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OxyS and RprA are two small noncoding RNAs (sRNAs) that modulate the expression of  rpoS,  encoding an alternative sigma factor that activates transcription of multiple  Escherichia coli  stress-response genes. While RprA activates  rpoS  for translation, OxyS down-regulates the transcript. Crucially, the RNA binding protein Hfq is required for both sRNAs to function, although the specific role played by Hfq remains unclear. We have investigated RprA and OxyS interactions with Hfq using biochemical and biophysical approaches. In particular, we have obtained the molecular envelopes of the Hfq–sRNA complexes using small-angle scattering methods, which reveal key molecular details. These data indicate that Hfq does not substantially change shape upon complex formation, whereas the sRNAs do. We link the impact of Hfq binding, and the sRNA structural changes induced, to transcript stability with respect to RNase E degradation. In light of these findings, we discuss the role of Hfq in the opposing regulatory functions played by RprA and OxyS in  rpoS  regulation.

Hfq binding changes the structure ofEscherichia colismall noncoding RNAs OxyS and RprA, which are involved in the riboregulation ofrpoS