title: Identification of a conserved branched RNA structure that functions as a factor-independent terminator.
abstract: Anti-Q is a small RNA encoded on pCF10, an antibiotic resistance plasmid of Enterococcus faecalis, which negatively regulates conjugation of the plasmid. In this study we sought to understand how Anti-Q is generated relative to larger transcripts of the same operon. We found that Anti-Q folds into a branched structure that functions as a factor-independent terminator. In vitro and in vivo, termination is dependent on the integrity of this structure as well as the presence of a 3' polyuridine tract, but is not dependent on other downstream sequences. In vitro, terminated transcripts are released from RNA polymerase after synthesis. In vivo, a mutant with reduced termination efficiency demonstrated loss of tight control of conjugation function. A search of bacterial genomes revealed the presence of sequences that encode Anti-Q-like RNA structures. In vitro and in vivo experiments demonstrated that one of these functions as a terminator. This work reveals a previously unappreciated flexibility in the structure of factor-independent terminators and identifies a mechanism for generation of functional small RNAs; it should also inform annotation of bacterial sequence features, such as terminators, functional sRNAs, and operons.
authors.affiliation: Department of Microbiology, University of Minnesota, Minneapolis, MN 55455.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Johnson
authors.forename: Yuqing
authors.initials: Y
authors.lastname: Chen
authors.forename: Heejin
authors.initials: H
authors.lastname: Lee
authors.forename: Ailong
authors.initials: A
authors.lastname: Ke
authors.forename: Keith E
authors.initials: KE
authors.lastname: Weaver
authors.forename: Gary M
authors.initials: GM
authors.lastname: Dunny
mesh_terms: D001483:Base Sequence; D015152:Blotting, Northern; D015153:Blotting, Western; D003227:Conjugation, Genetic / Q000235:genetics / Q000502:physiology*; D013293:Enterococcus faecalis / Q000235:genetics*; D008969:Molecular Sequence Data; D016296:Mutagenesis; D010957:Plasmids / Q000235:genetics*; D059370:RNA Folding / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D013728:Terminator Regions, Genetic / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D012329:RNA, Bacterial
keywords: antisense; attenuation; cell–cell signaling; pheromone; transcription