title: RNA signals in the 3' terminus of the genome of Equine arteritis virus are required for viral RNA synthesis.
abstract: RNA virus genomes contain cis-acting sequences and structural elements involved in virus replication. Both full-length and subgenomic negative-strand RNA synthesis are initiated at the 3' terminus of the positive-strand genomic RNA of Equine arteritis virus (EAV). To investigate the molecular mechanism of EAV RNA synthesis, the RNA secondary structure of the 3'-proximal region of the genome was analysed by chemical and enzymic probing. Based on the RNA secondary structure model derived from this analysis, several deletions were engineered in a full-length cDNA copy of the viral genome. Two RNA domains were identified that are essential for virus replication and most likely play a key role in viral RNA synthesis. The first domain, located directly upstream of the 3' untranslated region (UTR) (nt 12610-12654 of the genome), is mainly single-stranded but contains one small stem-loop structure. The second domain is located within the 3' UTR (nt 12661-12690) and folds into a prominent stem-loop structure with a large loop region. The location of this stem-loop structure near the 3' terminus of the genome suggests that it may act as a recognition signal during the initiation of minus-strand RNA synthesis.
authors.affiliation: Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.
authors.forename: Nancy
authors.initials: N
authors.lastname: Beerens
authors.affiliation: Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Snijder
mesh_terms: D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D006224:Cricetinae; D007240:Equartevirus / Q000235:genetics* / Q000502:physiology*; D016679:Genome, Viral; D006736:Horses; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000096:biosynthesis* / Q000737:chemistry / Q000235:genetics*; D017384:Sequence Deletion; D012689:Sequence Homology, Nucleic Acid; D015398:Signal Transduction; D014162:Transfection; D014779:Virus Replication
chemical_list: D012367:RNA, Viral