Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage

Genes Dev. 2011 Feb 15;25(4):385-96. doi: 10.1101/gad.2001711. Epub 2011 Feb 2.


Small RNA (sRNA)-induced mRNA degradation occurs through binding of an sRNA to a target mRNA with the concomitant action of the RNA degradosome, which induces an endoribonuclease E (RNase E)-dependent cleavage and degradation of the targeted mRNA. Because many sRNAs bind at the ribosome-binding site (RBS), it is possible that the resulting translation block is sufficient to promote the rapid degradation of the targeted mRNA. Contrary to this mechanism, we report here that the pairing of the sRNA RyhB to the target mRNA sodB initiates mRNA degradation even in the absence of translation on the mRNA target. Remarkably, even though it pairs at the RBS, the sRNA RyhB induces mRNA cleavage in vivo at a distal site located >350 nucleotides (nt) downstream from the RBS, ruling out local cleavage near the pairing site. Both the RNA chaperone Hfq and the RNA degradosome are required for efficient cleavage at the distal site. Thus, beyond translation initiation block, sRNA-induced mRNA cleavage requires several unexpected steps, many of which are determined by structural features of the target mRNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Endoribonucleases / genetics
  • Endoribonucleases / metabolism
  • Endoribonucleases / physiology
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli / physiology
  • Lac Operon
  • Models, Biological
  • Multienzyme Complexes / genetics
  • Multienzyme Complexes / metabolism
  • Multienzyme Complexes / physiology
  • Organisms, Genetically Modified
  • Polyribonucleotide Nucleotidyltransferase / genetics
  • Polyribonucleotide Nucleotidyltransferase / metabolism
  • Polyribonucleotide Nucleotidyltransferase / physiology
  • Protein Biosynthesis / drug effects*
  • Protein Biosynthesis / physiology
  • Protein Synthesis Inhibitors / pharmacology
  • RNA Helicases / genetics
  • RNA Helicases / metabolism
  • RNA Helicases / physiology
  • RNA Processing, Post-Transcriptional / drug effects*
  • RNA Processing, Post-Transcriptional / genetics
  • RNA Processing, Post-Transcriptional / physiology
  • RNA Stability / drug effects*
  • RNA Stability / physiology
  • RNA, Messenger / metabolism
  • RNA, Small Interfering / pharmacology*
  • Superoxide Dismutase / genetics
  • Superoxide Dismutase / metabolism
  • Transduction, Genetic


  • Bacterial Proteins
  • Multienzyme Complexes
  • Protein Synthesis Inhibitors
  • RNA, Messenger
  • RNA, Small Interfering
  • degradosome
  • SodB protein, Bacteria
  • Superoxide Dismutase
  • Polyribonucleotide Nucleotidyltransferase
  • Endoribonucleases
  • ribonuclease E
  • RNA Helicases