title: Domain swapping between homologous bacterial small RNAs dissects processing and Hfq binding determinants and uncovers an aptamer for conditional RNase E cleavage.
abstract: In E. coli, small RNA GlmZ activates the glmS mRNA by base-pairing in an Hfq dependent manner. When not required, GlmZ is bound by adaptor protein RapZ and recruited to RNase E, which cleaves GlmZ in its base-pairing sequence. Small RNA GlmY counteracts cleavage of GlmZ by sequestration of RapZ. Although both sRNAs are highly homologous, only GlmZ specifically binds Hfq and undergoes cleavage by RNase E. We used domain swapping to identify the responsible modules. Two elements, the 3' terminal oligo(U) stretch and the base-pairing region enable GlmZ to interact with Hfq. Accordingly, Hfq inhibits cleavage of GlmZ, directing it to base-pairing. Intriguingly, the central stem loop of GlmZ is decisive for cleavage, whereas the sequence comprising the actual cleavage site is dispensable. Assisted by RapZ, RNase E cleaves any RNA fused to the 3' end of this module. These results suggest a novel mode for RNase E recognition, in which one of the required handholds in the substrate is replaced by an RNA binding protein. This device can generate RNAs of interest in their 5' monophosphorylated form on demand. As these species are rapidly degraded, this tool allows to regulate gene expression post-transcriptionally by modulation of RapZ levels.
authors.affiliation: Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Göpel
authors.affiliation: Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria.
authors.forename: Muna Ayesha
authors.initials: MA
authors.lastname: Khan
authors.affiliation: Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria boris.goerke@univie.ac.at.
authors.forename: Boris
authors.initials: B
authors.lastname: Görke
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020029:Base Pairing; D001665:Binding Sites; D004722:Endoribonucleases / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D035001:Host Factor 1 Protein / Q000235:genetics / Q000378:metabolism*; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D012329:RNA, Bacterial; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D016601:RNA-Binding Proteins; C524677:YhbJ protein, E coli; D004722:Endoribonucleases; C022537:ribonuclease E