Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome

Mol Microbiol. 2006 Jul;61(2):394-406. doi: 10.1111/j.1365-2958.2006.05246.x. Epub 2006 Jun 12.


In Escherichia coli the initial step in the processing or decay of many messenger and structural RNAs is mediated by the endonuclease RNase E, which forms the core of a large RNA-catalysis machine termed the degradosome. Previous experiments have identified a protein that globally modulates RNA abundance by binding to RNase E and regulating its endonucleolytic activity. Here we report the discovery of RraB, which interacts with a different site on RNase E and interferes with cleavage of a different set of transcripts. We show that expression of RraA or RraB in vivo is accompanied by dramatic, distinct, and inhibitor-specific changes in degradosome composition--and that these are in turn associated with alterations in RNA decay and global transcript abundance profiles that are dissimilar to the profile observed during simple RNase E deficiency. Our results reveal the existence of endonuclease binding proteins that modulate the remodelling of degradosome composition in bacteria and argue that such degradosome remodelling is a mechanism for the differential regulation of RNA cleavages in E. coli.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Endoribonucleases / genetics
  • Endoribonucleases / metabolism*
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Gene Expression Regulation, Bacterial
  • Multienzyme Complexes / genetics
  • Multienzyme Complexes / metabolism*
  • Polyribonucleotide Nucleotidyltransferase / genetics
  • Polyribonucleotide Nucleotidyltransferase / metabolism*
  • Protein Disulfide-Isomerases / genetics
  • Protein Disulfide-Isomerases / metabolism
  • Protein Interaction Mapping
  • Protein Structure, Tertiary
  • RNA Helicases / genetics
  • RNA Helicases / metabolism*
  • RNA Stability*
  • RNA, Messenger / metabolism*
  • Surface Plasmon Resonance


  • Escherichia coli Proteins
  • Multienzyme Complexes
  • RNA, Messenger
  • RraA protein, E coli
  • RraB protein, E coli
  • degradosome
  • Polyribonucleotide Nucleotidyltransferase
  • Endoribonucleases
  • ribonuclease E
  • RNA Helicases
  • Protein Disulfide-Isomerases