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

Area of Science:

• Plant biology
• Chronobiology
• Molecular genetics

Background:

• Circadian clocks regulate 24-hour biological rhythms, entrained by the day/night cycle.
• Plant clock models traditionally focused on transcriptional control, with limited understanding of post-transcriptional and post-translational regulation.

Purpose of the Study:

• To develop a mechanistic model of the plant circadian clock incorporating post-transcriptional and post-translational regulation.
• To investigate the roles of PSEUDO-RESPONSE REGULATOR 7 (PRR7) and ZEITLUPE in the clock's feedback circuit.
• To identify novel components and mechanisms regulating morning-expressed genes.

Main Methods:

• Development of a mechanistic model integrating post-transcriptional and post-translational regulation.
• Parameter constraint using experimental data.
• Model validation against experimental data in varying environments and mutant backgrounds.
• In silico prediction of a night inhibitor (NI) function and experimental validation.

Main Results:

• A revised model including PRR7 and ZEITLUPE accurately reflects experimental data and exhibits increased robustness.
• The model predicts that morning-expressed genes are activated upon release from a night inhibitor.
• Experimental validation confirmed the NI function and identified PRR5 as a contributing gene.
• Multiple PRR genes were shown to decouple late-night events from light-driven responses.

Conclusions:

• The revised model provides a more comprehensive framework for plant circadian clock mechanisms.
• PRR gene family members play a crucial role in uncoupling distinct phases of the circadian cycle.
• This uncoupling enhances the flexibility and precision of rhythmic gene regulation in plants.