Effects of post-transcriptional regulation on phenotypic noise in Escherichia coli

Nucleic Acids Res. 2013 May;41(9):4825-34. doi: 10.1093/nar/gkt184. Epub 2013 Mar 21.


Cell-to-cell variations in protein abundance, called noise, give rise to phenotypic variability between isogenic cells. Studies of noise have focused on stochasticity introduced at transcription, yet the effects of post-transcriptional regulatory processes on noise remain unknown. We study the effects of RyhB, a small-RNA of Escherichia coli produced on iron stress, on the phenotypic variability of two of its downregulated target proteins, using dual chromosomal fusions to fluorescent reporters and measurements in live individual cells. The total noise of each of the target proteins is remarkably constant over a wide range of RyhB production rates despite cells being in stress. In fact, coordinate downregulation of the two target proteins by RyhB reduces the correlation between their levels. Hence, an increase in phenotypic variability under stress is achieved by decoupling the expression of different target proteins in the same cell, rather than by an increase in the total noise of each. Extrinsic noise provides the dominant contribution to the total protein noise over the total range of RyhB production rates. Stochastic simulations reproduce qualitatively key features of our observations and show that a feed-forward loop formed by transcriptional extrinsic noise, an sRNA and its target genes exhibits strong noise filtration capabilities.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / biosynthesis
  • Bacterial Proteins / genetics
  • Down-Regulation
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / biosynthesis
  • Escherichia coli Proteins / genetics*
  • Gene Expression Regulation, Bacterial*
  • Iron / metabolism
  • Phenotype*
  • RNA, Small Untranslated / metabolism
  • Superoxide Dismutase / biosynthesis
  • Superoxide Dismutase / genetics
  • Transcription, Genetic


  • Bacterial Proteins
  • Escherichia coli Proteins
  • RNA, Small Untranslated
  • Iron
  • SodB protein, Bacteria
  • Superoxide Dismutase