PXD008355

PXD008355 is an original dataset announced via ProteomeXchange.

Title	A systematic phosphoproteome screen to identify targets of the Target of Rapamycin (TOR) kinase in Arabidopsis thaliana
Description	The target of rapamycin (TOR) kinase is a central regulatory hub that translates environmental and nutritional information into permissive or restrictive growth decisions. Although the TOR pathway is conserved among eukaryotes, plants developed unique adaptations to this pathway to cope with their autotrophic and sessile nature. Here, we captured for the first time a proteome-wide view of the plant TOR phosphorylation and interaction landscape. After sampling four biological repeats, proteins were extracted, digested and phosphopeptides were enriched. In total, 8302 phosphopeptides on 2558 proteins were identified from all samples. After label free quantitative analysis, a filtered dataset of 5500 phosphopeptides on 2056 proteins was retained. To identify TOR-dependent sites, the control-, AZD8055- and rapamycin-treated samples were statistically analyzed using a linear mixed model to evaluate the effect of the treatment, time and the interaction between both. For T10, T20 and T40, the sucrose control samples were compared to the AZD8055 or rapamycin samples. In addition, the AZD8055 samples were compared to the rapamycin samples, and the sucrose control samples (T10, T20, T40) were compared to T0. Overall, the strongest effect occurred with AZD8055. Therefore, an additional filter was applied retrieving only phosphopeptides that changed at least two-fold upon AZD8055 treatment. In total, 96 unambiguous TOR-dependent phosphosites were detected on 66 proteins, linking TOR to a plethora of biological processes.
HostingRepository	PRIDE
AnnounceDate	2019-07-17
AnnouncementXML	Submission_2019-07-17_06:19:22.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jelle Van Leene
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-04 01:13:09	ID requested
⏵ 1	2019-07-17 06:19:24	announced

Van Leene J, Han C, Gadeyne A, Eeckhout D, Matthijs C, Cannoot B, De Winne N, Persiau G, Van De Slijke E, Van de Cotte B, Stes E, Van Bel M, Storme V, Impens F, Gevaert K, Vandepoele K, De Smet I, De Jaeger G, Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase. Nat Plants, 5(3):316-327(2019) [pubmed]

curator keyword: Biological

submitter keyword: Target of Rapamycin (TOR), Arabidopsis, cell culture, phosphoproteomics, AZD8055, rapamycin, sucrose, label-free quantitative MS

Geert De Jaeger
contact affiliation	Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium VIB Center for Plant Systems Biology, 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

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/2019/07/PXD008355

PRIDE project URI

• PRIDE
  1. PXD008355
     1. Label: PRIDE project
     2. Name: A systematic phosphoproteome screen to identify targets of the Target of Rapamycin (TOR) kinase in Arabidopsis thaliana