Major role for mRNA binding and restructuring in sRNA recruitment by Hfq

Toby J. Soper, Kevin Doxzen, Sarah A. Woodson

Research output: Contribution to journalArticlepeer-review

59 Scopus citations


Bacterial small RNAs (sRNAs) modulate gene expression by base-pairing with target mRNAs. Many sRNAs require the Sm-like RNA binding protein Hfq as a cofactor. Well-characterized interactions between DsrA sRNA and the rpoS mRNA leader were used to understand how Hfq stimulates sRNA pairing with target mRNAs. DsrA annealing stimulates expression of rpoS by disrupting a secondary structure in the rpoS leader, which otherwise prevents translation. Both RNAs bind Hfq with similar affinity but interact with opposite faces of the Hfq hexamer. Using mutations that block interactions between two of the three components, we demonstrate that Hfq binding to a functionally critical (AAN)4 motif in rpoS mRNA rescues DsrA binding to a hyperstable rpoS mutant. We also show that Hfq cannot stably bridge the RNAs. Persistent ternary complexes only form when the two RNAs are complementary. Thus, Hfq mainly acts by binding and restructuring the rpoS mRNA. However, Hfq binding to DsrA is needed for maximum annealing in vitro, indicating that transient interactions with both RNAs contribute to the regulatory mechanism. Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish (US)
Pages (from-to)1544-1550
Number of pages7
Issue number8
StatePublished - Aug 2011
Externally publishedYes


  • Bacterial gene regulation
  • DsrA
  • Native gel electrophoresis
  • RNA chaperone
  • RNA-protein interactions
  • rpoS

ASJC Scopus subject areas

  • Molecular Biology


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