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

Pokhilko A, Hodge SK, Stratford K, Knox K, Edwards KD, Thomson AW, Mizuno T, Millar AJ - Mol. Syst. Biol. (2010)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, UK.

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.

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Related in: MedlinePlus

Mechanism of TOC1 regulation by GI. The predicted (A) and experimental (B) profiles of TOC1 expression in lhy/cca1 double and lhy/cca1/gi triple mutants. Green lines correspond to lhy/cca1 and red lines to lhy/cca1/gi. (A) TOC1 mRNA expression is shown by solid lines and the total content of ZTL protein is shown by dashed lines. (B) Bioluminescence of transgenic mutant plants carrying the TOC1:LUC reporter, in the lhy/cca1 double and lhy/cca1/gi triple mutant backgrounds (taken from our previous data (Locke et al, 2006)).
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f5: Mechanism of TOC1 regulation by GI. The predicted (A) and experimental (B) profiles of TOC1 expression in lhy/cca1 double and lhy/cca1/gi triple mutants. Green lines correspond to lhy/cca1 and red lines to lhy/cca1/gi. (A) TOC1 mRNA expression is shown by solid lines and the total content of ZTL protein is shown by dashed lines. (B) Bioluminescence of transgenic mutant plants carrying the TOC1:LUC reporter, in the lhy/cca1 double and lhy/cca1/gi triple mutant backgrounds (taken from our previous data (Locke et al, 2006)).

Mentions: To understand the influence of ZTL on the evening loop, we revisited our previous data on the kinetics of TOC1 expression in the lhy/cca1 double and lhy/cca1/gi triple mutant plants in LL conditions (Locke et al, 2006). Our simulations showed that the ZTL level would be low in lhy/cca1/gi (Figure 5A), because of the rapid degradation of ZTL in the absence of GI protein (Kim et al, 2007). The lower ZTL increased TOC1 protein levels in lhy/cca1/gi compared with lhy/cca1. Next, the negative feedback from TOC1 to Y resulted in decreased Y mRNA in lhy/cca1/gi. As Y activates TOC1 expression, this resulted in a lower level of TOC1 mRNA and reduction of oscillation amplitude in the lhy/cca1/gi mutant plants (Figure 5A and B). This prediction of the model suggested that GI stabilization of ZTL causes an unexpected, indirect activation of TOC1 expression, consistent with the 2.5-fold increase of mean TOC1:LUC expression observed in lhy/cca1 compared with lhy/cca1/gi (Locke et al, 2006). In summary, the above simulations of the wt, ztl and lhy/cca1/gi mutants showed good agreement of the updated ZTL mechanism with existing experimental data.


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

Pokhilko A, Hodge SK, Stratford K, Knox K, Edwards KD, Thomson AW, Mizuno T, Millar AJ - Mol. Syst. Biol. (2010)

Mechanism of TOC1 regulation by GI. The predicted (A) and experimental (B) profiles of TOC1 expression in lhy/cca1 double and lhy/cca1/gi triple mutants. Green lines correspond to lhy/cca1 and red lines to lhy/cca1/gi. (A) TOC1 mRNA expression is shown by solid lines and the total content of ZTL protein is shown by dashed lines. (B) Bioluminescence of transgenic mutant plants carrying the TOC1:LUC reporter, in the lhy/cca1 double and lhy/cca1/gi triple mutant backgrounds (taken from our previous data (Locke et al, 2006)).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2964123&req=5

f5: Mechanism of TOC1 regulation by GI. The predicted (A) and experimental (B) profiles of TOC1 expression in lhy/cca1 double and lhy/cca1/gi triple mutants. Green lines correspond to lhy/cca1 and red lines to lhy/cca1/gi. (A) TOC1 mRNA expression is shown by solid lines and the total content of ZTL protein is shown by dashed lines. (B) Bioluminescence of transgenic mutant plants carrying the TOC1:LUC reporter, in the lhy/cca1 double and lhy/cca1/gi triple mutant backgrounds (taken from our previous data (Locke et al, 2006)).
Mentions: To understand the influence of ZTL on the evening loop, we revisited our previous data on the kinetics of TOC1 expression in the lhy/cca1 double and lhy/cca1/gi triple mutant plants in LL conditions (Locke et al, 2006). Our simulations showed that the ZTL level would be low in lhy/cca1/gi (Figure 5A), because of the rapid degradation of ZTL in the absence of GI protein (Kim et al, 2007). The lower ZTL increased TOC1 protein levels in lhy/cca1/gi compared with lhy/cca1. Next, the negative feedback from TOC1 to Y resulted in decreased Y mRNA in lhy/cca1/gi. As Y activates TOC1 expression, this resulted in a lower level of TOC1 mRNA and reduction of oscillation amplitude in the lhy/cca1/gi mutant plants (Figure 5A and B). This prediction of the model suggested that GI stabilization of ZTL causes an unexpected, indirect activation of TOC1 expression, consistent with the 2.5-fold increase of mean TOC1:LUC expression observed in lhy/cca1 compared with lhy/cca1/gi (Locke et al, 2006). In summary, the above simulations of the wt, ztl and lhy/cca1/gi mutants showed good agreement of the updated ZTL mechanism with existing experimental data.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, UK.

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.

Show MeSH
Related in: MedlinePlus