title: Analysis of hepatitis C virus RNA dimerization and core-RNA interactions.
abstract: The core protein of hepatitis C virus (HCV) has been shown previously to act as a potent nucleic acid chaperone in vitro, promoting the dimerization of the 3'-untranslated region (3'-UTR) of the HCV genomic RNA, a process probably mediated by a small, highly conserved palindromic RNA motif, named DLS (dimer linkage sequence) [G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J. P. Lavergne, F. Penin and J. L. Darlix (2004) Nucleic Acids Res., 32, 2623-2631]. To investigate in depth HCV RNA dimerization, we generated a series of point mutations in the DLS region. We find that both the plus-strand 3'-UTR and the complementary minus-strand RNA can dimerize in the presence of core protein, while mutations in the DLS (among them a single point mutation that abolished RNA replication in a HCV subgenomic replicon system) completely abrogate dimerization. Structural probing of plus- and minus-strand RNAs, in their monomeric and dimeric forms, indicate that the DLS is the major if not the sole determinant of UTR RNA dimerization. Furthermore, the N-terminal basic amino acid clusters of core protein were found to be sufficient to induce dimerization, suggesting that they retain full RNA chaperone activity. These findings may have important consequences for understanding the HCV replicative cycle and the genetic variability of the virus.
authors.affiliation: LaboRetro, Unité INSERM de Virologie Humaine, Ecole Normale Supérieure de Lyon IFR, 128 Biosciences Lyon-Gerland, 69364 Lyon Cedex 07, France.
authors.forename: Roland
authors.initials: R
authors.lastname: Ivanyi-Nagy
authors.forename: Igor
authors.initials: I
authors.lastname: Kanevsky
authors.forename: Caroline
authors.initials: C
authors.lastname: Gabus
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Lavergne
authors.forename: Damien
authors.initials: D
authors.lastname: Ficheux
authors.forename: François
authors.initials: F
authors.lastname: Penin
authors.forename: Philippe
authors.initials: P
authors.lastname: Fossé
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Darlix
mesh_terms: D020413:3' Untranslated Regions / Q000737:chemistry*; D001483:Base Sequence; D019281:Dimerization; D016174:Hepacivirus / Q000235:genetics*; D018832:Molecular Chaperones / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D017434:Protein Structure, Tertiary; D012367:RNA, Viral / Q000737:chemistry*; D014758:Viral Core Proteins / Q000737:chemistry / Q000378:metabolism*
chemical_list: D020413:3' Untranslated Regions; D018832:Molecular Chaperones; D012367:RNA, Viral; D014758:Viral Core Proteins; C069130:nucleocapsid protein, Hepatitis C virus