Inositol pyrophosphates (PP-InsPs) are vital nutrient messengers that finely regulate plant phosphate homeostasis, vital for growth and development. The enzyme VIP1, member of the PPIP5K kinase family, central to this network, generates the key signaling molecule 1,5-InsP8 and also participates in its breakdown. Alongside VIP1, Plant and Fungi Atypical Dual Specificity Phosphatases (PFA-DSPs) and NUDIX hydrolases (NUDTs) contribute to PP-InsP catabolism, yet their specific roles remain unclear.

This study identifies and characterizes inositol pyrophosphate phosphatases from Arabidopsis thaliana and Marchantia polymorpha. Overexpression experiments with PFA-DSP and NUDT enzymes in Arabidopsis revealed altered PP-InsP levels and stunted growth, highlighting their importance in cellular signaling.

Investigations using nudt17/18/21 knock-out mutants in Arabidopsis unveiled nuanced regulatory mechanisms governing PP-InsP pools and gene expression patterns without apparent growth defects. In contrast, loss-of-function mutants of Marchantia, Mppfa-dsp1ge, Mpnudt1ge, and Mpvip1ge, exhibited profound growth and developmental phenotypes, emphasizing their critical roles in PP-InsP regulation.

Analysis of Mppfa-dsp1ge and Mpvip1ge mutants in Marchantia revealed their involvement in phosphate signaling, nitrate homeostasis, and cell wall architecture. The synergistic effects observed in Mppfa-dsp1ge Mpvip1Δpdge double mutants underscored the collective impact of pyrophosphate phosphatases on plant PP-InsP pools and growth.

In conclusion, this study sheds light on the regulatory roles of VIP1, PFA-DSPs, and NUDTs in modulating PP-InsP dynamics, unraveling nutrient signaling crucial for plant growth and development.