Absolutely delighted to see our most recent paper published in npj Systems Biology and Applications today. This paper involves the full MyCIB team (Charlie Hodgman, Chungui Lu and myself), with work carried out by Ishan Ajmera. Ishan joined us as an MSc student on the (now closed) MSc in Integrative Systems Biology, was one of our star students, stayed for PhD, and is now a post-doc in the school. This work is from his PhD, and is a beautiful example of how experiment and modelling can be used together to provide new understanding and testable hypotheses. Citation and Abstract:
Ajmera I, Shi J, Giri J, Wu P, Stekel DJ, Lu C and Hodgman TC 2018. Regulatory feedback response mechanisms to phosphate starvation in rice. npj Systems Biology and Applications 4:4. doi:10.1038/s41540-017-0041-0.
Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding of the molecular mechanisms underlying phosphate uptake by investigating the transcriptional dynamics of two regulators: the Ubiquitin ligase PHO2 and the long non-coding RNA IPS1. Temporal measurements of RNA levels have been integrated into mechanistic mathematical models using advanced statistical techniques. Models based solely on current knowledge could not adequately explain the temporal expression profiles. Further modeling and bioinformatics analysis have led to the prediction of three regulatory features: the PHO2 protein mediates the degradation of its own transcriptional activator to maintain constant PHO2 mRNA levels; the binding affinity of the transcriptional activator of PHO2 is impaired by a phosphate-sensitive transcriptional repressor/inhibitor; and the extremely high levels of IPS1 and its rapid disappearance upon Pi re-supply are best explained by Pi-sensitive RNA protection. This work offers both new opportunities for plant phosphate research that will be essential for informing the development of phosphate efficient crop varieties, and a foundation for the development of models integrating phosphate with other stress responses.