Abundant clock proteins point to missing molecular regulation in the plant circadian clock
Abstract 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...
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| Language: | English |
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Springer Nature
2025-02-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.1038/s44320-025-00086-5 |
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| author | Uriel Urquiza-García Nacho Molina Karen J Halliday Andrew J Millar |
| author_facet | Uriel Urquiza-García Nacho Molina Karen J Halliday Andrew J Millar |
| author_sort | Uriel Urquiza-García |
| collection | DOAJ |
| description | Abstract 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 d ). We estimate the same K d from multiple results in vitro, extending the method to any promoter sequence. The detailed models simulated the K d 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. |
| format | Article |
| id | doaj-art-4b449909b89c4bd19d10c79fd5a99698 |
| institution | DOAJ |
| issn | 1744-4292 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-4b449909b89c4bd19d10c79fd5a996982025-08-20T03:03:20ZengSpringer NatureMolecular Systems Biology1744-42922025-02-0121436138910.1038/s44320-025-00086-5Abundant clock proteins point to missing molecular regulation in the plant circadian clockUriel Urquiza-García0Nacho Molina1Karen J Halliday2Andrew J Millar3Centre for Engineering Biology and School of Biological Sciences, C. H. Waddington Building, University of EdinburghCentre for Engineering Biology and School of Biological Sciences, C. H. Waddington Building, University of EdinburghSchool of Biological Sciences, Daniel Rutherford Building, University of EdinburghCentre for Engineering Biology and School of Biological Sciences, C. H. Waddington Building, University of EdinburghAbstract 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 d ). We estimate the same K d from multiple results in vitro, extending the method to any promoter sequence. The detailed models simulated the K d 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.https://doi.org/10.1038/s44320-025-00086-5Gene Regulatory NetworksBiological ClocksCircadian RhythmsMathematical ModellingPlant Biology |
| spellingShingle | Uriel Urquiza-García Nacho Molina Karen J Halliday Andrew J Millar Abundant clock proteins point to missing molecular regulation in the plant circadian clock Molecular Systems Biology Gene Regulatory Networks Biological Clocks Circadian Rhythms Mathematical Modelling Plant Biology |
| title | Abundant clock proteins point to missing molecular regulation in the plant circadian clock |
| title_full | Abundant clock proteins point to missing molecular regulation in the plant circadian clock |
| title_fullStr | Abundant clock proteins point to missing molecular regulation in the plant circadian clock |
| title_full_unstemmed | Abundant clock proteins point to missing molecular regulation in the plant circadian clock |
| title_short | Abundant clock proteins point to missing molecular regulation in the plant circadian clock |
| title_sort | abundant clock proteins point to missing molecular regulation in the plant circadian clock |
| topic | Gene Regulatory Networks Biological Clocks Circadian Rhythms Mathematical Modelling Plant Biology |
| url | https://doi.org/10.1038/s44320-025-00086-5 |
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