A simplified modelling framework facilitates more complex representations of plant circadian clocks

摘要

Mathematical models have been widely employed as a complement to experimental work in elucidating the underlying mechanistic behaviour of the plant circadian clock. In this study, we investigate the use of a simplified modelling strategy, the S-System framework, to reduce the computational complexity of such models. We test the efficacy of our approach by constructing S-System versions of five established plant clock models, which we fit to synthetic and experimental gene expression data. We demonstrate that the S-System formulation can generate fits to expression data that are very similar to those of its more complex counterparts, yielding predictions with better accuracy in some cases. Our work reveals three principal benefits of the S-System formalism in modelling gene regulatory networks (GRNs) characterised by entrainable oscillations, typified by the circadian clock. Firstly, it enables new interactions to be incorporated in a very easy manner. Secondly, it facilitates the inference of unknown regulation types. Thirdly, it mitigates the parameter identifiability problem, thereby making it a suitable modelling method for designing GRN control circuits for synthetic biology applications. Taken together, our findings identify the S-System framework as a promising alternative approach for computational modelling of oscillatory GRN networks.