PXD056943

PXD056943 is an original dataset announced via ProteomeXchange.

Title	NUDIX Hydrolases Target Specific Inositol Pyrophosphates and Regulate Phosphate ,and Iron Homeostasis, and the Expression of Defense Genes in Arabidopsis
Description	Inositol pyrophosphates (PP-InsPs) are important signaling molecules that regulate diverse cellular processes in eukaryotes, including energy homeostasis and phosphate (Pi) signaling. However, the enzymes responsible for their turnover in plants remain largely unknown. Using a non-hydrolysable PP-InsP analog in a pull-down approach, we identified a family of Arabidopsis Nudix hydrolases (NUDTs) that group into two closely related subclades. Through in vitro assays, heterologous expression systems, and higher-order gene-edited mutants, we explored the substrate specificities and physiological roles of these hydrolases. Using a combination of strong anion exchange (SAX)-HPLC, PAGE, and capillary electrophoresis electrospray ionization mass spectrometry (CE-ESI-MS), we found that their PP-InsP pyrophosphatase activity is enantiomer-selective and Mg2+-dependent. Specifically, subclade I NUDTs preferentially hydrolyze 4-InsP7, while subclade II NUDTs target 3-InsP7, with minor activity against other PP-InsPs, including 5-InsP7. In higher-order mutants of subclade II NUDTs, we observed defects in both Pi and iron homeostasis, accompanied by increased levels of 1/3-InsP7 and 5-InsP7, with a markedly larger increase in 1/3-InsP7. Furthermore, ectopic expression of NUDTs from both subclades induced local Pi starvation responses (PSRs). However, RNA-seq analysis of WT and nudt12/13/16 plants suggests that these NUDTs have PSR-independent roles, potentially involving 1/3-InsP7 in the regulation of plant defense. Expanding beyond subclade II NUDTs, we demonstrated susceptibility of the 3PP-position of PP-InsPs to enzymatic activities unrelated to NUDTs, and found that such activities are conserved across plants and humans. Additionally, we found that NUDT effectors from pathogenic ascomycete fungi exhibit a substrate specificity similar to subclade I NUDTs. Collectively, our study provides new insights into the roles of NUDTs in regulating PP-InsP signaling pathways in plants and highlights cross-kingdom conservation of enzymes involved in PP-InsP metabolism.
HostingRepository	PRIDE
AnnounceDate	2025-12-09
AnnouncementXML	Submission_2025-12-09_01:50:41.469.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sara Christina Stolze
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: NEWT:3702;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-18 06:00:45	ID requested
⏵ 1	2025-12-09 01:50:42	announced

10.1111/JIPB.70060;

submitter keyword: Nudix hydrolases (NUDTs),Inositol pyrophosphates (PP-InsPs)

Hirofumi Nakagami
contact affiliation	Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany
contact email	nakagami@mpipz.mpg.de
lab head
Sara Christina Stolze
contact affiliation	Plant Proteomics and Mass Spectrometry Group Max Planck Institute for Plant Breeding Research Carl-von-Linné Weg 10 50829 Cologne
contact email	stolze@mpipz.mpg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/12/PXD056943

PRIDE project URI

• PRIDE
  1. PXD056943
     1. Label: PRIDE project
     2. Name: NUDIX Hydrolases Target Specific Inositol Pyrophosphates and Regulate Phosphate ,and Iron Homeostasis, and the Expression of Defense Genes in Arabidopsis