A general mathematical framework for modelling subnetworks of the nuclear auxin pathway

Auxins, a group of plant hormones, play a crucial role in the functioning of various plant tissues and species. The Nuclear Auxin Pathway (NAP) is a network involving transcription factors (ARFs) and repressors (Aux/IAAs), which govern the response of individual cells to alterations in auxin concentration. This pathway is ubiquitous in land plants, with many species possessing multiple copies of each signaling component.

In this study, we introduce a general mathematical framework for modeling subnetworks of the NAP using ordinary differential equations (ODEs). This model is adaptable to any combination of transcriptional regulators, enabling the simulation of the promotion and repression of target genes. Through the application of this framework to published data, we observed that auxin treatment in Arabidopsis thaliana roots leads to distinct temporal response profiles for both target genes and the signaling components themselves.

To demonstrate the effectiveness of our modeling framework, we present examples of real and theoretical NAP subnetworks. By analyzing these networks and the effect of their dynamics on auxin-mediated transcriptional responses, we showcase the utility of our framework as a general-purpose tool for understanding the function of protein-protein and protein-DNA interactions within the NAP.

This research not only highlights the complexity of signalling pathways but also opens up new avenues for advancing our understanding of the NAP.