Regulatory feedback response mechanisms to phosphate starvation in rice

Ishan Ajmera,Dov J Stekel,Chungui Lu,Jing Shi,Jitender Giri,T Charlie Hodgman,Ping Wu

doi:10.1038/s41540-017-0041-0

Abstract

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.

Highlights

Ensuring a secure and sustainable food supply for the growing human population is a global priority
What causes the drop in PHO2 mRNA at early times upon Pi stress, given that corresponding levels of miR399 are quite low? Second, what causes the extreme elevation of induced by phosphate starvation 1 (IPS1) in response to Pi starvation, and its steep and sudden decline following Pi resupply? To address these questions, a new mathematical model for the regulation of phosphate uptake in plants has been developed by adopting the molecular network presented as Fig. 2a
Using the inferred Akaike Information Criterion (AIC), the values from statistical analysis indicate that the hypothesis models offer significantly better fits to the data than the original model, see Table 1

Summary

Introduction

Ensuring a secure and sustainable food supply for the growing human population is a global priority. MRNA and IPS1 levels in response to Pi starvation presented in Fig. 2; and published mRNA-SEQ data, for PHO2.20,21 Later, the base model was modified to test five competing hypotheses to explain unknown mechanisms regulating PHO2 transcription and two potential hypotheses for IPS1 dynamics (see below).

Results

Conclusion