Shared control of gene expression in bacteria by transcription factors and global physiology of the cell

Mol Syst Biol. 2013;9:634. doi: 10.1038/msb.2012.70.


Gene expression is controlled by the joint effect of (i) the global physiological state of the cell, in particular the activity of the gene expression machinery, and (ii) DNA-binding transcription factors and other specific regulators. We present a model-based approach to distinguish between these two effects using time-resolved measurements of promoter activities. We demonstrate the strength of the approach by analyzing a circuit involved in the regulation of carbon metabolism in E. coli. Our results show that the transcriptional response of the network is controlled by the physiological state of the cell and the signaling metabolite cyclic AMP (cAMP). The absence of a strong regulatory effect of transcription factors suggests that they are not the main coordinators of gene expression changes during growth transitions, but rather that they complement the effect of global physiological control mechanisms. This change of perspective has important consequences for the interpretation of transcriptome data and the design of biological networks in biotechnology and synthetic biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carbon / metabolism
  • Cyclic AMP / genetics
  • Cyclic AMP / metabolism
  • Cyclic AMP Receptor Protein / genetics
  • Cyclic AMP Receptor Protein / metabolism
  • Escherichia coli / growth & development
  • Escherichia coli / physiology*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Factor For Inversion Stimulation Protein / genetics
  • Factor For Inversion Stimulation Protein / metabolism
  • Gene Expression Regulation, Bacterial*
  • Gene Regulatory Networks
  • Models, Biological*
  • Reproducibility of Results
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism*


  • Cyclic AMP Receptor Protein
  • Escherichia coli Proteins
  • Factor For Inversion Stimulation Protein
  • Fis protein, E coli
  • Transcription Factors
  • crp protein, E coli
  • Carbon
  • Cyclic AMP