Revealing a two-loop transcriptional feedback mechanism in the cyanobacterial circadian clock

PLoS Comput Biol. 2013;9(3):e1002966. doi: 10.1371/journal.pcbi.1002966. Epub 2013 Mar 14.


Molecular genetic studies in the circadian model organism Synechococcus have revealed that the KaiC protein, the central component of the circadian clock in cyanobacteria, is involved in activation and repression of its own gene transcription. During 24 hours, KaiC hexamers run through different phospho-states during daytime. So far, it has remained unclear which phospho-state of KaiC promotes kaiBC expression and which opposes transcriptional activation. We systematically analyzed various combinations of positive and negative transcriptional feedback regulation by introducing a combined TTFL/PTO model consisting of our previous post-translational oscillator that considers all four phospho-states of KaiC and a transcriptional/translational feedback loop. Only a particular two-loop feedback mechanism out of 32 we have extensively tested is able to reproduce existing experimental observations, including the effects of knockout or overexpression of kai genes. Here, threonine and double phosphorylated KaiC hexamers activate and unphosphorylated KaiC hexamers suppress kaiBC transcription. Our model simulations suggest that the peak expression ratio of the positive and the negative component of kaiBC expression is the main factor for how the different two-loop feedback models respond to removal or to overexpression of kai genes. We discuss parallels between our proposed TTFL/PTO model and two-loop feedback structures found in the mammalian clock.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism*
  • Circadian Clocks / genetics
  • Circadian Clocks / physiology*
  • Circadian Rhythm Signaling Peptides and Proteins / genetics*
  • Circadian Rhythm Signaling Peptides and Proteins / metabolism*
  • Computational Biology
  • Computer Simulation
  • Cyanobacteria / genetics*
  • Cyanobacteria / metabolism*
  • Feedback, Physiological
  • Gene Expression Regulation, Bacterial
  • Models, Biological
  • Mutation
  • Phosphorylation
  • Transcription, Genetic


  • Bacterial Proteins
  • Circadian Rhythm Signaling Peptides and Proteins

Grant support

This work was financially supported through the German Ministry of Education and Research (BMBF), FORSYS partner program (grant number 0315294), the European Commission, FP7-ICT-2009-4, BACTOCOM, project number 248919, and Deutsche Forschungsgemeinschaft (DFG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.