title: Distinct and overlapping binding sites of Pseudomonas aeruginosa Hfq and RsmA proteins on the non-coding RNA RsmY.
abstract: In Pseudomonas aeruginosa the Rsm system is involved in regulation of quorum-sensing and virulence gene expression. Our recent studies revealed that the stability and abundance of the non-coding RNA RsmY, which antagonizes the translational regulator RsmA, is dependent on Hfq. Here, we show that Hfq and RsmA bind concurrently to RsmY. Enzymatic probing of RsmY RNA in the presence of RsmA and Hfq verified the proposed -GGA- motifs as RsmA binding sites and located Hfq binding sites in single-stranded regions adjacent to stem-loop structures, respectively. We conclude that distinct binding of Hfq and RsmA on RsmY RNA permits RsmY-mediated RsmA titration upon binding to and stabilization of RsmY RNA by Hfq. In addition, we provide evidence that Hfq sequesters RNase E cleavage sites on RsmY, which explains the previously observed dependence of RsmY RNA stability on Hfq.
authors.affiliation: Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University of Vienna, Campus Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria.
authors.forename: Theresa
authors.initials: T
authors.lastname: Sorger-Domenigg
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Sonnleitner
authors.forename: Vladimir R
authors.initials: VR
authors.lastname: Kaberdin
authors.forename: Udo
authors.initials: U
authors.lastname: Bläsi
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D001665:Binding Sites; D029968:Escherichia coli Proteins / Q000235:genetics*; D035001:Host Factor 1 Protein / Q000235:genetics*; D011550:Pseudomonas aeruginosa / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012097:Repressor Proteins / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D022661:RNA, Untranslated; D016601:RNA-Binding Proteins; D012097:Repressor Proteins; C095468:RsmA protein, Erwinia carotovora