Mechanism of phosphate sensing and signaling revealed by rice SPX1-PHR2 complex structure

Jia Zhou,Jian-Kang Zhu,Fangang Meng,Renyang Liu,Xinlong Xiao,Deqiang Yao,Qinli Hu,Shenghong Ge,Jin Ye,Mingguang Lei,Rujie Cai,Haojie Li,Weiman Xing,Chao Wang

doi:10.1038/s41467-021-27391-5

Abstract

Phosphate, a key plant nutrient, is perceived through inositol polyphosphates (InsPs) by SPX domain-containing proteins. SPX1 an inhibit the PHR2 transcription factor to maintain Pi homeostasis. How SPX1 recognizes an InsP molecule and represses transcription activation by PHR2 remains unclear. Here we show that, upon binding InsP6, SPX1 can disrupt PHR2 dimers and form a 1:1 SPX1-PHR2 complex. The complex structure reveals that SPX1 helix α1 can impose a steric hindrance when interacting with the PHR2 dimer. By stabilizing helix α1, InsP6 allosterically decouples the PHR2 dimer and stabilizes the SPX1-PHR2 interaction. In doing so, InsP6 further allows SPX1 to engage with the PHR2 MYB domain and sterically block its interaction with DNA. Taken together, our results suggest that, upon sensing the surrogate signals of phosphate, SPX1 inhibits PHR2 via a dual mechanism that attenuates dimerization and DNA binding activities of PHR2.

Highlights

Phosphate, a key plant nutrient, is perceived through inositol polyphosphates (InsPs) by SPX domain-containing proteins
The PHR transcription factors are the central regulators of Pi signaling, which bind to the PHR1-binding sequence (P1BS) in the promoter regions of phosphate starvation-induced (PSI) genes[10]
SPX1 and PHR2 formed a complex with a 1:1 stoichiometry in the presence of InsP6 and the PHR2 dimer was disrupted during the complex formation

Summary

Introduction

A key plant nutrient, is perceived through inositol polyphosphates (InsPs) by SPX domain-containing proteins. Previous studies indicated that rice SPX1 interacts with PHR2 in a Pidependent manner and acts as an inhibitor to repress PHR2 transcription activation under Pi-replete conditions[17] These findings implied the important roles of SPX domain-containing proteins in sensing Pi. Recent structural analysis of the SPX-domain, in conjunction with in vivo studies, has provided compelling evidence supporting the functions of the SPX domain as Pi sensors. SPX domains do not appear to sense inorganic Pi directly, but instead recognize soluble inositol polyphosphates (InsPs), such as InsP7 or InsP8, which act as a proxy for the cellular Pi status[18,19] Such a mechanism has recently been unveiled by the crystal structures of SPX domains in complex with InsP6, a commercially available substitute of InsP7 and InsP818,20–22. Our structure unravels a unique dual mechanism by which SPX1 mediates Pi sensing and signaling

Methods

Results

Conclusion