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

The circadian clock orchestrates biological processes so that they occur at specific times of the day, thereby facilitating adaptation to diurnal and seasonal environmental changes. In plants, mathematical modelling has been comprehensively integrated with experimental studies to gain a better mechanistic understanding of the complex genetic regulatory network comprising the clock. However, with an increasing number of circadian genes being discovered, there is a pressing need for methods facilitating the expansion of computational models to incorporate these newly-discovered components. Conventionally, plant clock models have comprised differential equation systems based on Michaelis-Menten kinetics. However, the difficulties associated with modifying interactions using this approach—and the concomitant problem of robustly identifying regulation types—has contributed to a complexity bottleneck, with quantitative fits to experimental data rapidly becoming computationally intractable for models possessing more than ≈50 parameters. Here, we address these issues by constructing the first plant clock models based on the S-System formalism originally developed by Savageau for analysing biochemical networks. We show that despite its relative simplicity, this approach yields clock models with comparable accuracy to the conventional Michaelis-Menten formalism. The S-System formulation also confers several key advantages in terms of model construction and expansion. In particular, it simplifies the inclusion of new interactions, whilst also facilitating the modification of regulation types, thereby making it well-suited to network inference. Furthermore, S-System models mitigate the issue of parameter identifiability. Finally, by applying linear systems theory to the models considered, we provide some justification for the increased use of aggregated protein equations in recent plant clock modelling, replacing the separate cytoplasmic/nuclear protein compartments that were characteristic of the earlier models. We conclude that as well as providing a simplified framework for model development, the S-System formalism also possesses significant potential as a robust modelling method for designing synthetic gene circuits.Author summary: 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.