title: Terminal structures of West Nile virus genomic RNA and their interactions with viral NS5 protein.
abstract: Genome cyclization is essential for flavivirus replication. We used RNases to probe the structures formed by the 5'-terminal 190 nucleotides and the 3'-terminal 111 nucleotides of the West Nile virus (WNV) genomic RNA. When analyzed individually, the two RNAs adopt stem-loop structures as predicted by the thermodynamic-folding program. However, when mixed together, the two RNAs form a duplex that is mediated through base-pairings of two sets of RNA elements (5'CS/3'CSI and 5'UAR/3'UAR). Formation of the RNA duplex facilitates a conformational change that leaves the 3'-terminal nucleotides of the genome (position -8 to -16) to be single-stranded. Viral NS5 binds specifically to the 5'-terminal stem-loop (SL1) of the genomic RNA. The 5'SL1 RNA structure is essential for WNV replication. The study has provided further evidence to suggest that flavivirus genome cyclization and NS5/5'SL1 RNA interaction facilitate NS5 binding to the 3' end of the genome for the initiation of viral minus-strand RNA synthesis.
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA.
authors.forename: Hongping
authors.initials: H
authors.lastname: Dong
authors.forename: Bo
authors.initials: B
authors.lastname: Zhang
authors.forename: Pei-Yong
authors.initials: PY
authors.lastname: Shi
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002460:Cell Line; D002522:Chlorocebus aethiops; D006224:Cricetinae; D016679:Genome, Viral / Q000235:genetics; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D023302:Protein Footprinting; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000378:metabolism; D014709:Vero Cells; D017361:Viral Nonstructural Proteins / Q000737:chemistry / Q000378:metabolism*; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014902:West Nile virus / Q000235:genetics / Q000378:metabolism / Q000502:physiology*
chemical_list: C096041:NS5 protein, flavivirus; D012367:RNA, Viral; D011994:Recombinant Proteins; D017361:Viral Nonstructural Proteins; D014764:Viral Proteins