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Date publication
février 2025
Journal
Molecular systems biology
Auteurs
Membres identifiés du Cancéropôle Est :
Dr MOLINA Nacho
Tous les auteurs :
Urquiza-García U, Molina N, Halliday KJ, Millar AJ
Lien Pubmed
Résumé
Understanding the biochemistry behind whole-organism traits such as flowering time is a longstanding challenge, where mathematical models are critical. Very few models of plant gene circuits use the absolute units required for comparison to biochemical data. We refactor two detailed models of the plant circadian clock from relative to absolute units. Using absolute RNA quantification, a simple model predicted abundant clock protein levels in Arabidopsis thaliana, up to 100,000 proteins per cell. NanoLUC reporter protein fusions validated the predicted levels of clock proteins in vivo. Recalibrating the detailed models to these protein levels estimated their DNA-binding dissociation constants (K). We estimate the same K from multiple results in vitro, extending the method to any promoter sequence. The detailed models simulated the K range estimated from LUX DNA-binding in vitro but departed from the data for CCA1 binding, pointing to further circadian mechanisms. Our analytical and experimental methods should transfer to understand other plant gene regulatory networks, potentially including the natural sequence variation that contributes to evolutionary adaptation.
Mots clés
Biological Clocks, Circadian Rhythms, Gene Regulatory Networks, Mathematical Modelling, Plant Biology
Référence
Mol Syst Biol. 2025 02 20;:
