PXD054002-1

PXD054002 is an original dataset announced via ProteomeXchange.

Title	A Nitrogen-specific Interactome Analysis Sheds Light on the Role of the SnRK1 and TOR Kinases in Plant Nitrogen Signaling - part2 kinase assay
Description	Nitrogen (N) is of utmost importance for plant growth and development. Multiple studies have shown that N signaling is tightly coupled with carbon (C) levels, but the interplay between C/N metabolism and growth remains largely an enigma. Nonetheless, the protein kinases sucrose non-fermenting 1 (SNF1)-related kinase 1 (SnRK1) and target of rapamycin (TOR), two ancient central metabolic regulators, are emerging as key integrators that link C/N status with growth. Despite their pivotal importance, the exact mechanisms behind the sensing of N status and its integration with C availability to drive metabolic decisions are largely unknown. Especially for SnRK1 it is not clear how this kinase responds to altered N levels. Therefore, we first monitored N-dependent SnRK1 kinase activity at high resolution with our in vivo separation of phase-based activity reporter of kinase (SPARK), revealing a contrasting N-dependency in shoot and root tissues. Next, using affinity purification (AP) and proximity labeling (PL) coupled to mass spectrometry (MS) experiments, we constructed an N-specific SnRK1 and TOR interactome in Arabidopsis thaliana cell cultures during N-starved and  repleted growth conditions. To broaden our understanding of the N-dependency of the TOR/SnRK1 signaling pathway, the resulting network was compared to corresponding C-related networks, identifying a large number of novel, N-specific interactors. Moreover, through integration of N dependent transcriptome and phosphoproteome data, we were able to pinpoint additional N dependent network components, revealing SnRK1 regulatory proteins that might function at the crosstalk of C/N signaling. Finally, confirmation of known and identification of novel interactors, such as IRE1A and RAB18, indicate that the endoplasmic reticulum functions as a key regulatory hub for TOR and SnRK1 via integration of C/N signaling. Part2, kinase assay on RAB18, PANK2, SEC12 and NLP8.
HostingRepository	PRIDE
AnnounceDate	2024-11-12
AnnouncementXML	Submission_2024-11-12_03:40:52.286.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD054002
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jelle Van Leene
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-17 03:16:22	ID requested
⏵ 1	2024-11-12 03:40:52	announced

10.1016/J.MCPRO.2024.100842;

10.6019/PXD054002;

submitter keyword: AP-MS,Arabidopsis, TOR complex, proximity labeling, SnRK1 complex, Nitrogen signaling

Geert De
contact affiliation	Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
contact email	geert.dejaeger@psb.vib-ugent.be
lab head
Jelle Van Leene
contact affiliation	VIB-UGHENT
contact email	jelee@psb.vib-ugent.be
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD054002
     1. Label: PRIDE project
     2. Name: A Nitrogen-specific Interactome Analysis Sheds Light on the Role of the SnRK1 and TOR Kinases in Plant Nitrogen Signaling - part2 kinase assay