C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA.
The bacterial Sm protein and RNA chaperone Hfq stabilizes small noncoding RNAs (sRNAs) and facilitates their annealing to mRNA targets involved in stress tolerance and virulence. Although an arginine patch on the Sm core is needed for Hfq's RNA chaperone activity, the function of Hfq's intrinsically disordered C-terminal domain (CTD) has remained unclear. Here, we use stopped flow spectroscopy to show that the CTD of Escherichia coli Hfq is not needed to accelerate RNA base pairing but is required for the release of dsRNA. The Hfq CTD also mediates competition between sRNAs, offering a kinetic advantage to sRNAs that contact both the proximal and distal faces of the Hfq hexamer. The change in sRNA hierarchy caused by deletion of the Hfq CTD in E. coli alters the sRNA accumulation and the kinetics of sRNA regulation in vivo. We propose that the Hfq CTD displaces sRNAs and annealed sRNA⋅mRNA complexes from the Sm core, enabling Hfq to chaperone sRNA-mRNA interactions and rapidly cycle between competing targets in the cell.
Cell, Molecular, Developmental Biology, and Biophysics Program, Johns Hopkins University, Baltimore, MD 21218.
Andrew
A
Santiago-Frangos
Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892.
Kumari
K
Kavita
Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892.
Daniel J
DJ
Schu
Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892; gottesms@helix.nih.gov swoodson@jhu.edu.
Susan
S
Gottesman
Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 gottesms@helix.nih.gov swoodson@jhu.edu.
Sarah A
0000-0003-0170-1987
SA
Woodson
D020029:Base Pairing; D035001:Host Factor 1 Protein / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins
D035001:Host Factor 1 Protein; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D016601:RNA-Binding Proteins; D011994:Recombinant Proteins
ChiX; RNA chaperone; intrinsically disordered protein; posttranscriptional regulation; small noncoding RNA
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