title: Novel requirements in peripheral structures of the extended satellite 2 hammerhead.
abstract: A number of RNAs that infect plants self-cleave using a domain called the hammerhead. The consensus plant hammerhead has three base paired stem structures. Stems I and III flank the cleaved phosphodiester and are connected to stem II by two unpaired and highly conserved sequences. We demonstrated previously that satellite 2 transcripts from the newt, Notophthalmus viridescens, use a modified hammerhead structure for self-cleavage. Here we show that hammerheads with similar modifications occur in satellite 2 from species representing two additional families of salamanders (Ambystoma talpoideum and Amphiuma tridactylum). The distinctive features of the modified satellite 2 hammerheads include unusually short stem III regions and internally looped extensions to stem I that are required for cleavage. However, despite the strict nucleotide requirement in the internal stem I loop of the newt hammerhead, the details of the stem I extensions differ in the three salamanders. An analysis of chimeric transcripts indicated that, in order for a specific stem I extension to be functional, it must be compatible with other regions of the modified satellite 2 hammerhead. One such region is stem II, and a mutational analysis has confirmed that there are specific sequence and/or structural requirements in stem II.
authors: Department of Chemistry, Florida State University, Tallahassee 32306-3050, USA.
authors: T A
authors: TA
authors: Garrett
authors: L M
authors: LM
authors: Pabón-Peña
authors: N
authors: N
authors: Gokaldas
authors: L M
authors: LM
authors: Epstein
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009673:Notophthalmus viridescens / Q000235:genetics; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D014158:Transcription, Genetic; D014562:Caudata / Q000235:genetics
chemical_list: D012313:RNA