Mathematical Modelling Plant Signalling Networks

Abstract

Abstract. During the last two decades, molecular genetic studies and the completion of the sequencing of the Arabidopsis thaliana genome have increased knowledge of hormonal regulation in plants. These signal transduction pathways act in concert through gene regulatory and signalling networks whose main components have begun to be elucidated. Our understanding of the resulting cellular processes is hindered by the complex, and sometimes counter-intuitive, dynamics of the networks, which may be interconnected through feedback controls and crossregulation. Mathematical modelling provides a valuable tool to investigate such dynamics and to perform in silico experiments that may not be easily carried out in a laboratory. In this article, we firstly review general methods for modelling gene and signalling networks and their application in plants. We then describe specific models of hormonal perception and cross-talk in plants. This sub-cellular analysis paves the way for more comprehensive mathematical studies of hormonal transport and signalling in a multi-scale setting.

The Regulatory Role of Key Metabolites in the Control of Cell Signaling

“…These observations suggest that the SnRK1 complex is constitutively active, while it is repressed under energy abundance conditions. This sort of control is the reverse of those of SNF1 and AMPK complexes, but is coherent with the general feature of plant cell signaling to prefer negative regulations rather than activations [87].…”

SnRK1 activation, signaling, and networking for energy homeostasis

“…Interestingly, plants seem to more generally prefer negative regulation, as illustrated by the many hormone signalling pathways that make use of (often ubiquitination and proteasome-mediated) inactivation and removal of repressor proteins. This apparently enables faster downstream responses [18], but more extensive (mathematical) modeling and experimentation may confirm additional benefits of such systems for plants.…”

Default Activation and Nuclear Translocation of the Plant Cellular Energy Sensor SnRK1 Regulate Metabolic Stress Responses and Development

“…SnRK1 controls energy homeostasis and thereby plant growth and development as well as biotic and abiotic stress tolerance (Tsai and Gazzarrini, 2014;Broeckx et al, 2016;Hulsmans et al, 2016;Baena-González and Hanson, 2017;Wurzinger et al, 2018). Plants in general seem to prefer negative regulatory mechanisms, with many (notably hormone signaling) pathways that involve inactivation (and degradation) of repressor proteins, likely enabling more robust, reliable, and flexible signal integration and possibly also faster downstream responses (Muraro et al, 2013). Consistent with inactivation under energy-rich conditions and the release of inhibition (rather than direct activation) by energy depletion, sugar phosphates such as Glc-6-P and trehalose-6-P (T6P) were found to inhibit the plant SnRK1 kinase (Toroser et al, 2000;Zhang et al, 2009;Nunes et al, 2013).…”