Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq

Mol Microbiol. 2006 Aug;61(4):1013-22. doi: 10.1111/j.1365-2958.2006.05288.x. Epub 2006 Jul 12.


SgrS is an Hfq-binding small antisense RNA that is induced upon phosphosugar stress. It forms a ribonucleoprotein complex with RNase E through Hfq to mediate silencing of the target ptsG mRNA encoding the membrane component of the glucose-specific phosphoenolpyruvate phosphotransferase system. Although SgrS is believed to act on ptsG mRNA through base pairing between complementary regions, this was not previously tested experimentally. We addressed the question of whether SgrS indeed forms an RNA-RNA duplex with ptsG mRNA to exert its regulatory function. Specific single nucleotide substitutions around the Shine-Dalgarno (SD) sequence of ptsG completely eliminated SgrS action while compensatory mutations in SgrS restored it. A systematic mutational analysis of both ptsG and SgrS RNAs revealed that six base pairs around SD sequence of ptsG are particularly important for SgrS action. We also showed in vitro that SgrS forms a stable duplex with the ptsG mRNA, and that Hfq markedly facilitates the rate of duplex formation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Blotting, Northern
  • Blotting, Western
  • Electrophoretic Mobility Shift Assay
  • Escherichia coli / chemistry
  • Escherichia coli / genetics*
  • Escherichia coli / physiology
  • Escherichia coli Proteins / physiology*
  • Host Factor 1 Protein / physiology*
  • Phosphoenolpyruvate Sugar Phosphotransferase System / genetics
  • Point Mutation
  • RNA Interference
  • RNA, Antisense / genetics
  • RNA, Antisense / metabolism*
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism*
  • RNA, Double-Stranded / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*


  • Escherichia coli Proteins
  • Hfq protein, E coli
  • Host Factor 1 Protein
  • RNA, Antisense
  • RNA, Bacterial
  • RNA, Double-Stranded
  • RNA, Messenger
  • Phosphoenolpyruvate Sugar Phosphotransferase System
  • phosphoenolpyruvate-glucose phosphotransferase