Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells

BMC Syst Biol. 2013 Dec 12;7:138. doi: 10.1186/1752-0509-7-138.


Background: Carbon catabolite repression (CCR) is critical for optimal bacterial growth, and in bacterial (and yeast) cells it leads to their selective consumption of a single substrate from a complex environment. However, the root cause(s) for the development of this regulatory mechanism is unknown. Previously, a flux balance model (FBAwMC) of Escherichia coli metabolism that takes into account the crowded intracellular milieu of the bacterial cell correctly predicted selective glucose uptake in a medium containing five different carbon sources, suggesting that CCR may be an adaptive mechanism that ensures optimal bacterial metabolic network activity for growth.

Results: Here, we show that slowly growing E. coli cells do not display CCR in a mixed substrate culture and gradual activation of CCR correlates with an increasing rate of E. coli cell growth and proliferation. In contrast, CCR mutant cells do not achieve fast growth in mixed substrate culture, and display differences in their cell volume and density compared to wild-type cells. Analyses of transcriptome data from wt E. coli cells indicate the expected regulation of substrate uptake and metabolic pathway utilization upon growth rate change. We also find that forced transient increase of intracellular crowding or transient perturbation of CCR delay cell growth, the latter leading to associated cell density-and volume alterations.

Conclusions: CCR is activated at an increased bacterial cell growth rate when it is required for optimal cell growth while intracellular macromolecular density is maintained within a narrow physiological range. In addition to CCR, there are likely to be other regulatory mechanisms of cell metabolism that have evolved to ensure optimal cell growth in the context of the fundamental biophysical constraint imposed by intracellular molecular crowding.

Publication types

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

MeSH terms

  • Biological Transport
  • Biomass
  • Carbon / metabolism*
  • Cell Count
  • Cell Culture Techniques
  • Cell Proliferation
  • Escherichia coli / cytology*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Gene Expression Profiling
  • Models, Biological
  • Systems Biology*


  • Carbon