title: Insights into transcription termination of Hfq-binding sRNAs of Escherichia coli and characterization of readthrough products.
abstract: The genes encoding Hfq-dependent sRNAs possess a typical Rho-independent transcription terminator. Here, we have studied the molecular events occurring at Rho-independent terminators of sRNA genes, focusing on two well-characterized Hfq-binding sRNAs, SgrS and RyhB. We constructed several hybrid genes in which the DNA sequence corresponding to a strong Rho-independent terminator was placed just downstream from the Rho-independent terminators of sRNA genes. By using this system, we demonstrate that transcripts frequently read through the Rho-independent terminators of sgrS and ryhB in normally growing cells. We show that Hfq does not affect the transcriptional readthrough event itself. We also find that the readthrough products no longer bind to Hfq in vivo. We have developed a competition assay based on a biotin-streptavidin system to analyze the interaction of Hfq and a particular RNA molecule in vitro. By using this method, we verify that the 3'-extended form of SgrS does not bind to Hfq in vitro. Finally, we demonstrate that transcription termination is significantly enhanced under stress conditions where transcription initiation of sRNA genes on the chromosome is induced. We conclude that the production of sRNAs is regulated not only at the step of transcription initiation but also at the step of transcription termination. The mechanism by which transcription termination is enhanced under stress conditions remains to be understood.
authors.affiliation: Faculty of Pharmaceutical Sciences, Suzuka University of Medical Sciences, Suzuka, Mie 513-0816, Japan.
authors.forename: Teppei
authors.initials: T
authors.lastname: Morita
authors.affiliation: Faculty of Pharmaceutical Sciences, Suzuka University of Medical Sciences, Suzuka, Mie 513-0816, Japan.
authors.forename: Masaki
authors.initials: M
authors.lastname: Ueda
authors.affiliation: Faculty of Pharmaceutical Sciences, Suzuka University of Medical Sciences, Suzuka, Mie 513-0816, Japan.
authors.forename: Kento
authors.initials: K
authors.lastname: Kubo
authors.affiliation: Faculty of Pharmaceutical Sciences, Suzuka University of Medical Sciences, Suzuka, Mie 513-0816, Japan.
authors.forename: Hiroji
authors.initials: H
authors.lastname: Aiba
mesh_terms: D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D035001:Host Factor 1 Protein / Q000378:metabolism*; D066298:In Vitro Techniques; D012329:RNA, Bacterial / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000378:metabolism*; D012234:Rho Factor / Q000235:genetics; D061785:Transcription Initiation, Genetic; D061806:Transcription Termination, Genetic
chemical_list: D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated; D012234:Rho Factor; C526013:SgrT protein, E coli
keywords: Hfq; Rho-independent terminator; bacterial sRNA; termination and stress; transcriptional readthrough