Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model

Alexandra Pokhilko, Sarah K. Hodge, Kevin Stratford, Kirsten Knox, Kieron D. Edwards, Adrian W. Thomson, Takeshi Mizuno, Andrew J. Millar

Research output: Contribution to journalArticle

101 Citations (Scopus)

Abstract

Circadian clocks generate 24-h rhythms that are entrained by the day/night cycle. Clock circuits include several light inputs and interlocked feedback loops, with complex dynamics. Multiple biological components can contribute to each part of the circuit in higher organisms. Mechanistic models with morning, evening and central feedback loops have provided a heuristic framework for the clock in plants, but were based on transcriptional control. Here, we model observed, post-transcriptional and post-translational regulation and constrain many parameter values based on experimental data. The model's feedback circuit is revised and now includes PSEUDO-RESPONSE REGULATOR 7 (PRR7) and ZEITLUPE. The revised model matches data in varying environments and mutants, and gains robustness to parameter variation. Our results suggest that the activation of important morning-expressed genes follows their release from a night inhibitor (NI). Experiments inspired by the new model support the predicted NI function and show that the PRR5 gene contributes to the NI. The multiple PRR genes of Arabidopsis uncouple events in the late night from light-driven responses in the day, increasing the flexibility of rhythmic regulation. Molecular Systems Biology 6: 416; published online 21 September 2010; doi:10.1038/msb.2010.69

Original languageEnglish
Article number416
Number of pages10
JournalMolecular Systems Biology
Volume6
DOIs
Publication statusPublished - Sep 2010

Keywords

  • Arabidopsis thaliana
  • biological clocks
  • circadian rhythms
  • mathematical model
  • systems biology
  • pseudo-response regulators
  • arabidopsis-thaliana
  • targeted degradation
  • blue-light
  • rhythms
  • gigantea
  • gene
  • oscillator
  • roles
  • PRR7

Cite this

Pokhilko, A., Hodge, S. K., Stratford, K., Knox, K., Edwards, K. D., Thomson, A. W., ... Millar, A. J. (2010). Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model. Molecular Systems Biology, 6, [416]. https://doi.org/10.1038/msb.2010.69

Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model. / Pokhilko, Alexandra; Hodge, Sarah K.; Stratford, Kevin; Knox, Kirsten; Edwards, Kieron D.; Thomson, Adrian W.; Mizuno, Takeshi; Millar, Andrew J.

In: Molecular Systems Biology, Vol. 6, 416, 09.2010.

Research output: Contribution to journalArticle

Pokhilko, A, Hodge, SK, Stratford, K, Knox, K, Edwards, KD, Thomson, AW, Mizuno, T & Millar, AJ 2010, 'Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model' Molecular Systems Biology, vol. 6, 416. https://doi.org/10.1038/msb.2010.69
Pokhilko, Alexandra ; Hodge, Sarah K. ; Stratford, Kevin ; Knox, Kirsten ; Edwards, Kieron D. ; Thomson, Adrian W. ; Mizuno, Takeshi ; Millar, Andrew J. / Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model. In: Molecular Systems Biology. 2010 ; Vol. 6.
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