title: Two-piece tmRNA in cyanobacteria and its structural analysis.
abstract: tmRNA acts to rescue stalled bacterial ribosomes while encoding a peptide tag added trans-translationally to the nascent peptide, targeting it for proteolysis. The permuted gene structure found in a group of cyanobacteria is shown to produce a two-piece mature tmRNA, as had been observed previously for the independently permuted gene of alpha-proteobacteria. The pieces have been mapped onto the gene sequence and aligned for the permuted cyanobacterial tmRNA sequences, including four novel sequences. Structural probing and base pair co-variations support a secondary structure model in which two pairings in the tRNA-like domain hold the two pieces together, and the coding piece bearing the tag reading frame additionally contains a single transient pseudoknot and three other stem-loops. This represents a dramatic reduction in pseudoknot number from the five present in one-piece cyanobacterial tmRNA.
authors.affiliation: Laboratoire de Biochimie Pharmaceutique, Faculté de Pharmacie, Université de Rennes I, UPRES Jeune Equipe 2311, IFR 97, 2 avenue du Pr Léon Bernard, 35043 Rennes cedex, France.
authors.forename: Cyril
authors.initials: C
authors.lastname: Gaudin
authors.forename: Xiong
authors.initials: X
authors.lastname: Zhou
authors.forename: Kelly P
authors.initials: KP
authors.lastname: Williams
authors.forename: Brice
authors.initials: B
authors.lastname: Felden
mesh_terms: D001483:Base Sequence; D000458:Cyanobacteria / Q000235:genetics*; D005798:Genes, Bacterial; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012322:RNA Precursors / Q000032:analysis; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D012322:RNA Precursors; D012329:RNA, Bacterial; C096222:tmRNA