title: Characterization of the initiation sites of both polarity strands of a viroid RNA reveals a motif conserved in sequence and structure.
abstract: Viroids replicate through a rolling-circle mechanism in which the infecting circular RNA and its complementary (-) strand are transcribed. The precise site at which transcription starts was investigated for the avocado sunblotch viroid (ASBVd), the type species of the family of viroids with hammerhead ribozymes. Linear ASBVd (+) and (-) RNAs begin with a UAAAA sequence that maps to similar A+U-rich terminal loops in their predicted quasi-rod-like secondary structures. The sequences around the initiation sites of ASBVd, which replicates and accumulates in the chloroplast, are similar to the promoters of a nuclear-encoded chloroplastic RNA polymerase (NEP), supporting the involvement of an NEP-like activity in ASBVd replication. Since RNA folding appears to be kinetically determined, the specific location of both ASBVd initiation sites provides a mechanistic insight into how the nascent ASBVd strands may fold in vivo. The approach used here, in vitro capping and RNase protection assays, may be useful for investigating the initiation sites of other small circular RNA replicons.
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Avenida de los Naranjos s/n, Valencia 46022, Spain.
authors.forename: J A
authors.initials: JA
authors.lastname: Navarro
authors.forename: R
authors.initials: R
authors.lastname: Flores
mesh_terms: D001483:Base Sequence; D002467:Cell Nucleus; D002736:Chloroplasts / Q000201:enzymology / Q000821:virology; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism; D019770:Lauraceae / Q000821:virology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000096:biosynthesis / Q000235:genetics*; D012315:RNA Caps / Q000378:metabolism; D016337:RNA, Catalytic / Q000235:genetics* / Q000378:metabolism; D000079962:RNA, Circular; D012367:RNA, Viral / Q000096:biosynthesis / Q000235:genetics*; D018741:Replication Origin; D012093:Replicon; D014772:Viroids / Q000235:genetics* / Q000502:physiology; D014779:Virus Replication
chemical_list: D012315:RNA Caps; D016337:RNA, Catalytic; D000079962:RNA, Circular; D012367:RNA, Viral; D012313:RNA; C409038:nucleus-encoded phage-type RNA polymerase; D012321:DNA-Directed RNA Polymerases