title: Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition.
abstract: Many bacteria use small RNAs (sRNAs) and the RNA chaperone Hfq to regulate mRNA stability and translation. Hfq, a ring-shaped homohexamer, has multiple faces that can bind both sRNAs and their mRNA targets. We find that Hfq has at least two distinct ways in which it interacts with sRNAs; these different binding properties have strong effects on the stability of the sRNA in vivo and the sequence requirements of regulated mRNAs. Class I sRNAs depend on proximal and rim Hfq sites for stability and turn over rapidly. Class II sRNAs are more stable and depend on the proximal and distal Hfq sites for stabilization. Using deletions and chimeras, we find that while Class I sRNAs regulate mRNA targets with previously defined ARN repeats, Class II sRNAs regulate mRNAs carrying UA-rich rim-binding sites. We discuss how these different binding modes may correlate with different roles in the cell, with Class I sRNAs acting as emergency responders and Class II sRNAs acting as silencers.
authors.affiliation: Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Schu
authors.affiliation: Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA.
authors.forename: Aixia
authors.initials: A
authors.lastname: Zhang
authors.affiliation: Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, USA gottesms@helix.nih.gov storzg@mail.nih.gov.
authors.forename: Susan
authors.initials: S
authors.lastname: Gottesman
authors.affiliation: Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA gottesms@helix.nih.gov storzg@mail.nih.gov.
authors.forename: Gisela
authors.initials: G
authors.lastname: Storz
mesh_terms: D020029:Base Pairing; D015152:Blotting, Northern; D017931:DNA Primers / Q000235:genetics; D048168:Escherichia coli K12 / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism*; D035001:Host Factor 1 Protein / Q000378:metabolism*; D008958:Models, Molecular; D010957:Plasmids / Q000235:genetics; D011485:Protein Binding; D012333:RNA, Messenger / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000378:metabolism*; D001616:beta-Galactosidase
chemical_list: D017931:DNA Primers; D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D001616:beta-Galactosidase
keywords: ChiX; Hfq; MgrR; RyhB