the HCV polyprotein coding sequence. By combining our experimental data with computer predictions, we have derived a secondary-structure model of this region. In our model, the last 220 nucleotides, where initiation of the (+) strand RNA synthesis presumably takes place, fold into five stable stem-loops, forming domain I. Domain I is linked to an overall less stable structure, named domain II, containing the sequences complementary to the pseudoknot of the internal ribosomal entry site in the 5' (+) UTR. Our results show that, even though the (-) strand 3'-terminal region has the antisense sequence of the 5' (+) UTR, it does not fold into its mirror image. Interestingly, comparison of the replication initiation sites on both strands reveals common structural features that may play key functions in the replication process.
Schuster
Catherine
C
U544 INSERM, Institut de Virologie, 67000 Strasbourg, France. Catherine.schuster@viro-ulp.u-strasbg.fr
Isel
Catherine
C
Imbert
Isabelle
I
Ehresmann
Chantal
C
Marquet
Roland
R
Kieny
Marie Paule
MP
D001483:Base Sequence; D004279:DNA, Viral / Q000235:genetics; D016174:Hepacivirus / Q000737:chemistry* / Q000235:genetics / Q000502:physiology; D006801:Humans; D008958:Models, Molecular; D015336:Molecular Probe Techniques; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D014779:Virus Replication
D004279:DNA, Viral; D012367:RNA, Viral